Gene Expression Omnibus (GEO) Overview Version´╝Ü2014-04-12Japanese page
An overview of the GEO entries broken down by the measurement platforms and the features of the measured samples.
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Data Unit : [ DataSet / Sample / Platform ] Show explanation>> <<Hide explanation
DataSet : Series(GSE) x Platform(GPL). A set of related gene expression data.
Sample : Biological materials.
platform : Methods or instruments used for the gene expression profilings.
The numbers shown in the tabs are the numbers of the data (series, samples or platforms) belonging to the groups.
  Human
(615,734)
  Primates
(5,814)
  Rodents
(225,055)
  Mammals
(20,968)
  Vertebrates
(22,581)
  Invertebrates
(46,584)
  Plants
(107,706)
  Bacteria
(45,091)
  Viruses
(1,432)
  Phages
(112)
  Unclassified
(6,986)
  All
(1,101,311)
 
  SAGE NlaIII
(4)
  SAGE RsaI
(0)
  SAGE Sau3A
(0)
  MPSS
(0)
  GeneChip
(637)
  Tiling Array
(86)
  cDNA Array
(1,377)
  Oligo Array
(3,118)
  Bead Array
(576)
  Protein Array
(0)
  Antibody
(0)
  RT-PCR
(0)
  HT-Seq
(1,091)
  Other
(85)
  All
(6,986)
 
  brain
(173)
  blood
(611)
  connective
(248)
  reproductive
(13)
  muscular
(109)
  digestive
(596)
  liver
(178)
  lung
(73)
  urinary
(42)
  endo/exo-crine
(127)
  embryo
(30)
  adult aerial structure
(0)
  young aerial structure
(0)
  root
(6)
  meristem/growing tissue
(0)
  flower/sexual organ
(0)
  seed/fruit/grain
(6)
  pooled
(439)
  unclassified
(4,335)
  all
(6,986)
 
1   |   2   |   3   |   4   |   5      »      [350]
Sample ID Title Number of Data Institute Submission date Platform Sample type Species Organ class Reasoning of the classification
Keywords used for the classification are shown with bold font.
1 GSM2388 human-macaque testis 668 National Institute of Infectious Diseases 2002-08-13 [cDNA Array] QtsA cDNA clones (GPL206) RNA Macaca fascicularis,Homo sapiens
Macaca fascicularis,Homo sapiens
testis cynomolgus monkey testis human testis
2 GSM24699 24550 MeasuredBioAssayData&DerivedBioAssayData 43,008 Stanford Microarray Database (SMD) 2004-06-08 [cDNA Array] SHBR (GPL1283) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens
pooled Whole blood (10 ml) for ten unrelated common chimpanzees (Pan troglodytes) was kindly provided by Dr. Harold M. McClure at the Yerkes Regional Primate Center of Emory University (Atlanta, GA). The ten chimpanzees included five males and five females. We isolated and transformed lymphocytes with frozen virus stocks by using a standard Epstein-Barr virus transformation protocol (1). For the human samples, we randomly selected lymphoblastoid cell lines for nine unrelated humans from a collection previously established in our laboratory (reference 1). All cell lines were maintained at 37 degrees C in 5% CO2, and with DMEM (Gibco-BRL) supplemented with 2 mM L-glutamine (Gibco-BRL, Carlsbad, CA), 100 U/ml penicillin, 100 microg/ml streptomycin (BioWhittaker, East Rutherford, NJ), and 10% FCS (Sigma, St. Louis, MO). All cell lines were maintained under the same conditions for more than 3 months, and were harvested on the same day. To minimize differences in growth behavior and morphology between different cell lines, we fed and split them at comparable growth points. Because growth rates differed between different lines, the splitting schedule and feeding cycle for individual lines varied. reference 1: Risch N, Spiker D, Lotspeich L, Nouri N, Hinds D, Hallmayer J, Kalaydjieva L, McCague P, Dimiceli S, Pitts T, Nguyen L, Yang J, Harper C, Thorpe D, Vermeer S, Young H, Hebert J, Lin A, Ferguson J, Chiotti C, Wiese-Slater S, Rogers T, Salmon B, Nicholas P, Myers RM, and et al. A genomic screen of autism: evidence for a multilocus etiology. Am J Hum Genet 65: 493-507., 1999. PolyA+ RNAs were isolated from approximated 107 cells by using the FAST TRACK 2.0 kit (Invitrogen, Carlsbad, CA) following the manufacturer's instructions. Equal amounts of poly-A RNA from nine human cell lines were pooled to serve as the common reference sample for each of the individual 19 samples. The human cDNA microarrays used in this study were obtained from the Stanford Functional Genomic Facility (http://www.microarray.org). We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html). Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ml containing 2 mg mRNA / 4 mg oligo (dT) primer / 0.5 mM each dATP, dCTP, dGTP / 0.2 mM dTTP / 0.1 mM Cy3/5-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ) / 0.01 M DTT / 400 units Superscript II reverse transcriptase (Life Technologies). We labeled the reference sample with Cy3-dUTP; thus in this study the Cy5/Cy3 ratio is taken as the measure of transcript levels in individual test samples. After incubation at 42 degrees C for 2-3 hours, the RNA was degraded by adding 15 ml of 0.1 N NaOH at 70 degrees C for 10 minutes, and was neutralized by adding 15 ml of 0.1 N HCl. Equal amounts of the Cy3 and Cy5 probes were combined and concentrated by using a Microcon YM-100 column (Millipore). After 20 mg Cot1 human DNA (Gibco-BRL), 20 mg PolyA RNA (Sigma, #P9403) and 20 mg tRNA (Gibco-BRL, #15401-011) were added, the probes were purified. For final probe preparation, 6 ml of 20x SSC (BioWhittaker, MD) and 1 ml of 10% SDS were added. The probes were denatured at 100 degrees C for 3 minutes, incubated at 37 degrees C for 30 minutes, and placed on the array under a 24 mm x 60 mm glass cover slip (Fisher). The slides were incubated at 65 degrees C for 16 hours in a hybridization chamber (GeneMachine, San Carlos, California). Slides were washed in graded SSC with 0.1% SDS: 2x for 2 to 5 minutes, 1x for 2 minutes, and 0.1x for 2 minutes, and spun dry. Fluorescent array images were collected for Cy3 and Cy5 channels by using a GenePix 4000B scanner (Axon Instruments, Foster City, CA) at a resolution of 5 mm per pixel.
3 GSM24700 24551 MeasuredBioAssayData&DerivedBioAssayData 43,008 Stanford Microarray Database (SMD) 2004-06-08 [cDNA Array] SHBR (GPL1283) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens
pooled Whole blood (10 ml) for ten unrelated common chimpanzees (Pan troglodytes) was kindly provided by Dr. Harold M. McClure at the Yerkes Regional Primate Center of Emory University (Atlanta, GA). The ten chimpanzees included five males and five females. We isolated and transformed lymphocytes with frozen virus stocks by using a standard Epstein-Barr virus transformation protocol (1). For the human samples, we randomly selected lymphoblastoid cell lines for nine unrelated humans from a collection previously established in our laboratory (reference 1). All cell lines were maintained at 37 degrees C in 5% CO2, and with DMEM (Gibco-BRL) supplemented with 2 mM L-glutamine (Gibco-BRL, Carlsbad, CA), 100 U/ml penicillin, 100 microg/ml streptomycin (BioWhittaker, East Rutherford, NJ), and 10% FCS (Sigma, St. Louis, MO). All cell lines were maintained under the same conditions for more than 3 months, and were harvested on the same day. To minimize differences in growth behavior and morphology between different cell lines, we fed and split them at comparable growth points. Because growth rates differed between different lines, the splitting schedule and feeding cycle for individual lines varied. reference 1: Risch N, Spiker D, Lotspeich L, Nouri N, Hinds D, Hallmayer J, Kalaydjieva L, McCague P, Dimiceli S, Pitts T, Nguyen L, Yang J, Harper C, Thorpe D, Vermeer S, Young H, Hebert J, Lin A, Ferguson J, Chiotti C, Wiese-Slater S, Rogers T, Salmon B, Nicholas P, Myers RM, and et al. A genomic screen of autism: evidence for a multilocus etiology. Am J Hum Genet 65: 493-507., 1999. PolyA+ RNAs were isolated from approximated 107 cells by using the FAST TRACK 2.0 kit (Invitrogen, Carlsbad, CA) following the manufacturer's instructions. Equal amounts of poly-A RNA from nine human cell lines were pooled to serve as the common reference sample for each of the individual 19 samples. The human cDNA microarrays used in this study were obtained from the Stanford Functional Genomic Facility (http://www.microarray.org). We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html). Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ml containing 2 mg mRNA / 4 mg oligo (dT) primer / 0.5 mM each dATP, dCTP, dGTP / 0.2 mM dTTP / 0.1 mM Cy3/5-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ) / 0.01 M DTT / 400 units Superscript II reverse transcriptase (Life Technologies). We labeled the reference sample with Cy3-dUTP; thus in this study the Cy5/Cy3 ratio is taken as the measure of transcript levels in individual test samples. After incubation at 42 degrees C for 2-3 hours, the RNA was degraded by adding 15 ml of 0.1 N NaOH at 70 degrees C for 10 minutes, and was neutralized by adding 15 ml of 0.1 N HCl. Equal amounts of the Cy3 and Cy5 probes were combined and concentrated by using a Microcon YM-100 column (Millipore). After 20 mg Cot1 human DNA (Gibco-BRL), 20 mg PolyA RNA (Sigma, #P9403) and 20 mg tRNA (Gibco-BRL, #15401-011) were added, the probes were purified. For final probe preparation, 6 ml of 20x SSC (BioWhittaker, MD) and 1 ml of 10% SDS were added. The probes were denatured at 100 degrees C for 3 minutes, incubated at 37 degrees C for 30 minutes, and placed on the array under a 24 mm x 60 mm glass cover slip (Fisher). The slides were incubated at 65 degrees C for 16 hours in a hybridization chamber (GeneMachine, San Carlos, California). Slides were washed in graded SSC with 0.1% SDS: 2x for 2 to 5 minutes, 1x for 2 minutes, and 0.1x for 2 minutes, and spun dry. Fluorescent array images were collected for Cy3 and Cy5 channels by using a GenePix 4000B scanner (Axon Instruments, Foster City, CA) at a resolution of 5 mm per pixel.
4 GSM24701 24552 MeasuredBioAssayData&DerivedBioAssayData 43,008 Stanford Microarray Database (SMD) 2004-06-08 [cDNA Array] SHBR (GPL1283) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens
pooled Whole blood (10 ml) for ten unrelated common chimpanzees (Pan troglodytes) was kindly provided by Dr. Harold M. McClure at the Yerkes Regional Primate Center of Emory University (Atlanta, GA). The ten chimpanzees included five males and five females. We isolated and transformed lymphocytes with frozen virus stocks by using a standard Epstein-Barr virus transformation protocol (1). For the human samples, we randomly selected lymphoblastoid cell lines for nine unrelated humans from a collection previously established in our laboratory (reference 1). All cell lines were maintained at 37 degrees C in 5% CO2, and with DMEM (Gibco-BRL) supplemented with 2 mM L-glutamine (Gibco-BRL, Carlsbad, CA), 100 U/ml penicillin, 100 microg/ml streptomycin (BioWhittaker, East Rutherford, NJ), and 10% FCS (Sigma, St. Louis, MO). All cell lines were maintained under the same conditions for more than 3 months, and were harvested on the same day. To minimize differences in growth behavior and morphology between different cell lines, we fed and split them at comparable growth points. Because growth rates differed between different lines, the splitting schedule and feeding cycle for individual lines varied. reference 1: Risch N, Spiker D, Lotspeich L, Nouri N, Hinds D, Hallmayer J, Kalaydjieva L, McCague P, Dimiceli S, Pitts T, Nguyen L, Yang J, Harper C, Thorpe D, Vermeer S, Young H, Hebert J, Lin A, Ferguson J, Chiotti C, Wiese-Slater S, Rogers T, Salmon B, Nicholas P, Myers RM, and et al. A genomic screen of autism: evidence for a multilocus etiology. Am J Hum Genet 65: 493-507., 1999. PolyA+ RNAs were isolated from approximated 107 cells by using the FAST TRACK 2.0 kit (Invitrogen, Carlsbad, CA) following the manufacturer's instructions. Equal amounts of poly-A RNA from nine human cell lines were pooled to serve as the common reference sample for each of the individual 19 samples. The human cDNA microarrays used in this study were obtained from the Stanford Functional Genomic Facility (http://www.microarray.org). We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html). Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ml containing 2 mg mRNA / 4 mg oligo (dT) primer / 0.5 mM each dATP, dCTP, dGTP / 0.2 mM dTTP / 0.1 mM Cy3/5-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ) / 0.01 M DTT / 400 units Superscript II reverse transcriptase (Life Technologies). We labeled the reference sample with Cy3-dUTP; thus in this study the Cy5/Cy3 ratio is taken as the measure of transcript levels in individual test samples. After incubation at 42 degrees C for 2-3 hours, the RNA was degraded by adding 15 ml of 0.1 N NaOH at 70 degrees C for 10 minutes, and was neutralized by adding 15 ml of 0.1 N HCl. Equal amounts of the Cy3 and Cy5 probes were combined and concentrated by using a Microcon YM-100 column (Millipore). After 20 mg Cot1 human DNA (Gibco-BRL), 20 mg PolyA RNA (Sigma, #P9403) and 20 mg tRNA (Gibco-BRL, #15401-011) were added, the probes were purified. For final probe preparation, 6 ml of 20x SSC (BioWhittaker, MD) and 1 ml of 10% SDS were added. The probes were denatured at 100 degrees C for 3 minutes, incubated at 37 degrees C for 30 minutes, and placed on the array under a 24 mm x 60 mm glass cover slip (Fisher). The slides were incubated at 65 degrees C for 16 hours in a hybridization chamber (GeneMachine, San Carlos, California). Slides were washed in graded SSC with 0.1% SDS: 2x for 2 to 5 minutes, 1x for 2 minutes, and 0.1x for 2 minutes, and spun dry. Fluorescent array images were collected for Cy3 and Cy5 channels by using a GenePix 4000B scanner (Axon Instruments, Foster City, CA) at a resolution of 5 mm per pixel.
5 GSM24702 24553 MeasuredBioAssayData&DerivedBioAssayData 43,008 Stanford Microarray Database (SMD) 2004-06-08 [cDNA Array] SHBR (GPL1283) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens
pooled Whole blood (10 ml) for ten unrelated common chimpanzees (Pan troglodytes) was kindly provided by Dr. Harold M. McClure at the Yerkes Regional Primate Center of Emory University (Atlanta, GA). The ten chimpanzees included five males and five females. We isolated and transformed lymphocytes with frozen virus stocks by using a standard Epstein-Barr virus transformation protocol (1). For the human samples, we randomly selected lymphoblastoid cell lines for nine unrelated humans from a collection previously established in our laboratory (reference 1). All cell lines were maintained at 37 degrees C in 5% CO2, and with DMEM (Gibco-BRL) supplemented with 2 mM L-glutamine (Gibco-BRL, Carlsbad, CA), 100 U/ml penicillin, 100 microg/ml streptomycin (BioWhittaker, East Rutherford, NJ), and 10% FCS (Sigma, St. Louis, MO). All cell lines were maintained under the same conditions for more than 3 months, and were harvested on the same day. To minimize differences in growth behavior and morphology between different cell lines, we fed and split them at comparable growth points. Because growth rates differed between different lines, the splitting schedule and feeding cycle for individual lines varied. reference 1: Risch N, Spiker D, Lotspeich L, Nouri N, Hinds D, Hallmayer J, Kalaydjieva L, McCague P, Dimiceli S, Pitts T, Nguyen L, Yang J, Harper C, Thorpe D, Vermeer S, Young H, Hebert J, Lin A, Ferguson J, Chiotti C, Wiese-Slater S, Rogers T, Salmon B, Nicholas P, Myers RM, and et al. A genomic screen of autism: evidence for a multilocus etiology. Am J Hum Genet 65: 493-507., 1999. PolyA+ RNAs were isolated from approximated 107 cells by using the FAST TRACK 2.0 kit (Invitrogen, Carlsbad, CA) following the manufacturer's instructions. Equal amounts of poly-A RNA from nine human cell lines were pooled to serve as the common reference sample for each of the individual 19 samples. The human cDNA microarrays used in this study were obtained from the Stanford Functional Genomic Facility (http://www.microarray.org). We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html). Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ml containing 2 mg mRNA / 4 mg oligo (dT) primer / 0.5 mM each dATP, dCTP, dGTP / 0.2 mM dTTP / 0.1 mM Cy3/5-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ) / 0.01 M DTT / 400 units Superscript II reverse transcriptase (Life Technologies). We labeled the reference sample with Cy3-dUTP; thus in this study the Cy5/Cy3 ratio is taken as the measure of transcript levels in individual test samples. After incubation at 42 degrees C for 2-3 hours, the RNA was degraded by adding 15 ml of 0.1 N NaOH at 70 degrees C for 10 minutes, and was neutralized by adding 15 ml of 0.1 N HCl. Equal amounts of the Cy3 and Cy5 probes were combined and concentrated by using a Microcon YM-100 column (Millipore). After 20 mg Cot1 human DNA (Gibco-BRL), 20 mg PolyA RNA (Sigma, #P9403) and 20 mg tRNA (Gibco-BRL, #15401-011) were added, the probes were purified. For final probe preparation, 6 ml of 20x SSC (BioWhittaker, MD) and 1 ml of 10% SDS were added. The probes were denatured at 100 degrees C for 3 minutes, incubated at 37 degrees C for 30 minutes, and placed on the array under a 24 mm x 60 mm glass cover slip (Fisher). The slides were incubated at 65 degrees C for 16 hours in a hybridization chamber (GeneMachine, San Carlos, California). Slides were washed in graded SSC with 0.1% SDS: 2x for 2 to 5 minutes, 1x for 2 minutes, and 0.1x for 2 minutes, and spun dry. Fluorescent array images were collected for Cy3 and Cy5 channels by using a GenePix 4000B scanner (Axon Instruments, Foster City, CA) at a resolution of 5 mm per pixel.
6 GSM24703 24554 MeasuredBioAssayData&DerivedBioAssayData 43,008 Stanford Microarray Database (SMD) 2004-06-08 [cDNA Array] SHBR (GPL1283) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens
pooled Whole blood (10 ml) for ten unrelated common chimpanzees (Pan troglodytes) was kindly provided by Dr. Harold M. McClure at the Yerkes Regional Primate Center of Emory University (Atlanta, GA). The ten chimpanzees included five males and five females. We isolated and transformed lymphocytes with frozen virus stocks by using a standard Epstein-Barr virus transformation protocol (1). For the human samples, we randomly selected lymphoblastoid cell lines for nine unrelated humans from a collection previously established in our laboratory (reference 1). All cell lines were maintained at 37 degrees C in 5% CO2, and with DMEM (Gibco-BRL) supplemented with 2 mM L-glutamine (Gibco-BRL, Carlsbad, CA), 100 U/ml penicillin, 100 microg/ml streptomycin (BioWhittaker, East Rutherford, NJ), and 10% FCS (Sigma, St. Louis, MO). All cell lines were maintained under the same conditions for more than 3 months, and were harvested on the same day. To minimize differences in growth behavior and morphology between different cell lines, we fed and split them at comparable growth points. Because growth rates differed between different lines, the splitting schedule and feeding cycle for individual lines varied. reference 1: Risch N, Spiker D, Lotspeich L, Nouri N, Hinds D, Hallmayer J, Kalaydjieva L, McCague P, Dimiceli S, Pitts T, Nguyen L, Yang J, Harper C, Thorpe D, Vermeer S, Young H, Hebert J, Lin A, Ferguson J, Chiotti C, Wiese-Slater S, Rogers T, Salmon B, Nicholas P, Myers RM, and et al. A genomic screen of autism: evidence for a multilocus etiology. Am J Hum Genet 65: 493-507., 1999. PolyA+ RNAs were isolated from approximated 107 cells by using the FAST TRACK 2.0 kit (Invitrogen, Carlsbad, CA) following the manufacturer's instructions. Equal amounts of poly-A RNA from nine human cell lines were pooled to serve as the common reference sample for each of the individual 19 samples. The human cDNA microarrays used in this study were obtained from the Stanford Functional Genomic Facility (http://www.microarray.org). We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html). Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ml containing 2 mg mRNA / 4 mg oligo (dT) primer / 0.5 mM each dATP, dCTP, dGTP / 0.2 mM dTTP / 0.1 mM Cy3/5-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ) / 0.01 M DTT / 400 units Superscript II reverse transcriptase (Life Technologies). We labeled the reference sample with Cy3-dUTP; thus in this study the Cy5/Cy3 ratio is taken as the measure of transcript levels in individual test samples. After incubation at 42 degrees C for 2-3 hours, the RNA was degraded by adding 15 ml of 0.1 N NaOH at 70 degrees C for 10 minutes, and was neutralized by adding 15 ml of 0.1 N HCl. Equal amounts of the Cy3 and Cy5 probes were combined and concentrated by using a Microcon YM-100 column (Millipore). After 20 mg Cot1 human DNA (Gibco-BRL), 20 mg PolyA RNA (Sigma, #P9403) and 20 mg tRNA (Gibco-BRL, #15401-011) were added, the probes were purified. For final probe preparation, 6 ml of 20x SSC (BioWhittaker, MD) and 1 ml of 10% SDS were added. The probes were denatured at 100 degrees C for 3 minutes, incubated at 37 degrees C for 30 minutes, and placed on the array under a 24 mm x 60 mm glass cover slip (Fisher). The slides were incubated at 65 degrees C for 16 hours in a hybridization chamber (GeneMachine, San Carlos, California). Slides were washed in graded SSC with 0.1% SDS: 2x for 2 to 5 minutes, 1x for 2 minutes, and 0.1x for 2 minutes, and spun dry. Fluorescent array images were collected for Cy3 and Cy5 channels by using a GenePix 4000B scanner (Axon Instruments, Foster City, CA) at a resolution of 5 mm per pixel.
7 GSM24704 24555 MeasuredBioAssayData&DerivedBioAssayData 43,008 Stanford Microarray Database (SMD) 2004-06-08 [cDNA Array] SHBR (GPL1283) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens
pooled Whole blood (10 ml) for ten unrelated common chimpanzees (Pan troglodytes) was kindly provided by Dr. Harold M. McClure at the Yerkes Regional Primate Center of Emory University (Atlanta, GA). The ten chimpanzees included five males and five females. We isolated and transformed lymphocytes with frozen virus stocks by using a standard Epstein-Barr virus transformation protocol (1). For the human samples, we randomly selected lymphoblastoid cell lines for nine unrelated humans from a collection previously established in our laboratory (reference 1). All cell lines were maintained at 37 degrees C in 5% CO2, and with DMEM (Gibco-BRL) supplemented with 2 mM L-glutamine (Gibco-BRL, Carlsbad, CA), 100 U/ml penicillin, 100 microg/ml streptomycin (BioWhittaker, East Rutherford, NJ), and 10% FCS (Sigma, St. Louis, MO). All cell lines were maintained under the same conditions for more than 3 months, and were harvested on the same day. To minimize differences in growth behavior and morphology between different cell lines, we fed and split them at comparable growth points. Because growth rates differed between different lines, the splitting schedule and feeding cycle for individual lines varied. reference 1: Risch N, Spiker D, Lotspeich L, Nouri N, Hinds D, Hallmayer J, Kalaydjieva L, McCague P, Dimiceli S, Pitts T, Nguyen L, Yang J, Harper C, Thorpe D, Vermeer S, Young H, Hebert J, Lin A, Ferguson J, Chiotti C, Wiese-Slater S, Rogers T, Salmon B, Nicholas P, Myers RM, and et al. A genomic screen of autism: evidence for a multilocus etiology. Am J Hum Genet 65: 493-507., 1999. PolyA+ RNAs were isolated from approximated 107 cells by using the FAST TRACK 2.0 kit (Invitrogen, Carlsbad, CA) following the manufacturer's instructions. Equal amounts of poly-A RNA from nine human cell lines were pooled to serve as the common reference sample for each of the individual 19 samples. The human cDNA microarrays used in this study were obtained from the Stanford Functional Genomic Facility (http://www.microarray.org). We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html). Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ml containing 2 mg mRNA / 4 mg oligo (dT) primer / 0.5 mM each dATP, dCTP, dGTP / 0.2 mM dTTP / 0.1 mM Cy3/5-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ) / 0.01 M DTT / 400 units Superscript II reverse transcriptase (Life Technologies). We labeled the reference sample with Cy3-dUTP; thus in this study the Cy5/Cy3 ratio is taken as the measure of transcript levels in individual test samples. After incubation at 42 degrees C for 2-3 hours, the RNA was degraded by adding 15 ml of 0.1 N NaOH at 70 degrees C for 10 minutes, and was neutralized by adding 15 ml of 0.1 N HCl. Equal amounts of the Cy3 and Cy5 probes were combined and concentrated by using a Microcon YM-100 column (Millipore). After 20 mg Cot1 human DNA (Gibco-BRL), 20 mg PolyA RNA (Sigma, #P9403) and 20 mg tRNA (Gibco-BRL, #15401-011) were added, the probes were purified. For final probe preparation, 6 ml of 20x SSC (BioWhittaker, MD) and 1 ml of 10% SDS were added. The probes were denatured at 100 degrees C for 3 minutes, incubated at 37 degrees C for 30 minutes, and placed on the array under a 24 mm x 60 mm glass cover slip (Fisher). The slides were incubated at 65 degrees C for 16 hours in a hybridization chamber (GeneMachine, San Carlos, California). Slides were washed in graded SSC with 0.1% SDS: 2x for 2 to 5 minutes, 1x for 2 minutes, and 0.1x for 2 minutes, and spun dry. Fluorescent array images were collected for Cy3 and Cy5 channels by using a GenePix 4000B scanner (Axon Instruments, Foster City, CA) at a resolution of 5 mm per pixel.
8 GSM24705 24556 MeasuredBioAssayData&DerivedBioAssayData 43,008 Stanford Microarray Database (SMD) 2004-06-08 [cDNA Array] SHBR (GPL1283) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens
pooled Whole blood (10 ml) for ten unrelated common chimpanzees (Pan troglodytes) was kindly provided by Dr. Harold M. McClure at the Yerkes Regional Primate Center of Emory University (Atlanta, GA). The ten chimpanzees included five males and five females. We isolated and transformed lymphocytes with frozen virus stocks by using a standard Epstein-Barr virus transformation protocol (1). For the human samples, we randomly selected lymphoblastoid cell lines for nine unrelated humans from a collection previously established in our laboratory (reference 1). All cell lines were maintained at 37 degrees C in 5% CO2, and with DMEM (Gibco-BRL) supplemented with 2 mM L-glutamine (Gibco-BRL, Carlsbad, CA), 100 U/ml penicillin, 100 microg/ml streptomycin (BioWhittaker, East Rutherford, NJ), and 10% FCS (Sigma, St. Louis, MO). All cell lines were maintained under the same conditions for more than 3 months, and were harvested on the same day. To minimize differences in growth behavior and morphology between different cell lines, we fed and split them at comparable growth points. Because growth rates differed between different lines, the splitting schedule and feeding cycle for individual lines varied. reference 1: Risch N, Spiker D, Lotspeich L, Nouri N, Hinds D, Hallmayer J, Kalaydjieva L, McCague P, Dimiceli S, Pitts T, Nguyen L, Yang J, Harper C, Thorpe D, Vermeer S, Young H, Hebert J, Lin A, Ferguson J, Chiotti C, Wiese-Slater S, Rogers T, Salmon B, Nicholas P, Myers RM, and et al. A genomic screen of autism: evidence for a multilocus etiology. Am J Hum Genet 65: 493-507., 1999. PolyA+ RNAs were isolated from approximated 107 cells by using the FAST TRACK 2.0 kit (Invitrogen, Carlsbad, CA) following the manufacturer's instructions. Equal amounts of poly-A RNA from nine human cell lines were pooled to serve as the common reference sample for each of the individual 19 samples. The human cDNA microarrays used in this study were obtained from the Stanford Functional Genomic Facility (http://www.microarray.org). We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html). Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ml containing 2 mg mRNA / 4 mg oligo (dT) primer / 0.5 mM each dATP, dCTP, dGTP / 0.2 mM dTTP / 0.1 mM Cy3/5-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ) / 0.01 M DTT / 400 units Superscript II reverse transcriptase (Life Technologies). We labeled the reference sample with Cy3-dUTP; thus in this study the Cy5/Cy3 ratio is taken as the measure of transcript levels in individual test samples. After incubation at 42 degrees C for 2-3 hours, the RNA was degraded by adding 15 ml of 0.1 N NaOH at 70 degrees C for 10 minutes, and was neutralized by adding 15 ml of 0.1 N HCl. Equal amounts of the Cy3 and Cy5 probes were combined and concentrated by using a Microcon YM-100 column (Millipore). After 20 mg Cot1 human DNA (Gibco-BRL), 20 mg PolyA RNA (Sigma, #P9403) and 20 mg tRNA (Gibco-BRL, #15401-011) were added, the probes were purified. For final probe preparation, 6 ml of 20x SSC (BioWhittaker, MD) and 1 ml of 10% SDS were added. The probes were denatured at 100 degrees C for 3 minutes, incubated at 37 degrees C for 30 minutes, and placed on the array under a 24 mm x 60 mm glass cover slip (Fisher). The slides were incubated at 65 degrees C for 16 hours in a hybridization chamber (GeneMachine, San Carlos, California). Slides were washed in graded SSC with 0.1% SDS: 2x for 2 to 5 minutes, 1x for 2 minutes, and 0.1x for 2 minutes, and spun dry. Fluorescent array images were collected for Cy3 and Cy5 channels by using a GenePix 4000B scanner (Axon Instruments, Foster City, CA) at a resolution of 5 mm per pixel.
9 GSM24706 24557 MeasuredBioAssayData&DerivedBioAssayData 43,008 Stanford Microarray Database (SMD) 2004-06-08 [cDNA Array] SHBR (GPL1283) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens
pooled Whole blood (10 ml) for ten unrelated common chimpanzees (Pan troglodytes) was kindly provided by Dr. Harold M. McClure at the Yerkes Regional Primate Center of Emory University (Atlanta, GA). The ten chimpanzees included five males and five females. We isolated and transformed lymphocytes with frozen virus stocks by using a standard Epstein-Barr virus transformation protocol (1). For the human samples, we randomly selected lymphoblastoid cell lines for nine unrelated humans from a collection previously established in our laboratory (reference 1). All cell lines were maintained at 37 degrees C in 5% CO2, and with DMEM (Gibco-BRL) supplemented with 2 mM L-glutamine (Gibco-BRL, Carlsbad, CA), 100 U/ml penicillin, 100 microg/ml streptomycin (BioWhittaker, East Rutherford, NJ), and 10% FCS (Sigma, St. Louis, MO). All cell lines were maintained under the same conditions for more than 3 months, and were harvested on the same day. To minimize differences in growth behavior and morphology between different cell lines, we fed and split them at comparable growth points. Because growth rates differed between different lines, the splitting schedule and feeding cycle for individual lines varied. reference 1: Risch N, Spiker D, Lotspeich L, Nouri N, Hinds D, Hallmayer J, Kalaydjieva L, McCague P, Dimiceli S, Pitts T, Nguyen L, Yang J, Harper C, Thorpe D, Vermeer S, Young H, Hebert J, Lin A, Ferguson J, Chiotti C, Wiese-Slater S, Rogers T, Salmon B, Nicholas P, Myers RM, and et al. A genomic screen of autism: evidence for a multilocus etiology. Am J Hum Genet 65: 493-507., 1999. PolyA+ RNAs were isolated from approximated 107 cells by using the FAST TRACK 2.0 kit (Invitrogen, Carlsbad, CA) following the manufacturer's instructions. Equal amounts of poly-A RNA from nine human cell lines were pooled to serve as the common reference sample for each of the individual 19 samples. The human cDNA microarrays used in this study were obtained from the Stanford Functional Genomic Facility (http://www.microarray.org). We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html). Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ml containing 2 mg mRNA / 4 mg oligo (dT) primer / 0.5 mM each dATP, dCTP, dGTP / 0.2 mM dTTP / 0.1 mM Cy3/5-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ) / 0.01 M DTT / 400 units Superscript II reverse transcriptase (Life Technologies). We labeled the reference sample with Cy3-dUTP; thus in this study the Cy5/Cy3 ratio is taken as the measure of transcript levels in individual test samples. After incubation at 42 degrees C for 2-3 hours, the RNA was degraded by adding 15 ml of 0.1 N NaOH at 70 degrees C for 10 minutes, and was neutralized by adding 15 ml of 0.1 N HCl. Equal amounts of the Cy3 and Cy5 probes were combined and concentrated by using a Microcon YM-100 column (Millipore). After 20 mg Cot1 human DNA (Gibco-BRL), 20 mg PolyA RNA (Sigma, #P9403) and 20 mg tRNA (Gibco-BRL, #15401-011) were added, the probes were purified. For final probe preparation, 6 ml of 20x SSC (BioWhittaker, MD) and 1 ml of 10% SDS were added. The probes were denatured at 100 degrees C for 3 minutes, incubated at 37 degrees C for 30 minutes, and placed on the array under a 24 mm x 60 mm glass cover slip (Fisher). The slides were incubated at 65 degrees C for 16 hours in a hybridization chamber (GeneMachine, San Carlos, California). Slides were washed in graded SSC with 0.1% SDS: 2x for 2 to 5 minutes, 1x for 2 minutes, and 0.1x for 2 minutes, and spun dry. Fluorescent array images were collected for Cy3 and Cy5 channels by using a GenePix 4000B scanner (Axon Instruments, Foster City, CA) at a resolution of 5 mm per pixel.
10 GSM24707 24558 MeasuredBioAssayData&DerivedBioAssayData 43,008 Stanford Microarray Database (SMD) 2004-06-08 [cDNA Array] SHBR (GPL1283) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens
pooled Whole blood (10 ml) for ten unrelated common chimpanzees (Pan troglodytes) was kindly provided by Dr. Harold M. McClure at the Yerkes Regional Primate Center of Emory University (Atlanta, GA). The ten chimpanzees included five males and five females. We isolated and transformed lymphocytes with frozen virus stocks by using a standard Epstein-Barr virus transformation protocol (1). For the human samples, we randomly selected lymphoblastoid cell lines for nine unrelated humans from a collection previously established in our laboratory (reference 1). All cell lines were maintained at 37 degrees C in 5% CO2, and with DMEM (Gibco-BRL) supplemented with 2 mM L-glutamine (Gibco-BRL, Carlsbad, CA), 100 U/ml penicillin, 100 microg/ml streptomycin (BioWhittaker, East Rutherford, NJ), and 10% FCS (Sigma, St. Louis, MO). All cell lines were maintained under the same conditions for more than 3 months, and were harvested on the same day. To minimize differences in growth behavior and morphology between different cell lines, we fed and split them at comparable growth points. Because growth rates differed between different lines, the splitting schedule and feeding cycle for individual lines varied. reference 1: Risch N, Spiker D, Lotspeich L, Nouri N, Hinds D, Hallmayer J, Kalaydjieva L, McCague P, Dimiceli S, Pitts T, Nguyen L, Yang J, Harper C, Thorpe D, Vermeer S, Young H, Hebert J, Lin A, Ferguson J, Chiotti C, Wiese-Slater S, Rogers T, Salmon B, Nicholas P, Myers RM, and et al. A genomic screen of autism: evidence for a multilocus etiology. Am J Hum Genet 65: 493-507., 1999. PolyA+ RNAs were isolated from approximated 107 cells by using the FAST TRACK 2.0 kit (Invitrogen, Carlsbad, CA) following the manufacturer's instructions. Equal amounts of poly-A RNA from nine human cell lines were pooled to serve as the common reference sample for each of the individual 19 samples. The human cDNA microarrays used in this study were obtained from the Stanford Functional Genomic Facility (http://www.microarray.org). We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html). Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ml containing 2 mg mRNA / 4 mg oligo (dT) primer / 0.5 mM each dATP, dCTP, dGTP / 0.2 mM dTTP / 0.1 mM Cy3/5-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ) / 0.01 M DTT / 400 units Superscript II reverse transcriptase (Life Technologies). We labeled the reference sample with Cy3-dUTP; thus in this study the Cy5/Cy3 ratio is taken as the measure of transcript levels in individual test samples. After incubation at 42 degrees C for 2-3 hours, the RNA was degraded by adding 15 ml of 0.1 N NaOH at 70 degrees C for 10 minutes, and was neutralized by adding 15 ml of 0.1 N HCl. Equal amounts of the Cy3 and Cy5 probes were combined and concentrated by using a Microcon YM-100 column (Millipore). After 20 mg Cot1 human DNA (Gibco-BRL), 20 mg PolyA RNA (Sigma, #P9403) and 20 mg tRNA (Gibco-BRL, #15401-011) were added, the probes were purified. For final probe preparation, 6 ml of 20x SSC (BioWhittaker, MD) and 1 ml of 10% SDS were added. The probes were denatured at 100 degrees C for 3 minutes, incubated at 37 degrees C for 30 minutes, and placed on the array under a 24 mm x 60 mm glass cover slip (Fisher). The slides were incubated at 65 degrees C for 16 hours in a hybridization chamber (GeneMachine, San Carlos, California). Slides were washed in graded SSC with 0.1% SDS: 2x for 2 to 5 minutes, 1x for 2 minutes, and 0.1x for 2 minutes, and spun dry. Fluorescent array images were collected for Cy3 and Cy5 channels by using a GenePix 4000B scanner (Axon Instruments, Foster City, CA) at a resolution of 5 mm per pixel.
11 GSM24708 24559 MeasuredBioAssayData&DerivedBioAssayData 43,008 Stanford Microarray Database (SMD) 2004-06-08 [cDNA Array] SHBR (GPL1283) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens
pooled Whole blood (10 ml) for ten unrelated common chimpanzees (Pan troglodytes) was kindly provided by Dr. Harold M. McClure at the Yerkes Regional Primate Center of Emory University (Atlanta, GA). The ten chimpanzees included five males and five females. We isolated and transformed lymphocytes with frozen virus stocks by using a standard Epstein-Barr virus transformation protocol (1). For the human samples, we randomly selected lymphoblastoid cell lines for nine unrelated humans from a collection previously established in our laboratory (reference 1). All cell lines were maintained at 37 degrees C in 5% CO2, and with DMEM (Gibco-BRL) supplemented with 2 mM L-glutamine (Gibco-BRL, Carlsbad, CA), 100 U/ml penicillin, 100 microg/ml streptomycin (BioWhittaker, East Rutherford, NJ), and 10% FCS (Sigma, St. Louis, MO). All cell lines were maintained under the same conditions for more than 3 months, and were harvested on the same day. To minimize differences in growth behavior and morphology between different cell lines, we fed and split them at comparable growth points. Because growth rates differed between different lines, the splitting schedule and feeding cycle for individual lines varied. reference 1: Risch N, Spiker D, Lotspeich L, Nouri N, Hinds D, Hallmayer J, Kalaydjieva L, McCague P, Dimiceli S, Pitts T, Nguyen L, Yang J, Harper C, Thorpe D, Vermeer S, Young H, Hebert J, Lin A, Ferguson J, Chiotti C, Wiese-Slater S, Rogers T, Salmon B, Nicholas P, Myers RM, and et al. A genomic screen of autism: evidence for a multilocus etiology. Am J Hum Genet 65: 493-507., 1999. PolyA+ RNAs were isolated from approximated 107 cells by using the FAST TRACK 2.0 kit (Invitrogen, Carlsbad, CA) following the manufacturer's instructions. Equal amounts of poly-A RNA from nine human cell lines were pooled to serve as the common reference sample for each of the individual 19 samples. The human cDNA microarrays used in this study were obtained from the Stanford Functional Genomic Facility (http://www.microarray.org). We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html). Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ml containing 2 mg mRNA / 4 mg oligo (dT) primer / 0.5 mM each dATP, dCTP, dGTP / 0.2 mM dTTP / 0.1 mM Cy3/5-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ) / 0.01 M DTT / 400 units Superscript II reverse transcriptase (Life Technologies). We labeled the reference sample with Cy3-dUTP; thus in this study the Cy5/Cy3 ratio is taken as the measure of transcript levels in individual test samples. After incubation at 42 degrees C for 2-3 hours, the RNA was degraded by adding 15 ml of 0.1 N NaOH at 70 degrees C for 10 minutes, and was neutralized by adding 15 ml of 0.1 N HCl. Equal amounts of the Cy3 and Cy5 probes were combined and concentrated by using a Microcon YM-100 column (Millipore). After 20 mg Cot1 human DNA (Gibco-BRL), 20 mg PolyA RNA (Sigma, #P9403) and 20 mg tRNA (Gibco-BRL, #15401-011) were added, the probes were purified. For final probe preparation, 6 ml of 20x SSC (BioWhittaker, MD) and 1 ml of 10% SDS were added. The probes were denatured at 100 degrees C for 3 minutes, incubated at 37 degrees C for 30 minutes, and placed on the array under a 24 mm x 60 mm glass cover slip (Fisher). The slides were incubated at 65 degrees C for 16 hours in a hybridization chamber (GeneMachine, San Carlos, California). Slides were washed in graded SSC with 0.1% SDS: 2x for 2 to 5 minutes, 1x for 2 minutes, and 0.1x for 2 minutes, and spun dry. Fluorescent array images were collected for Cy3 and Cy5 channels by using a GenePix 4000B scanner (Axon Instruments, Foster City, CA) at a resolution of 5 mm per pixel.
12 GSM24709 24560 MeasuredBioAssayData&DerivedBioAssayData 43,008 Stanford Microarray Database (SMD) 2004-06-08 [cDNA Array] SHBR (GPL1283) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens
pooled Whole blood (10 ml) for ten unrelated common chimpanzees (Pan troglodytes) was kindly provided by Dr. Harold M. McClure at the Yerkes Regional Primate Center of Emory University (Atlanta, GA). The ten chimpanzees included five males and five females. We isolated and transformed lymphocytes with frozen virus stocks by using a standard Epstein-Barr virus transformation protocol (1). For the human samples, we randomly selected lymphoblastoid cell lines for nine unrelated humans from a collection previously established in our laboratory (reference 1). All cell lines were maintained at 37 degrees C in 5% CO2, and with DMEM (Gibco-BRL) supplemented with 2 mM L-glutamine (Gibco-BRL, Carlsbad, CA), 100 U/ml penicillin, 100 microg/ml streptomycin (BioWhittaker, East Rutherford, NJ), and 10% FCS (Sigma, St. Louis, MO). All cell lines were maintained under the same conditions for more than 3 months, and were harvested on the same day. To minimize differences in growth behavior and morphology between different cell lines, we fed and split them at comparable growth points. Because growth rates differed between different lines, the splitting schedule and feeding cycle for individual lines varied. reference 1: Risch N, Spiker D, Lotspeich L, Nouri N, Hinds D, Hallmayer J, Kalaydjieva L, McCague P, Dimiceli S, Pitts T, Nguyen L, Yang J, Harper C, Thorpe D, Vermeer S, Young H, Hebert J, Lin A, Ferguson J, Chiotti C, Wiese-Slater S, Rogers T, Salmon B, Nicholas P, Myers RM, and et al. A genomic screen of autism: evidence for a multilocus etiology. Am J Hum Genet 65: 493-507., 1999. PolyA+ RNAs were isolated from approximated 107 cells by using the FAST TRACK 2.0 kit (Invitrogen, Carlsbad, CA) following the manufacturer's instructions. Equal amounts of poly-A RNA from nine human cell lines were pooled to serve as the common reference sample for each of the individual 19 samples. The human cDNA microarrays used in this study were obtained from the Stanford Functional Genomic Facility (http://www.microarray.org). We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html). Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ml containing 2 mg mRNA / 4 mg oligo (dT) primer / 0.5 mM each dATP, dCTP, dGTP / 0.2 mM dTTP / 0.1 mM Cy3/5-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ) / 0.01 M DTT / 400 units Superscript II reverse transcriptase (Life Technologies). We labeled the reference sample with Cy3-dUTP; thus in this study the Cy5/Cy3 ratio is taken as the measure of transcript levels in individual test samples. After incubation at 42 degrees C for 2-3 hours, the RNA was degraded by adding 15 ml of 0.1 N NaOH at 70 degrees C for 10 minutes, and was neutralized by adding 15 ml of 0.1 N HCl. Equal amounts of the Cy3 and Cy5 probes were combined and concentrated by using a Microcon YM-100 column (Millipore). After 20 mg Cot1 human DNA (Gibco-BRL), 20 mg PolyA RNA (Sigma, #P9403) and 20 mg tRNA (Gibco-BRL, #15401-011) were added, the probes were purified. For final probe preparation, 6 ml of 20x SSC (BioWhittaker, MD) and 1 ml of 10% SDS were added. The probes were denatured at 100 degrees C for 3 minutes, incubated at 37 degrees C for 30 minutes, and placed on the array under a 24 mm x 60 mm glass cover slip (Fisher). The slides were incubated at 65 degrees C for 16 hours in a hybridization chamber (GeneMachine, San Carlos, California). Slides were washed in graded SSC with 0.1% SDS: 2x for 2 to 5 minutes, 1x for 2 minutes, and 0.1x for 2 minutes, and spun dry. Fluorescent array images were collected for Cy3 and Cy5 channels by using a GenePix 4000B scanner (Axon Instruments, Foster City, CA) at a resolution of 5 mm per pixel.
13 GSM24710 24561 MeasuredBioAssayData&DerivedBioAssayData 43,008 Stanford Microarray Database (SMD) 2004-06-08 [cDNA Array] SHBR (GPL1283) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens
pooled Whole blood (10 ml) for ten unrelated common chimpanzees (Pan troglodytes) was kindly provided by Dr. Harold M. McClure at the Yerkes Regional Primate Center of Emory University (Atlanta, GA). The ten chimpanzees included five males and five females. We isolated and transformed lymphocytes with frozen virus stocks by using a standard Epstein-Barr virus transformation protocol (1). For the human samples, we randomly selected lymphoblastoid cell lines for nine unrelated humans from a collection previously established in our laboratory (reference 1). All cell lines were maintained at 37 degrees C in 5% CO2, and with DMEM (Gibco-BRL) supplemented with 2 mM L-glutamine (Gibco-BRL, Carlsbad, CA), 100 U/ml penicillin, 100 microg/ml streptomycin (BioWhittaker, East Rutherford, NJ), and 10% FCS (Sigma, St. Louis, MO). All cell lines were maintained under the same conditions for more than 3 months, and were harvested on the same day. To minimize differences in growth behavior and morphology between different cell lines, we fed and split them at comparable growth points. Because growth rates differed between different lines, the splitting schedule and feeding cycle for individual lines varied. reference 1: Risch N, Spiker D, Lotspeich L, Nouri N, Hinds D, Hallmayer J, Kalaydjieva L, McCague P, Dimiceli S, Pitts T, Nguyen L, Yang J, Harper C, Thorpe D, Vermeer S, Young H, Hebert J, Lin A, Ferguson J, Chiotti C, Wiese-Slater S, Rogers T, Salmon B, Nicholas P, Myers RM, and et al. A genomic screen of autism: evidence for a multilocus etiology. Am J Hum Genet 65: 493-507., 1999. PolyA+ RNAs were isolated from approximated 107 cells by using the FAST TRACK 2.0 kit (Invitrogen, Carlsbad, CA) following the manufacturer's instructions. Equal amounts of poly-A RNA from nine human cell lines were pooled to serve as the common reference sample for each of the individual 19 samples. The human cDNA microarrays used in this study were obtained from the Stanford Functional Genomic Facility (http://www.microarray.org). We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html). Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ml containing 2 mg mRNA / 4 mg oligo (dT) primer / 0.5 mM each dATP, dCTP, dGTP / 0.2 mM dTTP / 0.1 mM Cy3/5-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ) / 0.01 M DTT / 400 units Superscript II reverse transcriptase (Life Technologies). We labeled the reference sample with Cy3-dUTP; thus in this study the Cy5/Cy3 ratio is taken as the measure of transcript levels in individual test samples. After incubation at 42 degrees C for 2-3 hours, the RNA was degraded by adding 15 ml of 0.1 N NaOH at 70 degrees C for 10 minutes, and was neutralized by adding 15 ml of 0.1 N HCl. Equal amounts of the Cy3 and Cy5 probes were combined and concentrated by using a Microcon YM-100 column (Millipore). After 20 mg Cot1 human DNA (Gibco-BRL), 20 mg PolyA RNA (Sigma, #P9403) and 20 mg tRNA (Gibco-BRL, #15401-011) were added, the probes were purified. For final probe preparation, 6 ml of 20x SSC (BioWhittaker, MD) and 1 ml of 10% SDS were added. The probes were denatured at 100 degrees C for 3 minutes, incubated at 37 degrees C for 30 minutes, and placed on the array under a 24 mm x 60 mm glass cover slip (Fisher). The slides were incubated at 65 degrees C for 16 hours in a hybridization chamber (GeneMachine, San Carlos, California). Slides were washed in graded SSC with 0.1% SDS: 2x for 2 to 5 minutes, 1x for 2 minutes, and 0.1x for 2 minutes, and spun dry. Fluorescent array images were collected for Cy3 and Cy5 channels by using a GenePix 4000B scanner (Axon Instruments, Foster City, CA) at a resolution of 5 mm per pixel.
14 GSM24711 24562 MeasuredBioAssayData&DerivedBioAssayData 43,008 Stanford Microarray Database (SMD) 2004-06-08 [cDNA Array] SHBR (GPL1283) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens
pooled Whole blood (10 ml) for ten unrelated common chimpanzees (Pan troglodytes) was kindly provided by Dr. Harold M. McClure at the Yerkes Regional Primate Center of Emory University (Atlanta, GA). The ten chimpanzees included five males and five females. We isolated and transformed lymphocytes with frozen virus stocks by using a standard Epstein-Barr virus transformation protocol (1). For the human samples, we randomly selected lymphoblastoid cell lines for nine unrelated humans from a collection previously established in our laboratory (reference 1). All cell lines were maintained at 37 degrees C in 5% CO2, and with DMEM (Gibco-BRL) supplemented with 2 mM L-glutamine (Gibco-BRL, Carlsbad, CA), 100 U/ml penicillin, 100 microg/ml streptomycin (BioWhittaker, East Rutherford, NJ), and 10% FCS (Sigma, St. Louis, MO). All cell lines were maintained under the same conditions for more than 3 months, and were harvested on the same day. To minimize differences in growth behavior and morphology between different cell lines, we fed and split them at comparable growth points. Because growth rates differed between different lines, the splitting schedule and feeding cycle for individual lines varied. reference 1: Risch N, Spiker D, Lotspeich L, Nouri N, Hinds D, Hallmayer J, Kalaydjieva L, McCague P, Dimiceli S, Pitts T, Nguyen L, Yang J, Harper C, Thorpe D, Vermeer S, Young H, Hebert J, Lin A, Ferguson J, Chiotti C, Wiese-Slater S, Rogers T, Salmon B, Nicholas P, Myers RM, and et al. A genomic screen of autism: evidence for a multilocus etiology. Am J Hum Genet 65: 493-507., 1999. PolyA+ RNAs were isolated from approximated 107 cells by using the FAST TRACK 2.0 kit (Invitrogen, Carlsbad, CA) following the manufacturer's instructions. Equal amounts of poly-A RNA from nine human cell lines were pooled to serve as the common reference sample for each of the individual 19 samples. The human cDNA microarrays used in this study were obtained from the Stanford Functional Genomic Facility (http://www.microarray.org). We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html). Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ml containing 2 mg mRNA / 4 mg oligo (dT) primer / 0.5 mM each dATP, dCTP, dGTP / 0.2 mM dTTP / 0.1 mM Cy3/5-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ) / 0.01 M DTT / 400 units Superscript II reverse transcriptase (Life Technologies). We labeled the reference sample with Cy3-dUTP; thus in this study the Cy5/Cy3 ratio is taken as the measure of transcript levels in individual test samples. After incubation at 42 degrees C for 2-3 hours, the RNA was degraded by adding 15 ml of 0.1 N NaOH at 70 degrees C for 10 minutes, and was neutralized by adding 15 ml of 0.1 N HCl. Equal amounts of the Cy3 and Cy5 probes were combined and concentrated by using a Microcon YM-100 column (Millipore). After 20 mg Cot1 human DNA (Gibco-BRL), 20 mg PolyA RNA (Sigma, #P9403) and 20 mg tRNA (Gibco-BRL, #15401-011) were added, the probes were purified. For final probe preparation, 6 ml of 20x SSC (BioWhittaker, MD) and 1 ml of 10% SDS were added. The probes were denatured at 100 degrees C for 3 minutes, incubated at 37 degrees C for 30 minutes, and placed on the array under a 24 mm x 60 mm glass cover slip (Fisher). The slides were incubated at 65 degrees C for 16 hours in a hybridization chamber (GeneMachine, San Carlos, California). Slides were washed in graded SSC with 0.1% SDS: 2x for 2 to 5 minutes, 1x for 2 minutes, and 0.1x for 2 minutes, and spun dry. Fluorescent array images were collected for Cy3 and Cy5 channels by using a GenePix 4000B scanner (Axon Instruments, Foster City, CA) at a resolution of 5 mm per pixel.
15 GSM24712 24563 MeasuredBioAssayData&DerivedBioAssayData 43,008 Stanford Microarray Database (SMD) 2004-06-08 [cDNA Array] SHBR (GPL1283) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens
pooled Whole blood (10 ml) for ten unrelated common chimpanzees (Pan troglodytes) was kindly provided by Dr. Harold M. McClure at the Yerkes Regional Primate Center of Emory University (Atlanta, GA). The ten chimpanzees included five males and five females. We isolated and transformed lymphocytes with frozen virus stocks by using a standard Epstein-Barr virus transformation protocol (1). For the human samples, we randomly selected lymphoblastoid cell lines for nine unrelated humans from a collection previously established in our laboratory (reference 1). All cell lines were maintained at 37 degrees C in 5% CO2, and with DMEM (Gibco-BRL) supplemented with 2 mM L-glutamine (Gibco-BRL, Carlsbad, CA), 100 U/ml penicillin, 100 microg/ml streptomycin (BioWhittaker, East Rutherford, NJ), and 10% FCS (Sigma, St. Louis, MO). All cell lines were maintained under the same conditions for more than 3 months, and were harvested on the same day. To minimize differences in growth behavior and morphology between different cell lines, we fed and split them at comparable growth points. Because growth rates differed between different lines, the splitting schedule and feeding cycle for individual lines varied. reference 1: Risch N, Spiker D, Lotspeich L, Nouri N, Hinds D, Hallmayer J, Kalaydjieva L, McCague P, Dimiceli S, Pitts T, Nguyen L, Yang J, Harper C, Thorpe D, Vermeer S, Young H, Hebert J, Lin A, Ferguson J, Chiotti C, Wiese-Slater S, Rogers T, Salmon B, Nicholas P, Myers RM, and et al. A genomic screen of autism: evidence for a multilocus etiology. Am J Hum Genet 65: 493-507., 1999. PolyA+ RNAs were isolated from approximated 107 cells by using the FAST TRACK 2.0 kit (Invitrogen, Carlsbad, CA) following the manufacturer's instructions. Equal amounts of poly-A RNA from nine human cell lines were pooled to serve as the common reference sample for each of the individual 19 samples. The human cDNA microarrays used in this study were obtained from the Stanford Functional Genomic Facility (http://www.microarray.org). We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html). Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ml containing 2 mg mRNA / 4 mg oligo (dT) primer / 0.5 mM each dATP, dCTP, dGTP / 0.2 mM dTTP / 0.1 mM Cy3/5-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ) / 0.01 M DTT / 400 units Superscript II reverse transcriptase (Life Technologies). We labeled the reference sample with Cy3-dUTP; thus in this study the Cy5/Cy3 ratio is taken as the measure of transcript levels in individual test samples. After incubation at 42 degrees C for 2-3 hours, the RNA was degraded by adding 15 ml of 0.1 N NaOH at 70 degrees C for 10 minutes, and was neutralized by adding 15 ml of 0.1 N HCl. Equal amounts of the Cy3 and Cy5 probes were combined and concentrated by using a Microcon YM-100 column (Millipore). After 20 mg Cot1 human DNA (Gibco-BRL), 20 mg PolyA RNA (Sigma, #P9403) and 20 mg tRNA (Gibco-BRL, #15401-011) were added, the probes were purified. For final probe preparation, 6 ml of 20x SSC (BioWhittaker, MD) and 1 ml of 10% SDS were added. The probes were denatured at 100 degrees C for 3 minutes, incubated at 37 degrees C for 30 minutes, and placed on the array under a 24 mm x 60 mm glass cover slip (Fisher). The slides were incubated at 65 degrees C for 16 hours in a hybridization chamber (GeneMachine, San Carlos, California). Slides were washed in graded SSC with 0.1% SDS: 2x for 2 to 5 minutes, 1x for 2 minutes, and 0.1x for 2 minutes, and spun dry. Fluorescent array images were collected for Cy3 and Cy5 channels by using a GenePix 4000B scanner (Axon Instruments, Foster City, CA) at a resolution of 5 mm per pixel.
16 GSM24713 24564 MeasuredBioAssayData&DerivedBioAssayData 43,008 Stanford Microarray Database (SMD) 2004-06-08 [cDNA Array] SHBR (GPL1283) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens
pooled Whole blood (10 ml) for ten unrelated common chimpanzees (Pan troglodytes) was kindly provided by Dr. Harold M. McClure at the Yerkes Regional Primate Center of Emory University (Atlanta, GA). The ten chimpanzees included five males and five females. We isolated and transformed lymphocytes with frozen virus stocks by using a standard Epstein-Barr virus transformation protocol (1). For the human samples, we randomly selected lymphoblastoid cell lines for nine unrelated humans from a collection previously established in our laboratory (reference 1). All cell lines were maintained at 37 degrees C in 5% CO2, and with DMEM (Gibco-BRL) supplemented with 2 mM L-glutamine (Gibco-BRL, Carlsbad, CA), 100 U/ml penicillin, 100 microg/ml streptomycin (BioWhittaker, East Rutherford, NJ), and 10% FCS (Sigma, St. Louis, MO). All cell lines were maintained under the same conditions for more than 3 months, and were harvested on the same day. To minimize differences in growth behavior and morphology between different cell lines, we fed and split them at comparable growth points. Because growth rates differed between different lines, the splitting schedule and feeding cycle for individual lines varied. reference 1: Risch N, Spiker D, Lotspeich L, Nouri N, Hinds D, Hallmayer J, Kalaydjieva L, McCague P, Dimiceli S, Pitts T, Nguyen L, Yang J, Harper C, Thorpe D, Vermeer S, Young H, Hebert J, Lin A, Ferguson J, Chiotti C, Wiese-Slater S, Rogers T, Salmon B, Nicholas P, Myers RM, and et al. A genomic screen of autism: evidence for a multilocus etiology. Am J Hum Genet 65: 493-507., 1999. PolyA+ RNAs were isolated from approximated 107 cells by using the FAST TRACK 2.0 kit (Invitrogen, Carlsbad, CA) following the manufacturer's instructions. Equal amounts of poly-A RNA from nine human cell lines were pooled to serve as the common reference sample for each of the individual 19 samples. The human cDNA microarrays used in this study were obtained from the Stanford Functional Genomic Facility (http://www.microarray.org). We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html). Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ml containing 2 mg mRNA / 4 mg oligo (dT) primer / 0.5 mM each dATP, dCTP, dGTP / 0.2 mM dTTP / 0.1 mM Cy3/5-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ) / 0.01 M DTT / 400 units Superscript II reverse transcriptase (Life Technologies). We labeled the reference sample with Cy3-dUTP; thus in this study the Cy5/Cy3 ratio is taken as the measure of transcript levels in individual test samples. After incubation at 42 degrees C for 2-3 hours, the RNA was degraded by adding 15 ml of 0.1 N NaOH at 70 degrees C for 10 minutes, and was neutralized by adding 15 ml of 0.1 N HCl. Equal amounts of the Cy3 and Cy5 probes were combined and concentrated by using a Microcon YM-100 column (Millipore). After 20 mg Cot1 human DNA (Gibco-BRL), 20 mg PolyA RNA (Sigma, #P9403) and 20 mg tRNA (Gibco-BRL, #15401-011) were added, the probes were purified. For final probe preparation, 6 ml of 20x SSC (BioWhittaker, MD) and 1 ml of 10% SDS were added. The probes were denatured at 100 degrees C for 3 minutes, incubated at 37 degrees C for 30 minutes, and placed on the array under a 24 mm x 60 mm glass cover slip (Fisher). The slides were incubated at 65 degrees C for 16 hours in a hybridization chamber (GeneMachine, San Carlos, California). Slides were washed in graded SSC with 0.1% SDS: 2x for 2 to 5 minutes, 1x for 2 minutes, and 0.1x for 2 minutes, and spun dry. Fluorescent array images were collected for Cy3 and Cy5 channels by using a GenePix 4000B scanner (Axon Instruments, Foster City, CA) at a resolution of 5 mm per pixel.
17 GSM24714 24575 MeasuredBioAssayData&DerivedBioAssayData 43,008 Stanford Microarray Database (SMD) 2004-06-08 [cDNA Array] SHBR (GPL1283) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens
pooled Whole blood (10 ml) for ten unrelated common chimpanzees (Pan troglodytes) was kindly provided by Dr. Harold M. McClure at the Yerkes Regional Primate Center of Emory University (Atlanta, GA). The ten chimpanzees included five males and five females. We isolated and transformed lymphocytes with frozen virus stocks by using a standard Epstein-Barr virus transformation protocol (1). For the human samples, we randomly selected lymphoblastoid cell lines for nine unrelated humans from a collection previously established in our laboratory (reference 1). All cell lines were maintained at 37 degrees C in 5% CO2, and with DMEM (Gibco-BRL) supplemented with 2 mM L-glutamine (Gibco-BRL, Carlsbad, CA), 100 U/ml penicillin, 100 microg/ml streptomycin (BioWhittaker, East Rutherford, NJ), and 10% FCS (Sigma, St. Louis, MO). All cell lines were maintained under the same conditions for more than 3 months, and were harvested on the same day. To minimize differences in growth behavior and morphology between different cell lines, we fed and split them at comparable growth points. Because growth rates differed between different lines, the splitting schedule and feeding cycle for individual lines varied. reference 1: Risch N, Spiker D, Lotspeich L, Nouri N, Hinds D, Hallmayer J, Kalaydjieva L, McCague P, Dimiceli S, Pitts T, Nguyen L, Yang J, Harper C, Thorpe D, Vermeer S, Young H, Hebert J, Lin A, Ferguson J, Chiotti C, Wiese-Slater S, Rogers T, Salmon B, Nicholas P, Myers RM, and et al. A genomic screen of autism: evidence for a multilocus etiology. Am J Hum Genet 65: 493-507., 1999. PolyA+ RNAs were isolated from approximated 107 cells by using the FAST TRACK 2.0 kit (Invitrogen, Carlsbad, CA) following the manufacturer's instructions. Equal amounts of poly-A RNA from nine human cell lines were pooled to serve as the common reference sample for each of the individual 19 samples. The human cDNA microarrays used in this study were obtained from the Stanford Functional Genomic Facility (http://www.microarray.org). We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html). Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ml containing 2 mg mRNA / 4 mg oligo (dT) primer / 0.5 mM each dATP, dCTP, dGTP / 0.2 mM dTTP / 0.1 mM Cy3/5-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ) / 0.01 M DTT / 400 units Superscript II reverse transcriptase (Life Technologies). We labeled the reference sample with Cy3-dUTP; thus in this study the Cy5/Cy3 ratio is taken as the measure of transcript levels in individual test samples. After incubation at 42 degrees C for 2-3 hours, the RNA was degraded by adding 15 ml of 0.1 N NaOH at 70 degrees C for 10 minutes, and was neutralized by adding 15 ml of 0.1 N HCl. Equal amounts of the Cy3 and Cy5 probes were combined and concentrated by using a Microcon YM-100 column (Millipore). After 20 mg Cot1 human DNA (Gibco-BRL), 20 mg PolyA RNA (Sigma, #P9403) and 20 mg tRNA (Gibco-BRL, #15401-011) were added, the probes were purified. For final probe preparation, 6 ml of 20x SSC (BioWhittaker, MD) and 1 ml of 10% SDS were added. The probes were denatured at 100 degrees C for 3 minutes, incubated at 37 degrees C for 30 minutes, and placed on the array under a 24 mm x 60 mm glass cover slip (Fisher). The slides were incubated at 65 degrees C for 16 hours in a hybridization chamber (GeneMachine, San Carlos, California). Slides were washed in graded SSC with 0.1% SDS: 2x for 2 to 5 minutes, 1x for 2 minutes, and 0.1x for 2 minutes, and spun dry. Fluorescent array images were collected for Cy3 and Cy5 channels by using a GenePix 4000B scanner (Axon Instruments, Foster City, CA) at a resolution of 5 mm per pixel.
18 GSM24715 24576 MeasuredBioAssayData&DerivedBioAssayData 43,008 Stanford Microarray Database (SMD) 2004-06-08 [cDNA Array] SHBR (GPL1283) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens
pooled Whole blood (10 ml) for ten unrelated common chimpanzees (Pan troglodytes) was kindly provided by Dr. Harold M. McClure at the Yerkes Regional Primate Center of Emory University (Atlanta, GA). The ten chimpanzees included five males and five females. We isolated and transformed lymphocytes with frozen virus stocks by using a standard Epstein-Barr virus transformation protocol (1). For the human samples, we randomly selected lymphoblastoid cell lines for nine unrelated humans from a collection previously established in our laboratory (reference 1). All cell lines were maintained at 37 degrees C in 5% CO2, and with DMEM (Gibco-BRL) supplemented with 2 mM L-glutamine (Gibco-BRL, Carlsbad, CA), 100 U/ml penicillin, 100 microg/ml streptomycin (BioWhittaker, East Rutherford, NJ), and 10% FCS (Sigma, St. Louis, MO). All cell lines were maintained under the same conditions for more than 3 months, and were harvested on the same day. To minimize differences in growth behavior and morphology between different cell lines, we fed and split them at comparable growth points. Because growth rates differed between different lines, the splitting schedule and feeding cycle for individual lines varied. reference 1: Risch N, Spiker D, Lotspeich L, Nouri N, Hinds D, Hallmayer J, Kalaydjieva L, McCague P, Dimiceli S, Pitts T, Nguyen L, Yang J, Harper C, Thorpe D, Vermeer S, Young H, Hebert J, Lin A, Ferguson J, Chiotti C, Wiese-Slater S, Rogers T, Salmon B, Nicholas P, Myers RM, and et al. A genomic screen of autism: evidence for a multilocus etiology. Am J Hum Genet 65: 493-507., 1999. PolyA+ RNAs were isolated from approximated 107 cells by using the FAST TRACK 2.0 kit (Invitrogen, Carlsbad, CA) following the manufacturer's instructions. Equal amounts of poly-A RNA from nine human cell lines were pooled to serve as the common reference sample for each of the individual 19 samples. The human cDNA microarrays used in this study were obtained from the Stanford Functional Genomic Facility (http://www.microarray.org). We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html). Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ml containing 2 mg mRNA / 4 mg oligo (dT) primer / 0.5 mM each dATP, dCTP, dGTP / 0.2 mM dTTP / 0.1 mM Cy3/5-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ) / 0.01 M DTT / 400 units Superscript II reverse transcriptase (Life Technologies). We labeled the reference sample with Cy3-dUTP; thus in this study the Cy5/Cy3 ratio is taken as the measure of transcript levels in individual test samples. After incubation at 42 degrees C for 2-3 hours, the RNA was degraded by adding 15 ml of 0.1 N NaOH at 70 degrees C for 10 minutes, and was neutralized by adding 15 ml of 0.1 N HCl. Equal amounts of the Cy3 and Cy5 probes were combined and concentrated by using a Microcon YM-100 column (Millipore). After 20 mg Cot1 human DNA (Gibco-BRL), 20 mg PolyA RNA (Sigma, #P9403) and 20 mg tRNA (Gibco-BRL, #15401-011) were added, the probes were purified. For final probe preparation, 6 ml of 20x SSC (BioWhittaker, MD) and 1 ml of 10% SDS were added. The probes were denatured at 100 degrees C for 3 minutes, incubated at 37 degrees C for 30 minutes, and placed on the array under a 24 mm x 60 mm glass cover slip (Fisher). The slides were incubated at 65 degrees C for 16 hours in a hybridization chamber (GeneMachine, San Carlos, California). Slides were washed in graded SSC with 0.1% SDS: 2x for 2 to 5 minutes, 1x for 2 minutes, and 0.1x for 2 minutes, and spun dry. Fluorescent array images were collected for Cy3 and Cy5 channels by using a GenePix 4000B scanner (Axon Instruments, Foster City, CA) at a resolution of 5 mm per pixel.
19 GSM24716 24577 MeasuredBioAssayData&DerivedBioAssayData 43,008 Stanford Microarray Database (SMD) 2004-06-08 [cDNA Array] SHBR (GPL1283) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens
pooled Whole blood (10 ml) for ten unrelated common chimpanzees (Pan troglodytes) was kindly provided by Dr. Harold M. McClure at the Yerkes Regional Primate Center of Emory University (Atlanta, GA). The ten chimpanzees included five males and five females. We isolated and transformed lymphocytes with frozen virus stocks by using a standard Epstein-Barr virus transformation protocol (1). For the human samples, we randomly selected lymphoblastoid cell lines for nine unrelated humans from a collection previously established in our laboratory (reference 1). All cell lines were maintained at 37 degrees C in 5% CO2, and with DMEM (Gibco-BRL) supplemented with 2 mM L-glutamine (Gibco-BRL, Carlsbad, CA), 100 U/ml penicillin, 100 microg/ml streptomycin (BioWhittaker, East Rutherford, NJ), and 10% FCS (Sigma, St. Louis, MO). All cell lines were maintained under the same conditions for more than 3 months, and were harvested on the same day. To minimize differences in growth behavior and morphology between different cell lines, we fed and split them at comparable growth points. Because growth rates differed between different lines, the splitting schedule and feeding cycle for individual lines varied. reference 1: Risch N, Spiker D, Lotspeich L, Nouri N, Hinds D, Hallmayer J, Kalaydjieva L, McCague P, Dimiceli S, Pitts T, Nguyen L, Yang J, Harper C, Thorpe D, Vermeer S, Young H, Hebert J, Lin A, Ferguson J, Chiotti C, Wiese-Slater S, Rogers T, Salmon B, Nicholas P, Myers RM, and et al. A genomic screen of autism: evidence for a multilocus etiology. Am J Hum Genet 65: 493-507., 1999. PolyA+ RNAs were isolated from approximated 107 cells by using the FAST TRACK 2.0 kit (Invitrogen, Carlsbad, CA) following the manufacturer's instructions. Equal amounts of poly-A RNA from nine human cell lines were pooled to serve as the common reference sample for each of the individual 19 samples. The human cDNA microarrays used in this study were obtained from the Stanford Functional Genomic Facility (http://www.microarray.org). We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html). Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ml containing 2 mg mRNA / 4 mg oligo (dT) primer / 0.5 mM each dATP, dCTP, dGTP / 0.2 mM dTTP / 0.1 mM Cy3/5-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ) / 0.01 M DTT / 400 units Superscript II reverse transcriptase (Life Technologies). We labeled the reference sample with Cy3-dUTP; thus in this study the Cy5/Cy3 ratio is taken as the measure of transcript levels in individual test samples. After incubation at 42 degrees C for 2-3 hours, the RNA was degraded by adding 15 ml of 0.1 N NaOH at 70 degrees C for 10 minutes, and was neutralized by adding 15 ml of 0.1 N HCl. Equal amounts of the Cy3 and Cy5 probes were combined and concentrated by using a Microcon YM-100 column (Millipore). After 20 mg Cot1 human DNA (Gibco-BRL), 20 mg PolyA RNA (Sigma, #P9403) and 20 mg tRNA (Gibco-BRL, #15401-011) were added, the probes were purified. For final probe preparation, 6 ml of 20x SSC (BioWhittaker, MD) and 1 ml of 10% SDS were added. The probes were denatured at 100 degrees C for 3 minutes, incubated at 37 degrees C for 30 minutes, and placed on the array under a 24 mm x 60 mm glass cover slip (Fisher). The slides were incubated at 65 degrees C for 16 hours in a hybridization chamber (GeneMachine, San Carlos, California). Slides were washed in graded SSC with 0.1% SDS: 2x for 2 to 5 minutes, 1x for 2 minutes, and 0.1x for 2 minutes, and spun dry. Fluorescent array images were collected for Cy3 and Cy5 channels by using a GenePix 4000B scanner (Axon Instruments, Foster City, CA) at a resolution of 5 mm per pixel.
20 GSM24717 24578 MeasuredBioAssayData&DerivedBioAssayData 43,008 Stanford Microarray Database (SMD) 2004-06-08 [cDNA Array] SHBX (GPL1282) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens
pooled Whole blood (10 ml) for ten unrelated common chimpanzees (Pan troglodytes) was kindly provided by Dr. Harold M. McClure at the Yerkes Regional Primate Center of Emory University (Atlanta, GA). The ten chimpanzees included five males and five females. We isolated and transformed lymphocytes with frozen virus stocks by using a standard Epstein-Barr virus transformation protocol (1). For the human samples, we randomly selected lymphoblastoid cell lines for nine unrelated humans from a collection previously established in our laboratory (reference 1). All cell lines were maintained at 37 degrees C in 5% CO2, and with DMEM (Gibco-BRL) supplemented with 2 mM L-glutamine (Gibco-BRL, Carlsbad, CA), 100 U/ml penicillin, 100 microg/ml streptomycin (BioWhittaker, East Rutherford, NJ), and 10% FCS (Sigma, St. Louis, MO). All cell lines were maintained under the same conditions for more than 3 months, and were harvested on the same day. To minimize differences in growth behavior and morphology between different cell lines, we fed and split them at comparable growth points. Because growth rates differed between different lines, the splitting schedule and feeding cycle for individual lines varied. reference 1: Risch N, Spiker D, Lotspeich L, Nouri N, Hinds D, Hallmayer J, Kalaydjieva L, McCague P, Dimiceli S, Pitts T, Nguyen L, Yang J, Harper C, Thorpe D, Vermeer S, Young H, Hebert J, Lin A, Ferguson J, Chiotti C, Wiese-Slater S, Rogers T, Salmon B, Nicholas P, Myers RM, and et al. A genomic screen of autism: evidence for a multilocus etiology. Am J Hum Genet 65: 493-507., 1999. PolyA+ RNAs were isolated from approximated 107 cells by using the FAST TRACK 2.0 kit (Invitrogen, Carlsbad, CA) following the manufacturer's instructions. Equal amounts of poly-A RNA from nine human cell lines were pooled to serve as the common reference sample for each of the individual 19 samples. The human cDNA microarrays used in this study were obtained from the Stanford Functional Genomic Facility (http://www.microarray.org). We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html). Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ml containing 2 mg mRNA / 4 mg oligo (dT) primer / 0.5 mM each dATP, dCTP, dGTP / 0.2 mM dTTP / 0.1 mM Cy3/5-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ) / 0.01 M DTT / 400 units Superscript II reverse transcriptase (Life Technologies). We labeled the reference sample with Cy3-dUTP; thus in this study the Cy5/Cy3 ratio is taken as the measure of transcript levels in individual test samples. After incubation at 42 degrees C for 2-3 hours, the RNA was degraded by adding 15 ml of 0.1 N NaOH at 70 degrees C for 10 minutes, and was neutralized by adding 15 ml of 0.1 N HCl. Equal amounts of the Cy3 and Cy5 probes were combined and concentrated by using a Microcon YM-100 column (Millipore). After 20 mg Cot1 human DNA (Gibco-BRL), 20 mg PolyA RNA (Sigma, #P9403) and 20 mg tRNA (Gibco-BRL, #15401-011) were added, the probes were purified. For final probe preparation, 6 ml of 20x SSC (BioWhittaker, MD) and 1 ml of 10% SDS were added. The probes were denatured at 100 degrees C for 3 minutes, incubated at 37 degrees C for 30 minutes, and placed on the array under a 24 mm x 60 mm glass cover slip (Fisher). The slides were incubated at 65 degrees C for 16 hours in a hybridization chamber (GeneMachine, San Carlos, California). Slides were washed in graded SSC with 0.1% SDS: 2x for 2 to 5 minutes, 1x for 2 minutes, and 0.1x for 2 minutes, and spun dry. Fluorescent array images were collected for Cy3 and Cy5 channels by using a GenePix 4000B scanner (Axon Instruments, Foster City, CA) at a resolution of 5 mm per pixel.
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