|
|
|
|
| 1 |
GSM24699 |
24550 MeasuredBioAssayData&DerivedBioAssayData |
43,008 |
Stanford Microarray Database (SMD) |
2004-06-08 |
[cDNAアレイ] SHBR (GPL1283) |
RNA |
Pan troglodytes,Homo sapiens
 |
混合 |
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. |
| 2 |
GSM24700 |
24551 MeasuredBioAssayData&DerivedBioAssayData |
43,008 |
Stanford Microarray Database (SMD) |
2004-06-08 |
[cDNAアレイ] SHBR (GPL1283) |
RNA |
Pan troglodytes,Homo sapiens
|
混合 |
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 |
GSM24701 |
24552 MeasuredBioAssayData&DerivedBioAssayData |
43,008 |
Stanford Microarray Database (SMD) |
2004-06-08 |
[cDNAアレイ] SHBR (GPL1283) |
RNA |
Pan troglodytes,Homo sapiens
|
混合 |
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 |
GSM24702 |
24553 MeasuredBioAssayData&DerivedBioAssayData |
43,008 |
Stanford Microarray Database (SMD) |
2004-06-08 |
[cDNAアレイ] SHBR (GPL1283) |
RNA |
Pan troglodytes,Homo sapiens
|
混合 |
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 |
GSM24703 |
24554 MeasuredBioAssayData&DerivedBioAssayData |
43,008 |
Stanford Microarray Database (SMD) |
2004-06-08 |
[cDNAアレイ] SHBR (GPL1283) |
RNA |
Pan troglodytes,Homo sapiens
|
混合 |
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 |
GSM24704 |
24555 MeasuredBioAssayData&DerivedBioAssayData |
43,008 |
Stanford Microarray Database (SMD) |
2004-06-08 |
[cDNAアレイ] SHBR (GPL1283) |
RNA |
Pan troglodytes,Homo sapiens
|
混合 |
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 |
GSM24705 |
24556 MeasuredBioAssayData&DerivedBioAssayData |
43,008 |
Stanford Microarray Database (SMD) |
2004-06-08 |
[cDNAアレイ] SHBR (GPL1283) |
RNA |
Pan troglodytes,Homo sapiens
|
混合 |
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 |
GSM24706 |
24557 MeasuredBioAssayData&DerivedBioAssayData |
43,008 |
Stanford Microarray Database (SMD) |
2004-06-08 |
[cDNAアレイ] SHBR (GPL1283) |
RNA |
Pan troglodytes,Homo sapiens
|
混合 |
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 |
GSM24707 |
24558 MeasuredBioAssayData&DerivedBioAssayData |
43,008 |
Stanford Microarray Database (SMD) |
2004-06-08 |
[cDNAアレイ] SHBR (GPL1283) |
RNA |
Pan troglodytes,Homo sapiens
|
混合 |
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 |
GSM24708 |
24559 MeasuredBioAssayData&DerivedBioAssayData |
43,008 |
Stanford Microarray Database (SMD) |
2004-06-08 |
[cDNAアレイ] SHBR (GPL1283) |
RNA |
Pan troglodytes,Homo sapiens
|
混合 |
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 |
GSM24709 |
24560 MeasuredBioAssayData&DerivedBioAssayData |
43,008 |
Stanford Microarray Database (SMD) |
2004-06-08 |
[cDNAアレイ] SHBR (GPL1283) |
RNA |
Pan troglodytes,Homo sapiens
|
混合 |
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 |
GSM24710 |
24561 MeasuredBioAssayData&DerivedBioAssayData |
43,008 |
Stanford Microarray Database (SMD) |
2004-06-08 |
[cDNAアレイ] SHBR (GPL1283) |
RNA |
Pan troglodytes,Homo sapiens
|
混合 |
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 |
GSM24711 |
24562 MeasuredBioAssayData&DerivedBioAssayData |
43,008 |
Stanford Microarray Database (SMD) |
2004-06-08 |
[cDNAアレイ] SHBR (GPL1283) |
RNA |
Pan troglodytes,Homo sapiens
|
混合 |
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 |
GSM24712 |
24563 MeasuredBioAssayData&DerivedBioAssayData |
43,008 |
Stanford Microarray Database (SMD) |
2004-06-08 |
[cDNAアレイ] SHBR (GPL1283) |
RNA |
Pan troglodytes,Homo sapiens
|
混合 |
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 |
GSM24713 |
24564 MeasuredBioAssayData&DerivedBioAssayData |
43,008 |
Stanford Microarray Database (SMD) |
2004-06-08 |
[cDNAアレイ] SHBR (GPL1283) |
RNA |
Pan troglodytes,Homo sapiens
|
混合 |
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 |
GSM24714 |
24575 MeasuredBioAssayData&DerivedBioAssayData |
43,008 |
Stanford Microarray Database (SMD) |
2004-06-08 |
[cDNAアレイ] SHBR (GPL1283) |
RNA |
Pan troglodytes,Homo sapiens
|
混合 |
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 |
GSM24715 |
24576 MeasuredBioAssayData&DerivedBioAssayData |
43,008 |
Stanford Microarray Database (SMD) |
2004-06-08 |
[cDNAアレイ] SHBR (GPL1283) |
RNA |
Pan troglodytes,Homo sapiens
|
混合 |
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 |
GSM24716 |
24577 MeasuredBioAssayData&DerivedBioAssayData |
43,008 |
Stanford Microarray Database (SMD) |
2004-06-08 |
[cDNAアレイ] SHBR (GPL1283) |
RNA |
Pan troglodytes,Homo sapiens
|
混合 |
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 |
GSM24717 |
24578 MeasuredBioAssayData&DerivedBioAssayData |
43,008 |
Stanford Microarray Database (SMD) |
2004-06-08 |
[cDNAアレイ] SHBX (GPL1282) |
RNA |
Pan troglodytes,Homo sapiens
|
混合 |
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 |
GSM1004260 |
25% Human / 75% Mouse Replicate 1 |
0 |
University of Miami |
2012-09-14 |
[HT-Seq] Illumina Genome Analyzer IIx (Homo sapiens; Mus musculus) (GPL16061) |
SRA |
Homo sapiens,Mus musculus
 |
混合 |
human breast & mouse normal lung tissue |
|
|
|