Gene Expression Omnibus (GEO) Overview Version：2013-06-15Japanese 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
(2,851)		   Primates
(60)		   Rodents
(2,590)		   Mammals
(41)		   Vertebrates
(39)		   Invertebrates
(59)		   Plants
(464)		   Bacteria
(78)		   Viruses
(0)		   Phages
(0)		   Unclassified
(120)		   All
(6,302)		  
  SAGE NlaIII
(0)		   SAGE RsaI
(0)		   SAGE Sau3A
(0)		   MPSS
(0)		   GeneChip
(0)		   Tiling Array
(0)		   cDNA Array
(120)		   Oligo Array
(0)		   Bead Array
(0)		   Protein Array
(0)		   Antibody
(0)		   RT-PCR
(0)		   HT-Seq
(0)		   Other
(0)		   All
(120)		  
  brain
(0)		   blood
(0)		   connective
(0)		   reproductive
(0)		   muscular
(0)		   digestive
(0)		   liver
(0)		   lung
(0)		   urinary
(0)		   endo/exo-crine
(0)		   embryo
(0)		   adult aerial structure
(0)		   young aerial structure
(0)		   root
(0)		   meristem/growing tissue
(0)		   flower/sexual organ
(0)		   seed/fruit/grain
(0)		   pooled
(89)		   unclassified
(31)		   all
(120)		  
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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 GSM35433 SHFD232 41,472 Stanford Microarray Database (SMD) 2004-11-17 [cDNA Array] SHFD (GPL1709) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens		 unclassified source_name:1847 aURNA title:SHFD232 description:Simple annotation: Normal tissue, cell line Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52954.gif; format: GIF Sample_label_ch1 = Cy3 Sample_label_ch2 = Cy5 For the second batch, we amplified the nine RNA samples by using the MessageAmp aRNA Amplification Kit (Ambion) according to manufacturer's specifications. Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ul containing 2 ug mRNA(or amplified RNA)/ 4 ug oligo (dT) primer / 0.5 uM each dATP, dCTP, dGTP / 0.2 uM dTTP / 0.1 uM 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 &amp;#8734;C for 2-3 hours, the RNA was degraded by adding 15 ul of 0.1 N NaOH at 70 &amp;#8734;C for 10 minutes, and was neutralized by adding 15 ul 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 ug Cot1 human DNA (Gibco-BRL), 20 ug PolyA RNA (Sigma, #P9403) and 20 ug tRNA (Gibco-BRL, #15401-011) were added, the probes were purified. For final probe preparation, 6 ul of 20x SSC (BioWhittaker, MD) and 1 ul of 10% SDS were added. The probes were denatured at 100 &amp;#8734;C for 3 minutes, incubated at 37 &amp;#8734;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 &amp;#8734;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. Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.49; Parameter Scan Time = 10:44:26; Parameter PMT Volts = 520; Parameter Scan Date = 2004-06-02; Parameter Pixel Size = 10; Parameter Laser on time = 19480; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.98; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.49; Parameter Scan Time = 10:44:26; Parameter PMT Volts = 620; Parameter Scan Date = 2004-06-02; Parameter Pixel Size = 10; Parameter Laser on time = 18883; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.40; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
2 GSM35434 SHFD231 41,472 Stanford Microarray Database (SMD) 2004-11-17 [cDNA Array] SHFD (GPL1709) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens		 unclassified source_name:CHRISTA aURNA title:SHFD231 description:Simple annotation: Normal tissue, cell line Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52953.gif; format: GIF Sample_label_ch1 = Cy3 Sample_label_ch2 = Cy5 For the second batch, we amplified the nine RNA samples by using the MessageAmp aRNA Amplification Kit (Ambion) according to manufacturer's specifications. Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ul containing 2 ug mRNA(or amplified RNA)/ 4 ug oligo (dT) primer / 0.5 uM each dATP, dCTP, dGTP / 0.2 uM dTTP / 0.1 uM 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 &amp;#8734;C for 2-3 hours, the RNA was degraded by adding 15 ul of 0.1 N NaOH at 70 &amp;#8734;C for 10 minutes, and was neutralized by adding 15 ul 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 ug Cot1 human DNA (Gibco-BRL), 20 ug PolyA RNA (Sigma, #P9403) and 20 ug tRNA (Gibco-BRL, #15401-011) were added, the probes were purified. For final probe preparation, 6 ul of 20x SSC (BioWhittaker, MD) and 1 ul of 10% SDS were added. The probes were denatured at 100 &amp;#8734;C for 3 minutes, incubated at 37 &amp;#8734;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 &amp;#8734;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. Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.13; Parameter Scan Time = 10:35:41; Parameter PMT Volts = 540; Parameter Scan Date = 2004-06-02; Parameter Pixel Size = 10; Parameter Laser on time = 19471; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.98; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.13; Parameter Scan Time = 10:35:41; Parameter PMT Volts = 600; Parameter Scan Date = 2004-06-02; Parameter Pixel Size = 10; Parameter Laser on time = 18875; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.40; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
3 GSM35438 SHFD229 41,472 Stanford Microarray Database (SMD) 2004-11-17 [cDNA Array] SHFD (GPL1709) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens		 unclassified source_name:84 aURNA title:SHFD229 description:Simple annotation: Normal tissue, cell line Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52955.gif; format: GIF Sample_label_ch1 = Cy3 Sample_label_ch2 = Cy5 For the second batch, we amplified the nine RNA samples by using the MessageAmp aRNA Amplification Kit (Ambion) according to manufacturer's specifications. Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ul containing 2 ug mRNA(or amplified RNA)/ 4 ug oligo (dT) primer / 0.5 uM each dATP, dCTP, dGTP / 0.2 uM dTTP / 0.1 uM 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 &amp;#8734;C for 2-3 hours, the RNA was degraded by adding 15 ul of 0.1 N NaOH at 70 &amp;#8734;C for 10 minutes, and was neutralized by adding 15 ul 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 ug Cot1 human DNA (Gibco-BRL), 20 ug PolyA RNA (Sigma, #P9403) and 20 ug tRNA (Gibco-BRL, #15401-011) were added, the probes were purified. For final probe preparation, 6 ul of 20x SSC (BioWhittaker, MD) and 1 ul of 10% SDS were added. The probes were denatured at 100 &amp;#8734;C for 3 minutes, incubated at 37 &amp;#8734;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 &amp;#8734;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. Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.74; Parameter Scan Time = 10:51:53; Parameter PMT Volts = 520; Parameter Scan Date = 2004-06-02; Parameter Pixel Size = 10; Parameter Laser on time = 19488; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.97; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.74; Parameter Scan Time = 10:51:53; Parameter PMT Volts = 620; Parameter Scan Date = 2004-06-02; Parameter Pixel Size = 10; Parameter Laser on time = 18891; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.41; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
4 GSM35430 SHFD228 41,472 Stanford Microarray Database (SMD) 2004-11-17 [cDNA Array] SHFD (GPL1709) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens		 unclassified source_name:1857 aURNA title:SHFD228 description:Simple annotation: Normal tissue, cell line Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52956.gif; format: GIF Sample_label_ch1 = Cy3 Sample_label_ch2 = Cy5 For the second batch, we amplified the nine RNA samples by using the MessageAmp aRNA Amplification Kit (Ambion) according to manufacturer's specifications. Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ul containing 2 ug mRNA(or amplified RNA)/ 4 ug oligo (dT) primer / 0.5 uM each dATP, dCTP, dGTP / 0.2 uM dTTP / 0.1 uM 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 &amp;#8734;C for 2-3 hours, the RNA was degraded by adding 15 ul of 0.1 N NaOH at 70 &amp;#8734;C for 10 minutes, and was neutralized by adding 15 ul 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 ug Cot1 human DNA (Gibco-BRL), 20 ug PolyA RNA (Sigma, #P9403) and 20 ug tRNA (Gibco-BRL, #15401-011) were added, the probes were purified. For final probe preparation, 6 ul of 20x SSC (BioWhittaker, MD) and 1 ul of 10% SDS were added. The probes were denatured at 100 &amp;#8734;C for 3 minutes, incubated at 37 &amp;#8734;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 &amp;#8734;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. Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.20; Parameter Scan Time = 11:27:54; Parameter PMT Volts = 540; Parameter Scan Date = 2004-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 19591; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.97; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.20; Parameter Scan Time = 11:27:54; Parameter PMT Volts = 610; Parameter Scan Date = 2004-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 18995; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.43; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
5 GSM35436 SHFD207 41,472 Stanford Microarray Database (SMD) 2004-11-17 [cDNA Array] SHFD (GPL1709) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens		 unclassified source_name:992 aURNA title:SHFD207 description:Simple annotation: Normal tissue, cell line Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52957.gif; format: GIF Sample_label_ch1 = Cy3 Sample_label_ch2 = Cy5 For the second batch, we amplified the nine RNA samples by using the MessageAmp aRNA Amplification Kit (Ambion) according to manufacturer's specifications. Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ul containing 2 ug mRNA(or amplified RNA)/ 4 ug oligo (dT) primer / 0.5 uM each dATP, dCTP, dGTP / 0.2 uM dTTP / 0.1 uM 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 &amp;#8734;C for 2-3 hours, the RNA was degraded by adding 15 ul of 0.1 N NaOH at 70 &amp;#8734;C for 10 minutes, and was neutralized by adding 15 ul 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 ug Cot1 human DNA (Gibco-BRL), 20 ug PolyA RNA (Sigma, #P9403) and 20 ug tRNA (Gibco-BRL, #15401-011) were added, the probes were purified. For final probe preparation, 6 ul of 20x SSC (BioWhittaker, MD) and 1 ul of 10% SDS were added. The probes were denatured at 100 &amp;#8734;C for 3 minutes, incubated at 37 &amp;#8734;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 &amp;#8734;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. Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.41; Parameter Scan Time = 11:36:44; Parameter PMT Volts = 540; Parameter Scan Date = 2004-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 19600; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.99; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.41; Parameter Scan Time = 11:36:44; Parameter PMT Volts = 610; Parameter Scan Date = 2004-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 19004; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.44; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
6 GSM35437 SHFD206 41,472 Stanford Microarray Database (SMD) 2004-11-17 [cDNA Array] SHFD (GPL1709) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens		 unclassified source_name:1143 aURNA title:SHFD206 description:Simple annotation: Normal tissue, cell line Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52958.gif; format: GIF Sample_label_ch1 = Cy3 Sample_label_ch2 = Cy5 For the second batch, we amplified the nine RNA samples by using the MessageAmp aRNA Amplification Kit (Ambion) according to manufacturer's specifications. Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ul containing 2 ug mRNA(or amplified RNA)/ 4 ug oligo (dT) primer / 0.5 uM each dATP, dCTP, dGTP / 0.2 uM dTTP / 0.1 uM 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 &amp;#8734;C for 2-3 hours, the RNA was degraded by adding 15 ul of 0.1 N NaOH at 70 &amp;#8734;C for 10 minutes, and was neutralized by adding 15 ul 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 ug Cot1 human DNA (Gibco-BRL), 20 ug PolyA RNA (Sigma, #P9403) and 20 ug tRNA (Gibco-BRL, #15401-011) were added, the probes were purified. For final probe preparation, 6 ul of 20x SSC (BioWhittaker, MD) and 1 ul of 10% SDS were added. The probes were denatured at 100 &amp;#8734;C for 3 minutes, incubated at 37 &amp;#8734;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 &amp;#8734;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. Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.65; Parameter Scan Time = 11:46:50; Parameter PMT Volts = 540; Parameter Scan Date = 2004-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 19609; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.98; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.65; Parameter Scan Time = 11:46:50; Parameter PMT Volts = 610; Parameter Scan Date = 2004-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 19013; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.44; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
7 GSM35435 SHFD205 41,472 Stanford Microarray Database (SMD) 2004-11-17 [cDNA Array] SHFD (GPL1709) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens		 unclassified source_name:1275 aURNA title:SHFD205 description:Simple annotation: Normal tissue, cell line Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52959.gif; format: GIF Sample_label_ch1 = Cy3 Sample_label_ch2 = Cy5 For the second batch, we amplified the nine RNA samples by using the MessageAmp aRNA Amplification Kit (Ambion) according to manufacturer's specifications. Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ul containing 2 ug mRNA(or amplified RNA)/ 4 ug oligo (dT) primer / 0.5 uM each dATP, dCTP, dGTP / 0.2 uM dTTP / 0.1 uM 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 &amp;#8734;C for 2-3 hours, the RNA was degraded by adding 15 ul of 0.1 N NaOH at 70 &amp;#8734;C for 10 minutes, and was neutralized by adding 15 ul 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 ug Cot1 human DNA (Gibco-BRL), 20 ug PolyA RNA (Sigma, #P9403) and 20 ug tRNA (Gibco-BRL, #15401-011) were added, the probes were purified. For final probe preparation, 6 ul of 20x SSC (BioWhittaker, MD) and 1 ul of 10% SDS were added. The probes were denatured at 100 &amp;#8734;C for 3 minutes, incubated at 37 &amp;#8734;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 &amp;#8734;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. Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.96; Parameter Scan Time = 12:03:41; Parameter PMT Volts = 530; Parameter Scan Date = 2004-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 19620; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.97; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.96; Parameter Scan Time = 12:03:41; Parameter PMT Volts = 630; Parameter Scan Date = 2004-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 19024; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.44; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
8 GSM35425 SHFC179 41,472 Stanford Microarray Database (SMD) 2004-11-17 [cDNA Array] SHFC (GPL1710) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens		 unclassified source_name:CLAWS aURNA title:SHFC179 description:Simple annotation: Normal tissue, cell line Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52947.gif; format: GIF Sample_label_ch1 = Cy3 Sample_label_ch2 = Cy5 We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html). Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.47; Parameter Scan Time = 14:31:33; Parameter PMT Volts = 600; Parameter Scan Date = 2004-03-16; Parameter Pixel Size = 10; Parameter Laser on time = 16901; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.97; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.47; Parameter Scan Time = 14:31:33; Parameter PMT Volts = 630; Parameter Scan Date = 2004-03-16; Parameter Pixel Size = 10; Parameter Laser on time = 16929; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.51; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
9 GSM35420 SHFC178 41,472 Stanford Microarray Database (SMD) 2004-11-17 [cDNA Array] SHFC (GPL1710) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens		 unclassified source_name:489 aURNA title:SHFC178 description:Simple annotation: Normal tissue, cell line Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52946.gif; format: GIF Sample_label_ch1 = Cy3 Sample_label_ch2 = Cy5 We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html). Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.05; Parameter Scan Time = 12:59:53; Parameter PMT Volts = 530; Parameter Scan Date = 2004-03-12; Parameter Pixel Size = 10; Parameter Laser on time = 16865; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.88; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.05; Parameter Scan Time = 12:59:53; Parameter PMT Volts = 540; Parameter Scan Date = 2004-03-12; Parameter Pixel Size = 10; Parameter Laser on time = 16892; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.46; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
10 GSM35421 SHFC177 41,472 Stanford Microarray Database (SMD) 2004-11-17 [cDNA Array] SHFC (GPL1710) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens		 unclassified source_name:203 aURNA title:SHFC177 description:Simple annotation: Normal tissue, cell line Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52945.gif; format: GIF Sample_label_ch1 = Cy3 Sample_label_ch2 = Cy5 We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html). Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.78; Parameter Scan Time = 12:43:41; Parameter PMT Volts = 590; Parameter Scan Date = 2004-03-12; Parameter Pixel Size = 10; Parameter Laser on time = 16848; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.91; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.78; Parameter Scan Time = 12:43:41; Parameter PMT Volts = 600; Parameter Scan Date = 2004-03-12; Parameter Pixel Size = 10; Parameter Laser on time = 16876; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.52; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
11 GSM35426 SHFC176 41,472 Stanford Microarray Database (SMD) 2004-11-17 [cDNA Array] SHFC (GPL1710) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens		 unclassified source_name:REBA aURNA title:SHFC176 description:Simple annotation: Normal tissue, cell line Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52944.gif; format: GIF Sample_label_ch1 = Cy3 Sample_label_ch2 = Cy5 We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html). Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.56; Parameter Scan Time = 12:32:33; Parameter PMT Volts = 550; Parameter Scan Date = 2004-03-12; Parameter Pixel Size = 10; Parameter Laser on time = 16837; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.90; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.56; Parameter Scan Time = 12:32:33; Parameter PMT Volts = 590; Parameter Scan Date = 2004-03-12; Parameter Pixel Size = 10; Parameter Laser on time = 16865; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.52; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
12 GSM35428 SHFC175 41,472 Stanford Microarray Database (SMD) 2004-11-17 [cDNA Array] SHFC (GPL1710) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens		 unclassified source_name:FAYE aURNA title:SHFC175 description:Simple annotation: Normal tissue, cell line Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52943.gif; format: GIF Sample_label_ch1 = Cy3 Sample_label_ch2 = Cy5 We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html). Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.13; Parameter Scan Time = 12:16:27; Parameter PMT Volts = 570; Parameter Scan Date = 2004-03-12; Parameter Pixel Size = 10; Parameter Laser on time = 16820; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.92; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.13; Parameter Scan Time = 12:16:27; Parameter PMT Volts = 610; Parameter Scan Date = 2004-03-12; Parameter Pixel Size = 10; Parameter Laser on time = 16848; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.52; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
13 GSM35422 SHFC123 41,472 Stanford Microarray Database (SMD) 2004-11-17 [cDNA Array] SHFC (GPL1710) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens		 unclassified source_name:LILI aURNA title:SHFC123 description:Simple annotation: Normal tissue, cell line Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52942.gif; format: GIF Sample_label_ch1 = Cy3 Sample_label_ch2 = Cy5 We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html). Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.55; Parameter Scan Time = 11:10:30; Parameter PMT Volts = 540; Parameter Scan Date = 2004-03-10; Parameter Pixel Size = 10; Parameter Laser on time = 16809; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.96; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.55; Parameter Scan Time = 11:10:30; Parameter PMT Volts = 600; Parameter Scan Date = 2004-03-10; Parameter Pixel Size = 10; Parameter Laser on time = 16837; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.47; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
14 GSM35427 SHFC122 41,472 Stanford Microarray Database (SMD) 2004-11-17 [cDNA Array] SHFC (GPL1710) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens		 unclassified source_name:LILI aURNA title:SHFC122 description:Simple annotation: Normal tissue, cell line Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52941.gif; format: GIF Sample_label_ch1 = Cy3 Sample_label_ch2 = Cy5 We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html). Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.25; Parameter Scan Time = 11:02:37; Parameter PMT Volts = 540; Parameter Scan Date = 2004-03-10; Parameter Pixel Size = 10; Parameter Laser on time = 16801; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.96; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.25; Parameter Scan Time = 11:02:37; Parameter PMT Volts = 600; Parameter Scan Date = 2004-03-10; Parameter Pixel Size = 10; Parameter Laser on time = 16829; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.47; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
15 GSM35423 SHFB26 41,472 Stanford Microarray Database (SMD) 2004-11-17 [cDNA Array] SHFB (GPL1711) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens		 unclassified source_name:J89 aURNA title:SHFB26 description:Simple annotation: Normal tissue, cell line Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52950.gif; format: GIF Sample_label_ch1 = Cy3 Sample_label_ch2 = Cy5 We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html). Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.39; Parameter Scan Time = 15:11:10; Parameter PMT Volts = 570; Parameter Scan Date = 2004-03-16; Parameter Pixel Size = 10; Parameter Laser on time = 16942; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.96; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.39; Parameter Scan Time = 15:11:10; Parameter PMT Volts = 630; Parameter Scan Date = 2004-03-16; Parameter Pixel Size = 10; Parameter Laser on time = 16969; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.45; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
16 GSM35424 SHFB25 41,472 Stanford Microarray Database (SMD) 2004-11-17 [cDNA Array] SHFB (GPL1711) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens		 unclassified source_name:797 aURNA title:SHFB25 description:Simple annotation: Normal tissue, cell line Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52949.gif; format: GIF Sample_label_ch1 = Cy3 Sample_label_ch2 = Cy5 We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html). Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.29; Parameter Scan Time = 15:01:28; Parameter PMT Volts = 560; Parameter Scan Date = 2004-03-16; Parameter Pixel Size = 10; Parameter Laser on time = 16932; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.96; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.29; Parameter Scan Time = 15:01:28; Parameter PMT Volts = 610; Parameter Scan Date = 2004-03-16; Parameter Pixel Size = 10; Parameter Laser on time = 16959; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.46; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
17 GSM35431 SHFB240 41,472 Stanford Microarray Database (SMD) 2004-11-17 [cDNA Array] SHFB (GPL1711) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens		 unclassified source_name:BROOK aURNA title:SHFB240 description:Simple annotation: Normal tissue, cell line Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52952.gif; format: GIF Sample_label_ch1 = Cy3 Sample_label_ch2 = Cy5 For the second batch, we amplified the nine RNA samples by using the MessageAmp aRNA Amplification Kit (Ambion) according to manufacturer's specifications. Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ul containing 2 ug mRNA(or amplified RNA)/ 4 ug oligo (dT) primer / 0.5 uM each dATP, dCTP, dGTP / 0.2 uM dTTP / 0.1 uM 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 &amp;#8734;C for 2-3 hours, the RNA was degraded by adding 15 ul of 0.1 N NaOH at 70 &amp;#8734;C for 10 minutes, and was neutralized by adding 15 ul 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 ug Cot1 human DNA (Gibco-BRL), 20 ug PolyA RNA (Sigma, #P9403) and 20 ug tRNA (Gibco-BRL, #15401-011) were added, the probes were purified. For final probe preparation, 6 ul of 20x SSC (BioWhittaker, MD) and 1 ul of 10% SDS were added. The probes were denatured at 100 &amp;#8734;C for 3 minutes, incubated at 37 &amp;#8734;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 &amp;#8734;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. Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.10; Parameter Scan Time = 11:29:26; Parameter PMT Volts = 560; Parameter Scan Date = 2004-05-28; Parameter Pixel Size = 10; Parameter Laser on time = 19447; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.99; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.10; Parameter Scan Time = 11:29:26; Parameter PMT Volts = 620; Parameter Scan Date = 2004-05-28; Parameter Pixel Size = 10; Parameter Laser on time = 18851; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.44; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
18 GSM35429 SHFB24 41,472 Stanford Microarray Database (SMD) 2004-11-17 [cDNA Array] SHFB (GPL1711) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens		 unclassified source_name:PENOY aURNA title:SHFB24 description:Simple annotation: Normal tissue, cell line Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52948.gif; format: GIF Sample_label_ch1 = Cy3 Sample_label_ch2 = Cy5 We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html). Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.87; Parameter Scan Time = 14:40:41; Parameter PMT Volts = 570; Parameter Scan Date = 2004-03-16; Parameter Pixel Size = 10; Parameter Laser on time = 16911; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.96; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.87; Parameter Scan Time = 14:40:41; Parameter PMT Volts = 620; Parameter Scan Date = 2004-03-16; Parameter Pixel Size = 10; Parameter Laser on time = 16939; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.51; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
19 GSM35432 SHFB239 41,472 Stanford Microarray Database (SMD) 2004-11-17 [cDNA Array] SHFB (GPL1711) RNA Pan troglodytes,Homo sapiens
Pan troglodytes,Homo sapiens		 unclassified source_name:BJORN aURNA title:SHFB239 description:Simple annotation: Normal tissue, cell line Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52951.gif; format: GIF Sample_label_ch1 = Cy3 Sample_label_ch2 = Cy5 For the second batch, we amplified the nine RNA samples by using the MessageAmp aRNA Amplification Kit (Ambion) according to manufacturer's specifications. Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ul containing 2 ug mRNA(or amplified RNA)/ 4 ug oligo (dT) primer / 0.5 uM each dATP, dCTP, dGTP / 0.2 uM dTTP / 0.1 uM 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 &amp;#8734;C for 2-3 hours, the RNA was degraded by adding 15 ul of 0.1 N NaOH at 70 &amp;#8734;C for 10 minutes, and was neutralized by adding 15 ul 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 ug Cot1 human DNA (Gibco-BRL), 20 ug PolyA RNA (Sigma, #P9403) and 20 ug tRNA (Gibco-BRL, #15401-011) were added, the probes were purified. For final probe preparation, 6 ul of 20x SSC (BioWhittaker, MD) and 1 ul of 10% SDS were added. The probes were denatured at 100 &amp;#8734;C for 3 minutes, incubated at 37 &amp;#8734;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 &amp;#8734;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. Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.89; Parameter Scan Time = 11:21:14; Parameter PMT Volts = 560; Parameter Scan Date = 2004-05-28; Parameter Pixel Size = 10; Parameter Laser on time = 19440; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.98; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.89; Parameter Scan Time = 11:21:14; Parameter PMT Volts = 620; Parameter Scan Date = 2004-05-28; Parameter Pixel Size = 10; Parameter Laser on time = 18843; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.41; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
20 GSM36525 S.l. animal, 19 late torpor, reverse, brain 12,575 Stanford University 2004-11-29 [cDNA Array] Spermophilus lateralis array Mk 1 (GPL1706) RNA unidentified
unidentified		 pooled Spermophilus lateralis brain reference RNA Animal, 19 late torpor, reverse, brain
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