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°C for 2-3 hours, the RNA was degraded by adding 15 ul of 0.1 N NaOH at 70°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°C for 3 minutes, incubated at 37°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°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

source_name: BJORN


title: SHFD229

status: Public on Jun 08 2005

type: RNA

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

country: USA

institute: Stanford Microarray Database (SMD)

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°C for 2-3 hours, the RNA was degraded by adding 15 ul of 0.1 N NaOH at 70°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°C for 3 minutes, incubated at 37°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°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

molecule: total RNA

organism:
Pan troglodytes
Homo sapiens

source_name: 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°C for 2-3 hours, the RNA was degraded by adding 15 ul of 0.1 N NaOH at 70°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°C for 3 minutes, incubated at 37°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°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


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°C for 2-3 hours, the RNA was degraded by adding 15 ul of 0.1 N NaOH at 70°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°C for 3 minutes, incubated at 37°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°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

source_name: BROOK


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°C for 2-3 hours, the RNA was degraded by adding 15 ul of 0.1 N NaOH at 70°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°C for 3 minutes, incubated at 37°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°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