title: Human Skeletal Muscle Tissue

description: Human Skeletal Muscle Tissue

source_name: Human skeletal muscle tissue


title: Gills gene expression profiling from mussels in normal conditions (A)

status: Public on Oct 10 2006

type: RNA

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description:
Frozen gills (G), digestive gland (DG), foot/adductor muscles/ligaments (FML) and gonads/mantle (GM) tissues were dispersed separately into TRizol solution (Invitrogen, Carlsbad, CA, USA), and homogenized with an Diax 900 blender (Heidolph, Kelheim, Germany). Total RNA (15 µg), extracted following the manufacturer instructions, was reverse transcribed with SuperScript II (Invitrogen) and oligo-dT(18) as the primer, in the presence of either Cy3-dCTP or Cy5-dCTP (Amersham Biosciences, Uppsala, Sweden). Competitive hybridizations were carried out in a dual slide chamber (HybChamber, GeneMachines, San Carlos, CA, USA). Pellets of purified, labeled cDNAs were dissolved in hybridization buffer (Northern max, Ambion), applied on the MytArray 1.0, and covered with a 22×22 mm glass coverslip. After an overnight hybridization at 42°C, slides were washed sequentially for 4 min in buffer A (1X SSC/0.2% SDS) at 42°C, for 4 min buffer B (0.1X SSC/0.2% SDS) at room temperature and finally in 0.1X SSC for 2 min at room temperature. Digital images were generated in a GSI Lumonics LITE dual confocal laser scanner (ScanArray Microarray Analysis Software) and processed with QuantArray Analysis Software (GSI Lumonics, Ottawa, Canada). Normalized data were determined using the publicly available software MIDAS (TIGR Microarray Data Analysis System: http://www.tigr.org/softlab/). Normalized values (lowess normalization) were calculated for each spot, and converted in logarithmic scale. Final values correspond to log(2) ratio of the normalized intensities.
Keywords = gills
Keywords = normal conditions
Keywords = transcriptional profiling

molecule: total RNA

organism: Mytilus galloprovincialis

source_name: pool of 4 different mussel tissues (G, DG, FML and GM) in equal quantity - Reference

source_name: gills from mussels


title: Human Prostate Tissue

status: Public on Oct 07 2006

city: Berkeley

first: Jonathan

middle: L

last: Bingham

state: CA

address: 733 Allston Way

country: USA

institute: Jivan Biologics, Inc

description: Human Prostate Tissue

hyb_protocol: Following fragmentation, 5 microg of cRNA were hybridized for 16 hr at 42C

data_processing: Raw data from Mergen

organism: Homo sapiens

source_name: Human prostate tissue

label_protocol: Cy3-labeled cRNA were prepared from total RNA using Mergen protocol

tag: Adult male, single-patient, purchased from Ambion


title: Human Placenta Tissue

description: Human Placenta Tissue

source_name: Human placenta tissue


title: Human Pancreas Tissue

description: Human Pancreas Tissue

source_name: Human pancreas tissue


title: Human Kidney Tissue

description: Human Kidney Tissue

source_name: Human kidney tissue


title: Human Liver Tissue

description: Human Liver Tissue

source_name: Human liver tissue


title: Human Heart Tissue

description: Human Heart Tissue

source_name: Human heart tissue


title: Human Ovarian Tissue

description: Human Ovarian Tissue

source_name: Human ovarian tissue


title: Left arm fibroblasts, infiltrative BCC (S68.1 iii), serum starved

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: tumor, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/45146.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 770, 6740; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Julie,,Sneddon 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 = 39.38; Parameter Scan Time = 16:27:04; Parameter PMT Volts = 650; Parameter Scan Date = 2003-08-22; Parameter Pixel Size = 10; Parameter Laser on time = 120584; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.36; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Julie,,Sneddon 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 = 39.38; Parameter Scan Time = 16:27:04; Parameter PMT Volts = 740; Parameter Scan Date = 2003-08-22; Parameter Pixel Size = 10; Parameter Laser on time = 485693; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.00; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Julie,,Sneddon

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Stratagene UR

extract_protocol: StratageneRef; RNA for the reference was pooled from 11 cell lines - obtained from Stratagene.; Protocol Type = Biological Sample; Performer: Julie,,Sneddon

tag: Stratagene UR

source_name: S68.1 iii (left arm fibroblasts, infiltrative BCC) mRNA, serum starved

label_protocol: Brown Lab : human mRNA labeling del; Preparation of Fluorescent DNA Probe from HUMAN mRNA or Total RNA using Direct Incorporation  (Max Diehn/Ash Alizadeh  protocol; 3/15/01)  http://cmgm.stanford.edu/pbrown/protocols/4_human_RNA.html  Includes  I. Preparing fluoresenctly labeled cDNA (probe) II. Washing Arrays  for deletion; Protocol Type = Labeling; Performer: Julie,,Sneddon

growth_protocol: Fibroblast_serum_starvation; Fibroblasts were cultured in DMEM, 10% FBS, glutamine, penicillin-streptomycin at 5% C02 and 37 C.  48 hours before mRNA harvest, cells were subjected to serum starvation by changing medium to DMEM, 0.1% FBS, glutamine, penicillin-streptomycin.; Protocol Type = Growth Conditions; Performer: Julie,,Sneddon

extract_protocol:
fibroblast_from_tissue; Fibroblast cells were isolated from discarded human tissue.  Fat was removed using sterile scalpel and forceps; tissue was minced into ca. 1 mm cubes.  Incubation in a 6-well dish without medium at 37 0C for 10 minutes allowed for adhesion of the tissue to the plate.  Fresh media containing DMEM, 10% FBS, and penicillin-streptomycin was added, and samples were maintained at 37 0C and 5% CO2.  Media was replaced every 2 days.  Outgrowth of spindle-shaped cells was typically apparent after 5-15 days in culture.  When the cells were near confluence, they were subcultured with 0.25% trypsin-EDTA.  Cultures were expanded until sufficient for RNA isolations (typically 4 passages).; Protocol Type = Biological Sample; Performer: Julie,,Sneddon
FastTrack; mRNA was isolated using the FastTrack kit from Invitrogen, according to the manufacturer's instructions.; Protocol Type = Extract preparation; Performer: Julie,,Sneddon


title: BCC-6 fibroblasts, serum starved

description:
Simple annotation: tumor, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46641.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 7560; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Julie,,Sneddon 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 = 39.56; Parameter Scan Time = 16:12:31; Parameter PMT Volts = 610; Parameter Scan Date = 2003-11-06; Parameter Pixel Size = 10; Parameter Laser on time = 134930; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.38; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Julie,,Sneddon 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 = 39.56; Parameter Scan Time = 16:12:31; Parameter PMT Volts = 590; Parameter Scan Date = 2003-11-06; Parameter Pixel Size = 10; Parameter Laser on time = 499995; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.17; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Julie,,Sneddon

source_name: BCC-6 mRNA, serum starved

tag: BCC-6 mRNA, serum starved


title: Human Brain Tissue

description: Human Brain Tissue

source_name: Human brain tissue


title: Human Breast Tissue

description: Human Breast Tissue

source_name: Human breast tissue


title: Human Colon Tissue

description: Human Colon Tissue

source_name: Human colon tissue


title: Human Lung Tissue

description: Human Lung Tissue

source_name: Human lung tissue


title: Right medial chest fibroblasts (S68.3 ii), serum starved

description:
Simple annotation: Development, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/45148.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 770, 6740; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Julie,,Sneddon 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 = 39.19; Parameter Scan Time = 15:43:23; Parameter PMT Volts = 620; Parameter Scan Date = 2003-08-22; Parameter Pixel Size = 10; Parameter Laser on time = 120540; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.37; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Julie,,Sneddon 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 = 39.19; Parameter Scan Time = 15:43:23; Parameter PMT Volts = 620; Parameter Scan Date = 2003-08-22; Parameter Pixel Size = 10; Parameter Laser on time = 485649; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.02; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Julie,,Sneddon

source_name: S68.3 ii (right medial chest fibroblasts) mRNA, serum starved


title: Human Bladder Tissue

description: Human Bladder Tissue

source_name: Human bladder tissue


title: Human Fallopian Tissue

description: Human Fallopian Tissue

source_name: Human fallopian tissue


title: Human Adrenal Tissue

description: Human Adrenal Tissue

source_name: Human adrenal tissue


title: Right mid arm fibroblasts, normal skin (S68.2 i), serum starved

description:
Simple annotation: Development, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/45147.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 770, 6740; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Julie,,Sneddon 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 = 39.31; Parameter Scan Time = 16:03:09; Parameter PMT Volts = 630; Parameter Scan Date = 2003-08-22; Parameter Pixel Size = 10; Parameter Laser on time = 120559; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.36; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Julie,,Sneddon 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 = 39.31; Parameter Scan Time = 16:03:09; Parameter PMT Volts = 670; Parameter Scan Date = 2003-08-22; Parameter Pixel Size = 10; Parameter Laser on time = 485668; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.02; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Julie,,Sneddon

source_name: S68.2 i (right mid arm fibroblasts) mRNA, serum starved


title: Human Aorta Tissue

description: Human Aorta Tissue

source_name: Human aorta tissue


title: Daphnia_pulex:Juvenile female vs Adult male, replicate 2

status: Public on Oct 06 2006

city: Bloomington

first: John

middle: Kenneth

last: Colbourne

state: IN

department: Biology

institute: Indiana University

description: Four biological replicates (double dye-swaps) were used to assess differences between males and juvenile females under standard laboratory culture conditions.

hyb_protocol: Equal masses of cDNA from males and females were combined in a 1:3 volume with hybridization buffer (50% formamide, 5X SSC, 0.1% SDS, 10 μg calf thymus DNA) and denatured at 90°C for 4 min, quick chilled, and injected into a Lucidea Slidepro automated hybridization chamber (Amersham) containing a microarray slide pre-hybridized according to manufacturer’s instructions.  Following overnight hybridization, slides were washed twice at 60°C in 2X SSC + 0.2% SDS (15 min), once in 0.2X SSC + 0.2% SDS (10 min), once in 0.1X SSC (10 min) and once in 0.5X SSC (10 min).  Slides were dipped briefly in 100% isopropanol, centrifuged 5 min at 500 x g to dry, and scanned using an Axon 4200B scanner.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4200B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.0 analysis software.

data_processing: Data were filtered and extracted using GenePix v. 5.0 and imported in Bioconductor.  Normalization for M values was performed using spatial and intensity-dependent lowess smoothing in OLIN and differential expression was assessed using Limma.

organism: Daphnia pulex

source_name: Adult males

label_protocol: 20 micrograms total RNA reverse transribed into cDNA using Indirect cDNA Labeling Kit reagents (Invitrogen), according to manufacturer's protocol.

growth_protocol: Cultured at 20 degrees centigrade, in water from Lake Lemon, IN, filtered through 0.45 micron nylon, at 1 animal per 5 ml, fed Scenedesmus algae

extract_protocol: Using Qiagen RNeasy Mini Kit reagents and protocol, except that Trizol was used for initial homogenization, and DNAse digestion was performed on-column.

tag: Age 8 days

source_name: Juvenile females

tag: 6 days old


title: Daphnia_pulex:Adult female vs Adult male, replicate 1

treatment_protocol: Cultured at 20 degrees centigrade, in water from Lake Lemon, IN, filtered through 0.45 micron nylon, at 1 animal per 5 ml, fed Scenedesmus algae

tag: 8 days old

source_name: Adult females


title: BCC-4 fibroblasts, serum starved

description:
Simple annotation: tumor, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55297.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 960, 5400; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Julie,,Sneddon 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 = 39.12; Parameter Scan Time = 09:33:12; Parameter PMT Volts = 560; Parameter Scan Date = 2004-07-19; Parameter Pixel Size = 10; Parameter Laser on time = 176923; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.42; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Julie,,Sneddon 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 = 39.12; Parameter Scan Time = 09:33:12; Parameter PMT Volts = 630; Parameter Scan Date = 2004-07-19; Parameter Pixel Size = 10; Parameter Laser on time = 541727; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.95; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Julie,,Sneddon

source_name: BCC-4 mRNA, serum starved

tag: BCC-4 mRNA, serum starved


title: Daphnia_pulex:Juvenile female vs Adult male, replicate 3

tag: 6 Days old

tag: 8 Days old


title: Daphnia_pulex:Adult female vs Adult male, replicate 4


title: Daphnia_pulex:Adult female vs Adult male, replicate 2


title: Daphnia_pulex:Juvenile female vs Adult male, replicate 1


title: Daphnia_pulex:Adult female vs Adult male, replicate 3


title: Daphnia_pulex:Juvenile female vs Adult male, replicate 4


title: CD11b_Tumor bearing at time 24_replicate2

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

description: Global transcriptional analysis to explore the gene expression pattern of CD11b purified from the mouse spleen (tumor free and tumor bearing mice)

hyb_protocol: Standard Affymetrix procedures (see GeneChip? Expression Analysis Technical Manual)

data_processing: Affymetrix MAS5.0 procedure

label: Biotin

organism: Mus musculus

source_name: CD11b+ sorted cells from mouse spleen

label_protocol: 5 μg of total RNA were used to generate double-stranded cDNA (Invitrogen). Synthesis of Biotin-labeled cRNA was performed using the BioArrayTM HighYieldTM RNA Transcript Labeling Kit (ENZO Biochem).

extract_protocol: Total RNA was extracted by TRIzol (Invitrogen) from CD11b+ sorted cells according to the manufacturer?s instructions with little modifications. The quality and quantity of RNA sample were determined by Agilent RNA 6000 Nano Chip (Agilent Technologies). cDNA from purified total RNA was produced by M-MLV reverse transcriptase (Invitrogen) following manufacturer protocol. All the pre-hybridization quality controls were performed with the Agilent 2100 bioanalyzer (Agilent Technologies).

tag: BALB/c

tag: Gender

value: female

tag: Age

value: 8-12 weeks

tag: Tissue

value: spleen


title: CD11b_Tumor bearing at time 0_replicate3

scan_protocol: Standard Affymetrix procedures (see GeneChip? Expression Analysis Technical Manual)


title: Mtb stationary phase rep1

city: Suwon

first: ChangMuk

last: Lee

address: 224, Suinro, Gwonseon-Gu

department: Microbial Genetics Division

country: South Korea

institute: National Institute of Agricultural Biotechnology

description: The array hybridization was performed to compare general gene expression change between an exponential growth phase and late-log phase. Wild-type Mtb cells were directly inoculated from freezing stock until OD~0.5, which was chosen as a reference exponential growth stage. Samples were prepared after further growth until the OD values doubles in the same medium as was in the reference cells.

hyb_protocol: Hybridization, blocking and washing was performed following the procedure provided at TIGR, PFGRC; http://pfgrc.tigr.org/protocols/protocols.shtml

scan_protocol: QuantArray (ver. 3.0, Perkin Elmer) was used for 16-bit TIFF image quantification and initial data visualization.

data_processing: scale pin MAD and ratio-intensity Quantile normalization by using R (ver. 2.1.1) package (http://www.bioconductor.org) & S-plus ArrayAnalyzer (ver2.0)

organism: Mycobacterium tuberculosis

source_name: Reference signal, M. tuberculosis H37Rv, mid-log, OD=0.53

label_protocol: Labeled cDNA was prepared as follows: 10 μg of total RNA and 2 μg of random oligonucleotide hexamers (Invitrogen, CA) were incubated 15 min at 65 °C, cooled on ice, combined with Stratascript RTase buffer, 0.5 mM dATP, 0.5 mM dGTP, 0.5 mM dCTP, 0.02 mM dUTP, 1.5 nmol aminoallyl-dUTP (Amersham, NJ), and 2 μl Stratascript RTase II (Invitrogen, CA) in a total volume of 30 μl. This mixture was incubated 10 min at room temperature, and 42 °C overnight. Synthesized cDNA was purified by QIAquick PCR purification kit (Qiagen, CA) according to the manufacturer’s recommendation. The aminoallyl-dUTP-conjugated cDNA probes was spin-dried (SpeedVac, Savant), resuspended in 50 mM sodium carbonate buffer (pH 9.3) and cyanine monofunctional dyes (Amersham) for 1 h at room temperature followed by quenching with 4 M hydoxylamine. Cyanine-labeled probes were purified again by QIAquick PCR purification kit.

growth_protocol: M. tuberculosis H37Rv was grown in Middlebrook 7H9 (supplemented with 0.05% Tween-80, 10% oleic acid-albumin-dextrose-catalase enrichment and 0.2% glycerol). RNA was extracted from cells growing exponentially at an optical density (A600) of approximately 0.5 in Middlebrook 7H9 medium (pH 7.0).

extract_protocol: Cell was harvested and quickly forzen in dry ice-ethanol bath. Total M. tuberculosis RNA was isolated using glass beads (Bio101, Lysing Matrix B), a TRIzol (Invitrogen) extraction, and RNeasy (Qiagen) purification according to the manufacturers' recommendations.

treatment_protocol: There is no specific stress factors for this sample in terms of O2, nutrient, temperature and pH. Cells were harvested based on the optical density.

tag: Strain; M. tuberculosis virulent strain H37Rv

tag: Growth day; 6 day in liquid Middlebook 7H9 at 37 degree of Celsius

source_name: Sample signal, M. tuberculosis H37Rv, stationary phase, OD=1.42

growth_protocol: M. tuberculosis H37Rv was grown in Middlebrook 7H9 (supplemented with 0.05% Tween-80, 10% oleic acid-albumin-dextrose-catalase enrichment and 0.2% glycerol). RNA was extracted from cells at an approximately double culture time compared to mid-log phase (12 days, A600=1.42) in Middlebrook 7H9 medium (pH 7.0).

extract_protocol: Cell was harvested and quickly forzen in dry ice-ethanol bath. Total M. tuberculosis RNA was isolated using glass bead (Bio101, Lysing Matrix B), a TRIzol (Invitrogen) extraction, and RNeasy (Qiagen) purification following manufacturers' recommendation.

treatment_protocol: There is no specific stress factors for this sample in terms of O2, Nutrient, temperature and pH. Cells were harvested based on the optical density.

tag: Growth day; 12 day in liquid Middlebook 7H9 at 37 degree of Celsius


title: CD11b_Tumor bearing at time 24_replicate1


title: BCC-3 fibroblasts, serum starved

description:
Simple annotation: tumor, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46553.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1000, 7200; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Julie,,Sneddon 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 = 39.24; Parameter Scan Time = 15:19:25; Parameter PMT Volts = 600; Parameter Scan Date = 2003-11-06; Parameter Pixel Size = 10; Parameter Laser on time = 134872; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.38; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Julie,,Sneddon 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 = 39.24; Parameter Scan Time = 15:19:25; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-06; Parameter Pixel Size = 10; Parameter Laser on time = 499937; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.11; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Julie,,Sneddon

source_name: Stratagene UR

source_name: BCC-3 mRNA, serum starved

tag: BCC-3 mRNA, serum starved


title: Mtb late-log phase rep2

description: The array hybridization was performed to compare general gene expression change between an exponential growth phase and late-log phase. Wild-type Mtb cells were inoculated and grown until OD~0.5, which is chosen as a reference exponential growth stage. Samples were prepared after further growth until the OD values doubles in teh same medium as was in the reference cells.

scan_protocol: QuantArray (ver. 3.0, Perkin Elmer) was used for 16-bit TIFF image quantification and initial visualization.

data_processing: scale-pin MAD and ratio-intensity Quantile normalization using R (version 2.1.1) package (http://www.bioconductor.org) & S-plus ArrayAnalyzer(ver. 2.0)

source_name: Reference signal, M. tuberculosis H37Rv, mid-log, OD=0.65

growth_protocol: M. tuberculosis H37Rv was grown in Middlebrook 7H9 (supplemented with 0.05% Tween-80, 10% oleic acid-albumin-dextrose-catalase enrichment and 0.2% glycerol). RNA was extracted from cells growing exponentially at an optical density (A600) of approximately 0.5 in liquid Middlebrook 7H9 medium (pH7.0).

extract_protocol: Cell was harvested and quickly frozen in dry ice-ethanol bath. Total RNA was isolated using galss beads (Bio1010, Lysing matrix B), a TRIzol (InVitrogen) extraction and RNease (Qiagen) purification according to the manufacturers' recommendations.

treatment_protocol: There is no specific stress factors applied for this sample in terms of O2, nutrient, temperature and pH. Cells were harvested based on the optical density.

tag: Growth day; 6day in liquid Middlebrook 7H9 at 37 degree of Celsius

source_name: Sample signal, M. tuberculosis H37Rv, late-log, OD=1.18

growth_protocol: M. tuberculosis H37Rv was grown in Middlebrook 7H9 (supplemented with 0.05% Tween-80, 10% oleic acid-albumin-dextrose-catalase enrichment and 0.2% glycerol). RNA was extracted from cells growing exponentially at an optical density (A600) of approximately 1.0 in liquid Middlebrook 7H9 medium (pH7.0).

tag: Growth day; 8day in liquid Middlebrook 7H9 at 37 degree of Celsius


title: Mtb late-log phase rep5

description: The microarray hybridization was performed to compare general gene expression changes between an exponential growth phase and late-log phase. Wild-type Mtb cells were inoculated in the complete liquid medium, and grown until OD~0.5, which is chosen as a reference exponential growth stage. Samples were prepared after further growth until the OD values doubles in the same medium as was in the reference culture.

scan_protocol: QuantArray (ver. 3.0, Perkin Elmer) was used for 16-bit TIFF image quantification and intial visualization.

data_processing: scale-pin MAD and ratio-intensity Quantile normalization using R (ver. 2.1.1) package (http://www.bioconductor.org) & S-plus ArrayAnalyzer (ver.2.0)

source_name: Reference signal, M. tuberculosis H37Rv, mid-log, OD=0.64

extract_protocol: Cell was harvested and quickly frozen in dry ice-ethanol bath. Total RNA was isolated using glass beads (Bio101, LysingMatrix B), a TRIzol (InVitrogen) extraction and RNeasy (Qiagen) purification according to the manufacturers' recommendations.

tag: Growth day; 6 day in liquid Middlebrook 7H9 at 37 degree of Celsius

source_name: Sample signal, M. tuberculosis H37Rv, late-log, OD=1.17

tag: Growth day; 8 day in liquid Middlebrook 7H9 at 37 degree of Celsius


title: Mtb late-log phase rep4

data_processing: scal-pin MAD and ratio-intensity Quantile normalization using R (ver. 2.1.1) package (http://www.bioconductor.org) & S-plus ArrayAnalyzer (ver.2.0)


title: Mtb late-log phase rep3

data_processing: scal pin MAD and ratio-intensity Quantile normalization using R (ver. 2.1.1) package (http://www.bioconductor.org) & S-plus ArrayAnalyzer (ver.2.0)


title: CD11b_Tumor bearing at time 0_replicate2


title: CD11b_Tumor bearing at time 24_replicate3


title: IM CD34+ Pool II

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

institute: Centre for Regenerative Medicine

description: The biotin-labeled target synthesis reactions, as well as the Affymetrix HG-U133A GeneChip arrays hybridization, staining, and scanning, were performed using Affymetrix standard protocols (Affymetrix, Santa Clara, CA).

hyb_protocol: The fragmented cRNA was then hybridized to an identical lot of Affymetrix HG-U133A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.

scan_protocol: GeneChip were finally scanned using the GA2500 Affymetrix GeneChip scanner.

data_processing: GeneChip Operating Software (GCOS)

label: biotin-labeled

source_name: IM CD34+ progenitors cells

label_protocol: Biotin-labeled labeled cRNA  was purified using RNeasy spin columns (Qiagen, Valencia, CA) and fragmented (20 µg) following the Affymetrix GeneChip protocol. The assessment of cRNA concentration/quality and  fragmentation was performed with the Agilent RNA chips.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen-Life Technologies, Paisley, UK). Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA with the Agilent 2100 Bioanalyzer. In order to obtain enough RNA to perform the Affymetrix analysis, 0.6 µg of RNA from CD34+ cells of 5 different normal donors or IM patients were pooled, so as to obtain 3 pools each comprising 3 µg RNA.

tag: CD34+ hemopoietic progenitors purified from peripheral blood of Idiopathic Myelofibrosis (IM) patients


title: IM CD34+ Pool I


title: IM CD34+ Pool III


title: CD11b_Tumor bearing at time 0_replicate1


title: CD11b_Tumor free_replicate3


title: BM CD34+ Pool III

source_name: Bone Marrow CD34+ progenitors cells

tag: CD34+ hemopoietic progenitors purified from bone marrow of healthy controls


title: CD11b_Tumor free_replicate2


title: Mtb late-log phase rep1

data_processing: scale pin MAD and ratio-intensity Quantile normalization using R (ver. 2.1.1) package (http://www.bioconductor.org) & S-plus ArrayAnalyzer (ver2.0)

source_name: Reference, M. tuberculosis H37Rv, mid-log, OD=0.53

tag: Strain; M. tuberculosis viruence strain H37Rv

tag: Growth day at 37 degree of Celsius

value: 6 days

source_name: Sample, M. tuberculosis H37Rv, late-log, OD=1.17

growth_protocol: M. tuberculosis H37Rv was grown in Middlebrook 7H9 (supplemented with 0.05% Tween-80, 10% oleic acid-albumin-dextrose-catalase enrichment and 0.2% glycerol). RNA was extracted from cells at an approximately doubled optical density (A600=1.17) of in Middlebrook 7H9 medium (pH 7.0).

value: 8 days


title: CD11b_Tumor free_replicate1

hyb_protocol: Standard Affymetrix procedures (see GeneChip® Expression Analysis Technical Manual)

extract_protocol: Total RNA was extracted by TRIzol (Invitrogen) from CD11b+ sorted cells according to the manufacturer’s instructions with little modifications. The quality and quantity of RNA sample were determined by Agilent RNA 6000 Nano Chip (Agilent Technologies). cDNA from purified total RNA was produced by M-MLV reverse transcriptase (Invitrogen) following manufacturer protocol. All the pre-hybridization quality controls were performed with the Agilent 2100 bioanalyzer (Agilent Technologies).


title: BM CD34+ Pool I


title: BM CD34+ Pool II


title: WT 3

status: Public on Oct 05 2006

city: Charlestown

first: Dimitri

last: Krainc

state: MA

address: 114 16th Street

department: Neurology

institute: Massachusetts General Hospital

description: PGC-1a null (PGC-1a-/- ) and wild-type (PGC-1a+/+) mice were obtained by breeding heterozygous (PGC-1a+/-) founder mice as described (Leone et al., 2005).

data_processing: MAS 5.0

label: biotin

source_name: WT striatum

extract_protocol: Qiagen RNeasy

value: striatum

value: 6 months

value: F


title: WT 2


title: NB4 30min control vs NB4 30min LT

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: Labeling of RNA for hybridization was performed using the Low RNA Input Linear Amp Kit from Agilent Technologies according to the supplier’s instructions. Briefly, 500ng total RNA was reverse transcribed with an oligo-dT-T7 promoter primer and MMLV-RT. Second strand synthesis was carried out with random hexamers. Fluorescent antisense cRNA was synthesized with either cyanine 3-CTP (Cy3-CTP) or cyanine 5-CTP (Cy5-CTP) and T7 polymerase. Purified products were quantified at A552nm for Cy3-CTP and A650nm for Cy5-CTP. Prior to hybridization, 2 µg labeled cRNA each were fragmented, mixed with control targets and with hybridization buffer according to the supplier's protocol (Agilent Technologies). Hybridizations were performed at 60 °C for 17 h. Slides were washed according to manufacturer's protocol (SSC wash protocol) and scanning of the arrays was performed at a 5µm resolution using a DNA microarray laser scanner (Agilent Technologies). Features were extracted from raw image data using the Agilent Technologies image analysis software (G2567AA Feature Extraction Software, Version A7.5.1) and default settings. Background subtraction was accomplished by 'spacial detrend'. The arrays were normalized using rank consistency filtering of normalization feature selection, together with a combination linear and LOWESS curve fitting method. Ratios were calculated by most conservative estimate between a universal error model and propagated error. Data analysis was performed using the Rosetta Inpharmatics Resolver software package Build 4.1. Ratio profiles were generated from raw scan data using a processing pipeline which includes pre-processing (Feature Extraction) and post-processing (Rosetta Resolver) of data, and error model adjustments to the raw scan data. Ratio profiles were combined in an error-weighted fashion by Resolver to create ratio experiments. To compensate for dye-specific effects, and to ensure validity of the data, a color swap analysis (fluorescence reversal) was performed. Expression patterns were identified using stringent analysis criteria of 1.5-fold expression cut-offs of the ratio experiments and an anti-correlation of the dye reversal ratio hybridizations. Anti-correlation was determined by using the 'compare function' to compare two color-swap dye-reversal hybridizations and to decide how similar or dissimilar they were. In this way, only anti-correlated spots that had on the one array a red colour and on the other one a green colour and vice versa were selected. We compared color-swap dye-reversal hybridizations of individual 2 two-channel hybridizations and calculated correlation coefficients for the data sets resulting in unchanged genes, query signature genes, target signature genes, common signature genes and anti-correlated genes. By combining the < 1.5 fold and the anti-correlation criteria we filtered out data points with low P-value, making the analysis highly robust and reproducible. After applying this strategy, all valid data points had an error-weighted P-value < 0.01. In addition, by using this strategy data selection was independent of the error models implemented in the Rosetta Resolver system.

data_processing: Agilent Feature Extraction and Rosetta Resolver

source_name: NB4 ctrl 30 min

tag: NB4 control

source_name: NB4 LT 30 min

tag: NB4 Bacillus anthracis lethal toxin (LT) treatment


title: WT 1

tag: Gender


title: PGC-1a KO 3

molecule: cytoplasmic RNA

source_name: PGC1-a KO striatum

tag: Age


title: NB4 120min LT vs. NB4 120min control

data_processing: Agilent Feature Extraction, Rosetta Resolver

source_name: NB4 LT 120 min

source_name: NB4 ctrl 120 min


title: NB4 120min control vs. NB4 120min LT


title: PGC-1a KO 2

tag: Tissue


title: control with no rejection con7

status: Public on Oct 04 2006

city: Philadelphia

first: Thomas

last: Cappola

state: PA

address: 6 Penn Tower, 3400 Spruce Street

department: Penn Cardiovascular Institute

institute: Univeristy of Pennsylvania School of Medicine

description: Gene expression data from whole periheral blood in heart transplant recipients with no rejection

hyb_protocol: Following fragmentation cRNA were hybridized with HU133A arrays according to Affymetrix protocol.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Data were normalized using Robust Multi-Array Analysis (RMA). www.bioconductor.org

source_name: whole peripheral blood RNA; heart transplant no rejection

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: PaxGene preserved RNA

tag: whole peripheral blood RNA


title: MM-081_2

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

description:
gene expression profiles of purified plasma cells (PCs) obtained from MM-004 patient.
Keywords = Gene expression profiling
Keywords = Multiple myeloma
Keywords = TC classification
Keywords = Cyclin D
Keywords = IGH translocation

data_processing: After scanning, the CEL files were processed using standard Robust Multi-Array average (RMA) procedure to generate gene expression intensity values. Detection calls were calculated using the default parameters of Affymetrix MAS 5.0 software package.

label: biotin-labeled UTP and CTP

source_name: CD138+ plasma cells obtained from bone marrow of MM patient

tag: for full details see Table 1, Appendix_A from Agnelli, et al., "Molecular classification of multiple myeloma

value: a distinct transcriptional profile characterizes patients expressing CCND1 and negative for 14q32 translocations", J Clin Onc, in press


title: control with no rejection con5


title: PGC-1a KO 1

source_name: PGC-1a KO mouse striatum


title: Gene expression comparing between wild type [Cy3-red] and fosBd/d [Cy5-green] ES cells

city: Fukuoka

first: Yoshinori

middle: N

last: Ohnishi

state: Fukuoka

address: 3-1-1 Maidashi Higashi-ku

department: Department of Immunobiology and Neuroscience

country: Japan

institute: Medical Institute of Bioregulation, Kyushu University

description:
Total RNA was purified from ES cells grown in the absence of feeder cells using the Isogen kit (Nippon Gene), according to the manufacturer’s instructions. For DNA microarray experiments, Total RNA (10 microg) were labeled using the Agilent Linear Amplification/Labeling Kit (Agilent Technologies) according to the manufacturer's instructions. One microgram of each Cy3-labeled wild-type and Cy5-labeled mutant cDNA or each Cy3-labeled mutant and Cy5-labeled wild-type cDNA, respectively, were mixed, then hybridized to Agilent Mouse cDNA Microarrays (G4104A, design file number: 000522R000679, Agilent Technologies) with 8500 unique clones from Incyte’s mouse UniGene 1 clone set, according to the manufacturer's hybridization protocol. After the washing step, the microarray slides were analyzed with an Agilent G2565AA microarray scanner system. These experiments were carried out in duplicate using exchanged dye-labeled cDNA probes (i.e., Cy3 and Cy5 dye-swapping experiments).
You can get the detail information of columns below site.
http://www.chem.agilent.com/temp/radAEB25/00047887.pdf

data_processing: Data analysis was performed using Agilent Feature Extraction software (Ver. A.6.1.1)

source_name: wild type ES cells

tag: total RNA extracted from wild type ES cells

source_name: mutant ES cell line carrying homozygous fosBd/d alleles which encode exclusively DFosB

tag: total RNA extracted from mutant mouse embryonic stem (ES) cell line carrying homozygous fosBd/d alleles which encode exclusively DeltaFosB


title: control with no rejection con6


title: control with no rejection con4


title: NB4 30min LT vs. NB4 30min control


title: Gene expression comparing between fosB-wild type [Cy3-red] and fosB-null [Cy5-green] ES cells

source_name: fosB-null ES cells

tag: total RNA extracted from fosB-null ES cells


title: BCC-6 fibroblasts, serum starved

first: Julie

middle: B.

last: Sneddon

address: Beckman Center, Room 400

department: Stanford Biochemistry

institute: Stanford

description:
tumor, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46641.gif; format: GIF
Disease State: tumor-derived

source_name: Stratagene UR

tag: RNA for the reference was pooled from 11 cell lines - obtained from Stratagene.

source_name: BCC-6 mRNA, serum starved

label_protocol: Preparation of Fluorescent DNA Probe from HUMAN mRNA or Total RNA using Direct Incorporation; (Max Diehn/Ash Alizadeh  protocol; 3/15/01); http://cmgm.stanford.edu/pbrown/protocols/4_human_RNA.html

extract_protocol:
mRNA was isolated using the FastTrack kit from Invitrogen, according to the manufacturer's instructions.
Fibroblast cells were isolated from discarded human tissue.  Fat was removed using sterile scalpel and forceps; tissue was minced into ca. 1 mm cubes.  Incubation in a 6-well dish without medium at 37 0C for 10 minutes allowed for adhesion of the tissue to the plate.
Fresh media containing DMEM, 10% FBS, and penicillin-streptomycin was added, and samples were maintained at 37 0C and 5% CO2.  Media was replaced every 2 days.  Outgrowth of spindle-shaped cells was typically apparent after 5-15 days in culture.  When the cells were near confluence, they were subcultured with 0.25% trypsin-EDTA.  Cultures were expanded until sufficient for RNA isolations (typically 4 passages).

treatment_protocol: Fibroblasts were cultured in DMEM, 10% FBS, glutamine, penicillin-streptomycin at 5% C02 and 37 C.  48 hours before mRNA harvest, cells were subjected to serum starvation by changing medium to DMEM, 0.1% FBS, glutamine, penicillin-streptomycin.

tag: BCC-6 mRNA, serum starved


title: follow-up sample after treatment of rejection post7

description: Gene expression data from whole periheral blood in heart transplant recipients after treatment and resolution of rejection

source_name: whole peripheral blood RNA; heart transplant post-rejection (paired with r7)


title: control with no rejection con1


title: control with no rejection con3


title: control with no rejection con2


title: Left temple fibroblasts (S63.1 i), serum starved

description:
tumor, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48248.gif; format: GIF
Disease State: non-tumor-derived

source_name: S63.1 i (left temple fibroblasts) mRNA, serum starved


title: Right preauric skin fibroblasts (S55.1), serum starved

description:
tumor, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47262.gif; format: GIF
Disease State: non-tumor-derived

source_name: S55.1 (right preauric skin) mRNA, serum starved


title: Right scalp fibroblasts (A14.1), serum starved

description:
tumor, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47261.gif; format: GIF
Disease State: non-tumor-derived

source_name: A14.1 (right scalp fibroblasts) mRNA, serum starved


title: follow-up sample after treatment of rejection post5

source_name: whole peripheral blood RNA; heart transplant post-rejection (paired with r5)


title: Gene expression comparing between fosBd/d [Cy3-red] and wild type [Cy5-green] ES cells

source_name: fosBd/d ES cells


title: BCC-3 fibroblasts, serum starved

description:
tumor, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46553.gif; format: GIF
Disease State: tumor-derived

source_name: BCC-3 mRNA, serum starved

tag: BCC-3 mRNA, serum starved


title: Left arm fibroblasts, infiltrative BCC (S68.1 iii), serum starved

description:
tumor, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/45146.gif; format: GIF
Disease State: tumor-derived

source_name: S68.1 iii (left arm fibroblasts, infiltrative BCC) mRNA, serum starved


title: BCC-4 fibroblasts, serum starved

description:
tumor, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55297.gif; format: GIF
Disease State: tumor-derived

source_name: BCC-4 mRNA, serum starved

tag: BCC-4 mRNA, serum starved


title: follow-up sample after treatment of rejection post1

source_name: whole peripheral blood RNA; heart transplant post-rejection (paired with r1)


title: patient with rejection r7

description: Gene expression data from whole periheral blood in heart transplant recipients with acute cellular rejection

source_name: whole peripheral blood RNA; heart transplant rejection


title: Right mid arm fibroblasts, normal skin (S68.2 i), serum starved

description:
Development, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/45147.gif; format: GIF
Disease State: non-tumor-derived

source_name: S68.2 i (right mid arm fibroblasts) mRNA, serum starved


title: follow-up sample after treatment of rejection post3

source_name: whole peripheral blood RNA; heart transplant post-rejection (paired with r3)


title: BCC-2 fibroblasts, serum starved

description:
tumor, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52928.gif; format: GIF
Disease State: tumor-derived

source_name: BCC-2 mRNA, serum starved

tag: BCC-2 mRNA, serum starved


title: patient with rejection r6


title: Gene expression comparing between fosB-null [Cy3-red] and wild type [Cy5-green] ES cells

source_name: fosB-null ES cells

source_name: wild type ES cells


title: patient with rejection r2


title: patient with rejection r4


title: patient with rejection r3


title: follow-up sample after treatment of rejection post4

source_name: whole peripheral blood RNA; heart transplant post-rejection (paired with r4)


title: patient with rejection r5


title: CD34+ Untreated at 24 hours_2

description: The biotin-labeled target synthesis reactions, as well as the Affymetrix HG-U133A GeneChip arrays hybridization, staining, and scanning, were performed, starting from 2ug of total cellular RNA, using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). The fragmented cRNAs (20ug) were then hybridized to an identical lot of Affymetrix HG-U133A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument?s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification. GeneChip were finally scanned using the GA2500 Affymetrix GeneChip scanner.

source_name: CD34+ progenitors cells

extract_protocol: Total RNA was isolated from each cell population using RNeasy MinElute Cleanup kit (Qiagen, Valencia, CA) following manufacturer's recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 bioanalyzer. RNAs originating from the 6 donors were pooled in order to obtain at least 2 mg/sample in both untreated and treated cells.

treatment_protocol: Highly purified CD34+ cells from 6 healthy donors were seeded at 1000000 cells/ml in serum free medium (EX vivo 15) w/o cytokines and maintened in this culture conditions for 24 hours.

tag: CD34+ hemopoietic progenitors purified from peripheral blood.


title: CD34+ Treated 10 uM UTP and 150ng/ml CXCL12 at 24 hours

treatment_protocol: Highly purified CD34+ cells from 6 healthy donors were seeded at 1000000 cells/ml in serum free medium (EX vivo 15) w/o cytokines and treated with 10 mM UTP and 150ng/ml CXCL12 for 24 hours.


title: CD34+ Treated 150ng/ml CXCL12 at 24 hours

treatment_protocol: Highly purified CD34+ cells from 6 healthy donors were seeded at 1000000 cells/ml in serum free medium (EX vivo 15) w/o cytokines and treated with 150ng/ml CXCL12 for 24 hours.


title: CD34+ Treated 10 uM UTP at 24 hours_2

treatment_protocol: Highly purified CD34+ cells from 6 healthy donors were seeded at 1000000 cells/ml in serum free medium (EX vivo 15) w/o cytokines and treated with 10 mM UTP for 24 hours.


title: Right medial chest fibroblasts (S68.3 ii), serum starved

description:
Development, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/45148.gif; format: GIF
Disease State: non-tumor-derived

source_name: Stratagene UR

source_name: S68.3 ii (right medial chest fibroblasts) mRNA, serum starved


title: patient with rejection r1


title: BCC-P15-PB1 - mAdbID:60709

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

description: mAdb experiment ID: 60709

hyb_protocol: Sample Hybrization Protocol Wash procedure: Washing: 1. Wash with 2x SSC + 0.1% SDS to remove coverslip. 2. Wash with 1x SSC for 1 min. 3. Wash with 0.2x SSC for 1 min. 4. Wash with 0.05x SSC for 10-20 seconds. 5. Centrifuge slide at 80-100 g for 3 min. Other: Hybridization: Combine Cy3 and Cy5 labeled target (adjust the color to purple) and complete dry the sample by speed vacuum . Add 37ul of the following mixture to the dried target (for 20x40mm slide): 1ul 50x Denhardtüs blocking solution (Sigma Cat# 2532) 1ul poly dA (8mg/ml Pharmacia Cat# 27-7988-01) 1ul yeast tRNA (4mg/ml Sigma Cat# R8759) 10ul Human Cot I DNA (1mg/ml Gibco BRL Cat# 15279-011) 3ul 20X SSC 1ul 10% SDS 20ul of DEPC H2O Heat for 2 min at 99oC and Cool to RT. Apply target mixture to array slide, add coverslip, place in humidified hyb chamber, and hybridize at 65oC over night.

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

source_name: PBMC Pooled Donor Reference Sample

label_protocol:
Cy3 Sample Labeling Protocol
Other: Target labeling by reverse transcription: 4ul First strand buffer 1ul dN6 primer (8ug/ul; Boehringer Mannheim Cat# 1034731 resuspended in 250ul DEPC H2O) 2ul 10X low T - dNTP (5mM A, C and GTP, 2mM dTTP) 2ul Cy-dUTP (1mM Cy3) 2ul 0.1 M DTT 1ul RNasin 3-6ug amplified mRNA in 7 ul DEPC H2O Mix well and heat to 65C for 5min then cool down to 42C. Add 1.5ul SSII and Incubate for 90 min at 42C. Add 2.5ul 500mM EDTA and heat to 65C for 1min. Add 5ul 1M NaOH and incubate at 65C for 15min to hydrolyze RNA. Add 12.5ul 1M Tris immediately to neutralize the pH. Add 35ul of 1xTE. Target clean up: Prepare Bio-6 column and run target solution through it. Collect flow through and add 200ul 1xTE. Concentrate target to ~20ul using a microcon YM-30 column (Millipore Cat# 42410).

extract_protocol:
Sample Extraction Protocol
Other: RNA isolation from skin samples and modified RNA amplification for microarrays and Taqman real time PCR Total RNA was isolated using RNeasy minikits (Qiagen, Germantown, MD). Amplified antisense RNA (aRNA) was prepared from total RNA (0.5-3 ug) according to a modified version (see modification to original protocol, A-C below) of the protocol previously described by us (Wang et al Nature biotech 2000;17(4):457-459). The modifications introduced for total RNA isolation were the following: A) Tissue was homogenized through a 15ml disposable small tissue grinder (Fisher Scientific cat# 06-434A) containing originally 150ul of lysis buffer (RLT buffer + 2ul- betaME) and subsequently an additional 200 ul of lysis buffer to complete tissue homogenization and lysis. The lysate was then transferred to a QIAshreddder spin column and centrifuged at for 2 minutes at max speed. B) To remove proteins that interfered with RNA isolation, 590ul double-distilled water were added to the homogenate followed by 10ul PROTEINASE K solution (Qiagen) and mixed thoroughly by pipetting. The homogenate was then incubated at 55C for 10 minutes and centrifuged for 3 min at 13000 rpm at room temp. The supernatant (approximately 900ul) was then combined and mixed well with 0.5 volumes (usually 450 ul) of ethanol (96-100%) into a new Rnase-Dnase free tube mixed well by pipetting. To Separate RNA from DNA. 700ul of the sample (including any precipitate that may have formed) were transferred into a RNeasy mini column placed in a 2ml collection tube. Total RNA was isolated according to the manufacturer protocol. The modifications introduced for Antisense RNA amplification were the following: C) First strand cDNA synthesis was accomplished in the presence of 1ul SUPERase÷In (Ambion Cat# 2696 stored at Ÿ20 øC) instead of Rnasein Ambion Cat# 2696 stored at Ÿ20 øC) and ThermoScript RT (Gibco BRL Cat# 12236-022) instead of Superscript . One microliter of BSA (2ug/ul) was added as a carrier to each samples to increase RNA yield. D) A higher concentration of 1st round of amplification material was achieved by resuspending antisense RNA into « (11 ul) of original procedure volume and taking all of 1st round amplification-material to the second round of amplification. Quality of RNA was tested by Agilent technologies and spectophotometry (OD). Antisense RNA was either used for probe preparation and microarray analysis or for Taqman real time PCR. For microarray analysis test samples were labeled with Cy5-dUTP (Amersham, Piscataway, NJ) while the reference sample (pooled normal donor PBMC) was labeled with Cy3-dUTP. Test-reference sample pairs were mixed and co-hybridized to 17K-cDNA microarrays generated in our lab (gal file http://nciarray.nci.nih.gov/gal_files/gal_custom_current.shtml, Hs-CCDTM17.5k-1px.gal

tag: Cell type

value: peripheral blood mononuclear cells

label_protocol:
Cy5 Sample Labeling Protocol
Other: Target labeling by reverse transcription: 4ul First strand buffer 1ul dN6 primer (8ug/ul; Boehringer Mannheim Cat# 1034731 resuspended in 250ul DEPC H2O) 2ul 10X low T - dNTP (5mM A, C and GTP, 2mM dTTP) 2ul Cy-dUTP (1mM Cy5) 2ul 0.1 M DTT 1ul RNasin 3-6ug amplified mRNA in 7 ul DEPC H2O Mix well and heat to 65C for 5min then cool down to 42C. Add 1.5ul SSII and Incubate for 90 min at 42C. Add 2.5ul 500mM EDTA and heat to 65C for 1min. Add 5ul 1M NaOH and incubate at 65C for 15min to hydrolyze RNA. Add 12.5ul 1M Tris immediately to neutralize the pH. Add 35ul of 1xTE. Target clean up: Prepare Bio-6 column and run target solution through it. Collect flow through and add 200ul 1xTE. Concentrate target to ~20ul using a microcon YM-30 column (Millipore Cat# 42410).

value: skin

tag: Disease state

value: basal cell carcinoma


title: BCC-P135-PB1 - mAdbID:59838

description: mAdb experiment ID: 59838


title: BCC-P135-PB3 - mAdbID:59837

description: mAdb experiment ID: 59837

treatment_protocol:
Treatment type: compound
Agent: Imiquimod/Aldara
Treatment dose: 12.5 mg/dose
Treatment time: 4 days
Other: Cohort was treated twice a day for 4 days for a total of 8 doses.


title: BCC-P18-PB3 - mAdbID:65139

description: mAdb experiment ID: 65139

treatment_protocol:
Treatment type: compound
Agent: Imiquimod/Aldara
Treatment dose: 12.5 mg/dose
Treatment time: 2 days
Other: Cohort was treated twice a day for 2 days for a total of 4 doses.


title: follow-up sample after treatment of rejection post2

source_name: whole peripheral blood RNA; heart transplant post-rejection (paired with r2)


title: BCC-P42-PB1 - mAdbID:59815

description: mAdb experiment ID: 59815


title: BCC-P137-PB1 - mAdbID:59817

description: mAdb experiment ID: 59817


title: BCC-P42-PB3 - mAdbID:59816

description: mAdb experiment ID: 59816


title: BCC-P40-PB3 - mAdbID:59812

description: mAdb experiment ID: 59812


title: follow-up sample after treatment of rejection post6

source_name: whole peripheral blood RNA; heart transplant post-rejection (paired with r6)


title: BCC-P137-PB3 - mAdbID:59818

description: mAdb experiment ID: 59818

treatment_protocol:
Treatment type: placebo
Agent: vehicle cream
Treatment time: 8 days
Other: Cohort was treated twice a day for 8 days for a total of 8 doses.


title: BCC-P40-PB1 - mAdbID:59810

description: mAdb experiment ID: 59810


title: BCC-P41-PB1 - mAdbID:59813

description: mAdb experiment ID: 59813


title: BCC-P38-PB1 - mAdbID:59808

description: mAdb experiment ID: 59808


title: BCC-P36-PB1 - mAdbID:59806

description: mAdb experiment ID: 59806


title: BCC-P38-PB3 - mAdbID:59809

description: mAdb experiment ID: 59809


title: Follicular dendritic cell 1

city: Tsurumi, Yokohama

first: Masaki

last: Hikida

state: Kanagawa

address: 1-7-22 Suehiro-cho

department: RCAI

institute: RIKEN

description: total RNA was prepared from in vitro cultured follicular dendritic cells

data_processing: raw data

source_name: Follicular denderitic cell

label_protocol: One-Cycle Target Labeling Kit


title: Follicular dendritic cell 2

tag: Total RNA was prepared from in vitro cultured follicular dendritic cell


title: BCC-P233-PB1 - mAdbID:50646

description: mAdb experiment ID: 50646


title: BCC-P233-PB3 - mAdbID:50647

description: mAdb experiment ID: 50647

treatment_protocol:
Treatment type: compound
Agent: Imiquimod/Aldara
Treatment dose: 12.5 mg/dose
Treatment time: 8 days
Other: Cohort was treated once a day for 8 days for a total of 8 doses.


title: Bone marrow derived dendritic cell 2

description: total RNA were prepared from bone marrow derived dendritic cell

source_name: Bone marrow derived dendritic cell

tag: Total RNA was prepared from bone marrow derived dendritic cell


title: O4-4B

city: Bethesda

first: Joe

middle: A

last: Nielsen

state: MD

address: 49 Convent Drive BD49,5A75

institute: NIH/NINDS

description: Single A2B5+ and single O4+ cells were sorted directly from whole brain dissociates using flow cytometry

data_processing: Affymetrix CEL files were imported into Genespring and GCRMA was used for preprocessing of the data.  The data was normalized in Genespring using global per chip and per gene normalization

organism: Rattus norvegicus

source_name: whole brain

tag: Postnatal day7 male Sprague Dawley pups


title: BCC-P36-PB3 - mAdbID:59807

description: mAdb experiment ID: 59807

treatment_protocol:
Treatment type: placebo
Agent: vehicle cream
Treatment time: 4 days
Other: Cohort was treated twice a day for 4 days for a total of 4 doses.

tag: Tissue


title: O4-3B


title: Bone marrow derived dendritic cell

tag: total RNA were prepared from

tag: bone marrow derived dendritic cell


title: O4-2B


title: BCC-P41-PB3 - mAdbID:59814

description: mAdb experiment ID: 59814

treatment_protocol:
Treatment type: placebo
Agent: vehicle cream
Treatment time: 4 days
Other: Cohort was treated twice a day for 4 days for a total of 8 doses.


title: BCC-P134-PB1 - mAdbID:50644

description: mAdb experiment ID: 50644


title: BCC-P26-PB1 - mAdbID:50661

description: mAdb experiment ID: 50661


title: BCC-P134-PB3 - mAdbID:50645

description: mAdb experiment ID: 50645


title: BCC-P129-PB3 - mAdbID:50641

description: mAdb experiment ID: 50641


title: O4-1B


title: BCC-P129-PB1 - mAdbID:50638

description: mAdb experiment ID: 50638


title: BCC-P30-PB3 - mAdbID:50639

description: mAdb experiment ID: 50639


title: BCC-P132-PB3 - mAdbID:50643

description: mAdb experiment ID: 50643


title: A2B5-5B


title: BCC-P132-PB1 - mAdbID:50642

description: mAdb experiment ID: 50642


title: BCC-P28-PB3 - mAdbID:50637

description: mAdb experiment ID: 50637

treatment_protocol:
Treatment type: compound
Agent: Imiquimod/Aldara
Treatment dose: 12.5 mg/dose
Treatment time: 4 days
Other: Cohort was treated once a day for 4 days for a total of 4 doses.


title: A2B5-2B


title: BCC-P30-PB1 - mAdbID:50636

description: mAdb experiment ID: 50636


title: SMmuscle_NNgenotype_T12_rep1

city: Brisbane

first: Ross

last: Tellam

state: QLD

address: 306 Carmody Road St.Lucia

department: Level 6 Queensland Biosciences Precinct

country: Australia

institute: CSIRO Animal, Food and Health Sciences

description: Gene expression data from the Callipyge genotype (NN) at birth (T=12) from muscle type (SM)

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Bovine Genomer Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 200.

organism: Ovis aries

source_name: Semitendonosis (SM) muscle sample, Callipyge genotype (NN) at birth (T=12), technical rep1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Animals were reared and euthanased in accordance with the animal ethics guidelines of Utah State University (Utah, USA)

treatment_protocol: Skeletal muscle samples were obtained from a flock of Dorset/Suffolk/Rambouillet cross-bred sheep raised at Utah State University. Matings were conducted to produce the genotypes for transcript profiling comparisons, particularly the genotypes NN and NCpat , where NN is the wild type and NCpat is the paternal heterozygote. The genotypes of all animals were confirmed using a genotyping test (Freking et al. 2002; Smit et al. 2003). Longissimus dorsi (LD) skeletal muscle samples were obtained from 8 male lambs representing four of each genotype, at birth (T0) and 11-12 weeks of age (T12). In addition, samples were also taken of semimembranosis (SM) and semitendonosis (ST) skeletal muscles from wild type lambs at 12 weeks of age. All muscles were carefully dissected out and weighed. Samples were then collected from each muscle at pre-determined sites. The samples were dissected from the animal within 15 minutes of euthanasia and immediately frozen under liquid nitrogen and stored at –80oC.

tag: Genotype

value: NN

tag: Age

value: T=12 weeks


title: STmuscle_NNgenotype_T12_rep1

description: Gene expression data from the Callipyge genotype (NN) at birth (T=12) from muscle type (ST)

source_name: Semitendonosis (ST) muscle sample, Callipyge genotype (NN) at birth (T=12), technical rep1


title: BCC-P214-PB1 - mAdbID:47173

description: mAdb experiment ID: 47173


title: BCC-P26-PB3 - mAdbID:50633

description: mAdb experiment ID: 50633

treatment_protocol:
Treatment type: placebo
Agent: vehicle cream
Treatment time: 2 days
Other: Cohort was treated twice a day for 2 days for a total of 4 doses.


title: BCC-P24-PB1 - mAdbID:47172

description: mAdb experiment ID: 47172


title: A2B5-3B


title: A2B5-4B


title: BCC-P23-PB3 - mAdbID:47171

description: mAdb experiment ID: 47171


title: BCC-P28-PB1 - mAdbID:50632

description: mAdb experiment ID: 50632


title: A2B5-1B


title: SMmuscle_NNgenotype_T12_rep2

source_name: Semitendonosis (SM) muscle sample, Callipyge genotype (NN) at birth (T=12), technical rep2


title: BCC-P24-PB3 - mAdbID:47175

description: mAdb experiment ID: 47175


title: STmuscle_NNgenotype_T12_rep2

source_name: Semitendonosis (ST) muscle sample, Callipyge genotype (NN) at birth (T=12), technical rep2


title: BCC-P214-PB3 - mAdbID:47174

description: mAdb experiment ID: 47174


title: BCC-P21-PB3 - mAdbID:47166

description: mAdb experiment ID: 47166


title: LDmuscle_NCgenotype_T12_rep2

description: Gene expression data from the Callipyge genotype (NC) at birth (T=12) from muscle type (LD)

source_name: Longissimus dorsi (LD) muscle sample, Callipyge genotype (NC) at birth (T=12), technical rep2

value: NC (CmatN) maternal heterozygote


title: BCC-P27-PB1 - mAdbID:50630

description: mAdb experiment ID: 50630


title: BCC-P27-PB3 - mAdbID:50635

description: mAdb experiment ID: 50635


title: BCC-P22-PB3 - mAdbID:47168

description: mAdb experiment ID: 47168


title: BCC-P23-PB1 - mAdbID:47170

description: mAdb experiment ID: 47170


title: LDmuscle_NNgenotype_T12_rep2

description: Gene expression data from the Callipyge genotype (NN) at birth (T=12) from muscle type (LD)

source_name: Longissimus dorsi (LD) muscle sample, Callipyge genotype (NN) at birth (T=12), technical rep2


title: SSmuscle_NNgenotype_T12_rep1

description: Gene expression data from the Callipyge genotype (NN) at birth (T=12) from muscle type (SS)

source_name: Supraspinatus (SS) muscle sample, Callipyge genotype (NN) at birth (T=12), technical rep1


title: LDmuscle_NCgenotype_T12_rep1

source_name: Longissimus dorsi (LD) muscle sample, Callipyge genotype (NC) at birth (T=12), technical rep1


title: SSmuscle_NNgenotype_T12_rep2

source_name: Supraspinatus (SS) muscle sample, Callipyge genotype (NN) at birth (T=12), technical rep2


title: LDmuscle_NNgenotype_T12_rep1

source_name: Longissimus dorsi (LD) muscle sample, Callipyge genotype (NN) at birth (T=12), technical rep1


title: BCC-P22-PB1 - mAdbID:47167

description: mAdb experiment ID: 47167


title: Cu shock treatment rep2

city: Chicago

first: Gail

middle: M

last: Teitzel

state: IL

department: MGCB

institute: University of Chicago

description: Cu shock treatment

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

organism: Pseudomonas aeruginosa

source_name: 10mM Cu shock treatment

label_protocol: Approximately 36 µg of total RNA was processed to produce biotinylated cRNA targets.

growth_protocol: grown in LB with 100 mM MOPS at 37C

extract_protocol: 2 mL of culture was added to 4 mL RNAlater (Ambion). Total RNA was extracted using an RNeasy kit (Qiagen).

treatment_protocol: early log phase (OD600=0.2) treated with 10 mM Cu for 45 min

tag: Pseudomonas aeruginosa PAO1


title: SSmuscle_CNgenotype_T12_rep2

description: Gene expression data from the Callipyge genotype (CN) at birth (T=12) from muscle type (SS)

source_name: Supraspinatus (SS) muscle sample, Callipyge genotype (CN) at birth (T=12), technical rep2

value: CN (NCpat) paternal heterozygote


title: SSmuscle_CNgenotype_T12_rep1

source_name: Supraspinatus (SS) muscle sample, Callipyge genotype (CN) at birth (T=12), technical rep1


title: control for Cu shock treatment rep2

description: Cu shock control treatment

source_name: control for 10mM Cu shock treatment

treatment_protocol: early log phase (OD600=0.2) treated with HCl to bring pH to same levels as with 10 mM Cu for 45 min


title: BCC-P20-PB3 - mAdbID:47164

description: mAdb experiment ID: 47164

source_name: PBMC Pooled Donor Reference Sample


title: LDmuscle_CCgenotype_T12_rep2

description: Gene expression data from the Callipyge genotype (CC) at birth (T=12) from muscle type (LD)

source_name: Longissimus dorsi (LD) muscle sample, Callipyge genotype (CC) at birth (T=12), technical rep2

value: CC


title: control for Cu shock treatment rep1

description: Cu shock control treatment


title: LD muscle_CC genotype_T12_rep1

source_name: Longissimus dorsi (LD) muscle sample, Callipyge genotype (CC) at birth (T=12), technical rep1


title: BCC-P21-PB1 - mAdbID:47165

description: mAdb experiment ID: 47165


title: BCC-P15-PB3 - mAdbID:47154

description: mAdb experiment ID: 47154


title: adapted Cu treatment control rep2

description: adapted Cu treatment

source_name: adapted 10mM Cu treatment control

extract_protocol: 2 mL of culture was added to 4 mL RNAlater (Ambion).  Total RNA was extracted using an RNeasy kit (Qiagen).

treatment_protocol: grown to early log phase (OD600=0.2; approx 6h)


title: BCC-P20-PB1 - mAdbID:47163

description: mAdb experiment ID: 47163


title: Cu shock treatment rep1

description: Cu shock treatment


title: BCC-P18-PB1 - mAdbID:47161

description: mAdb experiment ID: 47161


title: BCC-P112-PB3 - mAdbID:47149

description: mAdb experiment ID: 47149


title: BCC-P17-PB3 - mAdbID:47159

description: mAdb experiment ID: 47159


title: BCC-P231-PB3 - mAdbID:41488

description: mAdb experiment ID: 41488


title: BCC-P17-PB1 - mAdbID:47156

description: mAdb experiment ID: 47156


title: LDmuscle_CNgenotype_T12_rep1

description: Gene expression data from the Callipyge genotype (CN) at birth (T=12) from muscle type (LD)

source_name: Longissimus dorsi (LD) muscle sample, Callipyge genotype (CN) at birth (T=12), technical rep1


title: BCC-P4-PB3 - mAdbID:47151

description: mAdb experiment ID: 47151


title: BCC-P231-PB1 - mAdbID:41487

description: mAdb experiment ID: 41487


title: LDmuscle_NNgenotype_T0_rep2

description: Gene expression data from the Callipyge genotype (NN) at birth (T=0) from muscle type (LD)

source_name: Longissimus dorsi (LD) muscle sample, Callipyge genotype (NN) at birth (T=0), technical rep2

value: T=0 birth


title: LDmuscle_NCgenotype_T0_rep2

description: Gene expression data from the Callipyge genotype (NC) at birth (T=0) from muscle type (LD)

source_name: Longissimus dorsi (LD) muscle sample, Callipyge genotype (NC) at birth (T=0), technical rep2


title: BCC-P4-PB1 - mAdbID:47150

description: mAdb experiment ID: 47150


title: BCC-P112-PB1 - mAdbID:47148

description: mAdb experiment ID: 47148


title: LDmuscle_NNgenotype_T0_rep1

source_name: Longissimus dorsi (LD) muscle sample, Callipyge genotype (NN) at birth (T=0), technical rep1


title: adapted Cu treatment control rep1

description: adapted Cu treatment


title: adapted Cu treatment rep2

description: adapted Cu treatment

source_name: adapted 10mM Cu treatment

treatment_protocol: grown to early log phase (OD600=0.2) with 10 mM Cu (approx 6h)


title: LDmuscle_CNgenotype_T12_rep2

source_name: Longissimus dorsi (LD) muscle sample, Callipyge genotype (CN) at birth (T=12), technical rep2


title: BCC-P13-PB1 - mAdbID:41486

description: mAdb experiment ID: 41486


title: LDmuscle_NCgenotype_T0_rep1

source_name: Longissimus dorsi (LD) muscle sample, Callipyge genotype (NC) at birth (T=0), technical rep1


title: BCC-P11-PB1 - mAdbID:41484

description: mAdb experiment ID: 41484


title: BCC-P13-PB3 - mAdbID:41485

description: mAdb experiment ID: 41485


title: adapted Cu treatment rep1

description: adapted Cu treatment


title: BCC-P10-PB3 - mAdbID:41480

description: mAdb experiment ID: 41480


title: BCC-P10-PB1 - mAdbID:41482

description: mAdb experiment ID: 41482


title: LDmuscle_CNgenotype_T0_rep2

description: Gene expression data from the Callipyge genotype (CN) at birth (T=0) from muscle type (LD)

source_name: Longissimus dorsi (LD) muscle sample, Callipyge genotype (CN) at birth (T=0), technical rep2


title: BCC-P8-PB1 - mAdbID:41478

description: mAdb experiment ID: 41478


title: BCC-P8-PB3 - mAdbID:41477

description: mAdb experiment ID: 41477


title: LDmuscle_CNgenotype_T0_rep1

source_name: Longissimus dorsi (LD) muscle sample, Callipyge genotype (CN) at birth (T=0), technical rep1


title: LDmuscle_CCgenotype_T0_rep1

description: Gene expression data from the Callipyge genotype (CC) at birth (T=0) from muscle type (LD)

source_name: Longissimus dorsi (LD) muscle sample, Callipyge genotype (CC) at birth (T=0), technical rep1


title: BCC-P5-PB1 - mAdbID:41475

description: mAdb experiment ID: 41475


title: BCC-P6-PB1 - mAdbID:41476

description: mAdb experiment ID: 41476


title: LDmuscle_CCgenotype_T0_rep2

source_name: Longissimus dorsi (LD) muscle sample, Callipyge genotype (CC) at birth (T=0), technical rep2


title: BCC-P2-PB3 - mAdbID:41468

description: mAdb experiment ID: 41468


title: BCC-P5-PB3 - mAdbID:41470

description: mAdb experiment ID: 41470


title: BCC-P6-PB3 - mAdbID:41471

description: mAdb experiment ID: 41471


title: BCC-P2-PB1 - mAdbID:41467

description: mAdb experiment ID: 41467


title: BCC-P3-PB1 - mAdbID:41469

description: mAdb experiment ID: 41469


title: BCC-P1-PB1 - mAdbID:41462

description: mAdb experiment ID: 41462


title: BCC-P1-PB3 - mAdbID:41465

description: mAdb experiment ID: 41465


title: BCC-P3-PB3 - mAdbID:41466

description: mAdb experiment ID: 41466


title: pk 2 6 (4/4/03)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39954.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 960, 6400; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Edward,,Boyden 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 = 31.64; Parameter Scan Time = 13:55:14; Parameter PMT Volts = 470; Parameter Scan Date = 2003-04-04; Parameter Pixel Size = 10; Parameter Laser on time = 26871; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.80; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden 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 = 31.64; Parameter Scan Time = 13:55:14; Parameter PMT Volts = 600; Parameter Scan Date = 2003-04-04; Parameter Pixel Size = 10; Parameter Laser on time = 96716; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: MRB 2nd round (4/4/03)

tag: MRB 2nd round (4/4/03)


title: pk 4-1 (9/23/02)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33678.gif

source_name: MRB 2nd round (9/23/02)

tag: MRB 2nd round (9/23/02)


title: pk 3-2 (11/24/02)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36626.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 7210; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Edward,,Boyden 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 = 37.16; Parameter Scan Time = 19:00:26; Parameter PMT Volts = 500; Parameter Scan Date = 2002-10-29; Parameter Pixel Size = 10; Parameter Laser on time = 80761; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 4.32; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.5; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden 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 = 37.16; Parameter Scan Time = 19:00:26; Parameter PMT Volts = 540; Parameter Scan Date = 2002-10-29; Parameter Pixel Size = 10; Parameter Laser on time = 77647; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.69; Parameter Scanning software version = 2.0.2.5; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden


title: BCC-P11-PB3 - mAdbID:41483

description: mAdb experiment ID: 41483

source_name: PBMC Pooled Donor Reference Sample


title: pk 2 5 (4/4/03)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39952.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 960, 6400; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Edward,,Boyden 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 = 32.58; Parameter Scan Time = 15:56:55; Parameter PMT Volts = 550; Parameter Scan Date = 2003-04-04; Parameter Pixel Size = 10; Parameter Laser on time = 26992; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.78; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden 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 = 32.58; Parameter Scan Time = 15:56:55; Parameter PMT Volts = 705; Parameter Scan Date = 2003-04-04; Parameter Pixel Size = 10; Parameter Laser on time = 96837; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.59; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden


title: pk 2-2 (11/24/02)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36625.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 770, 7600; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Edward,,Boyden 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 = 37.19; Parameter Scan Time = 17:19:01; Parameter PMT Volts = 500; Parameter Scan Date = 2002-10-29; Parameter Pixel Size = 10; Parameter Laser on time = 80674; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 4.32; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.5; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden 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 = 37.19; Parameter Scan Time = 17:19:01; Parameter PMT Volts = 510; Parameter Scan Date = 2002-10-29; Parameter Pixel Size = 10; Parameter Laser on time = 77560; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.70; Parameter Scanning software version = 2.0.2.5; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden


title: gc 2-3 (11/24/02)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35395.gif


title: gc 3-2 (11/24/02)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36536.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 7210; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Edward,,Boyden 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 = 37.16; Parameter Scan Time = 18:49:11; Parameter PMT Volts = 500; Parameter Scan Date = 2002-10-29; Parameter Pixel Size = 10; Parameter Laser on time = 80751; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 4.32; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.5; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden 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 = 37.16; Parameter Scan Time = 18:49:11; Parameter PMT Volts = 540; Parameter Scan Date = 2002-10-29; Parameter Pixel Size = 10; Parameter Laser on time = 77637; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.71; Parameter Scanning software version = 2.0.2.5; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden


title: pk 4  5 (4/22/03)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40600.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 520, 5440; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Edward,,Boyden 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 = 31.06; Parameter Scan Time = 14:23:46; Parameter PMT Volts = 545; Parameter Scan Date = 2003-04-22; Parameter Pixel Size = 10; Parameter Laser on time = 29043; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.85; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden 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 = 31.06; Parameter Scan Time = 14:23:46; Parameter PMT Volts = 680; Parameter Scan Date = 2003-04-22; Parameter Pixel Size = 10; Parameter Laser on time = 98874; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.55; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden

source_name: MRB 2nd round (4/22/03)

tag: MRB 2nd round (4/22/03)


title: pk 3 5 (4/4/03)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39953.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 960, 6400; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Edward,,Boyden 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 = 32.74; Parameter Scan Time = 17:01:45; Parameter PMT Volts = 560; Parameter Scan Date = 2003-04-04; Parameter Pixel Size = 10; Parameter Laser on time = 27056; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.78; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden 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 = 32.74; Parameter Scan Time = 17:01:45; Parameter PMT Volts = 730; Parameter Scan Date = 2003-04-04; Parameter Pixel Size = 10; Parameter Laser on time = 96902; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.60; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden


title: pk 3-1 (11/24/02)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35368.gif


title: gc 3-1 (11/24/02)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35366.gif


title: gc 2-1 (9/23/02)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33690.gif


title: gc 3-3 (2/4/03)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/39167.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 740, 7250; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Edward,,Boyden 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 = 31.97; Parameter Scan Time = 15:12:45; Parameter PMT Volts = 510; Parameter Scan Date = 2003-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 17225; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.66; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden 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 = 31.97; Parameter Scan Time = 15:12:45; Parameter PMT Volts = 560; Parameter Scan Date = 2003-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 87183; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.60; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden

source_name: MRB 2nd round (2/4/03)

tag: MRB 2nd round (2/4/03)


title: pk 1-3 (11/24/02)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36532.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 7210; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Edward,,Boyden 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 = 37.07; Parameter Scan Time = 18:32:06; Parameter PMT Volts = 530; Parameter Scan Date = 2002-10-29; Parameter Pixel Size = 10; Parameter Laser on time = 80733; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 4.32; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.5; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden 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 = 37.07; Parameter Scan Time = 18:32:06; Parameter PMT Volts = 510; Parameter Scan Date = 2002-10-29; Parameter Pixel Size = 10; Parameter Laser on time = 77619; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.69; Parameter Scanning software version = 2.0.2.5; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden


title: gc 4-1 (9/23/02)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33676.gif


title: gc 3-5 (4/22/03)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40596.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 520, 5440; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Edward,,Boyden 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 = 30.81; Parameter Scan Time = 13:26:16; Parameter PMT Volts = 550; Parameter Scan Date = 2003-04-22; Parameter Pixel Size = 10; Parameter Laser on time = 28986; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.83; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden 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 = 30.81; Parameter Scan Time = 13:26:16; Parameter PMT Volts = 675; Parameter Scan Date = 2003-04-22; Parameter Pixel Size = 10; Parameter Laser on time = 98817; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.55; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden


title: gc 1-2 (11/24/02)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35364.gif


title: Anergic2

first: yuanyuan

last: zha

department: Department of Pathology

description: we are interested in which genes are upregulated during T cell anergy. Thus, RNA from normal quiescent T cell clones were extracted to be compared to RNA extracted from anergic T cell clones

data_processing: Affymetrix Microarray Suite 4.0

molecule: polyA RNA

source_name: anergic Th1 T cell clone

label_protocol: Approximately 8 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: total RNA was extracted using Trizol  method (Invitrogen)

tag: anergized CD4 T cell clone


title: gc 2-4 (2/4/03)

last: Stanford Microarray Database

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/39165.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 740, 7250; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Edward,,Boyden 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 = 31.82; Parameter Scan Time = 14:45:20; Parameter PMT Volts = 500; Parameter Scan Date = 2003-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 17198; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.66; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden 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 = 31.82; Parameter Scan Time = 14:45:20; Parameter PMT Volts = 560; Parameter Scan Date = 2003-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 87156; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.58; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden


title: gc 1-1 (9/23/02)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33673.gif


title: pk 4-3 (11/24/02)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35380.gif


title: pk 1-1 (9/23/02)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33670.gif


title: pk 3-6 (5/7/03)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40729.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 740, 6910; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Edward,,Boyden 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 = 30.81; Parameter Scan Time = 13:36:48; Parameter PMT Volts = 525; Parameter Scan Date = 2003-05-07; Parameter Pixel Size = 10; Parameter Laser on time = 32176; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.80; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden 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 = 30.81; Parameter Scan Time = 13:36:48; Parameter PMT Volts = 640; Parameter Scan Date = 2003-05-07; Parameter Pixel Size = 10; Parameter Laser on time = 101977; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.51; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden

source_name: MRB 2nd round (5/7/03)

tag: MRB 2nd round (5/7/03)


title: pk 3-7 (5/7/03)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40760.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 740, 6910; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Edward,,Boyden 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 = 30.97; Parameter Scan Time = 13:50:56; Parameter PMT Volts = 525; Parameter Scan Date = 2003-05-07; Parameter Pixel Size = 10; Parameter Laser on time = 32191; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.74; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden 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 = 30.97; Parameter Scan Time = 13:50:56; Parameter PMT Volts = 655; Parameter Scan Date = 2003-05-07; Parameter Pixel Size = 10; Parameter Laser on time = 101991; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.51; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden


title: Anergic1

description: we are interested in which genes are upregulated during T cell anergy. Thus,RNA from normal quiescent T cell clones were extracted to be compared to RNA extracted from anergic T cell clones