title: Gerbil-passaged H. pylori strain B128 Trial 2

status: Public on Aug 16 2005

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs//7195.gif

source_name: TIGR/Astra Reference DNA

tag: TIGR/Astra Reference DNA

source_name: B128 Test DNA

tag: B128 Test DNA


title: Gerbil-passaged H. pylori strain B128

type: genomic

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

country: USA

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs//7138.gif

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

molecule: genomic DNA

organism: Helicobacter pylori


title: g1-1 genomic DNA vs Tigr/Astra reference

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-01/1898.gif

source_name: 1ug Tigr genomic DNA, 1 ug Astra genomic DNA

source_name: 1.7 ug g1-1 genomic DNA

tag: 1.7 ug g1-1 genomic DNA


title: G1 vs TIGR/Astra Genomic DNA

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2902.gif

source_name: TIGR/Astra Genomic DNA

tag: TIGR/Astra Genomic DNA

source_name: G1 Genomic DNA

tag: G1 Genomic DNA


title: Rat fatty liver16

status: Public on Sep 16 2004

type: RNA

city: Cambridge

first: Julian

last: Griffin

address: Tennis Court Road

department: Biochemistry

country: United Kingdom

institute: University of Cambridge

description:
Rats (Charles River UK Ltd.) were fed either standard laboratory chow, or chow supplemented with 1% orotic acid (Sigma Aldrich, UK) ad libitum. Orotic acid feeding is a well-characterised method for inducing reversible fatty liver disease in rodents. Rats were killed by cervical dislocation and the left lateral lobe of the liver excised. Tissues were snap frozen and stored in liquid nitrogen and/or at –80oC.

Keywords = orotic acid
Lot batch = 1

hyb_protocol: Biotinylated cRNA was fragmented and hybridised to RGU34A Affymetrix GeneChips according to standard Affymetrix protocols.

scan_protocol: Performed according to standard Affymetrix protocols.

data_processing: Data were analysed with the Affymetrix Microarray Suite 5.0 algorithm to generate a “signal” value and a “detection” label. Prior to normalisation, probes that generated an absent call in all cells were removed. Normalisation was calculated using a Global Scaling method based on the entire data set. Globally scaled values <10 were rounded up to 10.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Wistar rat liver tissue (control)

label_protocol: cDNA was generated from total RNA using SuperscriptTM Double-stranded cDNA Synthesis kit (Invitrogen, Life Technologies), cRNA was prepared by in vitro transcription (BioArray High Yield RNA transcript labelling kit Affymetrix, UK), and purified on an affinity resin column (RNeasy, Qiagen Ltd., UK).

extract_protocol: Total RNA was extracted by RNA Isolation Kit (Stratagene) from the livers of Wistar and Kyoto rats at day 0 (Wistar n=3, Kyoto n=2), day 1 and 3 (Wistar n=2, Kyoto n=2), and day 14 (Wistar n=3, Kyoto n=2).

tag: Kyoto rat liver tissue following animal exposure to orotic acid for 1 day


title: G1.1 Genomic DNA vs TIGR/Astra Trial 3

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-04/4133.gif

source_name: G1.1 Test DNA

tag: G1.1 Test DNA


title: Rat fatty liver14

source_name: Wistar rat liver tissue following animal exposure to orotic acid for 14 days


title: G1.1 Genomic DNA vs TIGR/Astra Trial 4

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-04/4667.gif


title: Rat fatty liver12

description:
Rats (Charles River UK Ltd.) were fed either standard laboratory chow, or chow supplemented with 1% orotic acid (Sigma Aldrich, UK) ad libitum. Orotic acid feeding is a well-characterised method for inducing reversible fatty liver disease in rodents. Rats were killed by cervical dislocation and the left lateral lobe of the liver excised. Tissues were snap frozen and stored in liquid nitrogen and/or at –80oC.

Keywords = orotic acid

source_name: Wistar rat liver tissue following animal exposure to orotic acid for 3 days

tag: Kyoto rat liver tissue following animal exposure to orotic acid for 3 days


title: glucose pulse (2g/l) on galactose chemostat (t=180min)

status: Public on Feb 03 2006

description:
Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58918.gif

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)

organism: Saccharomyces cerevisiae

source_name: ref- t=0

tag: ref- t=0


title: Rat fatty liver11


title: Rat fatty liver3

source_name: Kyoto rat liver tissue following animal exposure to orotic acid for 3 days


title: Rat fatty liver1

source_name: Kyoto rat liver tissue following animal exposure to orotic acid for 1 day


title: Rat fatty liver4

source_name: Kyoto Rat liver tissue following animal exposure to orotic acid for 3 days


title: 6Hs.194

status: Public on Feb 13 2004

city: San Francisco

first: Michael

middle: E.

last: Salazar

address: 1550 Fourth Street, RM 545

institute: University of California, San Francisco

description:
Total RNA from beta7 cells isolated from human PBMC (CD4+ and CD45RA- population)
Patient sex: male; Patient age: 28
Subject ID# 008
2 rounds amplification (Ambion's MessageAmp aRNA Kit)

organism: Homo sapiens


title: 6Hs.244.1

description:
Total RNA from beta7 cells isolated from human PBMC (CD4+ and CD45RA- population)
Patient sex: female; Patient age: 28
Subject ID# 011
2 rounds amplification (Ambion's MessageAmp aRNA Kit)


title: 6Hs.178.1


title: 6Hs.193.1


title: 6Hs.177.1


title: 6Hs.243.1


title: 6Hs.176

description:
Total RNA from beta7 cells isolated from human PBMC (CD4+ and CD45RA- population)
Patient sex: female; Patient age: 31
Subject ID# 010
2 rounds amplification (Ambion's MessageAmp aRNA Kit)


title: 6Hs.073

description:
Total RNA from beta7 cells isolated from human PBMC (CD4+ and CD45RA- population)
Patient sex: male; Patient age: 45
Subject ID# 007
2 rounds amplification (Ambion's MessageAmp aRNA Kit)


title: 6Hs.076

description:
Total RNA from beta7 cells isolated from human PBMC (CD4+ and CD45RA- population)
Patient sex: female; Patient age: 27
Subject ID# 006
2 rounds amplification (Ambion's MessageAmp aRNA Kit)


title: 6Hs.185.1


title: 6Hs.175


title: 6Hs.186.1


title: 6Hs.184.1


title: 6Hs.075


title: 6Hs.187.1


title: 6Hs.074


title: 6Hs.168

description:
Total RNA from beta7 cells isolated from human PBMC (CD4+ and CD45RA- population)
Patient sex: female; Patient age: 25
Subject ID# 003
2 rounds amplification (Ambion's MessageAmp aRNA Kit)


title: 6Hs.166

description:
Total RNA from beta7 cells isolated from human PBMC (CD4+ and CD45RA- population)
Patient sex: female; Patient age: 37
Subject ID# 004
2 rounds amplification (Ambion's MessageAmp aRNA Kit)


title: 6Hs.167.1


title: Hs_004_235


title: 6Hs.169.1


title: Hs_004_186_2

description:
Total RNA from beta7 cells isolated from human PBMC (CD4+ and CD45RA- population)
Patient sex: female; Patient age: 30
Subject ID# 001
2 rounds amplification (Ambion's MessageAmp aRNA Kit)


title: 6Hs.195.1


title: Hs_004_188

description:
Total RNA from beta7 cells isolated from human PBMC (CD4+ and CD45RA- population)
Patient sex: female; Patient age: 23
Subject ID# 009
2 rounds amplification (Ambion's MessageAmp aRNA Kit)


title: 6Hs.094


title: Hs_004_187_2


title: Hs_004_189_1


title: Tumor samples from patient No.84 PT84U95B

status: Public on Jan 16 2007

city: Houston

first: Federico

middle: Alberto

last: Monzon

state: TX

address: 6565 Fannin St, MS205

department: Pathology

institute: The Methodist Hospital

description: Gene expression data from primary prostate cancer

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U95B array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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.

source_name: PT84, tumor samples from patient No.84

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

extract_protocol: Total RNA was extracted with Qiagen Rneasy kit according to the manufacturer's instructions.

treatment_protocol: Fresh prostate tissues were recovered immediately after surgical removal. Tissues were dissected/trimmed to obtain pure tumor then snap frozen in liquid nitrogen within 30 mintues of excision and stored in -80C untill RNA extraction. An H&E stained frozen section of each sample was evaluated by a pathologist, to determine epithelial and stromal content and verify the presence of tumor in the sample. Only tumor tissues with less than 30% of tromal components were selected.

tag: Tissue

value: primary prostate tumor

tag: Tumor stage

tag: Gleason Grade


title: 37 week placenta basal plate 1 A

status: Public on Jan 11 2007

city: SAN FRANCISCO

first: Susan

last: Fisher

address: 513 PARNASSUS AVE

department: Obstretrics, Gynecology and Reproductive Sciences

institute: UCSF

description: 37 week placenta basal plate

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

source_name: placental basal plate

label_protocol: Approximately 2 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Clin Chem. 2006 Jan;52(1):159-60. Modification of the Standard Trizol-Based Technique Improves the Integrity of RNA Isolated from RNase-Rich Placental Tissue. Haimov-Kochman R, Fisher SJ, Winn VD.)

tag: Placenta, basal plate


title: Weigel_2-33_CHIP-213-C_Rep3_ATH1

status: Public on Jan 08 2007

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

description:
germplasm: flc-3
light regime1: short day
light regime2: long day
growth media type: soil
average daily humidity:
average daily temperature: 23C

data_processing: The data were analysed using Affymetrix Microarray Suite 5.0 (MAS5)

organism: Arabidopsis thaliana

treatment_protocol: LD 5 days

tag: Developmental stage

value: transition to flowering, 10-18 leaves

value: apical region

tag: Genetic variation

value: fast neutron flc allele in Col-0 background, early flowering


title: GM17749

status: Public on Jan 07 2007

city: Philadelphia

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

description: The cells were grown at a density of 5 x 105 cells/ ml in RPMI 1640 with 15% FBS, 100 U penicillin/ml, 100 ugm streptomycin sulfate/ml, 1% L-glutamine at 37°C in a humidified 5% CO2 chamber. RNA was extracted using the Qiagen mini-kits

source_name: lymphoblastoid cell lines from the CEU, CHB and JPT samples in the International HapMap Collection.

label_protocol: standard Affymetrix procedures

tag: lymphoblastoid cell line


title: NSH79 18-1 1wk: S, 2C

status: Public on Dec 15 2006

city: Seattle

first: Nina

middle: Reda

last: Salama

state: WA

address: 1100 Fairview Ave. N

department: Division of Human Biology

institute: Fred Hutchinson Cancer Research Center

description:
Simple annotation: Method testing, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51046.gif

hyb_protocol: pubmed ID 17101654

scan_protocol: pubmed ID 17101654 Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1070, 34400; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Baldwin 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 = 31.58; Parameter Scan Time = 11:57:49; Parameter PMT Volts = 420; Parameter Scan Date = 2004-04-13; Parameter Pixel Size = 10; Parameter Laser on time = 44482; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin 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 = 31.58; Parameter Scan Time = 11:57:49; Parameter PMT Volts = 530; Parameter Scan Date = 2004-04-13; Parameter Pixel Size = 10; Parameter Laser on time = 44490; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.81; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin

source_name: NSH79 18 input 1 S, 2C

label_protocol: pubmed ID 17101654

extract_protocol: pubmed ID 17101654

tag: NSH79 18 input 1 S, 2C

source_name: output mouse NSH79 18-1 1wk; S, 2C

tag: output mouse NSH79 18-1 1wk; S, 2C