title: colorectal cancer sample AUS2_042_p506 [exon-level]


title: colorectal cancer sample AUS2_030_p340 [exon-level]

status: Public on May 19 2011

type: RNA

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix)

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: For analysis at the exon level, raw data were processed (using a custom-made cdf-file; HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf) and analyzed for alternative splicing with the FIRMA algorithm (aroma.affymetrix). For gene-level analysis, raw data were processed with the RMA procedure using Expression Console (Affymetrix; gene-core analysis).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Colorectal cancer patient

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: For the colorectal cancer samples, total RNA was isolated from <30 mg tissue biopsies using the AllPrep DNA/RNA Mini kit (Qiagen), according to the manufacturer's protocol. For the normal colon mucosa samples, total RNA was isolated from <100 mg tissue biopsies using the Ambion RiboPure kit (Life Technologies), according to the manufacturer's protocol.

tag: tissue

value: colorectal cancer biopsy

tag: tumor stage

tag: msi-status

value: MSI-H


title: colorectal cancer sample AUS2_048_p344 [exon-level]

value: MSS


title: colorectal cancer sample AUS2_043_p1327 [exon-level]


title: colorectal cancer sample AUS2_031_p478 [exon-level]


title: colorectal cancer sample AUS2_026_p473 [exon-level]


title: colorectal cancer sample AUS2_050_p533 [exon-level]


title: colorectal cancer sample AUS2_068_p564 [exon-level]

value: MSI-L


title: colorectal cancer sample AUS2_019_p312 [gene-level]


title: colorectal cancer sample AUS2_029_p476 [exon-level]


title: colorectal cancer sample AUS2_036_p504 [exon-level]


title: colorectal cancer sample AUS2_041_p260 [exon-level]


title: colorectal cancer sample AUS2_019_p312 [exon-level]


title: colorectal cancer sample AUS2_022_p452 [exon-level]


title: colorectal cancer sample AUS2_038_p249 [exon-level]


title: colorectal cancer sample AUS2_028_p256 [exon-level]


title: colorectal cancer sample AUS2_024_p280 [exon-level]


title: colorectal cancer sample AUS2_012_p336 [exon-level]


title: colorectal cancer sample AUS2_010_p1622 [exon-level]


title: colorectal cancer sample AUS2_018_p1355 [exon-level]


title: colorectal cancer sample AUS2_027_p876 [exon-level]


title: colorectal cancer sample AUS2_011_p423 [exon-level]


title: colorectal cancer sample AUS2_017_p296 [exon-level]


title: colorectal cancer sample AUS2_013_p874 [exon-level]


title: colorectal cancer sample C985III [exon-level]

extract_protocol: Total RNA was isolated from <30 mg colorectal cancer biopsies using the AllPrep DNA/RNA Mini kit (Qiagen), according to the manufacturer's protocol.


title: colorectal cancer sample AUS2_012_p336 [gene-level]


title: colorectal cancer sample AUS2_003_p348 [exon-level]


title: colorectal cancer sample AUS2_086_p624 [exon-level]


title: colorectal cancer sample AUS2_010_p1622 [gene-level]


title: colorectal cancer sample C985III [gene-level]


title: colorectal cancer sample C980III [exon-level]


title: colorectal cancer sample C983III [gene-level]


title: colorectal cancer sample C965II [exon-level]


title: colorectal cancer sample C975III [exon-level]


title: colorectal cancer sample C981III [exon-level]


title: colorectal cancer sample C976II [exon-level]


title: colorectal cancer sample C970II [exon-level]


title: colorectal cancer sample C982III [exon-level]


title: colorectal cancer sample C982III [gene-level]


title: colorectal cancer sample C964II [exon-level]


title: colorectal cancer sample C981III [gene-level]


title: colorectal cancer sample C980III [gene-level]


title: colorectal cancer sample C932III [exon-level]


title: colorectal cancer sample C983III [exon-level]


title: colorectal cancer sample C937III [exon-level]


title: colorectal cancer sample C950II [exon-level]


title: colorectal cancer sample AUS2_037_p304 [exon-level]


title: colorectal cancer sample C946II [exon-level]


title: colorectal cancer sample C978II [exon-level]


title: colorectal cancer sample C895II [exon-level]


title: colorectal cancer sample C861y [exon-level]


title: colorectal cancer sample C891II [exon-level]


title: colorectal cancer sample C914III [exon-level]


title: colorectal cancer sample C896III [exon-level]


title: colorectal cancer sample C978II [gene-level]


title: colorectal cancer sample C950II [gene-level]


title: colorectal cancer sample C940III [exon-level]


title: colorectal cancer sample C935II [exon-level]


title: colorectal cancer sample C965II [gene-level]


title: colorectal cancer sample C940III [gene-level]


title: colorectal cancer sample C1402III [exon-level]


title: colorectal cancer sample C964II [gene-level]


title: colorectal cancer sample C975III [gene-level]


title: colorectal cancer sample C946II [gene-level]


title: colorectal cancer sample C914III [gene-level]


title: colorectal cancer sample C896III [gene-level]


title: colorectal cancer sample C970II [gene-level]


title: colorectal cancer sample C895II [gene-level]


title: colorectal cancer sample C932III [gene-level]


title: colorectal cancer sample C1395II [exon-level]


title: colorectal cancer sample C935II [gene-level]


title: colorectal cancer sample C861y [gene-level]


title: colorectal cancer sample C976II [gene-level]


title: colorectal cancer sample C937III [gene-level]


title: colorectal cancer sample C891II [gene-level]


title: colorectal cancer sample C1402III [gene-level]


title: colorectal cancer sample C1357II [exon-level]


title: colorectal cancer sample C1356III [exon-level]


title: colorectal cancer sample C1393III [gene-level]


title: colorectal cancer sample C1389III [exon-level]


title: colorectal cancer sample C1395II [gene-level]


title: colorectal cancer sample C1334III [exon-level]


title: colorectal cancer sample C1393III [exon-level]


title: colorectal cancer sample C1389III [gene-level]


title: colorectal cancer sample C1364II [exon-level]


title: colorectal cancer sample C1391II [gene-level]


title: colorectal cancer sample C1323III [exon-level]


title: colorectal cancer sample C1380III [exon-level]


title: colorectal cancer sample C1391II [exon-level]


title: colorectal cancer sample C1340III [exon-level]


title: colorectal cancer sample C1330III [exon-level]


title: colorectal cancer sample C1321II [exon-level]


title: colorectal cancer sample C1379II [exon-level]


title: colorectal cancer sample C1308III [exon-level]


title: colorectal cancer sample C1380III [gene-level]


title: colorectal cancer sample C1364II [gene-level]


title: colorectal cancer sample C1379II [gene-level]


title: colorectal cancer sample C1291II [exon-level]


title: colorectal cancer sample C1292III [exon-level]


title: colorectal cancer sample C1294II [exon-level]


title: colorectal cancer sample C1301III [exon-level]


title: colorectal cancer sample C1333III [exon-level]


title: colorectal cancer sample C1296II [exon-level]


title: colorectal cancer sample C1323III [gene-level]


title: colorectal cancer sample C1314III [exon-level]


title: colorectal cancer sample C1340III [gene-level]


title: colorectal cancer sample C1330III [gene-level]


title: colorectal cancer sample C1334III [gene-level]


title: colorectal cancer sample C1333III [gene-level]


title: colorectal cancer sample C1357II [gene-level]


title: colorectal cancer sample C1321II [gene-level]


title: colorectal cancer sample C1356III [gene-level]


title: colorectal cancer sample C1271III [exon-level]


title: colorectal cancer sample C1308III [gene-level]


title: colorectal cancer sample C1285III [exon-level]


title: colorectal cancer sample C1296II [gene-level]


title: colorectal cancer sample C1301III [gene-level]


title: colorectal cancer sample C1292III [gene-level]


title: colorectal cancer sample C1314III [gene-level]


title: colorectal cancer sample C1286III [exon-level]


title: colorectal cancer sample C1284III [exon-level]


title: colorectal cancer sample C1283II [exon-level]


title: colorectal cancer sample C1273II [exon-level]


title: colorectal cancer sample C1264II [exon-level]


title: colorectal cancer sample C1263II [exon-level]


title: colorectal cancer sample C1267III [exon-level]


title: colorectal cancer sample C1294II [gene-level]


title: colorectal cancer sample C1285III [gene-level]


title: colorectal cancer sample C1286III [gene-level]


title: colorectal cancer sample C1280III [exon-level]


title: colorectal cancer sample C1291II [gene-level]


title: colorectal cancer sample C1257II [exon-level]


title: colorectal cancer sample C1284III [gene-level]


title: colorectal cancer sample C1198III [exon-level]


title: colorectal cancer sample C1275III [exon-level]


title: colorectal cancer sample C1251III [exon-level]


title: colorectal cancer sample C1267III [gene-level]


title: colorectal cancer sample C1271III [gene-level]


title: colorectal cancer sample C1156II [exon-level]


title: colorectal cancer sample C1159III [exon-level]


title: colorectal cancer sample C1273II [gene-level]


title: colorectal cancer sample C1152III [exon-level]


title: colorectal cancer sample C1264II [gene-level]


title: colorectal cancer sample C1145III [exon-level]


title: colorectal cancer sample C1283II [gene-level]


title: colorectal cancer sample C1144III [exon-level]


title: colorectal cancer sample C1118III [exon-level]


title: colorectal cancer sample C1263II [gene-level]


title: colorectal cancer sample C1112II [exon-level]


title: colorectal cancer sample C1257II [gene-level]


title: colorectal cancer sample C1156II [gene-level]


title: colorectal cancer sample C1085II [exon-level]


title: colorectal cancer sample C1280III [gene-level]


title: colorectal cancer sample C1152III [gene-level]


title: colorectal cancer sample C1077III [exon-level]


title: colorectal cancer sample C1089II [exon-level]


title: colorectal cancer sample C1251III [gene-level]


title: colorectal cancer sample C1135II [exon-level]


title: colorectal cancer sample C1144III [gene-level]


title: colorectal cancer sample C1102II [exon-level]


title: colorectal cancer sample C1198III [gene-level]


title: colorectal cancer sample C1190II [gene-level]


title: colorectal cancer sample C1091II [exon-level]


title: colorectal cancer sample C1068III [exon-level]


title: colorectal cancer sample C1043II [exon-level]


title: colorectal cancer sample C1142III [gene-level]


title: colorectal cancer sample C1159III [gene-level]


title: colorectal cancer sample C1112II [gene-level]


title: colorectal cancer sample C1065III [exon-level]


title: colorectal cancer sample C1118III [gene-level]


title: colorectal cancer sample C1033III [exon-level]


title: colorectal cancer sample C1135II [gene-level]


title: colorectal cancer sample C1049II [exon-level]


title: colorectal cancer sample C1068III [gene-level]


title: colorectal cancer sample C1085II [gene-level]


title: colorectal cancer sample C1065III [gene-level]


title: colorectal cancer sample C1142III [exon-level]


title: colorectal cancer sample C1030II_2 [exon-level]


title: colorectal cancer sample C1022II [exon-level]


title: colorectal cancer sample C1043II [gene-level]


title: colorectal cancer sample C1089II [gene-level]


title: colorectal cancer sample C1102II [gene-level]


title: colorectal cancer sample C1018II [gene-level]


title: colorectal cancer sample C1034III [gene-level]


title: colorectal cancer sample C1022II [gene-level]


title: colorectal cancer sample C1034III [exon-level]


title: colorectal cancer sample C1030II_2 [gene-level]


title: colorectal cancer sample C1018II [exon-level]


title: colorectal cancer sample C1049II [gene-level]


title: colorectal cancer sample C1275III [gene-level]


title: colorectal cancer sample C1190II [exon-level]


title: colorectal cancer sample C1033III [gene-level]


title: 9.4 2DPA (inner ovule cells) vs. 0DPA (inner ovule cells)

status: Public on May 06 2011

city: Austin

first: Z Jeffrey

middle: Jeffrey

last: Chen

state: TX

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

country: USA

institute: The University of Texas at Austin

description: 2DPA inner ovule cells vs. 0DPA inner ovule cells

hyb_protocol: One Cy3-dCTP reaction is mixed with one Cy5-dCTP reaction to make one probe. Therefore, two “identical” probes each containing an equal amount of Cy3- and Cy5-labeled cDNAs were hybridized with two slides, which constituted one dye-swap experiment. The dye-swap was repeated once as a technical replication. The large dye-swap (four slides) was repeated using another biological sample (e.g., RNAs isolated from different pools of 3-DPA ovules). Therefore, each experiment consists of four technical replications and two biological replications in a total of eight slides (Chen et al. 2004). Hybridization was performed overnight (∼14 h) at 65°C. After hybridization, the slides were washed twice for 4 min each in 2X SSC, 0.2% SDS, again twice for 2 min each in 0.2XSSC, and twice for 2 min each in 0.05X SSC.

scan_protocol: The slides were scanned using GenePix 4000B (Axon, Foster City, CA), and the images were captured by GenePix Pro 4.1 software.

data_processing: The background correction was processed using Limma Package. After the data were processed using natural logarithm ratios of red and green hybridization signals, a robust and locally weighted linear regression (lowess) (Cleveland 1979) was used to remove non-linear components (e.g. dye and pin effects) (Quackenbush 2002). For the duplicate spots in each feature, we used an average value for data analysis. No additional steps for data normalization and background subtraction are needed for the AVONA model (Lee et al. 2004). The data were then subjected to the analysis of variance (ANOVA) test in a linear model to estimate the significant changes in gene expression caused by the two treatments (genotypes) (Black and Doerge 2002; Lee et al. 2004). A standard t-test statistic was used for this comparison based on the normality assumption for the residuals. The standard false discovery rate (FDR) (Hochberg and Tamhane 1987) was applied to control multiple testing errors using a significance level α= 0.05.

organism: Gossypium hirsutum

source_name: 2DPA inner ovule

label_protocol: RNA was amplified with a Amino Allyl MessageAmp™ aRNA amplification Kit (Ambion, Austin, TX). Two rounds of amplication were performed to get sufficient quantities of aRNA. Amplified RNA was coupled with Cy3 dyes (Amersham Biosciences, Piscataway, NJ) and purified using Qiagen RNeasy mini column (Qiagen, Germantown, MD). About 1 µg of fragmented Cy3-labeled aRNA probes was used for hybridization.

extract_protocol: Captured cells were homogenized in 500 µl of RNA extraction buffer (200 mM sodium borate decahydrate (pH 9), 30 mM ethylene glycol bis-N,N’-tetraacetic acid (EGTA), 1% (w/v) sodium dodecyl sulfate (SDS), 1% (w/v) sodium deoxycholate, 2% (w/v) polyvinylpyrrolidone (PVP), 0.5% (v/v) Nonidet-40 (NP-40), 10 mM dithiothreitol (DTT)). After 250 µl of ethanol was added to the captured cells, the sample was loaded onto a Qiagen RNeasy mini column (Qiagen, Valencia, CA) and washed as per the manufacturer’s recommendation.

tag: strain

value: Gossypium hirsutum L. cv. TM-1

value: inner ovule cells, captured by Laser Capture Microdissection (LCM)

tag: developmental stage

value: 2 days post-anthesis (2DPA)

source_name: 0DPA inner ovule cell

label_protocol: RNA was amplified with a Amino Allyl MessageAmp™ aRNA amplification Kit (Ambion, Austin, TX). Two rounds of amplication were performed to get sufficient quantities of aRNA. Amplified RNA was coupled with Cy5 dyes (Amersham Biosciences, Piscataway, NJ) and purified using Qiagen RNeasy mini column (Qiagen, Germantown, MD). About 1 µg of fragmented Cy5-labeled aRNA probes was used for hybridization.

value: 0 days post-anthesis (0DPA)


title: 10.2 0DPA (inner ovule cells) vs. 7DPA (ovule cells)

description: 0DPA inner ovule cells vs. 7DPA ovule cells

source_name: 0DPA inner ovule

source_name: 7DPA cotton ovule

value: ovule cells

value: 7 days post-anthesis (7DPA)


title: colorectal cancer sample C1145III [gene-level]


title: 10.4 0DPA (inner ovule cells) vs. 7DPA (ovule cells)


title: 8.4 0DPA (inner ovule cells) vs. -2DPA (inner ovule cells)

description: 0DPA inner ovule cells vs. -2DPA inner ovule cells

source_name: -2DPA inner ovule

value: -2 days post-anthesis (-2DPA)


title: 10.3 0DPA (inner ovule cells) vs. 7DPA (ovule cells)


title: 9.3 2DPA (inner ovule cells) vs. 0DPA (inner ovule cells)


title: 9.2 2DPA (inner ovule cells) vs. 0DPA (inner ovule cells)


title: 7.2 0DPA (ovule epidermal cells) vs. 7DPA (cotton fiber cells)

description: 0DPA ovule epidermal cells vs. 7DPA cotton fiber cells

source_name: 0DPA ovule epidermal cell

value: ovule epidermal cell, captured by Laser Capture Microdissection (LCM)

source_name: 7DPA cotton fiber

value: cotton fiber cells


title: 10.1 0DPA (inner ovule cells) vs. 7DPA (ovule cells)


title: 7.4 0DPA (ovule epidermal cells) vs. 7DPA (cotton fiber cells)

source_name: 0DPA ovule epidermal cells


title: 6.4 0DPA (ovule epidermal cells) vs. 2DPA (ovule epidermal cells)

description: 0DPA ovule epidermal cells vs. 2DPA ovule epidermal cells

source_name: 2DPA ovule epidermal cells


title: 8.1 0DPA (inner ovule cells) vs. -2DPA (inner ovule cells)


title: 6.2 0DPA (ovule epidermal cells) vs. 2DPA (ovule epidermal cells)


title: 7.3 0DPA (ovule epidermal cells) vs. 7DPA (cotton fiber cells)


title: 8.3 0DPA (inner ovule cells) vs. -2DPA (inner ovule cells)


title: 6.3 0DPA (ovule epidermal cells) vs. 2DPA (ovule epidermal cells)


title: colorectal cancer sample C1091II [gene-level]


title: 4.4 7DPA (inner ovule cells) vs. 7DPA (fiber cells)

description: 7DPA inner ovule cells vs. 7DPA cotton fiber cells

source_name: 7DPA inner ovule

value: inner ovule cells

value: cotton fiber


title: 4.3 7DPA (inner ovule cells) vs. 7DPA (fiber cells)


title: 6.1 0DPA (ovule epidermal cells) vs. 2DPA (ovule epidermal cells)


title: 4.2 7DPA (inner ovule cells) vs. 7DPA (fiber cells)


title: 5.1 0DPA (ovule epidermal cells) vs. -2DPA (ovule epidermal cells)

description: 0DPA ovule epidermal cells vs. -2DPA ovule epidermal cells

source_name: -2DPA ovule epidermal cell


title: 5.2 0DPA (ovule epidermal cells) vs. -2DPA (ovule epidermal cells)


title: 5.3 0DPA (ovule epidermal cells) vs. -2DPA (ovule epidermal cells)


title: 8.2 0DPA (inner ovule cells) vs. -2DPA (inner ovule cells)


title: 3.4 2DPA (inner ovule cells) vs. 2DPA (ovule epidermal cells)

description: 2DPA inner ovule cells vs. 2DPA ovule epidermal cells

value: inner ovule, captured by Laser Capture Microdissection (LCM)

source_name: 2DPA ovule epidermal cell


title: 9.1 2DPA (inner ovule cells) vs. 0DPA (inner ovule cells)


title: 7.1 0DPA (ovule epidermal cells) vs. 7DPA (cotton fiber cells)


title: 4.1 7DPA (inner ovule cells) vs. 7DPA (fiber cells)


title: 5.4 0DPA (ovule epidermal cells) vs. -2DPA (ovule epidermal cells)


title: 2.4 0DPA (inner ovule cells) vs. 0DPA (ovule epidermal cells)

description: 0DPA inner ovule cells vs. 0DPA ovule epidermal cells


title: 2.3 0DPA (inner ovule cells) vs. 0DPA (ovule epidermal cells)


title: 2.2 0DPA (inner ovule cells) vs. 0DPA (ovule epidermal cells)


title: 3.2 2DPA (inner ovule cells) vs. 2DPA (ovule epidermal cells)


title: 3.3 2DPA (inner ovule cells) vs. 2DPA (ovule epidermal cells)


title: 3.1 2DPA (inner ovule cells) vs. 2DPA (ovule epidermal cells)


title: 1.3 -2DPA (inner ovule cells) vs. -2DPA (ovule epidermal cells)

description: -2DPA inner ovule cells vs. -2DPA ovule epidermal cells


title: 1.4 -2DPA (inner ovule cells) vs. -2DPA (ovule epidermal cells)


title: 1.2 -2DPA (inner ovule cells) vs. -2DPA (ovule epidermal cells)


title: NA19210

status: Public on Apr 19 2011

type: genomic

city: Baltimore

first: Scott

middle: E.

last: Devine

state: MD

address: 801 W. Baltimore Street

institute: Institute for Genome Sciences

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19210.CEL

hyb_protocol: Standard Affymetrix 6.0 kits and protocols were used.

data_processing: Affymetrix APT software with BRLMM-P.  The APT select_probes routine was used to identify probes with AIC values <325 and FLDAB >3.  INDELs with >60 no calls also were eliminated.

molecule: genomic DNA

source_name: YRI

extract_protocol: Genomic DNA was purchased from Coriell.

tag: population

value: YRI


title: NA19204

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19204.CEL

scan_protocol: Standard Affymetrix 6.0 kits and protocols were used.


title: NA19201

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA19201.CEL

label_protocol: Standard Affymetrix 6.0 kits and protocols were used.


title: NA19206

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19206.CEL


title: NA19205

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19205.CEL


title: NA19209

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19209.CEL


title: NA19208

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19208v2.CEL


title: NA19203

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19203.CEL


title: NA19202

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA19202.CEL


title: NA19207

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19207.CEL


title: 2.1 0DPA (inner ovule cells) vs. 0DPA (ovule epidermal cells)


title: 1.1 -2DPA (inner ovule cells) vs. -2DPA (ovule epidermal cells)


title: heart_control_rep4

status: Public on Apr 26 2011

city: Kajang

first: Soon-Sen

last: Leow

state: Selangor

address: No. 6, Persiaran Institusi, Bandar Baru Bangi

country: Malaysia

institute: Malaysian Palm Oil Board

description: replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized with the rank invariant normalization in the Illumina BeadStudio 1.5.1.3 software

organism: Mus musculus

source_name: heart, control

label_protocol: Biotinylated cRNA was prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays

growth_protocol: Mice were given a normal diet for six weeks

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Mini Kit, followed by quantification using the NanoDrop spectrophotometer and qualitation using the Agilent Bioanalyzer

treatment_protocol: Control group was given distilled water while treatment group was given OPP (1500 ppm GAE) as drinks ad libitum

value: heart

tag: diet supplement

value: distilled water

value: BALB/c

tag: age

value: 12 weeks

tag: gender

value: male

tag: group

value: control


title: NA19200

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA19200.CEL


title: NA19194

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19194.CEL


title: liver_control_rep4

description: replicate 4

source_name: liver, control

value: liver


title: spleen_control_rep4

description: replicate 4

source_name: spleen, control

value: spleen


title: heart_control_rep2

description: replicate 2


title: heart_control_rep1

description: replicate 1


title: colorectal cancer sample C1077III [gene-level]

source_name: Colorectal cancer patient

value: colorectal cancer biopsy

value: MSS


title: spleen_control_rep3

description: replicate 3


title: liver_control_rep3

description: replicate 3


title: spleen_control_rep2

description: replicate 2


title: spleen_control_rep1

description: replicate 1


title: liver_control_rep2

description: replicate 2


title: heart_control_rep3

description: replicate 3


title: NA19192

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19192.CEL


title: NA19154

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA19154.CEL


title: NA19159

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA19159.CEL


title: NA19172

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19172.CEL


title: NA19171

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19171.CEL


title: NA19160

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA19160.CEL


title: liver_control_rep1

description: replicate 1


title: NA19173

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19173.CEL


title: NA19143

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA19143.CEL


title: NA19145

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA19145.CEL


title: NA19142

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19142.CEL


title: NA19152

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA19152.CEL


title: NA19140

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001b_NA19140b.CEL


title: NA19141

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19141.CEL


title: NA19161

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA19161.CEL


title: NA19193

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19193.CEL


title: NA19153

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA19153.CEL


title: NA19138

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA19138.CEL


title: NA19132, duplicate of NA19132b

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001b_NA19132b.CEL


title: NA19128

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19128.CEL


title: NA19144

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA19144.CEL


title: NA19120

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19120.CEL


title: NA19127

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19127.CEL


title: NA19137

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA19137.CEL


title: NA19102

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA19102.CEL


title: NA19101

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA19101.CEL


title: NA19100

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19100.CEL


title: NA19103

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19103.CEL


title: NA19119, technical replicate 2

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001b_NA19119b.CEL


title: NA19098

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19098.CEL


title: NA19099

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19099.CEL


title: NA19094

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA19094.CEL


title: NA18914

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18914.CEL


title: NA19093

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19093.CEL


title: NA18940

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18940_3.CEL

source_name: CHB

value: CHB


title: NA19092

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA19092.CEL


title: NA19131

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19131.CEL


title: NA18912

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18912.CEL


title: NA18870

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18870.CEL


title: NA18871

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18871.CEL


title: NA18913

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18913.CEL


title: NA18872

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18872.CEL


title: NA18863

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA18863.CEL


title: NA19116

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19116.CEL


title: NA18862, technical replicate 3

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001b_NA18862b.CEL


title: NA18862, technical replicate 2

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA18862_b.CEL


title: NA18862, technical replicate 1

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA18862.CEL


title: NA18860

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18860.CEL


title: NA18861

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA18861.CEL


title: NA18859

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18859.CEL


title: NA18856

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA18856.CEL


title: NA18858

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18858.CEL


title: NA18854

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA18854.CEL


title: NA18855

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA18855.CEL


title: NA18853

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA18853.CEL


title: NA18632

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18632_3.CEL


title: NA18624

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18624.CEL


title: NA18637

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18637_2.CEL


title: NA18635

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18635_A1.CEL


title: NA18623

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18623_B1.CEL


title: NA18622

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18622_B1.CEL


title: NA18611

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18611_B1.CEL


title: NA18621

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18621_B1.CEL


title: NA18612

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18612_B1.CEL


title: NA18620

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18620_3.CEL


title: NA18857

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA18857.CEL


title: NA18608

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18608_B1.CEL


title: NA18609

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18609_B1.CEL


title: NA18852

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA18852.CEL


title: NA18594

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18594_B1.CEL


title: NA18603

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18603_B1.CEL


title: NA18582

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18582_B1.CEL


title: NA18577

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18577_B1.CEL


title: NA18576

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18576_4.CEL


title: NA18573

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18573_B3.CEL


title: NA18572

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18572_3.CEL


title: NA18566

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18566_3.CEL


title: NA18571

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18571_3.CEL


title: NA18564

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18564_4.CEL


title: Bahati_NA15510_2.1

status: Public on May 01 2011

city: Seattle

first: Tomas

last: Marques-Bonet

state: WA

address: 1705 NE Pacific St,

department: Genome Sciences

institute: University of Washington

hyb_protocol: As described in Nimblegen protocol

scan_protocol: As described in Nimblegen protocol

data_processing: Normalized according to Nimblegen protocol

organism: Gorilla gorilla

source_name: Bahati

label_protocol: As described in Nimblegen protocol

extract_protocol: As described in Nimblegen protocol

tag: name

value: Bahati


title: NA18592

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18592_2.CEL


title: NA18570

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18570_3.CEL


title: NA18561

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18561_A3.CEL


title: NA18593

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18593_B1.CEL


title: NA18555

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18555_A2.CEL


title: NA18550

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18550_B1.CEL


title: NA18547

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18547_B1.CEL


title: NA18545

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18545_5.CEL


title: NA18537

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18537_B1.CEL


title: NA18540

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18540_B1.CEL


title: NA18579

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18579_B1.CEL


title: NA18542

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18542_B1.CEL


title: NA18532

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18532_B1.CEL


title: NA18562

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18562_B1.CEL


title: NA18526

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18526_B2.CEL


title: NA18524

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18524_B1.CEL


title: NA18529

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18529_B1.CEL


title: NA18522

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18522.CEL


title: NA18521

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18521.CEL


title: NA15510_Bahati_2.1

data_processing: Normalization (qspline) was performed using NimbleScan 2.4. Normalized log2 Cy3/Cy5.


title: NA18517

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18517.CEL


title: Clint_NA18507_GGOCustomchip

organism: Pan troglodytes

source_name: Clint

value: Clint


title: NA18507

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18507.CEL


title: NA18515

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18515.CEL


title: NA18516

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18516.CEL


title: NA18506

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18506.CEL


title: NA18505

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18505.CEL


title: NA18508

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18508.CEL


title: NA18504

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18504.CEL


title: NA18502

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18502.CEL


title: NA18503

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18503.CEL


title: NA15590

description:
Polymorphism Discovery Resource (PDR; Coriell; Collins et al. Genome Research 8, 1229-1231, 1999).

SED00001_NA15590_4.CEL

source_name: PDR

value: PDR


title: NA18500

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18500b.CEL


title: NA15510

description:
Polymorphism Discovery Resource (PDR; Coriell; Collins et al. Genome Research 8, 1229-1231, 1999).

SED00001_NA15510_A1.CEL


title: NA15594

description:
Polymorphism Discovery Resource (PDR; Coriell; Collins et al. Genome Research 8, 1229-1231, 1999).

SED00001_NA15594_005.CEL


title: NA18501

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18501.CEL


title: NA15386A

description:
Polymorphism Discovery Resource (PDR; Coriell; Collins et al. Genome Research 8, 1229-1231, 1999).

SED00001_NA15386A.CEL


title: NA15385

description:
Polymorphism Discovery Resource (PDR; Coriell; Collins et al. Genome Research 8, 1229-1231, 1999).

SED00001b_NA15385b.CEL


title: NA18523

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18523.CEL


title: NA19129

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19129.CEL


title: NA15242

description:
Polymorphism Discovery Resource (PDR; Coriell; Collins et al. Genome Research 8, 1229-1231, 1999).

SED00001_NA15242_005.CEL


title: NA15236

description:
Polymorphism Discovery Resource (PDR; Coriell; Collins et al. Genome Research 8, 1229-1231, 1999).

SED00001_NA15236_6.CEL


title: NA15324

description:
Polymorphism Discovery Resource (PDR; Coriell; Collins et al. Genome Research 8, 1229-1231, 1999).

SED00001_NA15324_A1.CEL


title: NA15227

description:
Polymorphism Discovery Resource (PDR; Coriell; Collins et al. Genome Research 8, 1229-1231, 1999).

SED00001b_NA15227b.CEL


title: NA18605

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18605_B1.CEL


title: NA18563

description:
Han Chinese (CHB; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA18563.CEL


title: NA15215A

description:
Polymorphism Discovery Resource (PDR; Coriell; Collins et al. Genome Research 8, 1229-1231, 1999).

SED00001_NA15215A.CEL


title: NA15213, technical replicate 2

description:
Polymorphism Discovery Resource (PDR; Coriell; Collins et al. Genome Research 8, 1229-1231, 1999).

SED00001_NA15213_006_2.CEL


title: NA15216

description:
Polymorphism Discovery Resource (PDR; Coriell; Collins et al. Genome Research 8, 1229-1231, 1999).

SED00001_NA15216_A2.CEL


title: NA15144C

description:
Polymorphism Discovery Resource (PDR; Coriell; Collins et al. Genome Research 8, 1229-1231, 1999).

SED00001_NA15144C.CEL


title: NA15221

description:
Polymorphism Discovery Resource (PDR; Coriell; Collins et al. Genome Research 8, 1229-1231, 1999).

SED00001b_NA15221b.CEL


title: NA15223

description:
Polymorphism Discovery Resource (PDR; Coriell; Collins et al. Genome Research 8, 1229-1231, 1999).

SED00001_NA15223_6v2.CEL


title: NA15224

description:
Polymorphism Discovery Resource (PDR; Coriell; Collins et al. Genome Research 8, 1229-1231, 1999).

SED00001_NA15224_4.CEL


title: NA15226

description:
Polymorphism Discovery Resource (PDR; Coriell; Collins et al. Genome Research 8, 1229-1231, 1999).

SED00001_NA15226A.CEL


title: NA15213, technical replicate 1

description:
Polymorphism Discovery Resource (PDR; Coriell; Collins et al. Genome Research 8, 1229-1231, 1999).

SED00001_NA15213_006.CEL


title: NA15072

description:
Polymorphism Discovery Resource (PDR; Coriell; Collins et al. Genome Research 8, 1229-1231, 1999).

SED00001_NA15072.CEL


title: NA15056

description:
Polymorphism Discovery Resource (PDR; Coriell; Collins et al. Genome Research 8, 1229-1231, 1999).

SED00001b_NA15056b.CEL


title: NA15036

description:
Polymorphism Discovery Resource (PDR; Coriell; Collins et al. Genome Research 8, 1229-1231, 1999).

SED00001_NA15036.CEL


title: NS12911

description:
HuRef (Levy et al. PLoS Biol. 5, e254, 2007).

SED00002_NS12911_1.CEL

source_name: HuRef

tag: sample type

value: HuRef


title: NA19240

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19240.CEL


title: NA15038

description:
Polymorphism Discovery Resource (PDR; Coriell; Collins et al. Genome Research 8, 1229-1231, 1999).

SED00001_NA15038.CEL


title: NA15029

description:
Polymorphism Discovery Resource (PDR; Coriell; Collins et al. Genome Research 8, 1229-1231, 1999).

SED00001_NA15029.CEL


title: NA19139

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00002_NA19139.CEL


title: NA15268

description:
Polymorphism Discovery Resource (PDR; Coriell; Collins et al. Genome Research 8, 1229-1231, 1999).

SED00001_NA15268.CEL


title: NA15245

description:
Polymorphism Discovery Resource (PDR; Coriell; Collins et al. Genome Research 8, 1229-1231, 1999).

SED00001_NA15245v2.CEL


title: NA19238, technical replicate 3

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001b_NA19238b.CEL


title: NA19238, technical replicate 2

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19238b.CEL


title: NA19238, technical replicate 1

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19238.CEL


title: NA19223

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19223.CEL


title: NA19222

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19222.CEL


title: NA19221

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19221.CEL


title: NA19211

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19211.CEL


title: NA19239

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19239.CEL


title: ON-CD8+T (CD62Llo/CD44hi), t=4,pool

status: Public on Mar 25 2011

city: Scottsdale

first: Cheryl

middle: E

last: Myers

state: AZ

address: 13400 E Shea Blvd

department: Immunology

institute: Mayo Clinic College of Medicine

description: Old CD8+T CD62Lhi CD44lo, t=4

hyb_protocol: Agilent In Situ Hybridization Kit Plus was used according to manufacturers instructions

scan_protocol: GE2-v5_95_Feb07 (Read Only), using Agilent Technologies Scanner G2505B US45102967

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.9.5.1.1). Using Genespring GX11, the data was normalized to the 75th percentile and a baseline transformation to median of all samples was performed. This list was further screened for a minimum of 2 fold change between the populations (A) at time point zero and at least two of the four other time points and (B) at least three of the four time points not including time point zero.

source_name: CD8+ Old Naïve Time 4

label_protocol: Agilent Low RNA Input Linear Amplification Kit PLUS  was used incorporating cy3, according to manufacturers instructions

growth_protocol: Naïve CD4 and CD8 T cell subpopulations were derived from young (4 months) and old (20 months) Balb/c mice through fluorescent cell sorting using CD4 or CD8 and CD62Llo and CD44hi. Four independent sortings were executed on separate days from biological samples to pool RNA for each time point in the time series activation dependant study.

extract_protocol: RLT buffer and RNeasy MicroKit (Qiagen) purification, according to manufacturers instructions, RNA was measured with the NanoDrop 1000 (Thermo Scientific) and integrity verified through  Agilent Bioanalyzer 2100  using the pico chip.

treatment_protocol: Respective T cell subpopulations were cultured for the specified time points in plates coated with stimulatory antibodies to CD3 and CD28.

value: 20 mo

tag: cell type

value: CD8+T (CD62Llo/CD44hi)

tag: treatment

value: stimulatory antibodies to CD3 and CD28

tag: time

value: 4 h


title: YN-CD8+T (CD62Llo/CD44hi), t=24,pool

description: Young CD8+T CD62Lhi CD44lo, t=24

source_name: CD8+ Young Naïve Time 24

value: BALB/c

value: 4 mo


title: YN-CD8+T (CD62Llo/CD44hi), t=0,pool rep3

description: Young CD8+T CD62Lhi CD44lo, t=0

source_name: CD8+ Young Naïve Time 0 replicate 3

value: 0 h


title: T2NF, Adipose Tissue,  Diet Induced Obesity vs. Chow Fed on SAMF Cy5

status: Public on Mar 01 2011

city: Calgary

first: Jane

last: Shearer

state: AB

address: 2500 University Drive NW

department: Kinesiology

country: Canada

institute: University of Calgary

description: Adipose Tissue tissue extracted after 20 weeks on a high fat diet - Biological replicate 6.

hyb_protocol: A hybridization solution was prepared by mixing DIG Easy Hyb, yeast tRNA and  fish sperm DNA in a 18:1:1 ratio; heating to 65 degrees celsius for 2 min and allowing the mixture to cool to room temperature. For each sample, 5 microliters of labeled cDNA was mixed with 60 microliters of the hybridization solution and heated to 65 degrees celsius, then allowed to cool to room temperature. The hybridization mixture was loaded onto array slides, incubated at 37 degrees celsius for 18 h, and scanned.

scan_protocol: Slides were scanned in a Perkin-Elmer ScanArray 5000TM using the Green HeNe 543.5 nm laser for excitation of Cy3 and the Red HeNe 632.8 nm laser for excitation of Cy5. The TIFF scans were imported into QuantArrayTM version 3.0 (Perkin-Elmer) microarray analysis software for spot identification/quantification and background estimation.

data_processing: Data was input into Gene Traffic DuoTM (Iobion), filtered to flag spots with intensities less than 100 U, and normalized according to the Lowess method. Data was analyzed using Significance Analysis of Microarrays.

source_name: Adipose Tissue

label_protocol: The FairPlay II Microarray Labeling Kit (Stratagene, La Jolla, CA, USA) was used to prepare cDNA and perform the microarrays. cDNA was synthesized using 10µg of total RNA, purified, and pooled for the control group. Next, pooled control cDNA and cDNA for each treatment subject were fluorescently labeled with an Alexa Fluor (AF) 555 or 647 dye (Alexa Fluor 555 and 647 DNA Labeling Kits; Invitrogen, Ontario, Canada).

growth_protocol: C57BL/6J mice were maintained in a humidity-controlled room with a 12h light/dark cycle. After 3wk of weaning, male littermates were randomly separated into control (n=6) and treatment (n=6) groups, and maintained in microisolator cages. After an acclimatization period of 1wk, animals were given free access to a chow diet (23% protein, 21% fat, and 55% carbohydrate) or a HF diet (15% protein, 59% fat, and 26% carbohydrate) for 20wk (58R3 – Testdiet; Purina, Richmond, IN, USA). Following the feeding period, animals were fasted for 6h, anesthetized with pentobarbital, and weighed.

extract_protocol: Tissue samples were homogenized at short intervals of time and total RNA was isolated using cold TRIzol to prevent RNA degradation (Invitrogen, Ontario, Canada).Specifically, optimized amounts of TRIzol were used for WAT (2mL TRIzol/100mg tissue) and the other tissues (1mL TRIzol/50-100mg tissue), and RNA isolation using Chloroform (EMD Chemicals, Inc., Gibbstown, NJ, USA) was performed twice for WAT. Next, total RNA was purified with wash buffers (RNeasy Mini Kit; Qiagen, Ontario, Canada) and deoxyribonuclease I (DNase I) (RNase-Free DNase Set; Qiagen, Ontario, Canada) according to the manufacturer’s protocol. The quality and quantity of RNA were determined by agarose gel electrophoresis and ultraviolet-visible (UV/VIS) spectroscopy.

treatment_protocol: Samples of WAT, liver, gastrocnemius muscle and heart were obtained, frozen with liquid nitrogen, and stored at -80oC until subsequent use.

tag: sex

value: Male

tag: diet

value: Chow

tag: feeding period

value: 20 wk

value: Total Pooled RNA from Chow Fed Mice

treatment_protocol: The FairPlay II Microarray Labeling Kit (Stratagene, La Jolla, CA, USA) was used to prepare cDNA and perform the microarrays. cDNA was synthesized using 10µg of total RNA, purified, and pooled. Next, pooled control cDNA was fluorescently labeled with an Alexa Fluor (AF) 555 or 647 dye (Alexa Fluor 555 and 647 DNA Labeling Kits; Invitrogen, Ontario, Canada). Mouse M7K microarray chip from the Southern Alberta Microarray Facility (University of Calgary, Calgary, AB) were used. The chip itself contains 6,792 70mer oligos designed against the UniGene database for mouse that clusters gene sequences into non-redundant sets. Qiagen/Operon designed and supplied the oligos used on the chip. The labeled cDNA was hybridized at 37oC for 18 h, and scanned via standard procedure. For every treatment sample and its corresponding control, two microarrays were performed in a dye-swap normalization experiment to reduce signal correlation bias and to ensure that both dyes were functional.

value: High Fat


title: ON-CD4+T (CD62Llo/CD44hi), t=24,pool

description: Old CD4+T CD62Lhi CD44lo, t=24

source_name: CD4+ Old Naïve Time 24

value: CD4+T (CD62Llo/CD44hi)


title: YN-CD8+T (CD62Llo/CD44hi), t=0,pool rep2

description: Young CD8+T CD62Lhi CD44lo, t=0

source_name: CD8+ Young Naïve Time 0 replicate 2


title: ON-CD8+T (CD62Llo/CD44hi), t=24,pool

description: Old CD8+T CD62Lhi CD44lo, t=24

source_name: CD8+ Old Naïve Time 24


title: ON-CD8+T (CD62Llo/CD44hi), t=0,pool rep3

description: Old CD8+T CD62Lhi CD44lo, t=0

source_name: CD8+ Old Naïve Time 0 replicate 3


title: ON-CD8+T (CD62Llo/CD44hi), t=72,pool

description: Old CD8+T CD62Lhi CD44lo, t=72

source_name: CD8+ Old Naïve Time 72


title: ON-CD4+T (CD62Llo/CD44hi), t=12,pool

description: Old CD4+T CD62Lhi CD44lo, t=12

source_name: CD4+ Old Naïve Time 12


title: YN-CD4+T (CD62Llo/CD44hi), t=0,pool rep 1

description: Young CD4+T CD62Lhi CD44lo, t=0

source_name: CD4+ Young Naïve Time 0 replicate 1


title: YN-CD4+T (CD62Llo/CD44hi), t=0,pool rep 2

description: Young CD4+T CD62Lhi CD44lo, t=0

source_name: CD4+ Young Naïve Time 0 replicate 2


title: ON-CD8+T (CD62Llo/CD44hi), t=0,pool rep1

description: Old CD8+T CD62Lhi CD44lo, t=0

source_name: CD8+ Old Naïve Time 0 replicate 1


title: YN-CD4+T (CD62Llo/CD44hi), t=72,pool

description: Young CD4+T CD62Lhi CD44lo, t=72

source_name: CD4+ Young Naïve Time 72


title: YN-CD4+T (CD62Llo/CD44hi), t=4,pool

description: Young CD4+T CD62Lhi CD44lo, t=4

source_name: CD4+ Young Naïve Time 4


title: YN-CD4+T (CD62Llo/CD44hi), t=24,pool

description: Young CD4+T CD62Lhi CD44lo, t=24

source_name: CD4+ Young Naïve Time 24


title: YN-CD4+T (CD62Llo/CD44hi), t=0,pool rep 3

description: Young CD4+T CD62Lhi CD44lo, t=0

source_name: CD4+ Young Naïve Time 0 replicate 3


title: YN-CD8+T (CD62Llo/CD44hi), t=0,pool rep1

description: Young CD8+T CD62Lhi CD44lo, t=0

source_name: CD8+ Young Naïve Time 0 replicate 1


title: ON-CD4+T (CD62Llo/CD44hi), t=0,pool rep3

description: Old CD4+T CD62Lhi CD44lo, t=0

source_name: CD4+ Old Naïve Time 0 replicate 3


title: ON-CD8+T (CD62Llo/CD44hi), t=0,pool rep2

description: Old CD8+T CD62Lhi CD44lo, t=0

source_name: CD8+ Old Naïve Time 0 replicate 2


title: ON-CD8+T (CD62Llo/CD44hi), t=12,pool

description: Old CD8+T CD62Lhi CD44lo, t=12

source_name: CD8+ Old Naïve Time 12


title: YN-CD8+T (CD62Llo/CD44hi), t=12,pool

description: Young CD8+T CD62Lhi CD44lo, t=12

source_name: CD8+ Young Naïve Time 12


title: YN-CD8+T (CD62Llo/CD44hi), t=4,pool

description: Young CD8+T CD62Lhi CD44lo, t=4

source_name: CD8+ Young Naïve Time 4


title: YN-CD8+T (CD62Llo/CD44hi), t=72,pool

description: Young CD8+T CD62Lhi CD44lo, t=72

source_name: CD8+ Young Naïve Time 72


title: ON-CD4+T (CD62Llo/CD44hi), t=4,pool

description: Old CD4+T CD62Lhi CD44lo, t=4

source_name: CD4+ Old Naïve Time 4


title: ON-CD4+T (CD62Llo/CD44hi), t=0,pool rep1

description: Old CD4+T CD62Lhi CD44lo, t=0

source_name: CD4+ Old Naïve Time 0 replicate 1


title: T2NF, Adipose Tissue,  Diet Induced Obesity vs. Chow Fed on SAMF Cy3

source_name: Adipose Tissue


title: YN-CD4+T (CD62Llo/CD44hi), t=12,pool

description: Young CD4+T CD62Lhi CD44lo, t=12

source_name: CD4+ Young Naïve Time 12


title: ON-CD4+T (CD62Llo/CD44hi), t=0,pool rep2

description: Old CD4+T CD62Lhi CD44lo, t=0

source_name: CD4+ Old Naïve Time 0 replicate 2


title: ON-CD4+T (CD62Llo/CD44hi), t=72,pool

description: Old CD4+T CD62Lhi CD44lo, t=72

source_name: CD4+ Old Naïve Time 72


title: T4NF, Adipose Tissue,  Diet Induced Obesity vs. Chow Fed on SAMF Cy3

description: Adipose Tissue tissue extracted after 20 weeks on a high fat diet - Biological replicate 1.


title: L5NF, Adipose Tissue,  Diet Induced Obesity vs. Chow Fed on SAMF Cy5

description: Adipose Tissue tissue extracted after 20 weeks on a high fat diet - Biological replicate 5.


title: T3NF, Adipose Tissue,  Diet Induced Obesity vs. Chow Fed on SAMF Cy3

description: Adipose Tissue tissue extracted after 20 weeks on a high fat diet - Biological replicate 3.


title: T4NF, Adipose Tissue,  Diet Induced Obesity vs. Chow Fed on SAMF Cy5


title: T3NF, Adipose Tissue,  Diet Induced Obesity vs. Chow Fed on SAMF Cy5


title: T7NF, Adipose Tissue,  Diet Induced Obesity vs. Chow Fed on SAMF Cy3

description: Adipose Tissue tissue extracted after 20 weeks on a high fat diet - Biological replicate 4.


title: T5NF,  Adipose Tissue,  Diet Induced Obesity vs. Chow Fed on SAMF Cy3

description: Adipose Tissue tissue extracted after 20 weeks on a high fat diet - Biological replicate 2.


title: T5NF, Adipose Tissue,  Diet Induced Obesity vs. Chow Fed on SAMF Cy5


title: T7NF, Adipose Tissue,  Diet Induced Obesity vs. Chow Fed on SAMF Cy5


title: L5NF, Adipose Tissue,  Diet Induced Obesity vs. Chow Fed on SAMF Cy3


title: 36-17G, Skeletal Muscle,  Diet Induced Obesity vs. Chow Fed on SAMF Cy3

description: Skeletal Muscle tissue extracted after 20 weeks on a high fat diet - Biological replicate 3.

source_name: Skeletal Muscle


title: 36-20G, Skeletal Muscle,  Diet Induced Obesity vs. Chow Fed on SAMF Cy3

description: Skeletal Muscle tissue extracted after 20 weeks on a high fat diet - Biological replicate 5.


title: P4G, Skeletal Muscle,  Diet Induced Obesity vs. Chow Fed on SAMF Cy5

description: Skeletal Muscle tissue extracted after 20 weeks on a high fat diet - Biological replicate 6.


title: 36-20G, Skeletal Muscle,  Diet Induced Obesity vs. Chow Fed on SAMF Cy5


title: 36-17G, Skeletal Muscle,  Diet Induced Obesity vs. Chow Fed on SAMF Cy5


title: 35-11G, Skeletal Muscle,  Diet Induced Obesity vs. Chow Fed on SAMF Cy3

description: Skeletal Muscle tissue extracted after 20 weeks on a high fat diet - Biological replicate 1.


title: P4G, Skeletal Muscle,  Diet Induced Obesity vs. Chow Fed on SAMF Cy3


title: 35-13G, Skeletal Muscle,  Diet Induced Obesity vs. Chow Fed on SAMF Cy5

description: Skeletal Muscle tissue extracted after 20 weeks on a high fat diet - Biological replicate 2.


title: 36-18G, Skeletal Muscle,  Diet Induced Obesity vs. Chow Fed on SAMF Cy3

description: Skeletal Muscle tissue extracted after 20 weeks on a high fat diet - Biological replicate 4.


title: 35-11G, Skeletal Muscle,  Diet Induced Obesity vs. Chow Fed on SAMF Cy5


title: 36-18,Heart,  Diet Induced Obesity vs. Chow Fed on SAMF Cy5

description: Heart tissue extracted after 20 weeks on a high fat diet - Biological replicate 5.

source_name: Heart


title: 36-18G, Skeletal Muscle,  Diet Induced Obesity vs. Chow Fed on SAMF Cy5


title: 35-14,Heart,  Diet Induced Obesity vs. Chow Fed on SAMF Cy3

description: Heart tissue extracted after 20 weeks on a high fat diet - Biological replicate 3.


title: 35-13G, Skeletal Muscle,  Diet Induced Obesity vs. Chow Fed on SAMF Cy3


title: 35-14,Heart,  Diet Induced Obesity vs. Chow Fed on SAMF Cy5


title: 36-17,Heart,  Diet Induced Obesity vs. Chow Fed on SAMF Cy5

description: Heart tissue extracted after 20 weeks on a high fat diet - Biological replicate 4.


title: 36-20,Heart,  Diet Induced Obesity vs. Chow Fed on SAMF Cy3

description: Heart tissue extracted after 20 weeks on a high fat diet - Biological replicate 6.


title: 36-20,Heart,  Diet Induced Obesity vs. Chow Fed on SAMF Cy5


title: 36-18,Heart,  Diet Induced Obesity vs. Chow Fed on SAMF Cy3


title: 36-17,Heart,  Diet Induced Obesity vs. Chow Fed on SAMF Cy3


title: 35-13,Heart,  Diet Induced Obesity vs. Chow Fed on SAMF Cy3

description: Heart tissue extracted after 20 weeks on a high fat diet - Biological replicate 2.


title: 35-11,Heart,  Diet Induced Obesity vs. Chow Fed on SAMF Cy3

description: Heart tissue extracted after 20 weeks on a high fat diet - Biological replicate 1.


title: T5L, Liver,  Diet Induced Obesity vs. Chow Fed on SAMF Cy5

description: Liver tissue extracted after 20 weeks on a high fat diet - Biological replicate 5.

source_name: Liver


title: 40L, Liver,  Diet Induced Obesity vs. Chow Fed on SAMF Cy3

description: Liver tissue extracted after 20 weeks on a high fat diet - Biological replicate 6.


title: T3L, Liver,  Diet Induced Obesity vs. Chow Fed on SAMF Cy5

description: Liver tissue extracted after 20 weeks on a high fat diet - Biological replicate 3.


title: T4L, Liver,  Diet Induced Obesity vs. Chow Fed on SAMF Cy3

description: Liver tissue extracted after 20 weeks on a high fat diet - Biological replicate 4.


title: T3L, Liver,  Diet Induced Obesity vs. Chow Fed on SAMF Cy3


title: 35-11,Heart,  Diet Induced Obesity vs. Chow Fed on SAMF Cy5


title: 40L, Liver,  Diet Induced Obesity vs. Chow Fed on SAMF Cy5


title: T2L, Liver,  Diet Induced Obesity vs. Chow Fed on SAMF Cy5

description: Liver tissue extracted after 20 weeks on a high fat diet - Biological replicate 2.


title: 35-13,Heart,  Diet Induced Obesity vs. Chow Fed on SAMF Cy5


title: T4L, Liver,  Diet Induced Obesity vs. Chow Fed on SAMF Cy5


title: T5L, Liver,  Diet Induced Obesity vs. Chow Fed on SAMF Cy3


title: T1L, Liver,  Diet Induced Obesity vs. Chow Fed on SAMF Cy3

description: Liver tissue extracted after 20 weeks on a high fat diet - Biological replicate 1.


title: T2L, Liver,  Diet Induced Obesity vs. Chow Fed on SAMF Cy3


title: T1L, Liver,  Diet Induced Obesity vs. Chow Fed on SAMF Cy5

growth_protocol: C57BL/6J mice were maintained in a humidity-controlled room with a 12h light/dark cycle. After 3wk of weaning, male littermates were randomly separated into control (n=6) and treatment (n=6) groups, and maintained in microisolator cages. After an acclimatization period of 1wk, animals were given free access to a chow diet (23% protein, 21% fat, and 55% carbohydrate) or a HF diet (15% protein, 59% fat, and 26% carbohydrate) for 20 wk (58R3 – Testdiet; Purina, Richmond, IN, USA). Following the feeding period, animals were fasted for 6h, anesthetized with pentobarbital, and weighed.


title: genomic DNA from chimpanzee heart 1 (replicate A)

status: Public on Feb 25 2011

city: Chicago

first: Athma

middle: A

last: Pai

state: IL

address: 920 E. 58th Street

institute: University of Chicago

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to the Illumina Infinium Human Methylation27 Beadchip using the Standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy3 and Cy5

source_name: heart

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using an QIAamp DNA Mini Kit (Qiagen)

value: male

tag: tissue

value: heart

tag: batch


title: genomic DNA from chimpanzee heart 4 (replicate A)


title: genomic DNA from chimpanzee heart 5 (replicate A)

value: female


title: genomic DNA from chimpanzee heart 6 (replicate B)


title: genomic DNA from chimpanzee heart 4 (replicate B)


title: genomic DNA from chimpanzee heart 1 (replicate B)


title: genomic DNA from chimpanzee heart 2 (replicate A)


title: genomic DNA from chimpanzee heart 3 (replicate A)


title: genomic DNA from chimpanzee heart 6 (replicate A)


title: genomic DNA from chimpanzee heart 2 (replicate B)


title: genomic DNA from chimpanzee heart 5 (replicate B)


title: genomic DNA from human heart 6 (replicate B)


title: genomic DNA from human heart 6 (replicate A)


title: genomic DNA from chimpanzee heart 3 (replicate B)


title: genomic DNA from human heart 4 (replicate A)


title: genomic DNA from human heart 5 (replicate B)


title: genomic DNA from human heart 2 (replicate B)


title: genomic DNA from human heart 3 (replicate A)


title: genomic DNA from human heart 5 (replicate A)


title: genomic DNA from human heart 4 (replicate B)


title: genomic DNA from human heart 1 (replicate B)


title: genomic DNA from human heart 1 (replicate A)


title: genomic DNA from chimpanzee kidney 5 (replicate A)

source_name: kidney

value: kidney


title: genomic DNA from chimpanzee kidney 6 (replicate A)


title: genomic DNA from chimpanzee kidney 5 (replicate B)


title: genomic DNA from chimpanzee kidney 4 (replicate A)


title: genomic DNA from chimpanzee kidney 3 (replicate B)


title: genomic DNA from chimpanzee kidney 6 (replicate B)


title: genomic DNA from chimpanzee kidney 1 (replicate B)


title: genomic DNA from human kidney 6 (replicate A)


title: genomic DNA from human kidney 6 (replicate B)


title: genomic DNA from chimpanzee kidney 3 (replicate A)


title: genomic DNA from chimpanzee kidney 4 (replicate B)


title: genomic DNA from human kidney 5 (replicate A)


title: genomic DNA from chimpanzee kidney 2 (replicate A)


title: genomic DNA from chimpanzee kidney 1 (replicate A)


title: genomic DNA from human kidney 4 (replicate B)


title: genomic DNA from human kidney 5 (replicate B)


title: genomic DNA from human kidney 3 (replicate B)


title: genomic DNA from human kidney 3 (replicate A)


title: genomic DNA from human kidney 2 (replicate B)


title: genomic DNA from human kidney 2 (replicate A)


title: genomic DNA from human kidney 1 (replicate B)


title: genomic DNA from human kidney 4 (replicate A)


title: genomic DNA from chimpanzee liver 6 (replicate B)

source_name: liver

value: liver


title: genomic DNA from chimpanzee liver 4 (replicate B)


title: genomic DNA from chimpanzee liver 6 (replicate A)


title: genomic DNA from human heart 3 (replicate B)


title: genomic DNA from chimpanzee liver 5 (replicate A)


title: genomic DNA from chimpanzee liver 5 (replicate B)


title: genomic DNA from chimpanzee liver 4 (replicate A)


title: genomic DNA from chimpanzee liver 2 (replicate B)


title: genomic DNA from chimpanzee liver 3 (replicate A)


title: genomic DNA from human kidney 1 (replicate A)


title: genomic DNA from human liver 6 (replicate B)


title: genomic DNA from human liver 5 (replicate B)


title: genomic DNA from chimpanzee liver 3 (replicate B)


title: genomic DNA from human liver 5 (replicate A)


title: genomic DNA from human liver 4 (replicate A)


title: genomic DNA from human liver 4 (replicate B)


title: genomic DNA from human liver 2 (replicate A)


title: genomic DNA from human liver 2 (replicate B)


title: genomic DNA from chimpanzee liver 1 (replicate A)


title: genomic DNA from chimpanzee liver 2 (replicate A)


title: genomic DNA from human liver 6 (replicate A)


title: genomic DNA from human liver 3 (replicate A)


title: genomic DNA from human liver 1 (replicate A)


title: F.pla_phenol, rep 3

status: Public on Jan 05 2011

city: Amherst

first: Dawn

last: Holmes

state: Massachusetts

address: 639 N Pleasant St Morrill IVN 422C

department: Microbiology

institute: University of Massachusetts Amherst

description: F. placidus grown with  0.5 mM phenol. Third biological replicate of three.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Ferroglobus placidus DSM 10642

source_name: 0.5 mM phenol as electron donor and 56 mM ferric citrate as electron acceptor

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Ferroglobus placidus DSM 10642 was grown in strict anaerobic conditions (80:20 N2/CO2) in medium previously described (Tor et al., Env. Micro. 2001, 3(4) p281) with 0.5 mM phenol as electron donor and Fe(III) citrate as electron acceptor. Cultures were incubated at 85C in the dark.

extract_protocol:
Cultures (100 ml in 156 ml serum bottles) were divided into 50 ml conical tubes (Falcon), and cells were pelleted with centrifugation at 3,000 xg for 15 min. Pellets were then immediately frozen in liquid nitrogen and stored at –80°C.

Total RNA was extracted according to the HG protocol described in Holmes et al., ISME Journal, 2011.

tag: strain

tag: electron donor

value: phenol

tag: electron donor type

value: aromatic compound


title: genomic DNA from human liver 1 (replicate B)


title: LM5674 surface biological replicate 4

status: Public on Dec 15 2010

city: Iowa City

first: Linda

last: McCarter

state: Iowa

address: 3-401 BSB  51 Newton Rd

institute: University of Iowa

hyb_protocol: Samples (~4.5 µg) were hybridized to the chips in the DNA Core Facility at the University of Iowa according to the standard Affymetrix protocols for E. coli

scan_protocol: Analysis was done using the following software available at the University of Iowa DNA facility: Affymetrix Gene Chip Operating Software (1.2.1), Affymetrix GeneChip® Genotyping Analysis Software (GTYPE) 4.0.

data_processing: Using the raw signal output generated by GTYPE, processing and comparisons were made by using R version 2.8.1 GUI 1.27 Tiger build 32-bit (5301) (http://www.r-project.org) within Bioconductor software for bioinformatics (http://www.bioconductor.org). The complete data set was preprocessed by using the GCRMA method to perform optical adjustment, background adjustment, normalization, and summarization functions

organism: Vibrio parahaemolyticus

source_name: S: wildtype strain on surface of agar plate

label_protocol: cDNA was synthesized according to the Affymetrix Prokaryotic Target Preparation Protocol using the Superscript II Reverse Transcriptase kit (Invitrogen) and pD(N)6 random hexamers (GE Healthcare). Approximately 36 µg of RNA was converted to ~7 µg cDNA, which was purified with the MinElute PCR purification kit (Qiagen) and fragmented with RQ1 DNase to yield fragments between 50 and 200 bp. cDNA was labeled with Biotin-ddUTP using the BioArray Terminal Labeling Kit (Enzo).

growth_protocol: To examine V. parahaemolyticus grown in liquid culture, a single colony was inoculated into 5 ml of HI medium and grown overnight with shaking.  This culture was sub-cultured by inoculating 500 µl into 10 ml of HI in a 125-ml flask and grown to mid-logarithmic phase, corresponding to an optical density at 600nm (OD600nm) of ~0.6.  The subculture was diluted to an OD600nm of 0.025 in 25 ml of HI in a 250-ml baffled flask and grown with shaking for 200 min at which time the cells were diluted into RNAprotect Bacteria Reagent (Qiagen) to a final OD600nm of 0.5.  To examine V. parahaemolyticus grown on plates, a single colony was streaked as a lawn over the entire surface of a fresh HI plate.  The following day, 5 ml of 0.3 M sucrose was used to suspend the cells on the plate, which were then diluted to an OD600nm of 0.05. Fifty µl of the diluted cells were spread onto an HI plate.  After 6 hours of growth, cells were harvested from the plate and diluted to OD600nm of 1.0 by using RNAprotect  that had been diluted 2-fold in 1x DPBS pH 7.1 (Gibco).

extract_protocol: Cells in RNAprotect were centrifuged and lysed by using lysozyme, proteinase K, and QIAzol (Qiagen) according to manufacturer’s protocol (Qiagen RNAprotect Bacteria Reagent Handbook). For each RNA preparation, 4 ml of liquid-grown cells or 2 ml of plate-grown cells were extracted and the RNA purified using 4 RNeasy minicolumns (Qiagen), which yielded ~50 µg RNA. This RNA was treated twice with RQ1 DNase (12 U, Promega) at 37ºC for one hour and purified after treatment using the RNeasy minikit

treatment_protocol: harvested cells were used for RNA isolation, examined microscopically to document average cell length, and analyzed for flagellin production by immunoblotting

tag: genetic modification

value: wild-type

tag: growth condition

value: Heart Infusion plate


title: genomic DNA from human liver 3 (replicate B)


title: LM5674 surface biological replicate 1


title: LM5674 surface biological replicate 2


title: LM5674 liquid dipyridyl phenamil biological replicate 2

source_name: PS2: wildtype strain in liquid with iron chelator and polar flagellar rotation inhibitor

value: Heart Infusion broth with 50 micromolar dipyridyl and 40 micromolar phenamil


title: LM5392 liquid dipyridyl

source_name: PS1: flaM- strain in liquid with iron chelator

value: flaM-

value: Heart Infusion broth with 50 micromolar dipyridyl


title: F.pla_phenol, rep 2

description: F. placidus grown with  0.5 mM phenol. Second biological replicate of three.


title: LM5674 surface biological replicate 3


title: F.pla_acetate, rep 3

description: F. placidus grown with 10 mM acetate. Third biological replicate of three.

source_name: 10 mM acetate as electron donor and 56 mM ferric citrate as electron acceptor

growth_protocol: Ferroglobus placidus DSM 10642 was grown in strict anaerobic conditions (80:20 N2/CO2) in medium previously described (Tor et al., Env. Micro. 2001, 3(4) p281) with 10 mM acetate as electron donor and Fe(III) citrate as electron acceptor. Cultures were incubated at 85C in the dark.

value: acetate

value: short organic acid


title: F.pla_benzoate, rep 1

description: F. placidus grown with 1 mM benzoate. First biological replicate of two.

source_name: 1 mM benzoate as electron donor and 56 mM ferric citrate as electron acceptor

growth_protocol: Ferroglobus placidus DSM 10642 was grown in strict anaerobic conditions (80:20 N2/CO2) in medium previously described (Tor et al., Env. Micro. 2001, 3(4) p281) with 1 mM benzoate as electron donor and Fe(III) citrate as electron acceptor. Cultures were incubated at 85 C in the dark.

value: benzoate

value: aromatic


title: F.pla_phenol, rep 1

description: F. placidus grown with 0.5 mM phenol. First biological replicate of three.


title: F.pla_acetate, rep 1

description: F. placidus grown with 10 mM acetate. First biological replicate of three.


title: LM7789 surface biological replicate 2

source_name: S(K-): lafK- strain grown on surface of agar plate

value: lafK-


title: LM7789 surface biological replicate 1


title: F.pla_acetate, rep 2

description: F. placidus grown with 10 mM acetate. Second biological replicate of three.


title: F.pla_benzoate, rep 2

description: F. placidus grown with 1 mM benzoate. Second biological replicate of two.


title: LM5674 liquid dipyridyl phenamil biological replicate 1


title: LM5674 liquid dipyridyl biological replicate 2

source_name: LD: wildtype strain in liquid culture with iron chelator


title: LM5674 liquid dipyridyl biological replicate 1


title: LM5674 liquid dipyridyl biological replicate 3


title: LM4262 liquid dipyridyl

source_name: PS1: motX- strain in liquid with iron chelator

value: motX-


title: S (1)

status: Public on Nov 05 2010

description: LM5674 surface biological replicate 1

source_name: S: wild-type strain on surface of agar plate

growth_protocol: To examine V. parahaemolyticus grown on plates with CaCl2 or ethylene glycol-bis(2-aminoethylether)-N,N,N′,N′-tetraacetic acid (EGTA), a single colony was streaked as a lawn over the entire surface of a fresh HI plate.  The following day, 5 ml of HI broth was used to suspend the cells on the plate, which were then diluted to an OD600nm = 0.05. Fifty µl of the diluted cells were spread onto an HI plate, or HI plate amended with 4 mM CaCl2 or 4 mM EGTA.  After 8 h of growth, cells were harvested from the plate and diluted to OD600nm of 1.0 by using RNAprotect (Qiagen) that had been diluted 2-fold in 1x DPBS pH 7.1 (Gibco).  To examine strains bearing the exsA expression plasmid or vector control, a single colony was streaked as a lawn on HI plates with gentamycin.  The following day these plates were suspended in sterile HI and diluted to OD600nm of 0.2. Fifty µl of the diluted cells were spread onto an HI plate with gentamycin and 1 mM IPTG.  After 4 hours of growth, cells were harvested as above in RNAprotect.

treatment_protocol: Harvested cells were used for RNA isolation

tag: genotype/variation


title: S (4)

description: LM5674 surface biological replicate 4


title: LM5674 liquid biological replicate 1

source_name: L: wildtype strain in liquid culture

value: Heart Infusion broth


title: S (2)

description: LM5674 surface biological replicate 2


title: S(K-) (1)

description: LM7789 surface biological replicate 1


title: S (3)

description: LM5674 surface biological replicate 3


title: S(K-) (2)

description: LM7789 surface biological replicate 2


title: PS2 (2)

description: LM5674 liquid dipyridyl phenamil biological replicate 2

source_name: PS2: wild-type strain in liquid with iron chelator and polar flagellar rotation inhibitor


title: PS2 (1)

description: LM5674 liquid dipyridyl phenamil biological replicate 1


title: LM5674 liquid biological replicate 2


title: LD (3)

description: LM5674 liquid dipyridyl biological replicate 3

source_name: LD: wild-type strain in liquid culture with iron chelator


title: PS1 (1)

description: LM4262 liquid dipyridyl


title: LD (2)

description: LM5674 liquid dipyridyl biological replicate 2


title: LD (1)

description: LM5674 liquid dipyridyl biological replicate 1


title: exsA (2)

description: LM8864_HI+gen+iptg_biological replicate 2

source_name: exsA: wild-type strian with exsA (vp1699) on IPTG inducbile plasmid grown on HI plates with gentamicin and IPTG

value: wild-type with exsA (vp1699)

value: Heart Infusion plate with gentamicin and IPTG


title: exsA (1)

description: LM8864_HI+gen+iptg_biological replicate 1


title: L (2)

description: LM5674 liquid biological replicate 2

source_name: L: wild-type strain in liquid culture


title: vector (2)

description: LM8863_HI+gen+iptg_biological replicate 2

source_name: vector: wild-type strain with vector control grown on plates with gentamicin and IPTG

value: wild-type with vector control


title: genomic DNA from human heart 2 (replicate A)

source_name: heart

value: male

value: heart


title: Ca(6) (1)

description: LM5674_HI+Ca6hours_biological replicate 1

source_name: Ca(6): wild-type strain grown on HI plate with added calcium

value: wild-type

value: Heart Infusion plate with added calcium


title: L (1)

description: LM5674 liquid biological replicate 1


title: vector (1)

description: LM8863_HI+gen+iptg_biological replicate 1


title: EGTA (2)

description: LM5674 HI + EGTA biological replicate 2

source_name: EGTA: wild-type strain grown on plate with 4 mM EGTA

value: Heart Infusion plate with EGTA


title: EGTA (1)

description: LM5674 HI + EGTA biological replicate 1


title: Ca (2)

description: LM5674_HI+Ca_biological replicate 2

source_name: Ca: wild-type strain grown on plate with 4 mM CaCl2


title: Ca (1)

description: LM5674_HI+Ca_biological replicate 1


title: PS1 (2)

description: LM5392 liquid dipyridyl

source_name: PS1: flaM- strain in liquid with iron chelator

value: flaM-


title: HI (1)

description: LM5674_HI_biological replicate 1

source_name: HI: wild-type strain grown on plate

value: Heart Infusion plate


title: HI (2)

description: LM5674_HI_biological replicate 2


title: Ca(6) (2)

description: LM5674_HI+Ca6hours_biological replicate 2


title: PC 2

status: Public on Oct 01 2010

city: Boston

first: Douglas

middle: M

last: Warner

state: MA

address: 136 Harrison

department: Molecular Biology & Microbiology

institute: Tufts University

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on E.coli 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station .

scan_protocol: GeneChips were scanned using the 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 100.

organism: Escherichia coli

source_name: cDNA made from strain PC1012(marArobsoxS) extracted from mouse kidney on day 2 post infection

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 1 ug total cDNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Bacteria were inoculated by direct injection of the mouse bladder, and kidney samples were taken at day 2 post-infection

extract_protocol: Infected kidney solutions were centrifuged at 5000xg for 10 min to separate bacteria (pellet) from kidney (surface of RNA-later solution) cells.  The kidney cells were evacuated from the top of the solution, and the remaining solution was spun once more at 12000xg for 10 min, followed by disposal of the supernatant.  Pelleted cells were resuspended in TE buffer and treated with lysozyme (Sigma) at 1mg/ml final concentration for 5 min, and samples of 3-5 infected mice were pooled together for each infection group.  Nucleic acids were extracted via the RNA extraction protocol and products of the RNAeasy kit (Qiagen).  Following column purification, RNA samples were treated with DNAse Turbo (Ambion) for 30 min at 37C, followed by quantification of RNA using a spectrophotometer.  Remaining polyadenylated eukaryotic RNA was depleted from the samples following the MicroEnrich (Ambion) protocol and resuspended in 20l of TE buffer.  RNA was quantified spectrophotometrically and equal amounts (~300-500ng) of KMD and PC1012 RNA samples were subjected to the MessageAmp (Ambion) RNA amplification protocol.  Resultant amplified RNA was quantified and equal amounts were used in the Affymetrix protocol for prokaryotic cDNA synthesis and biotin labeling.

treatment_protocol: Mouse kidneys were homogonized in RNALater solution (Ambion) and bacterial titers were taken.  Samples were pooled, and centrifuged as described below

tag: tissue source

value: kidney from CD-1 mice


title: Bj SFJ4-24 elevated CO2 condition vs ambient condition rep3

status: Public on Jul 29 2010

city: Saint Paul

first: Masayuki

last: Sugawara

state: MN

address: 250 Borloug Hall, 1991 Upper Buford Circle

department: Soil, Water, and Climate

institute: University of Minnesota

hyb_protocol: Both Cy3 and Cy5 labeled cDNAs to be compared were mixed, dried to completion, and then resuspended in 70 ul of preheated hybridization buffer (nuclease free water:formamide:20X SSC:1% SDS = 4:2.5:2.5:1) at 42°C. After adding 0.7 ul salmon sperm DNA (10 mg/ml) to prevent non-specific binding to the array, the mixture was hybridized at 42 C for 16 to 18 h. Hybridized arrays were washed with 1X SSC, 0.2% SDS at 42°C for 6 min, and, subsequently, with 0.1X SSC, 0.2% SDS at room temperature for 6 min, and twice with 0.1X SSC at room temperature for 3 min.

scan_protocol: The arrays were scanned using an Axon GenePix 4000B scanner (Molecular Devices Corp., Sunnyvale, CA). Signal intensities were analyzed using GenePix Pro 6.0 software (Molecular Devices Corp., Sunnyvale, CA).

data_processing: Signal intensities were normalized for spot and slide abnormalities using spatial lowess. Lowess adjusted data were subsequently analyzed by mixed effect microarray analysis of variance (MAANOVA) (Kerr et al. 2000). The resulting variety-by-gene interaction (VG) values were combined with the residual noise from each spot to obtain the filtered and adjusted expression values (Kerr et al. 2000; Kerr and Churchill 2001). Both lowess and MAANOVA are part of the R/maanova microarray statistical analysis package (http://www.jax.org/staff/churchill/labsite/). Expression values from two technical replicates in each array were combined, averaged, and subsequently subjected to significance analysis of microarray (SAM) data using the SAM package (Tusher et al. 2001). Significant genes were selected based on a 1.5-fold cut off threshold with a false discovery rate lower than 5%.

organism: Bradyrhizobium japonicum

source_name: Bradyrhizobium japonicum SFJ4-24 cells grown in the soybean rhizosphere under elevated CO2 condition (550 ppm) for 3 days

label_protocol: 10 ug of total RNA was used for cDNA synthesis with Superscript III reverse transcriptase and random hexamers (Invitrogen Corp.). After digesting the remaining RNA by RNase H (Invtrogen), cDNA was purified using a Microcon YM-30 column (Millipore) and concentration was determined.

growth_protocol: Bradyrhizobium japonicum strain was grown in 10 ml of AG medium (Sadowsky et al. 1987) until stationary phase, collected by centrifugation at 8,000 ×g for 10 min, and washed twice with sterilized, nitrogen-free, plant growth medium (Franco and Munns 1982). The resultant cells were re-suspended in 10 ml of the same plant growth medium to a final concentration of approximately 109 cells/ml. Germinated soybean seedlings (60 – 70) were each aseptically transferred into holes in the growth boxes filled with 300 ml of plant growth medium, and 3 ml washed bacterial suspension was added to provide approximately 107 cells/ml of growth medium. Three replicates seedling growth boxes were used for each CO2 treatment. Seedling boxes were covered with aluminum foil, transferred to a plant growth chamber, and the aeration pump (Luft Pump; Oceanic systems Inc. Dallas, TX) was immediately started. Each pump supplied aeration of three growth boxes, at a rate of 1.3 L /min. The seedling boxes were incubated for 3 days at 27°C in the dark. Kyoto, Japan). To investigate a directly influence of atmospheric elevated CO2 on gene expression in Bradyrhizobium cells, 3 ml of washed bacterial suspension was added in a growth boxes without plant seedlings, and the boxes were incubated at the same condition as above.

extract_protocol: Standard hot-phenol method

treatment_protocol: Germinated soybean seedlings in the growth boxes were incubated for 3 days at 27°C in the dark under elevated or amibient CO2 conditions. The elevated CO2 concentration in growth chambers was controlled by an APBA-250E indoor CO2 monitor (HORIBA, Kyoto, Japan), and maintained at 550 ppm or ambient CO2 concentration. All of the roots from three replicate hydroponic boxes were gently rinsed, several times in sterile fresh plant growth medium to remove loosely-adhering or non-attached bradyrhizobia. Rinsed roots were randomly cut with a sterilized scissor, and placed into 500 ml bottles containing 180 ml of ice- cold extraction buffer (0.1 % Na-pyrophosphate, pH 7.0, and 0.1 % Tween 20) and 20 ml of stop solution (5 % H2O-saturated phenol, pH 4.3, in 95% Ethanol). Bottles were agitated at approximately 220 strokes per min for 30 min by using an Eberbach model 6000 horizontal shaker (Eberbach Corp., Ann Arbor, MI). Extracts were filtered through three layers of Miracloth (Calbiochem Inc. LaJolla, CA) to remove plant cells and debris and filtrates were centrifuged at 8,000 ×g for 12 min. The resulting cell pellet were immediately flash frozen in liquid nitrogen, and stored in the freezer at -80 °C until RNA extraction.

source_name: Bradyrhizobium japonicum SFJ4-24 cells grown in the soybean rhizosphere under ambient CO2 condition (550 ppm) for 3 days


title: Bj SFJ4-24 elevated CO2 condition vs ambient condition rep4


title: Bj SFJ14-36 elevated CO2 condition vs ambient condition rep4

source_name: Bradyrhizobium japonicum SFJ14-36 cells grown in the soybean rhizosphere under elevated CO2 (550 ppm) condition for 3 days

source_name: Bradyrhizobium japonicum SFJ14-36 cells grown in the soybean rhizosphere under ambient CO2 condition for 3 days


title: Bj SFJ4-24 elevated CO2 condition vs ambient condition rep2


title: Bj SFJ4-24 elevated CO2 condition vs ambient condition rep1


title: Sarcoma tumor PT22DD

status: Public on Jul 06 2010

city: New York

first: Barry

middle: Stephen

last: Taylor

state: NY

address: 1275 York Avenue, Box #460

institute: Memorial Sloan-Kettering Cancer Center

description: Hybridized to 250K_Sty

hyb_protocol: Per manufacturer's instructions

scan_protocol: After hybridization, arrays were washed with Affymetrix fluidics station and scanned with the Gene Chip Scanner 3000 7G and Affymetrix Genotyping Tools Version 2.0

data_processing:
Signal instensities were were quantified and normalized with the Affymetrix Chromosomal Copy Number Analysis Tool (CNAT 4.0, 1.5.6_v3.1) and copy number was converted to tumor-to-normal log2 ratios using the algorithm described in Taylor BS, et al PLoS ONE 2008; 3(9):e3179. Cell line signal intensities were normalized to a baseline array with median intensity and quantile normalization in GenePattern based on the dChipSNP algorithm. SNP-level inteisities were obtained for these using the model-based PM/MM method. Data from each were compared to data from 1800 normal datasets, and the 5 normal samples with noise profiles most similar to each cell line were used to determine log2 ratios at each SNP locus.
The normalized tumor/normal ratio data described above are presented in the Sample data tables of the Tumor sample (normal Samples therefore do not have data tables).  The matrix of ratio data is also available as a text file on the Series record.

source_name: tumor DNA

label_protocol: PCR projects, after pooling, concentration, and fragmentation with Dnase I were labeled and denatured as per manufacturer's instructions with Bioprime Array CHG labeling kit (Invitrogen) using Cy3/Cy5.

extract_protocol: Genomic DNA was extracted from cyromoled-macrodissected tumor samples and from blood or normal adjacent tissue and digested with the StyI restriction enzyme

value: Soft-tissue sarcoma

tag: disease status

tag: sample id


title: Sarcoma tumor PT21DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT19DD

description: Hybridized to 250K_Sty


title: Bj SFJ14-36 elevated CO2 condition vs ambient condition rep3


title: Sarcoma tumor PT18DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT17DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT20DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT24DD

description: Hybridized to 250K_Sty


title: Control normal fat NF95

description: Gene expression data from control normal fat

scan_protocol: Flourescence was measured by confocal scanner (Agilent, Palo Alto, CA)

data_processing: Signal intensity data was generated with Affymetrix Microarray Suite version 5.0 software with default parameters. Expression values were estimated with robust multi-array average (RMA) using standard background correction. RMA-normalized expression data is provided in log base 2 scale.

label: Biotin

source_name: Human control normal fat

label_protocol: Per manufacturer's instructions

extract_protocol: Total RNA was extracted from macro-dissected cryomolds and homogenized in QIAzol lysis reagent

value: Human fat

value: Normal control


title: Control normal fat NF225


title: Bj SFJ14-36 elevated CO2 condition vs ambient condition rep1


title: Bj SFJ14-36 elevated CO2 condition vs ambient condition rep2


title: Control normal fat NF92


title: Control normal fat NF180


title: Sarcoma tumor PT7DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT175PL

description: Gene expression data from soft-tissue sarcoma tumor

source_name: Soft-tissue sarcoma


title: Sarcoma tumor PT43DD


title: Sarcoma tumor PT48DD


title: Sarcoma tumor PT177PL


title: Sarcoma tumor PT41DD


title: Sarcoma tumor PT6DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT33DD


title: Sarcoma tumor PT75LMS


title: Sarcoma tumor PT173PL


title: Sarcoma tumor PT47DD


title: Sarcoma tumor PT27DD


title: Sarcoma tumor PT46DD


title: Sarcoma tumor PT28DD


title: Control normal fat NF115


title: Control normal fat NF90


title: Sarcoma tumor PT34DD


title: Sarcoma tumor PT16DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT9DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT8DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT20DD


title: Sarcoma tumor PT2DD


title: Sarcoma tumor PT26DD


title: Sarcoma tumor PT1DD


title: Sarcoma tumor PT11DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT21DD


title: Sarcoma tumor PT8DD


title: Sarcoma tumor PT3DD


title: renal allograft biopsy,  (U of A/Chicago) 90A1AGX7

status: Public on May 24 2010

city: Edmonton

first: Jeff

last: Reeve

state: Alberta

address: 250 HMRC University of Alberta

institute: University of Alberta

description: Samples with the same initial numbers in the sample names are replicates from the same patient. For the main analysis, only the earliest biopsy per patient was used, and only in those patients with a biopsy taken > 1 year post-transplant

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HGU133 Plus 2.0 Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Gene Array Scanner (Affymetrix) and processed with GeneChip Operating Software Version 1.4.0 (Affynetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

source_name: renal allograft biopsy

label_protocol: RNA (1-2ug) was labeled using GeneChip HT One-Cycle Target Labeling and Control kit. Quality of labeled cRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to HGU133Plus2.0. GeneChip (Affymetrix, Santa Clara, CA).

growth_protocol: All human renal allograft biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

extract_protocol: Following homogenization of the tissue in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA), total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 4ug/core, (RNA integrity number >7).

treatment_protocol: The immunosuppressive treatment of the patients before the biopsy was based on individual treatment regiments; the treatment after the biopsy was adjusted based on the histopathological diagnosis.

tag: failed=1/non failed=0

tag: time of biopsy post transplant (days)

tag: time from biopsy to failure/censoring (days)

tag: rejection/non rejection

value: nonrej

tag: sample included in the main analysis- the first biopsy per patient from the 105 late (> 1 year) patients


title: renal allograft biopsy,  (U of A/Chicago) 95A2AGX7


title: Sarcoma tumor PT4DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT3DD

description: Hybridized to 250K_Sty


title: renal allograft biopsy,  (U of A/Chicago) 82A5AGX7

value: rej


title: renal allograft biopsy,  (U of A/Chicago) 85A1AGX7


title: renal allograft biopsy,  (U of A/Chicago) 94A2AGX7


title: renal allograft biopsy,  (U of A/Chicago) 97A2AGX7


title: Sarcoma tumor PT5DD


title: renal allograft biopsy,  (U of A/Chicago) 82A4AGX7


title: Sarcoma tumor PT24DD


title: renal allograft biopsy,  (U of A/Chicago) 80A7AGX7


title: renal allograft biopsy,  (U of A/Chicago) 82A3AGX7


title: renal allograft biopsy,  (U of A/Chicago) 86A1AGX7


title: renal allograft biopsy,  (U of A/Chicago) 96A6AGX11


title: renal allograft biopsy,  (U of A/Chicago) 89A1AGX7


title: renal allograft biopsy,  (U of A/Chicago) 84A2AGX7


title: Sarcoma tumor PT15DD


title: renal allograft biopsy,  (U of A/Chicago) 77A1AGX7


title: renal allograft biopsy,  (U of A/Chicago) 80A6AGX7


title: renal allograft biopsy,  (U of A/Chicago) 76A1AGX7


title: renal allograft biopsy,  (U of A/Chicago) 75A1AGX7


title: renal allograft biopsy,  (U of A/Chicago) 73A8AGX7


title: renal allograft biopsy,  (U of A/Chicago) 72A4AGX7


title: renal allograft biopsy,  (U of A/Chicago) 73A6AGX7


title: renal allograft biopsy,  (U of A/Chicago) 73A5AGX7


title: renal allograft biopsy,  (U of A/Chicago) 72A5AGX7


title: renal allograft biopsy,  (U of A/Chicago) 72A3AGX9


title: renal allograft biopsy,  (U of A/Chicago) 73A7AGX7


title: renal allograft biopsy,  (U of A/Chicago) 64A1AGX9


title: renal allograft biopsy,  (U of A/Chicago) 66A1AGX7


title: renal allograft biopsy,  (U of A/Chicago) 65A2AGX7


title: renal allograft biopsy,  (U of A/Chicago) 60A3AGX7


title: renal allograft biopsy,  (U of A/Chicago) 61A1AGX7


title: renal allograft biopsy,  (U of A/Chicago) 60A2AGX7


title: renal allograft biopsy,  (U of A/Chicago) 54A2AGX8


title: renal allograft biopsy,  (U of A/Chicago) 55A1AGX7


title: renal allograft biopsy,  (U of A/Chicago) 56A2AGX7


title: renal allograft biopsy,  (U of A/Chicago) 63A1AGX7


title: renal allograft biopsy,  (U of A/Chicago) 57A1AGX7


title: renal allograft biopsy,  (U of A/Chicago) 65A3AGX7