title: fine-00037: E10058_T


title: fine-00037: HF1345_T

status: Public on May 14 2015

type: RNA

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

country: USA

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Brain

tag: disease state

value: ASTROCYTOMA

tag: organism part

value: Brain

tag: tumor grading

value: Grade 2

tag: sample


title: fine-00037: HF1551_T

scan_protocol: See mage-tab files linked to series entry for additional details


title: fine-00037: HF0050_T

data_processing: See mage-tab files linked to series entry for additional details

value: GBM

value: Grade 4


title: fine-00037: E10210_T

label_protocol: See mage-tab files linked to series entry for additional details


title: fine-00037: HF0223_T

extract_protocol: See mage-tab files linked to series entry for additional details


title: fine-00037: E10262_T


title: fine-00037: E09800_T


title: fine-00037: E09818_T


title: fine-00037: HF1334_T


title: fine-00037: E08021_T

value: OLIGODENDROGLIOMA

value: Grade 3


title: fine-00037: E09743_T


title: fine-00037: E09985_T

value: UNKNOWN


title: fine-00037: HF1585_T


title: fine-00037: HF1032_T


title: fine-00037: E09797_T


title: fine-00037: NT5_T


title: fine-00037: E10264_T


title: fine-00037: 03461078_T


title: fine-00037: E10299_T


title: fine-00037: HF1380_T


title: fine-00037: E09688_T

value: MIXED


title: fine-00037: 03352571_T


title: fine-00037: HF0835_T


title: fine-00037: E09394_T


title: fine-00037: HF1178_T


title: fine-00037: E10136_T


title: fine-00037: E09398_T


title: fine-00037: E09483_T


title: fine-00037: E09546_T


title: fine-00037: NT3_T


title: fine-00037: E09967_T


title: fine-00037: 03504050_T


title: fine-00037: E09358_T


title: fine-00037: E09680_T


title: fine-00037: E10031_T


title: fine-00037: E09752_T


title: fine-00037: HF0291_T


title: fine-00037: E09906_T


title: fine-00037: E10226_T


title: fine-00037: 03522254_T


title: fine-00037: HF0178_T


title: fine-00037: E09900_T


title: fine-00037: E10025_T


title: fine-00037: E09451_T


title: fine-00037: E10556_T


title: fine-00037: E10488_T


title: fine-00037: HF0996_T


title: fine-00037: E10163_T


title: fine-00037: E09988_T


title: fine-00037: HF0329_T


title: fine-00037: E09975_T


title: fine-00037: E10041_T


title: BY-Cold-24h

city: Nanjing

first: Yue

last: Zhang

state: Jiangsu

address: Weigang No.1

department: Tea Science Research Institute

country: China

institute: Nanjing Agricultural University

hyb_protocol: Hybridization was performed overnight on a μParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://www.mirbase.org/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 L 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics)

data_processing: Data were analyzed by first subtracting the background, then the signals were normalized using a Lowess (locally weighted regression) filter. The raw microarray data set was filtered according to a standard procedure to exclude spots with minimum intensity. It was arbitrarily set to an intensity parameter of P100 for the miRNA microarray data. Spots with diameters less than 10 μm and flagged spots were also excluded from the analyses.

organism: Camellia sinensis

source_name: tea leaf

label_protocol: Labeling of total RNA was performed according to the protocol from LC Science for a single-color experiment with no modification.

extract_protocol: Total RNA from each tissue sample was extracted using TRK-1001 kit (LC Sciences) according to the manufacturer’s instructions.

tag: cultivar

value: Baiye 1

tag: tissue

value: leaf

tag: treatment


title: BY-CK

value: control


title: BY-Cold-4h


title: fine-00037: E09907_T


title: fine-00037: E09611B_T


title: fine-00037: HF0316_T


title: fine-00037: HF0268_T

value: Grade 1


title: YS-Cold-24h

value: Yingshuang


title: BY-Cold-12h


title: YS-Cold-12h


title: fine-00037: NT2_T


title: YS-Cold-4h


title: fine-00037: HF0152_T


title: fine-00037: E09862_T


title: fine-00037: E09907B_T


title: fine-00037: E09826_T


title: fine-00037: HF1671_T


title: YS-CK


title: fine-00037: 03506280_T


title: fine-00037: E09239_T


title: fine-00037: 03480779_T


title: fine-00037: E09914_T


title: fine-00037: HF0211_T


title: fine-00037: HF1677_T


title: fine-00037: E10250_T


title: fine-00037: E10022_T


title: fine-00037: E10462_T


title: fine-00037: E09833B_T


title: fine-00037: HF0608_T


title: Low-dose-rate_2Gy_rep6

city: New York

first: Sally

last: Amundson

state: NY

department: Center for Radiological Research

institute: Columbia University

description: Gene expression after 24hr with high-dose-rate irraidiated 2.2Gy mouse blood

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x GEx hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan setting with eXtended dynamic range, Scan area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software v10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended green Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers or Features not Positive and significant were excluded

organism: Mus musculus

source_name: Peripheral blood_LDR_2.2Gy_replicate 6

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the One-Color Qucik Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Male C57BL/6 mice were exposed with either high-dose-rate (0.85Gy/min) or low-dose-rate (0.0028Gy/min) irradiation to 1.1, 2.2 or 4.4-Gy X-rays. Sham irradiated controls, for both HDR and LDR, were treated exactly the same way as corresponding exposed samples but without irradiation exposure.

extract_protocol: The whole blood RNA was extracted using PAXgene blood RNA kit (Qiagen, NV) according to manufacturer’s instruction with on-column DNase I treatment, followed by removal of globin transcripts using the GLOBINclear kit (Ambion Inc., Austin, TX) to remove both a- and b-globin.

treatment_protocol: Twenty-four hours after the start of irradiation, mice were euthanized with CO2 and peripheral blood (appx. 0.5 ml) was collected via cardiac puncture, mixed in PAXgene blood RNA solution (1:4 ratio) and stored overnight at 4º C until processing for RNA extraction.

value: whole blood

tag: Sex

value: Male

tag: strain

value: high-dose-rate irraidiated 2.2Gy


title: fine-00037: E09602_T


title: fine-00037: E09833_T


title: fine-00037: E09960_T


title: fine-00037: HF0960_T


title: fine-00037: 81668782_T


title: Low-dose-rate_2Gy_rep3

description: Gene expression after 24hr with high-dose-rate irraidiated 1.1Gy mouse blood

source_name: Peripheral blood_LDR_2.2Gy_replicate 3

value: high-dose-rate irraidiated 1.1Gy


title: fine-00037: 03461404_T


title: Low-dose-rate_2Gy_rep1

description: Gene expression after 24hr with high-dose-rate irraidiated 4.4Gy mouse blood

source_name: Peripheral blood_LDR_2.2Gy_replicate 1

value: high-dose-rate irraidiated 4.4Gy


title: Low-dose-rate_2Gy_rep2

source_name: Peripheral blood_LDR_2.2Gy_replicate 2


title: fine-00037: E50123_T


title: Unirradiated control_0Gy_rep12

description: Gene expression after 24hr with low-dose-rate irraidiated 4.4Gy mouse blood

source_name: Peripheral blood_LDR_0Gy_replicate 6

value: low-dose-rate irraidiated 4.4Gy


title: fine-00037: HF1511_T

value: ASTROCYTOMA

value: Brain

value: Grade 2


title: fine-00037: E10193_T

value: GBM


title: fine-00037: E09378_T

value: UNKNOWN


title: Unirradiated control_0Gy_rep3

source_name: Peripheral blood_LDR_0Gy_replicate 1


title: fine-00037: HF0986_T

value: Grade 4


title: Unirradiated control_0Gy_rep11

source_name: Peripheral blood_LDR_0Gy_replicate 5


title: Low-dose-rate_1Gy_rep6

description: Gene expression after 24hr with low-dose-rate irraidiated 1.1Gy mouse blood

source_name: Peripheral blood_LDR_1.1Gy_replicate 6

value: low-dose-rate irraidiated 1.1Gy


title: fine-00037: HF1297_T


title: Low-dose-rate_1Gy_rep3

source_name: Peripheral blood_LDR_1.1Gy_replicate 3


title: fine-00037: HF0931_T


title: Low-dose-rate_1Gy_rep5

source_name: Peripheral blood_LDR_1.1Gy_replicate 5


title: Low-dose-rate_1Gy_rep4

source_name: Peripheral blood_LDR_1.1Gy_replicate 4


title: Low-dose-rate_1Gy_rep2

source_name: Peripheral blood_LDR_1.1Gy_replicate 2


title: fine-00037: E09730_T


title: Unirradiated control_0Gy_rep10

source_name: Peripheral blood_HDR_0Gy_replicate 6


title: Low-dose-rate_1Gy_rep1

source_name: Peripheral blood_LDR_1.1Gy_replicate 1


title: fine-00037: E09334_T

value: MIXED

value: Grade 3


title: fine-00037: HF1487_T

value: OLIGODENDROGLIOMA


title: fine-00037: HF1608_T


title: Unirradiated control_0Gy_rep9

source_name: Peripheral blood_HDR_0Gy_replicate 5


title: fine-00037: HF1397_T

source_name: Brain


title: fine-00037: HF1122_T


title: Unirradiated control_0Gy_rep8

source_name: Peripheral blood_HDR_0Gy_replicate 4


title: High-dose-rate_4Gy_rep3

source_name: Peripheral blood_HDR_4.4Gy_replicate 3


title: fine-00037: HF1227_T


title: High-dose-rate_4Gy_rep4

source_name: Peripheral blood_HDR_4.4Gy_replicate 4


title: fine-00037: E10026_T


title: High-dose-rate_4Gy_rep1

description: Gene expression after 24hr with low-dose-rate irraidiated 2.2Gy mouse blood

source_name: Peripheral blood_HDR_4.4Gy_replicate 1

value: low-dose-rate irraidiated 2.2Gy


title: fine-00037: E09742_T


title: fine-00037: HF0383_T


title: High-dose-rate_2Gy_rep4

description: Gene expression after 24hr in unirradiated mouse blood

source_name: Peripheral blood_HDR_2.2Gy_replicate 4

value: whole blood

value: unirradiated


title: High-dose-rate_4Gy_rep5

source_name: Peripheral blood_HDR_4.4Gy_replicate 5

value: Male


title: High-dose-rate_2Gy_rep2

source_name: Peripheral blood_HDR_2.2Gy_replicate 2


title: High-dose-rate_2Gy_rep1

source_name: Peripheral blood_HDR_2.2Gy_replicate 1

value: high-dose-rate irraidiated 1.1Gy


title: fine-00037: E09740_T


title: fine-00037: E09587_T


title: fine-00037: E09868_T


title: fine-00037: E50091_T


title: High-dose-rate_4Gy_rep6

source_name: Peripheral blood_HDR_4.4Gy_replicate 6


title: High-dose-rate_4Gy_rep2

source_name: Peripheral blood_HDR_4.4Gy_replicate 2


title: fine-00037: E10211_T


title: High-dose-rate_2Gy_rep6

source_name: Peripheral blood_HDR_2.2Gy_replicate 6


title: fine-00037: HF0914_T


title: fine-00037: E09867_T


title: High-dose-rate_2Gy_rep5

source_name: Peripheral blood_HDR_2.2Gy_replicate 5

value: high-dose-rate irraidiated 2.2Gy


title: fine-00037: E10038_T


title: fine-00037: MD550715_T


title: fine-00037: E10258_T


title: White Plymouth Rock (WR)

type: genomic

city: Shenzhen

first: Guoqiang

last: Yi

state: Guangdong

address: No 7,Pengfei Road,Dapeng District,Shenzhen

institute: Agricultural Genome Institute at Shenzhen

hyb_protocol: Hybridization was done for 40-72 h on 42℃ using NibleGen Hybridization System, and all the washing and drying steps were done without interruption.

scan_protocol: NimbleGem arrays were scanned at 2 μm resolution using a NimbleGem MS200 scanner with PMT 100%

data_processing: NimbleScan Software Version 2.6 (Roche NimbleGen, Inc) was used to extract the data. Considering we only analyzed raw CGH log2 ratio values not processed/normalized data, log2 ratio values were calculated between tests and reference.

molecule: genomic DNA

organism: Gallus gallus

source_name: Blood

label_protocol: 0.5 ug of test DNA were labeled with Cy3 and 0.5 ug of reference DNA were labeled with Cy5 following NimbleGen Arrays User's Guide.

extract_protocol: Genomic DNA was isolated using standard phenol/chloroform extraction methods.

value: blood

tag: breed

value: White Plymouth Rock (WR)

tag: gender

value: Female

value: Red Jungle Fowl


title: High-dose-rate_1Gy_rep5

source_name: Peripheral blood_HDR_1.1Gy_replicate 5


title: fine-00037: HF1587_T

value: ASTROCYTOMA

value: Brain


title: High-dose-rate_2Gy_rep3

source_name: Peripheral blood_HDR_2.2Gy_replicate 3


title: fine-00037: E09922_T

value: UNKNOWN


title: High-dose-rate_1Gy_rep6

source_name: Peripheral blood_HDR_1.1Gy_replicate 6


title: fine-00037: E10036_T

source_name: Brain


title: High-dose-rate_1Gy_rep1

source_name: Peripheral blood_HDR_1.1Gy_replicate 1


title: High-dose-rate_1Gy_rep2

source_name: Peripheral blood_HDR_1.1Gy_replicate 2


title: fine-00037: HF1255_T


title: fine-00037: HF0953_T

value: Grade 2


title: fine-00037: HF0163_T


title: High-dose-rate_1Gy_rep4

source_name: Peripheral blood_HDR_1.1Gy_replicate 4

value: high-dose-rate irraidiated 4.4Gy


title: Unirradiated control_0Gy_rep1

source_name: Peripheral blood_HDR_0Gy_replicate 1

value: low-dose-rate irraidiated 1.1Gy


title: Beijing You (BY)

value: Beijing You (BY)


title: fine-00037: E09231_T


title: Low-dose-rate_4Gy_rep5

source_name: Peripheral blood_LDR_4.4Gy_replicate 5

value: low-dose-rate irraidiated 4.4Gy


title: fine-00037: HF0066_T

value: GBM

value: Grade 4


title: Unirradiated control_0Gy_rep7

source_name: Peripheral blood_HDR_0Gy_replicate 3

value: whole blood

value: Male

value: low-dose-rate irraidiated 2.2Gy


title: Unirradiated control_0Gy_rep2

source_name: Peripheral blood_HDR_0Gy_replicate 2


title: Low-dose-rate_4Gy_rep6

source_name: Peripheral blood_LDR_4.4Gy_replicate 6


title: fine-00037: HF1232_T

value: Grade 3


title: Silkie (SK)

value: blood

value: Silkie (SK)


title: fine-00037: HF1667_T


title: Shouguang (SG)

value: Shouguang (SG)

value: Female

value: Red Jungle Fowl


title: Low-dose-rate_4Gy_rep4

source_name: Peripheral blood_LDR_4.4Gy_replicate 4


title: fine-00037: MD602958_T

value: Brain


title: Low-dose-rate_4Gy_rep3

source_name: Peripheral blood_LDR_4.4Gy_replicate 3

value: unirradiated


title: fine-00037: E09948_T

value: ASTROCYTOMA


title: Low-dose-rate_4Gy_rep2

source_name: Peripheral blood_LDR_4.4Gy_replicate 2


title: fine-00037: E09945_T

value: UNKNOWN


title: fine-00037: E09910_T


title: Luxi Game (LX)

value: Luxi Game (LX)


title: Tibetan (TB)

value: Tibetan (TB)


title: Dongxiang (DX)

value: Dongxiang (DX)


title: fine-00037: HF1509_T

value: GBM

value: Grade 4


title: Low-dose-rate_4Gy_rep1

source_name: Peripheral blood_LDR_4.4Gy_replicate 1

value: whole blood

value: Male


title: fine-00037: HF1628_T


title: Low-dose-rate_2Gy_rep4

source_name: Peripheral blood_LDR_2.2Gy_replicate 4

value: high-dose-rate irraidiated 1.1Gy


title: fine-00037: HF0377_T


title: Unirradiated control_0Gy_rep5

source_name: Peripheral blood_LDR_0Gy_replicate 3


title: fine-00037: E09787_T


title: Unirradiated control_0Gy_rep4

source_name: Peripheral blood_LDR_0Gy_replicate 2


title: Low-dose-rate_2Gy_rep5

source_name: Peripheral blood_LDR_2.2Gy_replicate 5


title: fine-00037: HF1186_T

source_name: Brain

value: Grade 3


title: fine-00037: HF0048_T

value: Grade 1


title: Unirradiated control_0Gy_rep6

source_name: Peripheral blood_LDR_0Gy_replicate 4


title: fine-00037: MD550239_T


title: fine-00037: E09430_T


title: fine-00037: NT6_T


title: 1WWT

city: Xaimen

first: Zhongxian

last: Lu

state: Fujian

address: Xiangan Nanlu Road

department: School of Pharmaceutical Sciences

institute: Xiamen University

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with ACGG soft using Affymetrix default analysis settings and normalized by RMA method.

source_name: Postnatal 1 week Shp2f/f mice testis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

extract_protocol: Total RNA of Testis tissues from Shp2f/f and SCSKO mice was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

tag: strain background

tag: genotype/variation

value: wild type; Shp2f/f

tag: age

value: Postnatal 1 week

value: testis


title: Wenchang (WC)

source_name: Blood

value: blood

value: Wenchang (WC)

value: Female

value: Red Jungle Fowl


title: 2WWT

source_name: Postnatal 2 weeks Shp2f/f mice testis

value: Postnatal 2 week


title: 2WKO

source_name: Postnatal 2 weeks SCSKO mice testis

value: SCSKO


title: 1WKO

source_name: Postnatal 1 week SCSKO mice testis


title: D3WT

source_name: Postnatal 3 days Shp2f/f mice testis

value: Postnatal 3 days


title: E16-5KO

source_name: 16.5 fetal day SCSKO mice testis

value: 16.5 fetal day


title: fine-00037: HF0212_T

value: GBM

value: Brain

value: Grade 4


title: fine-00037: E10318_T


title: fine-00037: E09139_T


title: High-dose-rate_1Gy_rep3

source_name: Peripheral blood_HDR_1.1Gy_replicate 3

value: whole blood

value: Male

value: high-dose-rate irraidiated 4.4Gy


title: D3KO

source_name: Postnatal 3 days SCSKO mice testis


title: fine-00037: E09673_T

value: ASTROCYTOMA

value: Grade 2


title: 9cRA-polyIC

city: Suzhou

first: feng

last: ma

address: 218 Xinghu Street, B5-527

department: Suzhou Institute of Systems Medicine

institute: CAMS

scan_protocol: Affymetrix standard protocols

data_processing: Microarray data were normalized using GCRMA

source_name: RAW264.7 cells treated with 9cRA and polyI:C

label_protocol: Biotin labeled to Affymetrix Mouse Genome 430.2 GeneChip microarrays (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix reagents and protocols (http://www.affymetrix.com).

growth_protocol: RAW264.7 were grown in DMEM containing 10%FBS and 1% penicillin/streptomycin, 37C and 10%CO2

extract_protocol: Total RNA was extracted by TRIzol

treatment_protocol: RAW 264.7 cells were pre-treated with DMSO or 100nM of 9cis-retinoic acid for 16hours.  The cells were then stimulated with polyI:C (6ug transfected) or LPS (500ng/mL) for 2 hours.

tag: cell line

value: 9cRA and polyI:C


title: fine-00037: E09681_T

value: OLIGODENDROGLIOMA

value: Grade 3


title: DMSO-polyIC

hyb_protocol: Affymetrix Mouse Genome  430.2 GeneChip microarrays (Affymetrix Inc., Santa Clara, CA, USA)

source_name: RAW264.7 cells treated with DMSO and polyI:C

value: DMSO and polyI:C


title: fine-00037: HF0894_T


title: E16-5WT

source_name: 16.5 fetal day Shp2f/f mice testis

value: wild type; Shp2f/f

value: testis


title: 9cRA-LPS

source_name: RAW264.7 cells treated with 9cRA and LPS

value: 9cRA and LPS


title: DMSO-LPS

source_name: RAW264.7 cells treated with DMSO and LPS

value: DMSO and LPS


title: fine-00037: E10021_T


title: fine-00037: E09454_T


title: fine-00037: E10054_T


title: fine-00037: HF0966_T


title: fine-00037: HF1058_T


title: fine-00037: 03431712_T


title: IL-2 deficient Lung, biological replicate 2

city: Worcester

first: Susan

middle: L

last: Swain

state: MA

address: 55 Lake Avenue North

department: Pathology

institute: University of Massachusetts Medical School

description: Gene expression data from primed  IL-2 deficient DO11.10 CD4 T cell effectors from the lung on day 7 post influenza infection

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on M430.2 GeneChip Arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: For publicaiton Cel files were analyzed with GeneSpringGX (Agilent) using default analysis settings and the PLIER normalization method.

label: Biotin

source_name: Primed IL-2 deficient DO11.10 CD4 T cell effectors from the lung on day 7 post influenza infection

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Congenic Thy1.1 donor WT or IL-2 deficient memory DO11.10 CD4 T cells were adoptively transferred to naïve Thy1.2 BALB/c mice in 200uL PBS.  Mice were subsequently infected with 0.1 LD50 A/PR8/34-OVAII influenza A virus.

extract_protocol: Total RNA was extracted from cells with RNeasy Mini Kit from QIAGEN and amplified (MessageAmp a RNA; Ambion) according to manufacturers instructions.

treatment_protocol: On day 7 post infection, donor CD4 T cells were re-isolated from adoptive hosts by enrichment with CD4 magnetic beads (Milteny) followed by facs sorting for Thy1.1 and CFSE-divided populations.

tag: strain (naïve mice)

value: BALB/c

value: IL-2 deficient memory DO11.10 CD4 T cells were adoptively transferred to naïve BALB/c mice

tag: infection of mice

value: A/PR8/34-OVAII influenza

tag: time

value: 7 days post infection

tag: cell type (effector precursor)

value: Primed IL-2 deficient DO11.10 donor CD4 T cells (re-isolated from adoptive hosts)


title: DMSO

source_name: RAW264.7 cells treated with DMSO only

value: DMSO only


title: WT Lung, biological replicate 1

description: Gene expression data from primed WT DO11.10 CD4 T cell effectors from the lung on day 7 post influenza infection

source_name: Primed WT DO11.10 CD4 T cell effectors from the lung on day 7 post influenza infection

value: WT memory DO11.10 CD4 T cells were adoptively transferred to naïve BALB/c mice

value: Primed WT DO11.10 donor CD4 T cells (re-isolated from adoptive hosts)


title: Uveal melanoma primary tissue 4 replicate

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

hyb_protocol: The labeled samples were dried completely in a vacuum concentrator and resuspended in 18 ul of nuclease free water. The hybridization mixture [10X GE blocking agent (4.5 ul), 2X Hi-RPM hybridization buffer (22.5ul)] along with labeled miRNA sample was heated for 5 min at 100 °C and immediately kept on ice. Each 45 ul sample was hybridized onto a microarray at 55 °C for 20 h. Slides were washed 5 min in GE wash buffer 1 at RT and again for 5 min in GE wash buffer 2 at 37 °C

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software

data_processing: miRNA based normalization was done using GeneSpring GX 11.5 Software. 90th Percentile Shift Normalization

source_name: monosomy 3 uveal melanoma tumor

label_protocol: miRNA labeling was performed as described in Agilent miRNA microarray protocol version 2.0 using Agilent miRNA labeling kit. 100 ng of total RNA was dephosphorylated with calf intestine alkaline phosphatase for 30 min at 37°C. Denaturation was performed by adding DMSO and incubating at 100°C for 7 min and immediately transferred to ice water bath. Ligation was performed with pCp-Cy3 at 16 °C for 2 hr.

extract_protocol: RNA was prepared using the mirVana kit from Ambion as per manufacturer's protocol.

tag: age (years)

value: male

tag: tissue origin

value: OD:EB (right eye:eyeball)

tag: sample/tissue type

value: Formalin-fixed parraffin embedded tumor sections

tag: sample/tissue info

value: LTD:6mmx5mm; Spindle cells; monosomy 3


title: Uveal melanoma primary tissue 5 replicate

value: female

value: OS:EB (left eye:eyeball)

value: LTD:6mmx10mm; Mixed cell type; Liver metasized; monosomy 3


title: Uveal melanoma primary tissue 6

source_name: disomy 3 uveal melanoma tumor

value: LTD:16mmx10mm; Mixed cell type, cilico choroidal ,orbital invasion


title: Uveal melanoma primary tissue 5


title: Uveal melanoma primary tissue 4


title: Uveal melanoma primary tissue 6 replicate

value: LTD:16mmx10mm; Mixed cell type, cilico choroidal, orbital invasion;disomy 3


title: fine-00037: MD547038_T

source_name: Brain

tag: disease state

value: ASTROCYTOMA

tag: organism part

value: Brain

tag: tumor grading

value: Grade 3

tag: sample


title: WT Lung, biological replicate 2

value: BALB/c

tag: treatment

value: A/PR8/34-OVAII influenza

value: 7 days post infection


title: IL-2 deficient Lung, biological replicate 1

value: IL-2 deficient memory DO11.10 CD4 T cells were adoptively transferred to naïve BALB/c mice

value: Primed IL-2 deficient DO11.10 donor CD4 T cells (re-isolated from adoptive hosts)


title: fine-00037: HF1606_T

value: Grade 2


title: Uveal melanoma primary tissue 3

tag: gender

value: LTD:15mmx16mm; Mixed cell type,extrascleral; cilico-choroidal involvement, Liver- metasized; monosomy 3


title: Uveal melanoma primary tissue 2

value: OD:EB (right eye:eyeball)

value: Formalin-fixed parraffin embedded tumor sections

value: LTD:9.5mmx4mm; Mixed cell type, intrascleral and vortex veins invasion, partially pigmented, spindle cells;disomy 3


title: 9cRA

source_name: RAW264.7 cells treated with 9cRA only

value: 9cRA only


title: fine-00037: E10512_T

value: GBM


title: fine-00037: HF1489_T


title: Uveal melanoma primary tissue 3 replicate

value: female

value: OS:EB (left eye:eyeball)


title: fine-00037: E09956_T


title: Uveal melanoma primary tissue 1

value: LTD:15mmx6mm; Spindle cells,intrascleral; disomy 3


title: fine-00037: HF0327_T

value: OLIGODENDROGLIOMA


title: fine-00037: E10002_T

value: Grade 4


title: fine-00037: HF0505_T


title: fine-00037: E09167_T

value: UNKNOWN


title: fine-00037: E09804_T

value: Brain


title: fine-00037: HF1280_T

value: ASTROCYTOMA

value: Grade 3


title: 111809_2936725839_011

city: Cambridge

first: Jadwiga

last: Bienkowska

address: 45 Fayette Str Apt 3

institute: BiogenIdec

hyb_protocol: standard Affymetrix protcol

scan_protocol: HTAPS scanner was used

data_processing: Data was normalized using  gcrma using R package for each set separately (Controls and SLE were normalized as one set).

source_name: DMARD-IR

label_protocol: NuGEN Ovation

growth_protocol: Whole Blood samples in collected fom PAXgene tubes

extract_protocol: The RNA was extracted with Trizol reagent (Life Technologies) and cleaned up with RNA easy (Qiagen) according to the manufacturer’s protocols.

tag: tissue

value: whole blood

tag: time-point

value: baseline

tag: disease

value: Rheumatoid Arthiritis (DMARD-IR)


title: fine-00037: 03465304_T

value: Grade 2


title: fine-00037: HF1097_T


title: fine-00037: E10097_T


title: 120109_2680669640_013


title: 120309_3049578640_044


title: 111909_2726469540_049


title: fine-00037: HF0303_T


title: 120109_2608222840_079


title: fine-00037: E10162_T


title: fine-00037: E09847_T


title: fine-00037: HF0460_T


title: 120209_2931990540_006


title: fine-00037: HF0757_T


title: fine-00037: 03434766_T


title: 120809_2608289740_003


title: 120209_2680725640_060


title: fine-00037: HF0616_T


title: fine-00037: HF0180_T


title: 120309_3049577940_038


title: 120309_2933611740_001


title: 120109_2548307740_002


title: fine-00037: MD548457_T


title: 120209_2608239540_004


title: fine-00037: E10103_T


title: 112309_2608255740_039


title: fine-00037: E10012_T


title: 120309_2608154840_003


title: fine-00037: 03439543_T


title: fine-00037: HF0251_T


title: 111809_2881494739_017


title: fine-00037: 03513467_T


title: fine-00037: HF0670_T


title: fine-00037: E10029_T


title: 022410_2881493939_026


title: fine-00037: 01074569_T


title: 041310_2742534539_045


title: 120809_2985561540_071


title: 120809_2680689540_032


title: 120109_3097937740_007


title: 120809_2985561940_079


title: fine-00037: HF0982_T


title: fine-00037: E10001_T


title: fine-00037: HF0142_T


title: 111909_2726475640_004


title: 111809_2988451939_027


title: fine-00037: HF0526_T


title: 022410_2608221740_055


title: fine-00037: HF0627_T


title: fine-00037: 03468400_T


title: fine-00037: E50057_T


title: fine-00037: E09622_T


title: 120809_3013094540_048


title: fine-00037: E09624_T


title: fine-00037: E09989_T


title: fine-00037: E09846_T


title: fine-00037: E09262_T

value: MIXED


title: 111809_3009231439_072


title: 041310_2679466939_066


title: 120209_2993662840_071


title: fine-00037: E09296_T


title: fine-00037: E09644_T


title: 120809_2985562540_089


title: 112309_2932681840_011


title: 113009_2679457439_012


title: fine-00037: 03089254_T


title: 022410_2548298640_076


title: fine-00037: E10692_T


title: 120309_2608289540_078


title: fine-00037: E09842_T


title: 111909_2801948739_088


title: 120309_2608155640_009


title: fine-00037: E10227_T


title: 111809_3000329939_033


title: 113009_2648620639_023


title: fine-00037: E09978_T


title: 111809_3009230839_054


title: fine-00037: E09899_T


title: fine-00037: 03479212_T


title: 022410_2607505440_071


title: fine-00037: 03448110B_T


title: 120109_2483197640_051


title: fine-00037: E10285_T


title: 111909_2640087439_063


title: 120209_2931983540_068


title: fine-00037: E09966_T


title: 120309_2551353940_042


title: fine-00037: E09531_T


title: 111909_2980486639_081


title: fine-00037: E09615_T


title: fine-00037: HF1475_T


title: fine-00037: 03184579_T


title: fine-00037: HF1613_T


title: 120809_3055447940_026


title: 120309_2831598840_070


title: 022410_2831599540_056


title: 120809_2680695640_066


title: 113009_2940642640_085


title: fine-00037: E09935_T


title: 111909_2640086639_094


title: fine-00037: E09971_T


title: 113009_2548298940_072


title: fine-00037: HF0089_T


title: 111809_3000330539_043


title: 111809_2980486439_058


title: fine-00037: E10072_T


title: fine-00037: E10062_T


title: fine-00037: E10192_T


title: 022410_2742534639_080


title: fine-00037: E09657_T


title: 111809_2957789839_065


title: fine-00037: HF0654_T


title: fine-00037: E10362_T


title: fine-00037: E09440_T


title: fine-00037: E10287_T


title: 113009_2980486739_005


title: 120109_2643114940_053


title: 120809_2992998440_095


title: 120209_3049577640_050


title: fine-00037: E09858_T


title: fine-00037: HF0232_T


title: fine-00037: E09708_T


title: fine-00037: 03484270_T


title: fine-00037: E10184_T


title: 112309_2608273540_050


title: 120109_2608238940_083


title: fine-00037: 03450728_T


title: fine-00037: E10252C_NT


title: 120109_2483174940_089


title: 111809_3073183439_073


title: 120309_2608172640_014


title: 120209_3048914440_085


title: 022410_2569823640_021


title: 111809_2957789439_055


title: fine-00037: E10252_T


title: 120109_2931920940_065


title: 120809_2932700740_012


title: fine-00037: 03822538_2_T


title: 041310_2742512939_028


title: 113009_3097937640_077


title: fine-00037: 03822538_T


title: fine-00037: E10252B_T


title: fine-00037: E09774_T


title: fine-00037: HF0183_T


title: fine-00037: E10252C_T


title: fine-00037: MD552910_T


title: 041310_2944158740_034


title: 022410_2726476640_087


title: 113009_2932396740_081


title: fine-00037: E09791_T


title: 113009_2726720439_038


title: fine-00037: E10267_T


title: fine-00037: HF0639_T


title: fine-00037: E10203_T


title: 120109_2608238740_071


title: fine-00037: E10286_T


title: fine-00037: MD607216_T


title: 120809_2680688740_068


title: 111809_3050741539_074


title: 120809_2608289440_020


title: fine-00037: MD545226_T


title: 120209_2608154940_076


title: 113009_2726721439_028


title: 112309_2608272740_053


title: fine-00037: HF0171_T


title: fine-00037: E09513_T


title: 120109_2547442640_004


title: 022410_2726667939_050


title: fine-00037: E09489_T


title: 111909_2608323540_015


title: 120309_2608155740_017


title: fine-00037: 03497265_T


title: fine-00037: HF0442.5_T


title: fine-00037: HF1139_T


title: fine-00037: HF1502_T


title: 120809_2992997940_064


title: fine-00037: E10271_T


title: 120109_2954552640_049


title: 120109_2983673440_037


title: fine-00037: E09993_T


title: fine-00037: E09885_T


title: fine-00037: E09478_T


title: 113009_2607505540_059


title: 120209_2608171840_087


title: 113009_2726666939_053


title: 022410_2726476740_008


title: fine-00037: 03463522_T


title: 111909_2726468640_039


title: fine-00037: E09419_T


title: fine-00037: HF1167_T


title: fine-00037: E09928_T


title: 041310_2608256540_069


title: 041310_2608272440_007


title: 111809_2988451539_020


title: fine-00037: E09855_T


title: fine-00037: E09495_T


title: 120209_3011863740_052


title: fine-00037: E10172_T


title: 120109_2608255840_075


title: fine-00037: E09654_T


title: 113009_2986664439_009


title: 113009_2727965739_016


title: fine-00037: E09233_T


title: 120309_2993663440_012


title: fine-00037: MD607103_T


title: fine-00037: E09405_T


title: 120809_2680711540_074


title: 113009_2932389940_075


title: fine-00037: 03451592_T


title: fine-00037: HF1618_T


title: fine-00037: E10003_T


title: 120809_2680710740_093


title: fine-00037: HF1325_T


title: 113009_2607504740_058


title: fine-00037: E09955_T


title: 120109_2680677840_033


title: 120209_2995591740_032


title: fine-00037: E09331_T


title: fine-00037: E10470_T


title: fine-00037: E09756_T


title: 113009_2664958940_073


title: 120809_2992997740_036


title: fine-00037: E09647_T


title: 120109_2680670740_057


title: 120109_2680677740_041


title: 120209_2993662740_079


title: 120309_2933611840_015


title: fine-00037: 03476542_T


title: fine-00037: E10300_T


title: fine-00037: HF0138_T


title: fine-00037: E10008_T


title: fine-00037: 03477889_T


title: 111809_2936726839_031


title: 022410_2727964939_078


title: fine-00037: 03514945_T


title: 112309_2957889939_092


title: 120109_2608238840_085


title: 120809_2608323740_013


title: fine-00037: HF0252_T


title: fine-00037: E10011_T


title: 120809_2680704740_028


title: fine-00037: E09542_T


title: 120809_2985560940_076


title: fine-00037: HF0285_T


title: 112309_2679445739_003


title: 120109_2483185640_031


title: fine-00037: HF0844_T


title: 111809_2801949739_007


title: fine-00037: E09264_T


title: 022410_2680696540_068


title: fine-00037: E10292_T


title: fine-00037: E09690_T


title: fine-00037: E09649_T


title: 120109_2726106840_077


title: 113009_2607504840_063


title: fine-00037: E09894_T


title: 113009_2726667639_056


title: fine-00037: E09471_T


title: 041310_2608255640_087


title: fine-00037: MD608660_T


title: 111909_2640067939_053


title: 120809_2680688840_054


title: fine-00037: HF0790_T


title: 120209_2608154740_090


title: 120809_2608306740_001


title: fine-00037: E10514_T


title: fine-00037: HF1458_T


title: 111909_2726483640_026


title: fine-00037: 03513138_T


title: fine-00037: E10216_T


title: fine-00037: E09744_T


title: fine-00037: E10710_T


title: fine-00037: HF1319_T


title: fine-00037: HF0543_T


title: fine-00037: 88375506_T


title: 111809_2881493839_014


title: 120809_2985562740_081


title: 120109_2983673740_016


title: 120309_2551354740_019


title: 120209_3011863640_030


title: 120809_2680695840_060


title: 111809_3000329539_023


title: fine-00037: E10662_T


title: 120309_3027766440_094


title: 120809_2985561740_056


title: fine-00037: E10662B_T


title: fine-00037: 03466950_T


title: fine-00037: 03495697_T


title: 120109_2483185940_038


title: fine-00037: 03473405_T


title: fine-00037: E09408_T


title: 120209_2995591540_058


title: fine-00037: HF1538_T


title: fine-00037: E09698_T


title: fine-00037: HF0850_T


title: fine-00037: E10027_T


title: 111909_3031904940_011


title: fine-00037: MD548092_T


title: 111809_3009230739_078


title: 120809_3070688940_030


title: 111809_3000329439_009


title: fine-00037: HF1409_T


title: fine-00037: HF1286_T


title: 113009_2547441940_094


title: fine-00037: HF1077_T


title: fine-00037: HF0088_T


title: fine-00037: HF0024_T


title: fine-00037: HF0891_T


title: fine-00037: E09238_T


title: fine-00037: HF1090_T


title: fine-00037: E09494_T


title: fine-00037: E09893_T


title: fine-00037: E10030_T


title: fine-00037: E09848_T


title: fine-00037: E09923_T


title: fine-00037: HF1156_T


title: fine-00037: HF1269_T


title: fine-00037: E10249_T


title: fine-00037: E09645_T


title: fine-00037: NT1_T


title: 022410_2831598940_019


title: 120209_3112324940_048


title: fine-00037: 03433293_T


title: 120209_3086029840_056


title: fine-00037: 03437595_T


title: 041310_2932389840_092


title: 120209_2933612440_074


title: fine-00037: HF0450_T


title: 120109_2983673940_052


title: 120809_2680688940_040


title: 041310_2947128640_073


title: fine-00037: E09890_T


title: 041310_3043090839_048


title: 111809_3073182539_056


title: 111809_2881494639_041


title: fine-00037: E10016_T


title: 120809_2680695740_024


title: 022410_2679458539_013


title: 120309_2608305940_082


title: 120309_2551354640_055


title: 120109_2726105440_091


title: 120809_2680696840_038


title: 111909_2947128840_010


title: 120209_3086030540_034


title: 041310_2608262840_068


title: fine-00037: E09819_T


title: 120209_2933611940_088


title: 041310_2547604740_017


title: fine-00037: HF0897_T


title: 120809_2608305840_014


title: 111909_2726482940_009


title: 111809_2988451739_008


title: fine-00037: HF0022_T


title: 022410_2648619739_015


title: fine-00037: HF1191_T


title: 120309_2608306640_074


title: fine-00037: E10182_T


title: fine-00037: E09996_T


title: 111909_2947128940_027


title: 111909_2648620539_070


title: 111909_2789731839_065


title: 111909_2726483840_036


title: fine-00037: NT7_T


title: 120209_2726106540_010


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title: fine-00037: E10191_T


title: fine-00037: E10306_T


title: 120309_2569832740_061


title: 111909_2547442940_052


title: fine-00037: HF1708_T


title: fine-00037: HF1338_T


title: fine-00037: HF0599_T


title: fine-00037: HF1381_T


title: 113009_2932388840_078


title: 111809_2801948839_019


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title: fine-00037: E10044_T


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title: fine-00037: HF1581_T


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title: 120109_2608204940_095


title: fine-00037: 03421536_T

value: UNCLASSIFIED


title: 120309_2569833640_025


title: 113009_2679457839_025


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title: fine-00037: HF1316_T


title: 120109_2680670640_021


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title: 120809_3013093940_027


title: fine-00037: HF0533_T


title: fine-00037: HF1493_T


title: 111909_2801949439_068


title: 022410_2957790539_030


title: 120209_3086029640_042


title: fine-00037: HF0087_T


title: fine-00037: HF0151_T


title: 041310_2988560739_090


title: 120109_2680669940_035


title: fine-00037: HF0954.2_T


title: fine-00037: E10076_T


title: fine-00037: 03460111_T


title: 113009_2726719839_049


title: 041310_2789732839_077


title: fine-00037: 03441358_T


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title: 120309_2608289840_084


title: 120309_3104359840_058


title: 120209_2931982840_082


title: fine-00037: E09595_T


title: fine-00037: HF0434_T


title: 041310_3050741739_074


title: 120209_2784027540_070


title: fine-00037: E09964_T


title: fine-00037: E09448_T


title: fine-00037: HF1517_T


title: fine-00037: E09369_T


title: 111909_2679446439_085


title: fine-00037: E10037_T


title: 120109_2608205840_073


title: 041310_2608255940_025


title: fine-00037: HF1292_T


title: 120809_2680703940_042


title: 120109_2608205540_067


title: 120109_2483179840_039


title: 120209_2680725740_038


title: fine-00037: HF1492_T


title: 120209_2680725540_054


title: fine-00037: E10595_T


title: 120309_2784027440_053


title: 111809_2881493739_044


title: fine-00037: E10265_T


title: fine-00037: E09755_T


title: 111909_3073182839_001


title: 120309_2995591640_052


title: fine-00037: 03471616_T


title: 022410_2680704540_047


title: 111909_2608322640_051


title: fine-00037: HF0408_T


title: fine-00037: E10305_T


title: 022410_2640067439_025


title: 120809_2680696640_046


title: fine-00037: E09917_T


title: 120209_3049578540_036


title: fine-00037: HF1344_T


title: fine-00037: HF1702_T


title: fine-00037: HF0184_T


title: fine-00037: E10144_T


title: 120309_2784027940_039


title: fine-00037: 03421899_T


title: 022410_2569824540_062


title: fine-00037: HF1000_T


title: 113009_2679457539_010


title: 120109_2483197740_015


title: fine-00037: HF1442_T


title: fine-00037: HF0606_T


title: 113009_2726668439_048


title: fine-00037: 03525342_T


title: fine-00037: E09832_T


title: fine-00037: HF1494_T


title: 111809_3073183639_075


title: fine-00037: HF1588_T


title: fine-00037: E09515_T


title: 111809_2936726739_005


title: 112309_2964236939_058


title: 120809_2608288940_018


title: fine-00037: E09214_T


title: fine-00037: HF1640_T


title: fine-00037: HF0244_T


title: 120109_2680678440_027


title: 111909_2726561839_089


title: 111909_2726475840_016


title: fine-00037: HF0031_T


title: 120809_2680711640_082


title: 041310_2962121739_060


title: fine-00037: E10615_T


title: 111809_2936726539_034


title: fine-00037: E10312_T


title: 022410_2962121939_059


title: fine-00037: HF0855_T


title: 041310_2608256440_002


title: 022410_2726482840_061


title: 022410_2680725840_018


title: fine-00037: E10248_T


title: 022410_2957789539_029


title: fine-00037: HF1568_T


title: fine-00037: HF0510_T


title: fine-00037: HF1382_T


title: 120109_2608239440_063


title: fine-00037: E10290_T


title: 120209_3011863840_022


title: fine-00037: E10158_T


title: 120109_2983673540_023


title: fine-00037: E10476_T


title: fine-00037: HF1540_T


title: fine-00037: HF0726_T


title: 120109_2680677640_047


title: 120209_2608171640_073


title: 041310_2932396840_023


title: 120309_2608289640_086


title: 022410_2679457639_012


title: fine-00037: E09535_T


title: fine-00037: E09920_T


title: fine-00037: HF0802_T


title: fine-00037: E10278_T


title: fine-00037: E09137_T


title: 022410_2742513439_034


title: 111809_3009231739_057


title: fine-00037: E09623_T


title: 111909_2640067639_058


title: 120809_2992998740_073


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title: 113009_2726667839_042


title: 041310_3009229739_013


title: fine-00037: E09770_T


title: fine-00037: E09137B_T


title: 113009_2940641840_068


title: fine-00037: E09860_T


title: fine-00037: E09810_T


title: 120209_2680718740_026


title: 041310_3050741439_075


title: 041310_2679446539_031


title: 120109_2608239740_069


title: fine-00037: E10105_T


title: fine-00037: E09704_T


title: 120809_2932018440_016


title: fine-00037: E10023_T


title: 120309_2783093840_022


title: fine-00037: E10551_T


title: fine-00037: HF1235_T


title: fine-00037: E09393_T


title: 111909_2608322940_018


title: fine-00037: HF1469_T


title: fine-00037: E10690_T


title: 112309_3026354739_035


title: fine-00037: E09629_T


title: 120809_3034936840_084


title: 022410_2932018840_067


title: 022410_2640086539_032


title: 022410_2965901739_043


title: fine-00037: E09511_T


title: fine-00037: E10196_T


title: fine-00037: HF0778_T


title: 120809_2680710840_087


title: fine-00037: 03418160_T


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title: 120809_2985561440_022


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title: 120209_2680726440_024


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title: 120209_2483180540_008


title: fine-00037: HF1318_T


title: fine-00037: HF1490_T


title: fine-00037: 00641238_T


title: fine-00037: 03272709_T


title: 041310_2679467839_067


title: 120309_2932681940_073


title: fine-00037: E09601_T


title: fine-00037: E09786_T


title: fine-00037: HF0108_T


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title: 111909_2726561739_061


title: fine-00037: HF1589_T


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title: 041310_2679467939_014


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title: 113009_2932389740_084


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title: 111809_2881494839_069


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title: 120209_2608155540_084


title: fine-00037: E09664_T


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title: 120109_3021164440_001


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title: fine-00037: MD570013_T


title: fine-00037: E09449_T


title: fine-00037: 03474525_T


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title: 120109_2643114740_017


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title: 041310_3057360940_029


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title: 112309_2932681540_014


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title: 120809_2992998540_058


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title: 120209_2608172540_065


title: fine-00037: MD554082_T


title: 113009_2726720939_015


title: 113009_2962122439_034


title: fine-00037: E10138_T


title: fine-00037: HF0963_T


title: fine-00037: E09982_T


title: 111909_2742513639_060


title: 111909_2947128740_025


title: fine-00037: E09997_T


title: fine-00037: HF1407_T


title: fine-00037: E09829_T


title: fine-00037: E09610_T


title: fine-00037: HF0512_T


title: 022410_3026353939_070


title: 112309_2608272940_036


title: 022410_2742535439_009


title: 041310_2965901939_061


title: 111909_2726720639_092


title: 041310_2726483540_041


title: 111809_3009229639_080


title: 022410_2551353740_064


title: fine-00037: E09938_T


title: fine-00037: HF1150_T


title: 120309_2551353840_028


title: fine-00037: E09930_T


title: 022410_2932397440_017


title: 120309_2831598640_092


title: 022410_2796710539_048


title: 022410_3109028739_027


title: 112309_2957890639_065


title: 022410_3009231539_028


title: 041310_3049577740_010


title: 073109_3038836838_030

source_name: TNF-IR

value: Rheumatoid Arthiritis (TNF-IR)


title: 112309_2988559939_082


title: 073109_1320953638_075


title: 112309_2679468439_018


title: 041310_2957890839_043


title: 041310_2986664539_044


title: 073109_3052754838_159


title: 073109_3156375838_090


title: 073109_3131866538_143


title: 032409_2566403638_012


title: 041310_2569832640_009


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title: 031709_2451661638_064


title: 032409_3017471538_058


title: 032409_2657979838_007


title: 073109_3051668838_054


title: 031709_2494533839_047


title: 073109_2981880739_019


title: 073109_3101212538_043


title: EXP-608: Blood_TCGA-AB-2946

source_name: Primary Blood Derived Cancer

tag: age

tag: french-american-british classification

tag: Sex

value: MALE

value: Blood

tag: cytogenetic

value: [Not Available]

value: BONE MARROW


title: 073109_3075409538_069


title: 032409_2402897738_050


title: 031709_2402895838_070


title: 073109_3110731638_070


title: 031709_2494533739_033


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title: 032409_2424676738_042


title: 073109_3188582838_047


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title: 031709_2690340438_066


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title: 031709_2595325638_075


title: 073109_2989671638_129


title: 031709_2880642638_021


title: 032409_2553006738_020


title: 031709_2475991738_052


title: 031709_2451661838_079


title: 073109_3187300639_022


title: 073109_2494545740_066


title: 073109_3075409738_095


title: 073109_2989671738_034


title: 031709_2602305538_084


title: 073109_3131866738_099


title: 073109_1284178538_078


title: 032409_2490099638_034


title: 032409_2490098938_049


title: 073109_2980627738_131


title: 073109_2402914739_063


title: 073109_2989671438_032


title: 073109_3064522538_145


title: 031709_2602305638_074


title: 032409_2989981638_060


title: 032409_2657980538_032


title: 031709_2657979938_053


title: 031709_2566296638_063


title: 073109_3042695838_124


title: 073109_3064514938_148


title: 073109_2994400538_110


title: 073109_2494549639_023


title: 031709_2980627538_039


title: 073109_3038836638_118


title: 073109_3122640939_109


title: 073109_3044467538_038


title: 073109_3075413638_152


title: 031709_2690339838_056


title: 073109_2602305938_136


title: EXP-608: Blood_TCGA-AB-2918

value: FEMALE

value: Trisomy 8


title: EXP-608: Blood_TCGA-AB-2922

value: M0 Undifferentiated

value: Normal


title: 073109_2962673938_012


title: 073109_3038055938_082


title: 073109_3044657838_150


title: 031709_2424672738_041


title: NOD_NAIVE_4

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

description: NOD  NAIVE replicate  4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were log2 transformed and normalised using quantile normalisation in R

source_name: NOD  NAIVE replicate  4

label_protocol: Biotinylated cRNA were prepared with Illumina  kit for Illumina arrays

extract_protocol: RNA was extracted

treatment_protocol: Total RNA was extracted from naïve and injured DRGs (6 DRGs per sample, 3 mice) across 9 strains and assessed with the Agilent Bioanalyzer (Agilent Technologies). Four biologically distinct replicates were run per sample for a total of 72 arrays.

tag: strain

value: NOD

value: NAIVE

value: dorsal root ganglion


title: 073109_3051669438_051

value: whole blood

value: baseline


title: EXP-608: Blood_TCGA-AB-2944


title: 073109_3110731738_092


title: 073109_2537724740_065


title: 073109_3148345738_161


title: C3H_AX5D_1

description: C3H  AX5D  replicate 1

source_name: C3H  AX5D  replicate 1


title: 032409_2402914738_038


title: 032409_2402901538_021


title: AJ_NAIVE_1

description: AJ  NAIVE  replicate 1

source_name: AJ  NAIVE  replicate 1

value: AJ


title: 031709_2676148839_005


title: 073109_1313035938_026


title: 031709_2691913438_030


title: 073109_3044467738_041


title: 032409_2566295738_028


title: 032409_2402901438_041


title: DBA_NAIVE_4

description: DBA  NAIVE replicate  4

source_name: DBA  NAIVE replicate  4

value: DBA


title: WSB_NAIVE_1

description: WSB  NAIVE replicate  1

source_name: WSB  NAIVE replicate  1

value: WSB


title: 032409_2447317738_008

value: Rheumatoid Arthiritis (TNF-IR)


title: WSB_NAIVE_2

description: WSB  NAIVE  replicate 2

source_name: WSB  NAIVE  replicate 2


title: 129_AX5D_2

description: 129  AX5D  replicate 2

source_name: 129  AX5D  replicate 2


title: 073109_2611732739_024


title: 129_NAIVE_4

description: 129  NAIVE replicate  4

source_name: 129  NAIVE replicate  4


title: 073109_3075413738_102


title: AJ_AX5D_4

description: AJ  AX5D  replicate 4

source_name: AJ  AX5D  replicate 4


title: 031709_2676148639_018


title: 031709_2537724739_009


title: NOD_AX5D_3

description: NOD  AX5D  replicate 3

source_name: NOD  AX5D  replicate 3


title: AJ_AX5D_2

description: AJ  AX5D replicate  2

source_name: AJ  AX5D replicate  2


title: 031709_2402909038_050


title: C3H_NAIVE_1

description: C3H  NAIVE replicate  1

source_name: C3H  NAIVE replicate  1


title: CAST_AX5D_2

description: CAST  AX5D replicate  2

source_name: CAST  AX5D replicate  2

value: CAST


title: C57_AX5D_2

description: C57  AX5D replicate  2

source_name: C57  AX5D replicate  2


title: C3H_AX5D_4

description: C3H  AX5D replicate  4

source_name: C3H  AX5D replicate  4


title: NOD_NAIVE_1

description: NOD  NAIVE  replicate 1

source_name: NOD  NAIVE  replicate 1


title: NZO_NAIVE_2

description: NZO  NAIVE replicate  2

source_name: NZO  NAIVE replicate  2

value: NZO


title: CAST_AX5D_3

description: CAST  AX5D replicate  3

source_name: CAST  AX5D replicate  3


title: DBA_AX5D_4

description: DBA  AX5D  replicate 4

source_name: DBA  AX5D  replicate 4


title: 031709_2789702938_086

source_name: TNF-IR


title: 073109_2962674638_057


title: 031709_2469757638_089


title: AJ_NAIVE_3

description: AJ  NAIVE  replicate 3

source_name: AJ  NAIVE  replicate 3


title: C3H_NAIVE_2

description: C3H  NAIVE  replicate 2

source_name: C3H  NAIVE  replicate 2


title: AJ_NAIVE_2

description: AJ  NAIVE  replicate 2

source_name: AJ  NAIVE  replicate 2


title: C57_NAIVE_4

description: C57  NAIVE replicate  4

source_name: C57  NAIVE replicate  4


title: 031709_2690339938_051


title: NZO_NAIVE_1

description: NZO  NAIVE replicate  1

source_name: NZO  NAIVE replicate  1


title: CAST_NAIVE_1

description: CAST  NAIVE  replicate 1

source_name: CAST  NAIVE  replicate 1


title: DBA_AX5D_1

description: DBA  AX5D  replicate 1

source_name: DBA  AX5D  replicate 1


title: WSB_AX5D_2

description: WSB  AX5D  replicate 2

source_name: WSB  AX5D  replicate 2


title: 031709_2624114638_025


title: 032409_2537724639_064


title: 031709_2424673538_065


title: NOD_AX5D_4

description: NOD  AX5D  replicate 4

source_name: NOD  AX5D  replicate 4


title: 073109_3038723538_006


title: 129_NAIVE_1

description: 129  NAIVE  replicate 1

source_name: 129  NAIVE  replicate 1


title: NZO_AX5D_4

description: NZO  AX5D  replicate 4

source_name: NZO  AX5D  replicate 4


title: 129_AX5D_4

description: 129  AX5D  replicate 4

source_name: 129  AX5D  replicate 4


title: WSB_AX5D_1

description: WSB  AX5D  replicate 1

source_name: WSB  AX5D  replicate 1


title: C57_AX5D_3

description: C57  AX5D  replicate 3

source_name: C57  AX5D  replicate 3


title: NZO_NAIVE_4

description: NZO  NAIVE  replicate 4

source_name: NZO  NAIVE  replicate 4


title: 073109_3022203538_001


title: CAST_NAIVE_3

description: CAST  NAIVE  replicate 3

source_name: CAST  NAIVE  replicate 3


title: CAST_NAIVE_2

description: CAST  NAIVE  replicate 2

source_name: CAST  NAIVE  replicate 2


title: 031709_2475992538_015

source_name: TNF-IR


title: CAST_NAIVE_4

description: CAST  NAIVE replicate  4

source_name: CAST  NAIVE replicate  4


title: C3H_NAIVE_4

description: C3H  NAIVE  replicate 4

source_name: C3H  NAIVE  replicate 4


title: C3H_AX5D_2

description: C3H  AX5D  replicate 2

source_name: C3H  AX5D  replicate 2


title: DBA_NAIVE_1

description: DBA  NAIVE  replicate 1

source_name: DBA  NAIVE  replicate 1


title: C57_AX5D_4

description: C57  AX5D  replicate 4

source_name: C57  AX5D  replicate 4


title: DBA_AX5D_2

description: DBA  AX5D  replicate 2

source_name: DBA  AX5D  replicate 2


title: WSB_AX5D_3

description: WSB  AX5D replicate  3

source_name: WSB  AX5D replicate  3


title: NZO_AX5D_3

description: NZO  AX5D  replicate 3

source_name: NZO  AX5D  replicate 3


title: 129_NAIVE_3

description: 129  NAIVE  replicate 3

source_name: 129  NAIVE  replicate 3


title: 031709_2649327938_061


title: C3H_NAIVE_3

description: C3H  NAIVE  replicate 3

source_name: C3H  NAIVE  replicate 3


title: 031709_2624114538_068


title: 032409_2657980638_029


title: NOD_NAIVE_2

description: NOD  NAIVE  replicate 2

source_name: NOD  NAIVE  replicate 2


title: 073109_3044658538_087


title: WSB_AX5D_4

description: WSB  AX5D  replicate 4

source_name: WSB  AX5D  replicate 4


title: DBA_AX5D_3

description: DBA  AX5D  replicate 3

source_name: DBA  AX5D  replicate 3


title: 073109_2962674538_009


title: 031709_2566403738_069


title: 032409_2717721438_062


title: 032409_2402892039_010


title: NZO_AX5D_2

description: NZO  AX5D  replicate 2

source_name: NZO  AX5D  replicate 2


title: 129_AX5D_3

description: 129  AX5D  replicate 3

source_name: 129  AX5D  replicate 3


title: 032409_2475991638_045


title: 031709_2789702838_011


title: CAST_AX5D_1

description: CAST  AX5D  replicate 1

source_name: CAST  AX5D  replicate 1


title: WSB_NAIVE_4

description: WSB  NAIVE  replicate 4

source_name: WSB  NAIVE  replicate 4


title: AJ_AX5D_3

description: AJ  AX5D  replicate 3

source_name: AJ  AX5D  replicate 3


title: C57_NAIVE_1

description: C57  NAIVE  replicate 1

source_name: C57  NAIVE  replicate 1


title: NOD_AX5D_2

description: NOD  AX5D  replicate 2

source_name: NOD  AX5D  replicate 2


title: 129_AX5D_1

description: 129  AX5D  replicate 1

source_name: 129  AX5D  replicate 1


title: DBA_NAIVE_2

description: DBA  NAIVE  replicate 2

source_name: DBA  NAIVE  replicate 2


title: EZ2-2_INPUT_EZ8s2_31C

city: Boston

first: Hun-Goo

last: Lee

address: 185 Cambridge St

department: Molecular Biology

institute: Mass General Hospital

description: input DNA

hyb_protocol: Hybridization of labeled DNA was done in 200ul of solution containing 1xMES, 3M TMAC, 40pM oligo B2, 100u/ml sonicated salmon sperm DNA, 0.02% Triton X100 for 18 hours at 45C with 45rpm rotation. Staining and washing was done using EukGE-WS2v4 protocol

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing:
The data was median scaled to 100 and the ratio of average ChIP to average Input was computed and smoothed by taking trimmed mean over sliding 675bp window. All operations were performed with TiMAT T2 v1.2.0
The .sgr files were produced with TiMAT T2 v1.2.0 and contain average ChIP/ average Input values smoothed by taking trimmed mean over sliding 675bp window. The coordinates of produced .sgr files were converted to UCSC 2006 version (dm3) by using liftover program from UCSC.

organism: Drosophila melanogaster

source_name: EZ2-2 at 31°C, input DNA from EZ8s2-31C chromatin

label_protocol: 2ug of amplified ChIP product was fragmented with DNAse I and labeled with TdT by biotin-11-ddATP incorporation

growth_protocol: EZ2-2 cells were grown in Schneider's medium (Gibco) supplemented with 10% FBS, 100U/ml of Penicillin G, 100ug/ml of Streptomycin sulfate and 292 ug/ml of L-glutamine.

extract_protocol: Live cells were crosslinked with 1.8% formaldehyde for 10 min at 25°C and soluble chromatin prepared as described in Schwartz et al., 2006. ChIP and sample amplification was done as described in Schwartz et al., 2006

treatment_protocol: EZ2-2 cells were grown at 25°C or 31°C for 12 days.

value: grown at 31°C for 12 days

tag: cell line

value: EZ2-2 ; E(z) temperature-sensitive cell line

tag: antibody


title: EZ2-2_INPUT_EZ8s2_25C

description: input DNA

source_name: EZ2-2 at 25°C, input DNA from EZ8s2-25C chromatin

value: grown at 25°C


title: NOD_NAIVE_3

description: NOD  NAIVE  replicate 3

source_name: NOD  NAIVE  replicate 3


title: NZO_NAIVE_3

description: NZO  NAIVE  replicate 3

source_name: NZO  NAIVE  replicate 3


title: 031709_2494553739_035

source_name: TNF-IR


title: 032409_2424676838_037


title: 129_NAIVE_2

description: 129  NAIVE  replicate 2

source_name: 129  NAIVE  replicate 2


title: 032409_2402892038_031


title: EZ2-2_INPUT_EZ8s1_31C

description: input DNA

source_name: EZ2-2 at 31°C, input DNA from EZ8s1-31C chromatin


title: EZ2-2_H3K4me1_31C

description: H3K4me1 ChIP with EZ2-2 cells from non-permissive temperature

source_name: EZ2-2 at 31°C, anti-H3K4me1 ChIP

value: H3K4me1 (Abcam, ab8895)


title: DBA_NAIVE_3

description: DBA  NAIVE  replicate 3

source_name: DBA  NAIVE  replicate 3


title: C57_NAIVE_2

description: C57  NAIVE  replicate 2

source_name: C57  NAIVE  replicate 2


title: C57_AX5D_1

description: C57  AX5D  replicate 1

source_name: C57  AX5D  replicate 1


title: 032409_2475991838_043


title: EZ2-2_H3K4me1_25C

description: H3K4me1 ChIP with EZ2-2 cells from permissive temperature

source_name: EZ2-2 at 25°C, anti-H3K4me1 ChIP


title: NZO_AX5D_1

description: NZO  AX5D  replicate 1

source_name: NZO  AX5D  replicate 1


title: CAST_AX5D_4

description: CAST  AX5D  replicate 4

source_name: CAST  AX5D  replicate 4


title: 071310_164130813_021

source_name: SLE

value: SLE (Systemic LUPUS Erythomatosus)


title: 071310_166593733_004


title: 032409_2690339638_039


title: C57_NAIVE_3

description: C57  NAIVE  replicate 3

source_name: C57  NAIVE  replicate 3


title: C3H_AX5D_3

description: C3H  AX5D  replicate 3

source_name: C3H  AX5D  replicate 3


title: EZ2-2_H3K27ac_25C

description: H3K27ac ChIP with EZ2-2 cells from permissive temperature

source_name: EZ2-2 at 25°C, anti-H3K27ac ChIP

value: H3K27ac (Abcam, ab4729)


title: NOD_AX5D_1

description: NOD  AX5D  replicate 1

source_name: NOD  AX5D  replicate 1

value: NOD


title: WSB_NAIVE_3

description: WSB  NAIVE  replicate 3

source_name: WSB  NAIVE  replicate 3

value: NAIVE


title: 071310_164130543_043


title: EZ2-2_H3K27me3_25C

description: H3K27me3 ChIP with EZ2-2 cells from permissive temperature

source_name: EZ2-2 at 25°C, anti-H3K27me3 ChIP

value: H3K27me3 (Abcam, ab6002)


title: 071910_166590503_026

value: whole blood


title: Sg4_INPUT_51c

description: input DNA

data_processing:
The data was median scaled to 100 and the ratio of average ChIP to average Input was computed and smoothed by taking trimmed mean over sliding 675bp window. All operations were performed with TiMAT v2.8.3.
The .sgr files were produced with TiMAT v2.8.3 and contain average ChIP/ average Input values smoothed by taking trimmed mean over sliding 675bp window. The coordinates of produced .sgr files were converted to UCSC 2006 version (dm3) by using liftover program from UCSC.

source_name: Sg4, input DNA from 51c chromatin

label_protocol: 2ug of amplified ChIP product was fragmented with DNAse I  and labeled with TdT by biotin-11-ddATP incorporation

growth_protocol: Sg4 cells were grown to a density of 5x10^6 cells/ml in Schneider's medium (Gibco) supplemented with 10% FBS, 100U/ml of Penicillin G, 100ug/ml of Streptomycin sulfate and 292 ug/ml of L-glutamine.

treatment_protocol: Sg4 cells were grown at 25°C. No treatment.

tag: chip antibody


title: EZ2-2_INPUT_EZ8s1_25C

description: input DNA

source_name: EZ2-2 at 25°C, input DNA from EZ8s1-25C chromatin


title: EZ2-2_H3K27me3_31C

description: H3K27me3 ChIP with EZ2-2 cells from non-permissive temperature

source_name: EZ2-2 at 31°C, anti-H3K27me3 ChIP


title: 071310_164131323_019

value: baseline


title: Sg4_INPUT_16c

description: input DNA

source_name: Sg4, input DNA from 16c chromatin


title: Sg4_UTX

description:
dUTX ChIP
Sg4_UTX_exp1
Sg4_UTX_exp2

source_name: Sg4, anti-UTX ChIP

value: dUTX (Pirrotta Lab; affinity purified)


title: Sg4_H3K27me2

description:
H3K27me2 ChIP
Sg4_H3K27me2_exp1
Sg4_H3K27me2_exp2

source_name: Sg4, anti-H3K27me2 (T. Jenuwein Lab) ChIP

value: H3K27me2 (from T. Jenuwein Lab)


title: EZ2-2_H3K27ac_31C

description: H3K27ac ChIP with EZ2-2 cells from non-permissive temperature

source_name: EZ2-2 at 31°C, anti-H3K27ac ChIP


title: Sg4_H3

description:
H3 ChIP
Sg4_H3_exp1
Sg4_H3_exp2

source_name: Sg4, anti-H3 ChIP


title: Sg4_INPUT_52c

description: input DNA

source_name: Sg4, input DNA from 52c chromatin


title: Sg4_INPUT_24c

description: input DNA

source_name: Sg4, input DNA from 24c chromatin


title: Sg4_INPUT_23c

description: input DNA

source_name: Sg4, input DNA from 23c chromatin


title: EXP-620: TCGA-F4-6805-01A-11D-1837-05

source_name: Primary solid tumor

tag: clinical m staging

tag: colon polyps history

value: NO

tag: pathologic t staging

tag: disease staging

value: Stage IIA

tag: pathologic n staging

value: FEMALE

value: Colon

tag: disease state

value: Colon Adenocarcinoma

value: COLON


title: EXP-620: TCGA-G4-6628-01A-11D-1837-05

value: Stage I

value: MALE

tag: organism part

tag: sample


title: EXP-620: TCGA-AZ-6606-01A-11D-1837-05

value: [Not Available]

value: Stage IV


title: EXP-620: TCGA-F4-6704-01A-11D-1837-05

value: MX

value: Stage IIIC

value: Colon Mucinous Adenocarcinoma


title: EXP-620: TCGA-F4-6806-01A-11D-1837-05


title: EXP-620: TCGA-F4-6807-01A-11D-1837-05

value: Stage IIIA


title: EXP-620: TCGA-CM-6679-01A-11D-1837-05


title: EXP-620: TCGA-CA-6717-01A-11D-1837-05

value: Stage II


title: EXP-620: TCGA-A6-5664-01A-21D-1837-05

value: YES


title: EXP-620: TCGA-CA-6719-01A-11D-1837-05


title: EXP-620: TCGA-AZ-4323-01A-21D-1837-05


title: EXP-620: TCGA-AA-3496-01A-21D-1837-05


title: EXP-620: TCGA-CK-6746-01A-11D-1837-05

value: Stage IIC


title: EXP-620: TCGA-AZ-6608-01A-11D-1837-05


title: EXP-620: TCGA-DM-A1HB-01A-22D-A17Z-05

value: NOT SPECIFIED


title: EXP-620: TCGA-CK-6748-01A-11D-1837-05


title: EXP-620: TCGA-F4-6809-01A-11D-1837-05

value: Stage IVA


title: EXP-620: TCGA-AZ-6607-01A-11D-1837-05


title: EXP-620: TCGA-A6-5656-01A-21D-1837-05


title: 071910_166593933_057

source_name: SLE

tag: tissue

value: whole blood

tag: time-point

value: baseline

tag: disease

value: SLE (Systemic LUPUS Erythomatosus)


title: 071910_166590333_047


title: 072010_162824823_048


title: 071310_166477923_092


title: 072010_166479533_155


title: 071910_166593033_146


title: 071310_164130423_015


title: 071310_166590113_026


title: EXP-620: TCGA-07-0227-20A-01D-1837-05

source_name: Control Analyte

tag: age

tag: Sex


title: EXP-620: TCGA-CM-6674-01A-11D-1837-05

value: NO

value: Stage IIA

value: Colon

value: Colon Adenocarcinoma

value: COLON


title: EXP-620: TCGA-F4-6703-01A-11D-1837-05

value: MALE


title: EXP-620: TCGA-CA-6715-01A-21D-1837-05

value: [Not Available]

value: Stage III


title: EXP-620: TCGA-CM-6677-01A-11D-1837-05

value: FEMALE


title: EXP-620: TCGA-CA-5254-01A-21D-1837-05

value: Stage II


title: EXP-620: TCGA-A6-6654-01A-21D-1837-05

value: YES

value: Stage IIIB


title: 071310_166594123_017


title: 071310_164129733_055


title: EXP-620: TCGA-CM-6678-01A-11D-1837-05


title: EXP-620: TCGA-CM-6680-01A-11D-1837-05


title: EXP-620: TCGA-AA-3511-01A-21D-1837-05


title: EXP-620: TCGA-AZ-6605-01A-11D-1837-05


title: EXP-620: TCGA-CK-6751-01A-11D-1837-05

value: MX

value: Stage I

value: Colon Mucinous Adenocarcinoma


title: EXP-620: TCGA-CM-6675-01A-11D-1837-05

value: Stage IVB


title: EXP-620: TCGA-AZ-4616-01A-21D-1837-05

value: Stage IV


title: EXP-620: TCGA-CA-6716-01A-11D-1837-05


title: EXP-620: TCGA-AD-6548-01A-11D-1837-05


title: EXP-620: TCGA-AA-3489-01A-21D-1837-05

value: NO


title: EXP-620: TCGA-G4-6309-01A-21D-1837-05


title: EXP-620: TCGA-AZ-6603-01A-11D-1837-05


title: EXP-620: TCGA-CM-4751-01A-02D-1837-05


title: EXP-620: TCGA-F4-6808-01A-11D-1837-05


title: EXP-620: TCGA-A6-6780-01A-11D-1837-05

value: Stage IIA


title: EXP-620: TCGA-A6-6782-01A-11D-1837-05

value: Stage IIB

value: Colon


title: EXP-620: TCGA-A6-6651-01A-21D-1837-05

value: Colon Adenocarcinoma

value: COLON


title: EXP-620: TCGA-CM-6676-01A-11D-1837-05

value: MALE


title: EXP-620: TCGA-CK-6747-01A-11D-1837-05

value: [Not Available]


title: EXP-620: TCGA-CM-5863-01A-21D-1837-05

value: FEMALE


title: 072010_166479233_128

value: whole blood

value: baseline

value: SLE (Systemic LUPUS Erythomatosus)


title: 072010_166594643_034


title: EXP-620: TCGA-CA-6718-01A-11D-1837-05

value: Stage II


title: EXP-620: TCGA-CM-6165-01A-11D-1651-05


title: EXP-620: TCGA-CM-6167-01A-11D-1651-05

value: Stage IIIC


title: 071310_162824813_077


title: EXP-620: TCGA-CA-5255-01A-11D-1837-05


title: EXP-620: TCGA-CM-6168-01A-11D-1651-05


title: 072010_162824833_123


title: EXP-620: TCGA-D5-5538-01A-01D-1651-05

value: Stage IIIB


title: 071410_166590053_079


title: EXP-620: TCGA-CM-6163-01A-11D-1651-05

value: Stage I


title: 072010_164131443_130


title: EXP-620: TCGA-CM-6162-01A-11D-1651-05

value: Colon Mucinous Adenocarcinoma


title: EXP-620: TCGA-CK-4948-01B-11D-1651-05

value: Stage IIIA


title: EXP-620: TCGA-CM-5862-01A-01D-1651-05

value: NO

value: Stage IVA


title: 071910_166594043_117


title: EXP-620: TCGA-CM-5864-01A-01D-1651-05

value: Colon


title: EXP-620: TCGA-CM-6164-01A-11D-1651-05

value: Stage IIA

value: Colon Adenocarcinoma


title: EXP-620: TCGA-CM-6169-01A-11D-1651-05

value: MALE

value: COLON


title: EXP-608: Blood_TCGA-AB-2931

source_name: Primary Blood Derived Cancer

tag: french-american-british classification

value: Blood

tag: cytogenetic

value: [Not Available]

value: BONE MARROW


title: EXP-620: TCGA-CA-5797-01A-01D-1651-05


title: EXP-620: TCGA-A6-5666-01A-01D-1651-05

value: Stage IIC


title: EXP-620: TCGA-CK-5913-01A-11D-1651-05

value: MX

value: Stage II

value: FEMALE


title: 072010_155533513_023

value: whole blood

value: baseline

value: SLE (Systemic LUPUS Erythomatosus)


title: 071310_166479053_042


title: 071910_166588823_115


title: 071910_164130133_013


title: EXP-620: TCGA-CM-6170-01A-11D-1651-05

value: YES

value: Stage I


title: 072010_166594133_021


title: EXP-620: TCGA-AY-5543-01A-01D-1651-05

value: NO

value: Stage IVA

value: Colon


title: EXP-620: TCGA-AZ-5403-01A-01D-1651-05

value: MALE

value: Colon Adenocarcinoma


title: EXP-620: TCGA-CK-5912-01A-11D-1651-05

value: COLON


title: EXP-620: TCGA-A6-5657-01A-01D-1651-05

value: Stage IIIB


title: EXP-620: TCGA-CM-5860-01A-01D-1651-05

value: Stage IIA


title: EXP-620: TCGA-CM-6172-01A-11D-1651-05


title: EXP-620: TCGA-A6-5665-01A-01D-1651-05


title: EXP-620: TCGA-CK-5916-01A-11D-1651-05

value: [Not Available]


title: EXP-620: TCGA-AM-5820-01A-01D-1651-05


title: EXP-620: TCGA-CM-6161-01A-11D-1651-05


title: EXP-620: TCGA-A6-5660-01A-01D-1651-05

value: Stage IIIC


title: EXP-620: TCGA-CA-5796-01A-01D-1651-05

value: Colon Mucinous Adenocarcinoma


title: EXP-620: TCGA-CK-4947-01B-11D-1651-05

value: FEMALE


title: EXP-620: TCGA-AV-A03D-20A-01D-A17Z-05

value: NOT SPECIFIED


title: EXP-620: TCGA-CM-5868-01A-01D-1651-05


title: EXP-620: TCGA-CM-6171-01A-11D-1651-05


title: EXP-620: TCGA-AM-5821-01A-01D-1651-05


title: EXP-620: TCGA-CK-5914-01A-11D-1651-05

value: MX

value: Stage III


title: 072010_166590003_127

value: whole blood

value: baseline

value: SLE (Systemic LUPUS Erythomatosus)


title: EXP-620: TCGA-D5-5539-01A-01D-1651-05

value: Stage IIIA


title: EXP-620: TCGA-CK-5915-01A-11D-1651-05

value: Stage I

value: Colon


title: EXP-620: TCGA-CM-6166-01A-11D-1651-05

value: NO

value: Colon Adenocarcinoma


title: EXP-620: TCGA-CM-5861-01A-01D-1651-05

value: COLON


title: EXP-620: TCGA-07-0227-20A-01D-1651-05


title: EXP-620: TCGA-A6-5661-01A-01D-1651-05

value: YES

value: Stage IIA


title: 071910_166590453_108


title: EXP-620: TCGA-A6-5662-01A-01D-1651-05

value: Stage IVA

value: MALE


title: 071310_166592533_036


title: EXP-620: TCGA-D5-5541-01A-01D-1651-05

value: Stage IIIB


title: 072010_166589543_129


title: 071910_162825323_035


title: 071410_166593443_082


title: EXP-620: TCGA-DM-A282-01A-12D-A16X-05

value: NOT SPECIFIED


title: EXP-620: TCGA-A6-5659-01A-01D-1651-05


title: EXP-620: TCGA-AD-5900-01A-11D-1651-05

value: MX

value: Colon Mucinous Adenocarcinoma


title: 071910_164129413_031

value: whole blood


title: 071310_166479633_035

value: baseline


title: EXP-620: TCGA-DM-A28G-01A-11D-A16X-05


title: EXP-620: TCGA-DM-A28A-01A-21D-A16X-05


title: 072010_166591343_151

value: SLE (Systemic LUPUS Erythomatosus)


title: EXP-620: TCGA-D5-5540-01A-01D-1651-05


title: EXP-620: TCGA-AV-A03D-20A-01D-A16X-05


title: EXP-620: TCGA-DM-A28E-01A-11D-A16X-05


title: EXP-620: TCGA-DM-A280-01A-12D-A16X-05


title: 071310_162824353_050


title: EXP-620: TCGA-DM-A28H-01A-11D-A16X-05


title: EXP-620: TCGA-DM-A28C-01A-11D-A16X-05


title: EXP-620: TCGA-DM-A28F-01A-11D-A16X-05


title: 071910_164129633_129


title: 072010_166480613_040


title: 072010_166480413_112


title: EXP-608: Blood_TCGA-AB-2932

value: Blood

value: Normal

value: BONE MARROW


title: EXP-620: TCGA-DM-A28M-01A-12D-A16X-05

value: Colon


title: EXP-620: TCGA-AD-6901-01A-11D-1926-05

value: [Not Available]

value: Colon Adenocarcinoma


title: Total RNA - REP4

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description: Total RNA. Replicate 4 of 4

hyb_protocol: Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino) ethanesulfonic acid, 1 M Na+, and 20mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05 µg/ml. Hybridization was performed for 16 h by incubating 200 µl of the sample to MOE 430 2.0 chips at 45ºC

scan_protocol: Each microarray was stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix) and scanned at 11µm resolution in a GeneChip® Scanner 3000 7G System (Affymetrix).

data_processing: Microarray analysis was performed using the affylmaGUI R package. Robust Multi-array Analysis (RMA) algorithm was used for background correction, normalization and expression levels summarization.

source_name: Total RNA

label_protocol: cDNA was synthesized from 4 µg of RNA using an oligodeoxythymidylic acid 24nt  primer with a T7 polymerase promoter site added to the 3´end. Following second-strand cDNA synthesis, the double-stranded cDNA was purified and used as template in the subsequent in vitro transcription (IVT) reaction. This in vitro transcription was performed using One-cycle target labelling and control reagents (Affymetrix) to produce biotin labelled cRNA.

growth_protocol: Cells were seeded on dishes previously incubated with matrigel (BD bioscience) for 1 hour and grown in RPMI (GIBCO) containing 10% bovine foetal serum.

extract_protocol: hStau1-associated RNAs were isolated by TAP purification (Villace et al, NAR 2004): cell extracts were obtained by lysis in a buffer containing 50 mM Tris-HCl, 100 mM NaCl, and 5 mM EDTA, pH 7.5 (TNE), 0.5% NP-40, 1 mM dithiothreitol (DTT), human placental RNase inhibitor (HPRI) (40 U/ml), and the complete protease inhibitor cocktail (Roche) for 30 min at 4°C. The supernatant was centrifuged at 10,000 rpm for 10 min and 4°C. The lysates were incubated with IgG-Sepharose (GE Healthcare) for 12 h at 4°C. The resin was washed 10 times with 10 resin volumes of IPP-150 (150 mM NaCl, 10 mM Tris-HCl, 0.1% NP40, pH 8.0) buffer and five times with 50 mM Tris-HCl, pH 8, 0.5 mM EDTA, 1 mM DTT. The complexes bound to the resin were digested with 1 U of tobacco etch virus (TEV) protease per 107 cells for 3 h at room temperature. The supernatant was collected, mixed with five washes of the resin with IPP150-CBB (150 mM NaCl, 10 mM Tris-HCl, 0.1% NP40, 10 mM 2-mercaptoethanol, 1 mM Mg(AcO)2, 1 mM imidazole, 2 mM CaCl2, pH 8.0) buffer and incubated with calmodulin-agarose resin (Stratagene) for 12 h at 4°C. The resin was washed 10 times in IPP150-CBB buffer and eluted in a buffer containing 10 mM Tris-HCl, pH 8, 0.1% NP-40, 10 mM β-mercaptoethanol, 1 mM imidazole, and 3 mM EGTA. hStau1-associated RNAs were obtained by treatment with 0.2 mg/ml proteinase K-0.5% SDS in TNE buffer for 30 min at 37°C. After phenol extraction, RNAs were precipitated with 2 volumes of ethanol and 20 μg of glycogen (Roche). RNAs from gel filtration fractions were obtained by treatment with 0.2 mg/ml proteinase K-0.5% SDS in TNE buffer for 30 min at 37°C. After phenol extraction, RNAs were precipitated with 2 volumes of ethanol and 20 μg of glycogen (Roche). Total RNA (not associated) from cell extracts was obtained using Trizol (Invitrogen) following the manufacturer’s instructions. RNAs were dephosphorylated with Shrimp Alkaline Phosphatase (USB-Affimetrix) for 30 minutes at 37ºC and subsequently phosphorylated by incubation with T4 Polynucleotide Kinase in the presence of 1 µM γ-32P-ATP. The integrity, pattern and size of the Stau-associated RNAs were analyzed in 4% and 15% polyacrylamide-urea gels. The integrity of each RNA preparation was tested using the Agilent 2100 Bioanalyzer.

treatment_protocol: Transfection of HEK293T cells was carried out with 25 μg of the plasmid pCHStau-TAP (Villace ,P., Marion,R.M. and Ortin,J. (2004) The composition of Staufen-containing RNA granules from human cells indicate a role in the regulated transport and translation of messenger RNAs. Nucleic Acids Res., 32, 2411–2420) per 150 mm dish, using the calcium-phosphate method. After incubation for 24 h at 37 ºC, the cells were washed with PBS, collected, centrifuged for 5 minutes at 1500 rpm and 4ºC and used for RNA or protein extraction.

tag: cell line


title: EXP-620: TCGA-DM-A285-01A-11D-A16X-05


title: Total RNA - REP3

description: Total RNA. Replicate 3 of 4


title: Total RNA - REP2

description: Total RNA. Replicate 2 of 4


title: EXP-620: TCGA-DM-A288-01A-11D-A16X-05


title: Total RNA - REP1

description: Total RNA. Replicate 1 of 4


title: 071910_166479943_144


title: Stau1-associated RNA - REP3

description: Stau1-associated RNA. Replicate 3 of 3

source_name: Stau1-associated RNA


title: EXP-620: TCGA-AD-6963-01A-11D-1926-05

value: COLON


title: 072010_166477233_015


title: EXP-620: TCGA-D5-6931-01A-11D-1926-05

value: NO

value: Stage IIIC


title: 072010_162825243_038


title: EXP-620: TCGA-DM-A28K-01A-21D-A16X-05


title: 071910_166594243_148


title: 071910_166593923_027


title: EXP-620: TCGA-D5-6922-01A-11D-1926-05

value: Stage IIIA

value: MALE


title: 071310_164130733_012


title: Stau1-associated RNA - REP1

description: Stau1-associated RNA- Replicate 1 of 3


title: EXP-620: TCGA-D5-6923-01A-11D-1926-05

value: Stage I

value: FEMALE


title: 072010_164131223_152


title: EXP-620: TCGA-G4-6304-01A-11D-1926-05

value: Stage IIB


title: EXP-620: TCGA-D5-6932-01A-11D-1926-05

value: Stage IIA


title: EXP-620: TCGA-D5-6930-01A-11D-1926-05

value: Colon Mucinous Adenocarcinoma


title: EXP-620: TCGA-D5-6920-01A-11D-1926-05


title: EXP-620: TCGA-AD-6899-01A-11D-1926-05

value: MX


title: EXP-620: TCGA-F4-6857-01A-11D-1926-05

value: NOT SPECIFIED


title: EXP-620: TCGA-D5-6929-01A-31D-1926-05

value: Stage IV


title: EXP-620: TCGA-AD-6895-01A-11D-1926-05


title: EXP-620: TCGA-D5-6898-01A-11D-1926-05


title: EXP-620: TCGA-F4-6856-01A-11D-1926-05


title: EXP-620: TCGA-D5-6928-01A-11D-1926-05


title: EXP-620: TCGA-AD-6890-01A-11D-1926-05


title: EXP-620: TCGA-F4-6855-01A-11D-1926-05


title: EXP-620: TCGA-D5-6534-01A-21D-1926-05

value: YES


title: S401_F_PRE

city: Washington

first: Monica

last: Hubal

state: DC

address: 111 Michigan Ave NW

department: Integrative Systems Biology

institute: Children's National Medical Center

description: Gene expression data from skeletal muscle in Subject 401 before (PRE) exercise training; subject group F.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133_Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G

data_processing: CHP files were produced in Expression Console using the PLIER algorithm. CHP files were imported into Partek Genomics Suite for statistical analysis. RM ANCOVA was used to test group and time factors, using sex and age as covariates. Regression analyses were used in genotype/gene expression or genotype/phenotype association testing.

source_name: vastus lateralis muscle; PRE exercise training

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA for two-cycle amplification (Expression Analysis Technical Manual, 2008, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions prior to processing for Affymetrix microarrays.

value: vastus lateralis

tag: exercise group

value: F (Resistance exercise)

tag: ethnicity

value: Caucasian

value: F

tag: subject id


title: EXP-620: TCGA-D5-5537-01A-21D-1926-05

tag: clinical m staging

tag: colon polyps history

value: NO

tag: pathologic t staging

value: Colon

value: Colon Adenocarcinoma

value: COLON


title: 072010_166592953_148

value: whole blood

value: baseline

value: SLE (Systemic LUPUS Erythomatosus)


title: EXP-620: TCGA-D5-6927-01A-21D-1926-05

tag: disease staging

value: Stage IIA

tag: pathologic n staging

value: MALE

tag: disease state


title: EXP-620: TCGA-F4-6854-01A-11D-1926-05

value: Stage IVA

value: FEMALE

tag: organism part

tag: sample


title: EXP-620: TCGA-AD-6889-01A-11D-1926-05

value: [Not Available]


title: EXP-620: TCGA-AD-6965-01A-11D-1926-05

value: MX


title: EXP-620: TCGA-AD-6888-01A-11D-1926-05

value: YES

value: Stage IIIB

value: NX


title: EXP-620: TCGA-D5-6926-01A-11D-1926-05

value: Stage IIIA


title: Stau1-associated RNA - REP2

description: Stau1-associated RNA. Replicate 2 of 3


title: EXP-620: TCGA-07-0227-20A-01D-1926-05

value: NOT SPECIFIED


title: EXP-620: TCGA-AD-6964-01A-11D-1926-05

value: NO

value: Colon


title: S367_F_POST

description: Gene expression data from skeletal muscle in Subject 367 after (POST) exercise training; subject group F.

source_name: vastus lateralis muscle; POST exercise training

tag: tissue

value: vastus lateralis

value: F (Resistance exercise)

value: Caucasian

value: F


title: S401_F_POST

description: Gene expression data from skeletal muscle in Subject 401 after (POST) exercise training; subject group F.

tag: age


title: S361_F_PRE

description: Gene expression data from skeletal muscle in Subject 361 before (PRE) exercise training; subject group F.

tag: Sex


title: S379_E_Pre

description: Gene expression data from skeletal muscle in Subject 379 before (PRE) exercise training; subject group E.

value: E (Aerobic + Resistance exercise)


title: EXP-620: TCGA-D5-6924-01A-11D-1926-05

value: Stage IIA

value: MALE

value: Colon Adenocarcinoma

value: COLON


title: EXP-620: TCGA-07-0227-20A-01D-1772-05


title: S359_E_POST

description: Gene expression data from skeletal muscle in Subject 359 after (POST) exercise training; subject group E.


title: 071410_166477833_003

value: whole blood

tag: time-point

value: baseline

tag: disease

value: SLE (Systemic LUPUS Erythomatosus)


title: S356_F_PRE

description: Gene expression data from skeletal muscle in Subject 356 before (PRE) exercise training; subject group F.


title: EXP-620: TCGA-D5-7000-01A-11D-1926-05

value: Stage I

value: FEMALE

value: Colon Mucinous Adenocarcinoma


title: S361_F_POST

description: Gene expression data from skeletal muscle in Subject 361 after (POST) exercise training; subject group F.


title: 072010_166588923_016


title: EXP-620: TCGA-A6-6781-01A-22D-1926-05

value: MX

value: [Not Available]

value: Stage IIIC


title: 072010_166479423_018


title: S366_F_PRE

description: Gene expression data from skeletal muscle in Subject 366 before (PRE) exercise training; subject group F.

value: vastus lateralis

value: F (Resistance exercise)

value: M


title: 071910_166479913_103


title: 072010_166592633_188


title: S387_E_POST

description: Gene expression data from skeletal muscle in Subject 387 after (POST) exercise training; subject group E.

value: E (Aerobic + Resistance exercise)

value: Caucasian


title: S387_E_PRE

description: Gene expression data from skeletal muscle in Subject 387 before (PRE) exercise training; subject group E.


title: EXP-620: TCGA-AZ-6601-01A-11D-1772-05

value: Stage II

value: MALE

value: Colon


title: 071410_166590943_001

value: whole blood


title: EXP-620: TCGA-G4-6303-01A-11D-1772-05

value: NO

value: Stage IV

value: Colon Adenocarcinoma

value: COLON


title: EXP-620: TCGA-A6-6650-01A-11D-1772-05

value: Stage IIA

value: FEMALE


title: EXP-620: TCGA-G4-6588-01A-11D-1772-05

value: YES


title: 071310_166479743_002

value: baseline

value: SLE (Systemic LUPUS Erythomatosus)


title: EXP-620: TCGA-G4-6299-01A-11D-1772-05

value: Stage IIIC


title: EXP-620: TCGA-G4-6626-01A-11D-1772-05


title: EXP-620: TCGA-G4-6627-01A-11D-1772-05


title: S357_F_PRE

description: Gene expression data from skeletal muscle in Subject 357 before (PRE) exercise training; subject group F.

value: vastus lateralis

value: F (Resistance exercise)

value: M


title: S379_E_POST

description: Gene expression data from skeletal muscle in Subject 379 after (POST) exercise training; subject group E.

value: E (Aerobic + Resistance exercise)

value: Caucasian

value: F


title: 072010_165619843_057

value: whole blood


title: S359_E_PRE

description: Gene expression data from skeletal muscle in Subject 359 before (PRE) exercise training; subject group E.


title: S367_F_PRE

description: Gene expression data from skeletal muscle in Subject 367 before (PRE) exercise training; subject group F.


title: EXP-620: TCGA-A6-6653-01A-11D-1772-05

value: Stage I

value: MALE

value: Colon


title: EXP-620: TCGA-AZ-6601-11A-01D-1772-05

source_name: Solid normal tissue

value: [Not Available]

value: Stage II

value: Colon Adenocarcinoma

value: COLON


title: S366_F_POST

description: Gene expression data from skeletal muscle in Subject 366 after (POST) exercise training; subject group F.


title: EXP-620: TCGA-F4-6569-01A-11D-1772-05


title: EXP-620: TCGA-G4-6625-11A-01D-1772-05

value: NO

value: Stage IIA

value: FEMALE


title: EXP-620: TCGA-AZ-6599-11A-01D-1772-05

value: MX


title: EXP-620: TCGA-A6-6652-01A-11D-1772-05

value: Stage IVA


title: EXP-620: TCGA-G4-6306-01A-11D-1772-05

value: YES


title: EXP-620: TCGA-D5-6529-01A-11D-1772-05


title: EXP-620: TCGA-F4-6459-01A-11D-1772-05

value: Stage IIIB


title: S356_F_POST

description: Gene expression data from skeletal muscle in Subject 356 after (POST) exercise training; subject group F.

value: vastus lateralis

value: F (Resistance exercise)

value: Caucasian


title: 072010_166591533_142

value: whole blood

value: baseline

value: SLE (Systemic LUPUS Erythomatosus)


title: EXP-620: TCGA-G4-6625-01A-21D-1772-05

value: Colon


title: EXP-620: TCGA-A6-6142-01A-11D-1772-05

value: [Not Available]


title: EXP-620: TCGA-A6-6137-01A-11D-1772-05

value: MALE

value: Colon Adenocarcinoma


title: EXP-620: TCGA-A6-6649-01A-11D-1772-05

value: COLON


title: EXP-620: TCGA-F4-6461-01A-11D-1772-05

value: NO

value: Stage IIIC


title: S354_E_POST

description: Gene expression data from skeletal muscle in Subject 354 after (POST) exercise training; subject group E.

value: E (Aerobic + Resistance exercise)

value: M


title: EXP-620: TCGA-A6-4105-01A-02D-1772-05

value: Stage IIA


title: EXP-620: TCGA-AZ-6600-01A-11D-1772-05

value: Stage IV


title: 072010_164130233_134


title: S352_F_POST

description: Gene expression data from skeletal muscle in Subject 352 after (POST) exercise training; subject group F.

value: vastus lateralis


title: S354_E_PRE

description: Gene expression data from skeletal muscle in Subject 354 before (PRE) exercise training; subject group E.


title: EXP-620: TCGA-AZ-6598-01A-11D-1772-05

value: MX

value: Stage II

value: FEMALE


title: S357_F_POST

description: Gene expression data from skeletal muscle in Subject 357 after (POST) exercise training; subject group F.

value: F (Resistance exercise)

value: Caucasian


title: S352_F_PRE

description: Gene expression data from skeletal muscle in Subject 352 before (PRE) exercise training; subject group F.


title: S336_F_POST

description: Gene expression data from skeletal muscle in Subject 336 after (POST) exercise training; subject group F.

value: F


title: EXP-620: TCGA-A6-6138-01A-11D-1772-05

value: Stage I

value: Colon


title: EXP-620: TCGA-F4-6570-01A-11D-1772-05

value: [Not Available]

value: Colon Adenocarcinoma


title: EXP-620: TCGA-AZ-6599-01A-11D-1772-05

value: MALE

value: COLON


title: EXP-620: TCGA-AZ-6600-11A-01D-1772-05


title: EXP-620: TCGA-A6-6140-01A-11D-1772-05

value: NO


title: S336_F_PRE

description: Gene expression data from skeletal muscle in Subject 336 before (PRE) exercise training; subject group F.


title: S335_E_POST

description: Gene expression data from skeletal muscle in Subject 335 after (POST) exercise training; subject group E.

value: E (Aerobic + Resistance exercise)

value: M


title: EXP-620: TCGA-A6-6648-01A-11D-1772-05

value: Stage IVA


title: EXP-620: TCGA-A6-6141-01A-11D-1772-05

value: YES

value: Stage IIA


title: EXP-620: TCGA-G4-6586-01A-11D-1772-05


title: EXP-620: TCGA-AZ-6598-11A-01D-1772-05

value: MX

value: Stage II


title: EXP-620: TCGA-F4-6460-01A-11D-1772-05

value: Stage IIIB

value: FEMALE


title: EXP-620: TCGA-G4-6294-01A-11D-1772-05

value: Stage IV


title: EXP-620: TCGA-AV-A03D-20A-01D-A153-05

value: NOT SPECIFIED


title: EXP-620: TCGA-DM-A1D7-01A-11D-A153-05

value: Colon


title: 072010_162825023_140

value: whole blood

value: baseline

value: SLE (Systemic LUPUS Erythomatosus)


title: 072010_166594653_118


title: 071910_166591943_048


title: 071310_165620403_049


title: S335_E_PRE

description: Gene expression data from skeletal muscle in Subject 335 before (PRE) exercise training; subject group E.

value: vastus lateralis

value: Caucasian


title: S334_D_POST

description: Gene expression data from skeletal muscle in Subject 334 after (POST) exercise training; subject group D.

value: D (Moderate aerobic exercise)


title: S330_B_POST

description: Gene expression data from skeletal muscle in Subject 330 after (POST) exercise training; subject group B.

value: B (Inactive control)

value: M


title: S334_D_PRE

description: Gene expression data from skeletal muscle in Subject 334 before (PRE) exercise training; subject group D.


title: EXP-620: TCGA-DM-A1HA-01A-11D-A153-05


title: 071310_166479723_075


title: S317_F_PRE

description: Gene expression data from skeletal muscle in Subject 317 before (PRE) exercise training; subject group F.

value: F (Resistance exercise)


title: EXP-620: TCGA-DM-A1D4-01A-21D-A153-05


title: EXP-620: TCGA-DM-A1DB-01A-11D-A153-05


title: 072010_166593153_117


title: 071310_166590743_014


title: 072010_164129323_059


title: S316_E_PRE

description: Gene expression data from skeletal muscle in Subject 316 before (PRE) exercise training; subject group E.

value: E (Aerobic + Resistance exercise)

value: African American


title: S326_B_PRE

description: Gene expression data from skeletal muscle in Subject 326 before (PRE) exercise training; subject group B.


title: EXP-620: TCGA-DM-A1D6-01A-21D-A153-05


title: 071910_162824913_019


title: 072010_166592143_036


title: S326_B_POST

description: Gene expression data from skeletal muscle in Subject 326 after (POST) exercise training; subject group B.


title: EXP-620: TCGA-DM-A1DA-01A-11D-A153-05


title: EXP-620: TCGA-DM-A0XF-01A-11D-A153-05


title: EXP-620: TCGA-DM-A0XD-01A-12D-A153-05


title: S330_B_PRE

description: Gene expression data from skeletal muscle in Subject 330 before (PRE) exercise training; subject group B.


title: EXP-620: TCGA-DM-A1D8-01A-11D-A153-05


title: EXP-620: TCGA-DM-A1D0-01A-11D-A153-05


title: EXP-620: TCGA-DM-A0X9-01A-11D-A153-05


title: 071910_166594613_151


title: EXP-620: TCGA-CM-5349-01A-21D-1721-05

value: NO

value: Stage IIA

value: Colon Adenocarcinoma

value: COLON


title: EXP-620: TCGA-DM-A1D9-01A-11D-A153-05

value: NOT SPECIFIED


title: EXP-620: TCGA-AA-3663-11A-01D-1721-05

value: Stage II

value: MALE

value: Colon


title: EXP-620: TCGA-CM-4743-01A-01D-1721-05


title: EXP-620: TCGA-D5-6539-01A-11D-1721-05

value: [Not Available]

value: Stage IIIA

value: FEMALE


title: EXP-620: TCGA-G4-6314-01A-11D-1721-05

value: Stage IV


title: EXP-620: TCGA-D5-6530-01A-11D-1721-05

value: Stage I


title: EXP-620: TCGA-AA-3712-11A-01D-1721-05

value: Stage III


title: EXP-620: TCGA-D5-6535-01A-11D-1721-05

value: MX

value: Stage IIIB


title: EXP-620: TCGA-AA-3663-01A-01D-1721-05


title: EXP-620: TCGA-G4-6310-01A-11D-1721-05


title: EXP-620: TCGA-D5-6540-01A-11D-1721-05

value: Colon Mucinous Adenocarcinoma


title: 071910_166592513_029

value: whole blood

value: baseline

value: SLE (Systemic LUPUS Erythomatosus)


title: 071910_166477623_119


title: S316_E_POST

description: Gene expression data from skeletal muscle in Subject 316 after (POST) exercise training; subject group E.

value: vastus lateralis

value: E (Aerobic + Resistance exercise)

value: African American

value: M


title: EXP-620: TCGA-G4-6323-01A-11D-1721-05

value: NO

value: Tis

value: Stage IA

value: MALE

value: Colon

value: Colon Adenocarcinoma

value: COLON


title: EXP-620: TCGA-CM-5344-01A-21D-1721-05

value: YES

value: FEMALE


title: EXP-620: TCGA-AU-3779-01A-01D-1721-05

value: Stage I


title: EXP-620: TCGA-A6-2675-11A-01D-1721-05

value: MX

value: Stage IIA


title: S314_E_POST

description: Gene expression data from skeletal muscle in Subject 314 after (POST) exercise training; subject group E.

value: F


title: 071910_166589613_116

value: whole blood

value: baseline

value: SLE (Systemic LUPUS Erythomatosus)


title: S281_C_PRE

description: Gene expression data from skeletal muscle in Subject 281 before (PRE) exercise training; subject group C.

value: vastus lateralis

value: C (High aerobic exercise)

value: Caucasian

value: M


title: 072010_166593353_135


title: 071310_164131113_090


title: EXP-620: TCGA-G4-6297-01A-11D-1721-05

value: Stage IV


title: S301_E_PRE

description: Gene expression data from skeletal muscle in Subject 301 before (PRE) exercise training; subject group E.

value: E (Aerobic + Resistance exercise)


title: EXP-620: TCGA-G4-6302-11A-01D-1721-05

value: NO

value: Colon

value: Colon Mucinous Adenocarcinoma


title: EXP-620: TCGA-AA-3713-01A-21D-1721-05

value: YES

value: MALE

value: Colon Adenocarcinoma

value: COLON


title: 071910_166479613_043


title: 072010_166588353_149


title: EXP-620: TCGA-AA-3655-11A-01D-1721-05

value: Stage II


title: EXP-620: TCGA-G4-6297-11A-01D-1721-05

value: FEMALE


title: EXP-620: TCGA-G4-6317-01A-11D-1721-05

value: MX

value: Stage IIIC


title: S281_C_POST

description: Gene expression data from skeletal muscle in Subject 281 after (POST) exercise training; subject group C.

value: vastus lateralis


title: EXP-620: TCGA-A6-5667-01A-21D-1721-05

value: [Not Available]

value: Stage IIIB


title: EXP-620: TCGA-AA-3697-01A-01D-1721-05

value: Stage III


title: EXP-620: TCGA-G4-6314-11A-01D-1721-05

value: Stage IV


title: EXP-620: TCGA-CM-5348-01A-21D-1721-05


title: 072010_166590953_054

value: whole blood

value: baseline

value: SLE (Systemic LUPUS Erythomatosus)


title: EXP-620: TCGA-A6-5667-11A-01D-1721-05

value: Colon


title: 071310_165620503_008


title: 072010_166592043_150


title: EXP-620: TCGA-A6-2675-01A-02D-1721-05

value: NO

value: Stage IIA


title: 071910_166593753_065


title: 071310_166480213_009


title: S277_C_POST

description: Gene expression data from skeletal muscle in Subject 277 after (POST) exercise training; subject group C.

value: C (High aerobic exercise)

value: Caucasian

value: M