title: Sample M483: whole liver tissue

description: Sample M483: whole liver tissue (HCC group)


title: Sample M479: whole liver tissue

status: Public on Nov 03 2016

type: RNA

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: Sample M479: whole liver tissue (HCC group)

hyb_protocol: Hybridization was performed on Affymetrix GeneChip miRNA 2.0 arrays using standard protocols available at www.affymetrix.com.

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: Scanned images of microarray chips were analyzed using Expression Console (Affymetrix) with the default settings. Raw data were processed using different algorithms. Detected Above Background algorithm (DABD) and RMA Background Adjustment algorithm were performed in order to remove the background value.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: whole liver sample

extract_protocol: RNA was extracted from liver tissues using Trizol and following manufacter’s manual instructions (Life Tecnologies, Carlsbad, CA). miRNA quantification was performed using the commercial kit Mir-X miRNA First-Strand Synthesis Kit doing as manufacter’s manual instructions (Takara Bio Europe/Clontech, Saint-Germain-en-Laye, France).

tag: tissue type

value: hepatocellular carcinoma

tag: group

value: HCC


title: Sample M477: whole liver tissue

description: Sample M477: whole liver tissue (HCC group)

label_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000


title: Sample M467: whole liver tissue

description: Sample M467: whole liver tissue (HCC group)


title: Sample M455: whole liver tissue

description: Sample M455: whole liver tissue (HCC group)


title: Sample M461: whole liver tissue

description: Sample M461: whole liver tissue (HCC group)


title: Sample M459: whole liver tissue

description: Sample M459: whole liver tissue (HCC group)


title: Sample M493: whole liver tissue

description: Sample M493: whole liver tissue (HCC group)


title: Sample M473: whole liver tissue

description: Sample M473: whole liver tissue (HCC group)


title: Sample M435: whole liver tissue

description: Sample M435: whole liver tissue (HCC group)


title: Sample M443: whole liver tissue

description: Sample M443: whole liver tissue (HCC group)


title: Sample M393: whole liver tissue

description: Sample M393: whole liver tissue (HCC group)


title: Sample M425: whole liver tissue

description: Sample M425: whole liver tissue (HCC group)


title: Sample M399: whole liver tissue

description: Sample M399: whole liver tissue (HCC group)


title: Sample M421: whole liver tissue

description: Sample M421: whole liver tissue (HCC group)


title: Sample M411: whole liver tissue

description: Sample M411: whole liver tissue (HCC group)


title: Sample M385: whole liver tissue

description: Sample M385: whole liver tissue (HCC group)


title: Sample M423: whole liver tissue

description: Sample M423: whole liver tissue (HCC group)


title: Sample M375: whole liver tissue

description: Sample M375: whole liver tissue (HCC group)


title: Sample M391: whole liver tissue

description: Sample M391: whole liver tissue (HCC group)


title: Sample M451: whole liver tissue

description: Sample M451: whole liver tissue (HCC group)


title: Sample M363: whole liver tissue

description: Sample M363: whole liver tissue (HCC group)


title: Sample M357: whole liver tissue

description: Sample M357: whole liver tissue (HCC group)


title: Sample M397: whole liver tissue

description: Sample M397: whole liver tissue (HCC group)


title: Sample M407: whole liver tissue

description: Sample M407: whole liver tissue (HCC group)


title: Sample M371: whole liver tissue

description: Sample M371: whole liver tissue (HCC group)


title: Sample M379: whole liver tissue

description: Sample M379: whole liver tissue (HCC group)


title: Sample M339: whole liver tissue

description: Sample M339: whole liver tissue (HCC group)


title: Sample M353: whole liver tissue

description: Sample M353: whole liver tissue (HCC group)


title: Sample M345: whole liver tissue

description: Sample M345: whole liver tissue (HCC group)


title: Sample M373: whole liver tissue

description: Sample M373: whole liver tissue (HCC group)


title: Sample M319: whole liver tissue

description: Sample M319: whole liver tissue (HCC group)


title: Sample M329: whole liver tissue

description: Sample M329: whole liver tissue (HCC group)


title: Sample M325: whole liver tissue

description: Sample M325: whole liver tissue (HCC group)


title: Sample M327: whole liver tissue

description: Sample M327: whole liver tissue (HCC group)


title: Sample M279: whole liver tissue

description: Sample M279: whole liver tissue (HCC group)


title: Sample M311: whole liver tissue

description: Sample M311: whole liver tissue (HCC group)


title: Sample M337: whole liver tissue

description: Sample M337: whole liver tissue (HCC group)


title: Sample M305: whole liver tissue

description: Sample M305: whole liver tissue (HCC group)


title: Sample M335: whole liver tissue

description: Sample M335: whole liver tissue (HCC group)


title: Sample M321: whole liver tissue

description: Sample M321: whole liver tissue (HCC group)


title: Sample M779: whole liver tissue

description: Sample M779: whole liver tissue (HCC group)


title: Sample M739: whole liver tissue

description: Sample M739: whole liver tissue (HCC group)


title: Sample M271: whole liver tissue

description: Sample M271: whole liver tissue (HCC group)


title: Sample M439: whole liver tissue

description: Sample M439: whole liver tissue (HCC group)


title: Sample B301: whole liver tissue

description: Sample B301: whole liver tissue (HCC group)


title: Sample B167: whole liver tissue

description: Sample B167: whole liver tissue (HCC group)


title: Sample M549: whole liver tissue

description: Sample M549: whole liver tissue (HCC group)


title: Sample M503: whole liver tissue

description: Sample M503: whole liver tissue (HCC group)


title: Sample M265: whole liver tissue

description: Sample M265: whole liver tissue (HCC group)


title: Sample M663: whole liver tissue

description: Sample M663: whole liver tissue (HCC group)


title: Sample M243: whole liver tissue

description: Sample M243: whole liver tissue (HCC group)


title: Sample M269: whole liver tissue

description: Sample M269: whole liver tissue (HCC group)


title: Sample M261: whole liver tissue

description: Sample M261: whole liver tissue (HCC group)


title: Sample M625: whole liver tissue

description: Sample M625: whole liver tissue (HCC group)


title: Sample M695: whole liver tissue

description: Sample M695: whole liver tissue (HCC group)


title: Sample M213: whole liver tissue

description: Sample M213: whole liver tissue (HCC group)


title: Sample M253: whole liver tissue

description: Sample M253: whole liver tissue (HCC group)


title: Sample M275: whole liver tissue

description: Sample M275: whole liver tissue (HCC group)


title: Sample M589: whole liver tissue

description: Sample M589: whole liver tissue (HCC group)


title: Sample M233: whole liver tissue

description: Sample M233: whole liver tissue (HCC group)


title: Sample M257: whole liver tissue

description: Sample M257: whole liver tissue (HCC group)


title: Sample M255: whole liver tissue

description: Sample M255: whole liver tissue (HCC group)


title: Sample M247: whole liver tissue

description: Sample M247: whole liver tissue (HCC group)


title: Sample M369: whole liver tissue

description: Sample M369: whole liver tissue (HCC group)


title: Sample M237: whole liver tissue

description: Sample M237: whole liver tissue (HCC group)


title: Sample M207: whole liver tissue

description: Sample M207: whole liver tissue (HCC group)


title: Sample M267: whole liver tissue

description: Sample M267: whole liver tissue (HCC group)


title: Sample M209: whole liver tissue

description: Sample M209: whole liver tissue (HCC group)


title: Sample M223: whole liver tissue

description: Sample M223: whole liver tissue (HCC group)


title: HCC cell line HuH28

description: HCC cell line HuH28 (HCC Cell line group)

source_name: HCC cell line

value: HCC Cell line


title: Sample M235: whole liver tissue

description: Sample M235: whole liver tissue (HCC group)


title: Pituitary_adenoma_NVPBEZ235_rep7

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from pituitary adenoma from rat treated with 20 mg/kg NVP-BEZ235

hyb_protocol: According to the Affymetrix expression protocol (HWS kit)

data_processing: RMA probeset summary and quantile normalisation (Expression console v.1.3.0.187, Affymetrix)

organism: Rattus norvegicus

source_name: Pituitary adenoma from rat treated with 20 mg/kg NVP-BEZ235

label_protocol: Ovation PicoSL WTA System V2 in combination with the Encore Biotin Module (Nugen)

growth_protocol: Animals per housed under spf conditions

extract_protocol: RNeasy Micro Kit (Qiagen) including DNase treatment

treatment_protocol: No treatment

tag: strain

value: Sprague-Dawley white eye/Wistar-Kyoto

tag: age

value: 8 months

tag: gender

value: Female

tag: genotype

value: p27Kip1 (Cdknb1) mutant, homozygous

tag: tissue

value: pituitary adenoma

tag: treatment

value: 20 mg/kg NVP-BEZ235


title: Pituitary_adenoma_control_rep7

description: Gene expression data from pituitary adenoma from rat treated with 20 mg/kg PEG; control

scan_protocol: According to the Affymetrix expression protocol

source_name: Pituitary adenoma from rat treated with 20 mg/kg PEG; control

value: Male

value: 20 mg/kg PEG; control


title: Sample B44: whole liver tissue

description: Sample B44: whole liver tissue (Normal group)

value: normal liver

value: Normal


title: Sample B51: whole liver tissue

description: Sample B51: whole liver tissue (Normal group)


title: Sample M229: whole liver tissue

description: Sample M229: whole liver tissue (HCC group)


title: HCC cell line HuH7

description: HCC cell line HuH7 (HCC Cell line group)


title: Pituitary_adenoma_NVPBEZ235_rep10


title: HCC cell line HuCCTI

description: HCC cell line HuCCTI (HCC Cell line group)


title: Pituitary_adenoma_NVPBEZ235_rep6


title: Pituitary_adenoma_NVPBEZ235_rep8


title: Pituitary_adenoma_control_rep5


title: Pituitary_adenoma_NVPBEZ235_rep5


title: Pituitary_adenoma_NVPBEZ235_rep1

description: Gene expression data from pituitary adenoma from rat treated with 30 mg/kg NVP-BEZ235

source_name: Pituitary adenoma from rat treated with 30 mg/kg NVP-BEZ235

value: 30 mg/kg NVP-BEZ235


title: Pituitary_adenoma_control_rep2


title: Sample B43: whole liver tissue

description: Sample B43: whole liver tissue (Normal group)


title: Pituitary_adenoma_control_rep4


title: Pituitary_adenoma_control_rep6


title: Sample B317: whole liver tissue

description: Sample B317: whole liver tissue (HCC group)


title: AP2IV-3 overexpression, pH7.8, 100 nM Shield 1, 36h, replicate 1

city: Tampa

first: Dong-Pyo

last: Hong

state: Florida

address: 3720 Spectrum Blvd, Suite304

country: USA

institute: University of south florida

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45 oC to the affymetrix U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned by using the Affymetrix GCS3000 scanner.

data_processing: Genespring GX v12.6.1 (Agilent)

organism: Toxoplasma gondii

source_name: tachyzoite (pH 7.8)

label_protocol: Ambion messageAmp premier

growth_protocol: parasites were grown in T175 flasks in human foreskin fibroblasts

extract_protocol: Qiagen RNA easy, double DNAse digestion

treatment_protocol: in vitro growth  at different pHs (pH7.0, pH7.8, pH8.2) in vitro, 32-48h

tag: Stage

value: bradyzoite

tag: ph

value: AP2IV-3 overexpression


title: Pituitary_adenoma_NVPBEZ235_rep4


title: Sample B46: whole liver tissue

description: Sample B46: whole liver tissue (Normal group)


title: Pituitary_adenoma_control_rep1


title: HCC cell line Hep3B

description: HCC cell line Hep3B (HCC Cell line group)


title: Parent, pH 7.8, 100 nM Shield 1, 36h, replicate 2

value: tachyzoite

value: wildtype (parental)


title: Pituitary_adenoma_NVPBEZ235_rep2


title: AP2IV-3 knockout, pH8.2, 48h, replicate 1

source_name: bradyzoite induced (pH 8.2)

value: AP2IV-3 Knockout


title: Sample B319: whole liver tissue

description: Sample B319: whole liver tissue (HCC group)

value: hepatocellular carcinoma

value: HCC


title: AP2IV-3 overexpression, pH7.0, 100 nM Shield 1, 32h, replicate 2

source_name: tachyzoite (pH 7.0)


title: AP2IV-3 overexpression, pH7.8, 100 nM Shield 1, 36h, replicate 2


title: HCC cell line HepG2

description: HCC cell line HepG2 (HCC Cell line group)

value: HCC Cell line


title: Parent, pH 7.8, 100 nM Shield 1, 36h, replicate 1


title: Parent, pH 8.2, 48h, replicate 1


title: AP2IV-3 overexpression, pH7.0, 100 nM Shield 1, 32h, replicate 1


title: Parent, pH 8.2, 48h, replicate 2


title: Pituitary_adenoma_NVPBEZ235_rep9

value: Sprague-Dawley white eye/Wistar-Kyoto

value: 8 months


title: AP2IV-3 knockout, pH8.2, 48h, replicate 2


title: Parent, pH 7.0, 100 nM Shield 1, 32h, replicate 2


title: Pituitary_adenoma_NVPBEZ235_rep3

value: Female

value: p27Kip1 (Cdknb1) mutant, homozygous

value: pituitary adenoma


title: Pituitary_adenoma_control_rep3

value: 20 mg/kg PEG; control


title: Sample B265: whole liver tissue

description: Sample B265: whole liver tissue (HCC group)


title: Sample B299: whole liver tissue

description: Sample B299: whole liver tissue (HCC group)


title: Sample B243: whole liver tissue

description: Sample B243: whole liver tissue (HCC group)


title: Parent, pH 7.0, 100 nM Shield 1, 32h, replicate 1


title: Sample B237: whole liver tissue

description: Sample B237: whole liver tissue (HCC group)


title: Sample B157: whole liver tissue

description: Sample B157: whole liver tissue (HCC group)


title: Sample B179: whole liver tissue

description: Sample B179: whole liver tissue (HCC group)


title: Sample B247: whole liver tissue

description: Sample B247: whole liver tissue (HCC group)


title: Sample B215: whole liver tissue

description: Sample B215: whole liver tissue (HCC group)


title: Sample B156: whole liver tissue

description: Sample B156: whole liver tissue (CH group)

value: cirrhotic liver

value: CH


title: Sample B178: whole liver tissue

description: Sample B178: whole liver tissue (CH group)


title: Sample B158: whole liver tissue

description: Sample B158: whole liver tissue (CH group)


title: Sample B181: whole liver tissue

description: Sample B181: whole liver tissue (HCC group)


title: Sample B161: whole liver tissue

description: Sample B161: whole liver tissue (HCC group)


title: Sample B214: whole liver tissue

description: Sample B214: whole liver tissue (CH group)


title: Sample B231: whole liver tissue

description: Sample B231: whole liver tissue (HCC group)


title: Sample B175: whole liver tissue

description: Sample B175: whole liver tissue (HCC group)


title: Sample B209: whole liver tissue

description: Sample B209: whole liver tissue (HCC group)


title: Sample B150: whole liver tissue

description: Sample B150: whole liver tissue (CH group)


title: Sample B159: whole liver tissue

description: Sample B159: whole liver tissue (HCC group)


title: Sample B152: whole liver tissue

description: Sample B152: whole liver tissue (CH group)


title: Sample B151: whole liver tissue

description: Sample B151: whole liver tissue (HCC group)


title: Sample B174: whole liver tissue

description: Sample B174: whole liver tissue (CH group)


title: Sample B135: whole liver tissue

description: Sample B135: whole liver tissue (HCC group)


title: Sample B111: whole liver tissue

description: Sample B111: whole liver tissue (HCC group)


title: Sample B134: whole liver tissue

description: Sample B134: whole liver tissue (CH group)


title: Sample B239: whole liver tissue

description: Sample B239: whole liver tissue (HCC group)


title: Sample B153: whole liver tissue

description: Sample B153: whole liver tissue (HCC group)


title: Sample B108: whole liver tissue

description: Sample B108: whole liver tissue (CH group)


title: GF esg[ts] gut, biological rep3

city: Edmonton

first: Edan

last: Foley

state: Alberta

address: 116 Street and 86 Ave

department: Medical Microbiology and Immunology

country: Canada

institute: University of Alberta

description: Gene expression data from GF esg[ts] guts

hyb_protocol: 12 ug of cRNA was used for fragmentation, fragmented cRNA was hybridized on GeneChip®Drosophila Genome 2.0 Array, washed and stained according to the Affymetrix protocol (User Guide GeneChip® 3' IVT PLUS Reagent Kit, 2013-2015, Affymetrix).

scan_protocol: Affymetrix GeneChip 3000 7G Scanner

data_processing: The data were analyzed with Expression Console (Affymetrix) using default analysis settings.

organism: Drosophila melanogaster

source_name: Drosophila GF esg[ts] guts 2 days post activation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix GeneChip 3' IVT plus protocol from 100 ng total RNA (User Guide GeneChip® 3' IVT PLUS Reagent Kit, 2013-2015, Affymetrix).

growth_protocol: Flies were raised on regular food or food containing an antibiotic cocktail for 10-11 days at 18°C to obtain conventionally reared (CR) or germ-free (GF) flies. The flies were then heat shifted to 29°C for 2 days to get ImdCA expression in gut progenitor cells.

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

treatment_protocol: After the 2 day heat shift, a total of 10 guts per sample (5 female, 5 male) were dissected into Trizol and used for RNA extraction.

value: dissected gut

value: w; esgGAL4, tubGAL80[ts], UASGFP/+;+/+


title: CR esg[ts] gut, biological rep3

description: Gene expression data from CR esg[ts] guts

source_name: Drosophila CR esg[ts] guts 2 days post activation


title: GF esg[ts]>ImdCA gut, biological rep1

description: Gene expression data from GF esg[ts]>ImdCA guts

source_name: Drosophila GF esg[ts]>ImdCA guts 2 days post activation

value: w; esgGAL4, tubGAL80[ts], UASGFP/+; UASImdCA/+


title: GF esg[ts] gut, biological rep2


title: Glioma cell U87- after FOXP3 transfection  48 hours

city: Tianjin

first: Jinhuan

last: wang

address: Room 6  Jizhao Road, Tianjin City

country: China

institute: Tianjin Huanhu Hospital

description: Gene expression after transfection  48 hours

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Glioma cell U87

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS 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: Glioma cell lines U87 were from Peking Union Medical College Cell Resource Center (Beijing, China) . Cells were cultured in Dulbecco’s modified essential medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin and 100 μg/mL streptomycin in a humidified atmosphere containing 5% CO2 at 37°C.

extract_protocol: Trizol (Invitrogen) was used to extract from total RNA from transfected cells according to the manufacturer’s instructions.

treatment_protocol: Cells were transfected with plasmid vectors mediated by lipofectamine 2000 (Invitrogen, Carlsbad, CA).

tag: cell line

tag: transfection

value: FOXP3 48 hours


title: CLL80_B24

city: Portland

first: Alexey

last: Danilov

state: OR

address: 3181 SW Sam Jackson Pk Rd

institute: Oregon Health and Science Univeristy

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalized using quantile normalisation with BRB Array Tools

source_name: Human CLL cells

label_protocol: Reverse transcription using an oligo(dT) primer bearing a T7 promoter and the high yield ArrayScriptTM reverse transcriptase were used to make cDNA. The cDNA was made double-stranded and purified to use as a template for in vitro transcription with T7 RNA Polymerase and the included biotin-NTP mix

growth_protocol: Cells were cultured in RPMI with 15% FBS

extract_protocol: B-cells isolated using B-cell purification kit (Multenyi Biotech). RNA isolated using RNEasy kit (Qiagen)

treatment_protocol: Cells were co-cultured with BAFF-expressing stroma for 18 hours. No drug treatment was introduced.

tag: cell type

value: CLL cells from patient with CLL


title: CR esg[ts]>ImdCA gut, biological rep1

description: Gene expression data from CR esg[ts]>ImdCA guts

source_name: Drosophila CR esg[ts]>ImdCA guts 2 days post activation


title: CLL71_B24

scan_protocol: Standard Illumina hybridization protocol


title: GF esg[ts]>ImdCA gut, biological rep3


title: Sample B109: whole liver tissue

description: Sample B109: whole liver tissue (HCC group)


title: GF esg[ts] gut, biological rep1


title: GF esg[ts]>ImdCA gut, biological rep2


title: CR esg[ts] gut, biological rep1


title: CLL71_B0


title: CR esg[ts] gut, biological rep2


title: Sample B325: whole liver tissue

description: Sample B325: whole liver tissue (HCC group)


title: CR esg[ts]>ImdCA gut, biological rep2


title: CLL80_B0


title: HDbrain: genomic DNA from InferiorParietal from Sample475

status: Public on Nov 02 2016

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

description: genomic DNA from human brain

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing:
BeadStudio software v3.2.
Unmethylated and methylated signal intensities and detection p values

label: Cy3 and Cy5

molecule: genomic DNA

source_name: InferiorParietal

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from fresh frozen tissue using AllPrep DNA/RNA mini kit according to standard instructions

tag: personid

tag: brainbank

value: NewZealand

tag: broadbrainregion

value: Parietal

tag: Sex

value: male

tag: disease

value: HD

tag: caglength

tag: dnamage

tag: dnamagewindsorized

tag: postmorteminterval


title: CLL58_B0


title: HDbrain: genomic DNA from CingulateGyrus from Sample473

description: genomic DNA from human brain

source_name: CingulateGyrus

value: Limbic

tag: age


title: HDbrain: genomic DNA from MotorCortex from Sample474

description: genomic DNA from human brain

source_name: MotorCortex

value: other

value: Control


title: Group B 1

city: chengdu

first: ping

middle: shi

last: liu

state: sichuan

address: guoxue road

department: Emergency Department

institute: West China Hospital of Sichuan University

description: aggressive fluid resuscitation

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA). After being washed in an ozone-free environment, the slides were scanned using the Axon GenePix 4000B microarray scanner.

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis.

data_processing: Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization.All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Differentially expressed genes were identified through Fold Change filtering.

source_name: aggressive fluid resuscitation

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). Briefly, ds-cDNA was incubated with 4 μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). One μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation.

growth_protocol: Ringer’s solution infusion to reach and maintain MAP at 50–60 mmHg, beginning immediately after the tail amputation

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Ringer’s solution infusion, with an attempt to maintain MAP over 80 mmHg, beginning immediately after the tail amputation

tag: strain

value: Sprague-Dawley (SD)

tag: gender

value: 90 and 120 days

tag: tissue

value: liver

tag: treatment group

value: aggressive fluid resuscitation


title: HDbrain: genomic DNA from InferiorParietal from Sample472

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SensoryCortex from Sample471

description: genomic DNA from human brain

source_name: SensoryCortex

value: Temporal


title: CLL58_B24


title: Group B 3

description: aggressive fluid resuscitation


title: HDbrain: genomic DNA from Hippocampus from Sample470

description: genomic DNA from human brain

source_name: Hippocampus

value: UCLA

value: AD


title: HDbrain: genomic DNA from MotorCortex from Sample469

description: genomic DNA from human brain


title: CD4+ T-cells, + OVA, replicate_3 [HT_MG-430_PM]

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Following fragmentation, 5-6 micrograms of biotin-labeled targets were hybridized for 16 hr at 45C on an array. HT_MG-430_PM GeneChips were washed and stained in the Affymetrix GeneTitan system.

scan_protocol: HT_MG-430_PM plate arrays were scanned using the Affymetrix GeneTitan system.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console Software v1.1.

organism: Mus musculus

source_name: CD4+ T cells from DO11.10 TCR transgenic mice, stimulate with cognate peptide on macrophages as antigen presenting cells

label_protocol: For samples analyzed on the Affymetrix HT_MG-430_PM array, biotinylated cRNA was prepared from 100 ng of total RNA according to the standard Affymetrix 3’ IVT Express protocol (GeneChip 3’ IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix).

growth_protocol: Macrophages isolated from the peritoneal cavity 3 days after thioglycollate. Cells were washed, counted and plated in 24 well plates. T cells are from axial and cervical lymph nodes.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) according to the manufacturer's protocol.

treatment_protocol: IL-4 and IL-10 (10 ng/mL each) 12-16 hours followed by washing and replacement of the media. All RPMI media is derived from RPMI-SILAC and arginine, leucine or lysine added back at the percentage of normal RPMI as described. All CD4+ cells were sorted after 48 hours (LVV samples) or 72 hours (arg samples) using an iCyt high speed sorter gating on viable singlets. Cells were stained with anti-CD4 antibodies and washed extensively in FACS buffer prior to sorting. Lysis in Trizol was immediately after sorting the maximum living cells from each sample.

tag: strain/background

value: Balb/c

tag: genotype/variation

value: DO11.10 TCR transgenic

value: CD4+ T cells from axial and cervical lymph nodes (with macrophages from peritoneal cavity present)

tag: treatment

value: OVA


title: Group A 2

description: limited fluid resuscitation group

source_name: limited fluid resuscitation group

value: limited fluid resuscitation group


title: CD4+ T-cells, + OVA + IL-4 + IL-10, replicate_2 [HT_MG-430_PM]

source_name: CD4+ T cells from DO11.10 TCR transgenic mice, stimulate with cognate peptide on macrophages as antigen presenting cells where the latter was stimulated with IL-4 and IL-10 overnight to induce arginase-1 expression

tag: cell type

value: OVA + IL-4 + IL-10


title: CD4+ T-cells, untreated, replicate_2 [HT_MG-430_PM]

source_name: CD4+ T cells from DO11.10 TCR transgenic mice, (no cognate peptide control) on macrophages as antigen presenting cells


title: CD4+ T-cells, untreated, replicate_1 [HT_MG-430_PM]


title: CD4+ T-cells, + OVA, replicate_2 [HT_MG-430_PM]


title: CD4+ T-cells, untreated, replicate_3 [HT_MG-430_PM]


title: HDbrain: genomic DNA from Frontal from Sample467

description: genomic DNA from human brain

source_name: Frontal

tag: personid

tag: brainbank

value: NewZealand

value: male


title: HDbrain: genomic DNA from SensoryCortex from Sample464

description: genomic DNA from human brain

tag: broadbrainregion

tag: Sex

value: HD


title: CD4+ T-cells, + OVA + IL-4 + IL-10, replicate_1 [HT_MG-430_PM]


title: HDbrain: genomic DNA from InferiorParietal from Sample463

description: genomic DNA from human brain

value: Parietal

tag: disease

tag: caglength


title: CD4+ T-cells, + OVA, replicate_1 [HT_MG-430_PM]


title: HDbrain: genomic DNA from Frontal from Sample468

description: genomic DNA from human brain

value: other

tag: dnamage

tag: dnamagewindsorized


title: CR esg[ts]>ImdCA gut, biological rep3

value: dissected gut

tag: genotype

value: w; esgGAL4, tubGAL80[ts], UASGFP/+; UASImdCA/+


title: HDbrain: genomic DNA from CingulateGyrus from Sample465

description: genomic DNA from human brain

value: Limbic

tag: age

value: female

tag: postmorteminterval


title: HDbrain: genomic DNA from Frontal from Sample466

description: genomic DNA from human brain

value: UCLA


title: Group A 1

description: limited fluid resuscitation group

tag: strain

value: Sprague-Dawley (SD)

tag: gender

value: 90 and 120 days

tag: tissue

value: liver


title: HDbrain: genomic DNA from Hippocampus from Sample462

description: genomic DNA from human brain


title: HDbrain: genomic DNA from VisualCortex from Sample461

description: genomic DNA from human brain

source_name: VisualCortex

value: Occipital

value: Control


title: Group A 3

description: limited fluid resuscitation group

tag: treatment group

value: limited fluid resuscitation group


title: HDbrain: genomic DNA from Frontal from Sample460

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Temporal from Sample458

description: genomic DNA from human brain

source_name: Temporal

value: Temporal

value: AD


title: HDbrain: genomic DNA from CaudateNucleus from Sample459

description: genomic DNA from human brain

source_name: CaudateNucleus

value: NewZealand


title: HDbrain: genomic DNA from Mid from Sample456

description: genomic DNA from human brain

source_name: Mid

value: male


title: HDbrain: genomic DNA from SuperiorParietal from Sample457

description: genomic DNA from human brain

source_name: SuperiorParietal

value: Parietal


title: HDbrain: genomic DNA from CaudateNucleus from Sample455

description: genomic DNA from human brain

value: other


title: Sample B110: whole liver tissue

description: Sample B110: whole liver tissue (CH group)

source_name: whole liver sample

tag: tissue type

value: cirrhotic liver

tag: group

value: CH


title: HDbrain: genomic DNA from SuperiorParietal from Sample451

description: genomic DNA from human brain

tag: personid

value: HD


title: HDbrain: genomic DNA from Frontal from Sample453

description: genomic DNA from human brain

tag: brainbank


title: HDbrain: genomic DNA from Frontal from Sample448

description: genomic DNA from human brain

tag: broadbrainregion


title: HDbrain: genomic DNA from CaudateNucleus from Sample449

description: genomic DNA from human brain

tag: Sex


title: HDbrain: genomic DNA from VisualCortex from Sample446

description: genomic DNA from human brain

value: female

tag: disease


title: HDbrain: genomic DNA from Occipital from Sample439

description: genomic DNA from human brain

source_name: Occipital

value: UCLA

tag: caglength


title: HDbrain: genomic DNA from Frontal from Sample441

description: genomic DNA from human brain

tag: dnamage


title: HDbrain: genomic DNA from VisualCortex from Sample447

description: genomic DNA from human brain

tag: dnamagewindsorized


title: HDbrain: genomic DNA from CingulateGyrus from Sample445

description: genomic DNA from human brain

source_name: CingulateGyrus

value: Limbic


title: HDbrain: genomic DNA from CRBM from Sample442

description: genomic DNA from human brain

source_name: CRBM


title: HDbrain: genomic DNA from Occipital from Sample450

description: genomic DNA from human brain


title: HDbrain: genomic DNA from MotorCortex from Sample444

description: genomic DNA from human brain

source_name: MotorCortex


title: HDbrain: genomic DNA from Occipital from Sample443

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Temporal from Sample437

description: genomic DNA from human brain


title: HDbrain: genomic DNA from VisualCortex from Sample438

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample436

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CingulateGyrus from Sample434

description: genomic DNA from human brain


title: HDbrain: genomic DNA from VisualCortex from Sample435

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CaudateNucleus from Sample433

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample430

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Temporal from Sample431

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample432

description: genomic DNA from human brain


title: HDbrain: genomic DNA from MotorCortex from Sample454

description: genomic DNA from human brain


title: HDbrain: genomic DNA from VisualCortex from Sample452

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample429

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CRBM from Sample440

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample427

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Temporal from Sample426

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample423

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample428

description: genomic DNA from human brain


title: HDbrain: genomic DNA from InferiorParietal from Sample424

description: genomic DNA from human brain

source_name: InferiorParietal


title: HDbrain: genomic DNA from Frontal from Sample425

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SensoryCortex from Sample422

description: genomic DNA from human brain

source_name: SensoryCortex


title: HDbrain: genomic DNA from SensoryCortex from Sample421

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Hippocampus from Sample420

description: genomic DNA from human brain

source_name: Hippocampus


title: HDbrain: genomic DNA from CingulateGyrus from Sample419

description: genomic DNA from human brain


title: Sample B307: whole liver tissue

description: Sample B307: whole liver tissue (HCC group)

value: hepatocellular carcinoma

value: HCC


title: HDbrain: genomic DNA from CingulateGyrus from Sample418

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample413

description: genomic DNA from human brain

value: Occipital


title: HDbrain: genomic DNA from SensoryCortex from Sample414

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SuperiorParietal from Sample410

description: genomic DNA from human brain

value: Control


title: HDbrain: genomic DNA from Frontal from Sample415

description: genomic DNA from human brain


title: HDbrain: genomic DNA from MotorCortex from Sample412

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CingulateGyrus from Sample411

description: genomic DNA from human brain


title: HDbrain: genomic DNA from MotorCortex from Sample416

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SuperiorParietal from Sample406

description: genomic DNA from human brain


title: HDbrain: genomic DNA from VisualCortex from Sample404

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Temporal from Sample405

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SensoryCortex from Sample409

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CaudateNucleus from Sample403

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Temporal from Sample402

description: genomic DNA from human brain


title: HDbrain: genomic DNA from VisualCortex from Sample401

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CRBM from Sample398

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CRBM from Sample397

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CaudateNucleus from Sample399

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample395

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample396

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample394

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample417

description: genomic DNA from human brain


title: HDbrain: genomic DNA from VisualCortex from Sample407

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample392

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample408

description: genomic DNA from human brain


title: HDbrain: genomic DNA from InferiorParietal from Sample387

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Temporal from Sample391

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample390

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample383

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CRBM from Sample384

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CRBM from Sample389

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample380

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Hippocampus from Sample386

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample388

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Temporal from Sample381

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample382

description: genomic DNA from human brain


title: Group B 2

description: aggressive fluid resuscitation

source_name: aggressive fluid resuscitation

value: Sprague-Dawley (SD)

value: 90 and 120 days

value: liver

value: aggressive fluid resuscitation


title: HDbrain: genomic DNA from CRBM from Sample378

description: genomic DNA from human brain

value: male


title: HDbrain: genomic DNA from Frontal from Sample377

description: genomic DNA from human brain

value: AD


title: HDbrain: genomic DNA from Occipital from Sample379

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SuperiorParietal from Sample375

description: genomic DNA from human brain

value: NewZealand

value: Parietal


title: HDbrain: genomic DNA from Occipital from Sample376

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CRBM from Sample393

description: genomic DNA from human brain

value: other


title: HDbrain: genomic DNA from CingulateGyrus from Sample374

description: genomic DNA from human brain

value: HD


title: HDbrain: genomic DNA from Frontal from Sample373

description: genomic DNA from human brain

value: female


title: HDbrain: genomic DNA from Occipital from Sample372

description: genomic DNA from human brain

value: UCLA


title: HDbrain: genomic DNA from Frontal from Sample371

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CaudateNucleus from Sample369

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Temporal from Sample368

description: genomic DNA from human brain

value: Temporal


title: HDbrain: genomic DNA from SensoryCortex from Sample367

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Temporal from Sample385

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample370

description: genomic DNA from human brain


title: HDbrain: genomic DNA from MotorCortex from Sample366

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CRBM from Sample363

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample361

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Temporal from Sample362

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Mid from Sample360

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample364

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Mid from Sample359

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample358

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Hippocampus from Sample357

description: genomic DNA from human brain

value: Limbic


title: HDbrain: genomic DNA from Hippocampus from Sample356

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SensoryCortex from Sample353

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CRBM from Sample354

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SensoryCortex from Sample352

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample349

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample355

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CRBM from Sample348

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Temporal from Sample347

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CRBM from Sample344

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SensoryCortex from Sample342

description: genomic DNA from human brain


title: Glioma cell U87- after control transfection  48 hours

source_name: Glioma cell U87

tag: cell line

tag: transfection

value: control 48 hours


title: HDbrain: genomic DNA from Frontal from Sample343

description: genomic DNA from human brain

tag: age

tag: postmorteminterval


title: HDbrain: genomic DNA from Temporal from Sample340

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CRBM from Sample341

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SuperiorParietal from Sample365

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample339

description: genomic DNA from human brain

value: Occipital


title: HDbrain: genomic DNA from CRBM from Sample338

description: genomic DNA from human brain

value: Control


title: HDbrain: genomic DNA from Frontal from Sample337

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample336

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Hippocampus from Sample351

description: genomic DNA from human brain


title: HDbrain: genomic DNA from InferiorParietal from Sample332

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SuperiorParietal from Sample334

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CaudateNucleus from Sample330

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SensoryCortex from Sample350

description: genomic DNA from human brain


title: HDbrain: genomic DNA from InferiorParietal from Sample328

description: genomic DNA from human brain


title: HDbrain: genomic DNA from InferiorParietal from Sample333

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample329

description: genomic DNA from human brain


title: HDbrain: genomic DNA from InferiorParietal from Sample331

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample325

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Temporal from Sample346

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CaudateNucleus from Sample327

description: genomic DNA from human brain


title: HDbrain: genomic DNA from MotorCortex from Sample345

description: genomic DNA from human brain


title: HDbrain: genomic DNA from InferiorParietal from Sample324

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Hippocampus from Sample323

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Hippocampus from Sample326

description: genomic DNA from human brain


title: HDbrain: genomic DNA from VisualCortex from Sample320

description: genomic DNA from human brain


title: HDbrain: genomic DNA from MotorCortex from Sample319

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Temporal from Sample322

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample321

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SensoryCortex from Sample335

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SensoryCortex from Sample318

description: genomic DNA from human brain


title: HDbrain: genomic DNA from InferiorParietal from Sample317

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SuperiorParietal from Sample316

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Temporal from Sample315

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SensoryCortex from Sample314

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CingulateGyrus from Sample313

description: genomic DNA from human brain


title: HDbrain: genomic DNA from InferiorParietal from Sample311

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample308

description: genomic DNA from human brain


title: HDbrain: genomic DNA from InferiorParietal from Sample307

description: genomic DNA from human brain


title: HDbrain: genomic DNA from MotorCortex from Sample309

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CaudateNucleus from Sample310

description: genomic DNA from human brain


title: HDbrain: genomic DNA from VisualCortex from Sample303

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample301

description: genomic DNA from human brain


title: HDbrain: genomic DNA from VisualCortex from Sample302

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SensoryCortex from Sample300

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample299

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CRBM from Sample297

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SensoryCortex from Sample296

description: genomic DNA from human brain


title: HDbrain: genomic DNA from MotorCortex from Sample295

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Hippocampus from Sample292

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SuperiorParietal from Sample294

description: genomic DNA from human brain


title: HDbrain: genomic DNA from VisualCortex from Sample293

description: genomic DNA from human brain


title: HDbrain: genomic DNA from VisualCortex from Sample291

description: genomic DNA from human brain


title: HDbrain: genomic DNA from MotorCortex from Sample290

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample289

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Temporal from Sample288

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample312

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CRBM from Sample286

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample285

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CingulateGyrus from Sample306

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CaudateNucleus from Sample305

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample304

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CaudateNucleus from Sample400

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample282

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CRBM from Sample281

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CingulateGyrus from Sample298

description: genomic DNA from human brain


title: HDbrain: genomic DNA from InferiorParietal from Sample276

description: genomic DNA from human brain


title: HDbrain: genomic DNA from InferiorParietal from Sample275

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample278

description: genomic DNA from human brain


title: HDbrain: genomic DNA from MotorCortex from Sample274

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample277

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample272

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SensoryCortex from Sample273

description: genomic DNA from human brain


title: CD4+ T-cells, + OVA + IL-4 + IL-10, replicate_3 [HT_MG-430_PM]

source_name: CD4+ T cells from DO11.10 TCR transgenic mice, stimulate with cognate peptide on macrophages as antigen presenting cells where the latter was stimulated with IL-4 and IL-10 overnight to induce arginase-1 expression

tag: strain/background

value: Balb/c

tag: genotype/variation

value: DO11.10 TCR transgenic

tag: cell type

value: CD4+ T cells from axial and cervical lymph nodes (with macrophages from peritoneal cavity present)

tag: treatment

value: OVA + IL-4 + IL-10


title: HDbrain: genomic DNA from Temporal from Sample279

description: genomic DNA from human brain


title: HDbrain: genomic DNA from VisualCortex from Sample268

description: genomic DNA from human brain

value: male


title: HDbrain: genomic DNA from Occipital from Sample269

description: genomic DNA from human brain

value: AD


title: HDbrain: genomic DNA from MotorCortex from Sample267

description: genomic DNA from human brain

value: NewZealand


title: HDbrain: genomic DNA from CRBM from Sample287

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CingulateGyrus from Sample271

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Mid from Sample266

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CRBM from Sample265

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample264

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Hippocampus from Sample263

description: genomic DNA from human brain


title: HDbrain: genomic DNA from MotorCortex from Sample284

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CaudateNucleus from Sample283

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CRBM from Sample261

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CingulateGyrus from Sample260

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CRBM from Sample262

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SuperiorParietal from Sample259

description: genomic DNA from human brain

value: Parietal


title: HDbrain: genomic DNA from MotorCortex from Sample257

description: genomic DNA from human brain

value: other


title: HDbrain: genomic DNA from InferiorParietal from Sample256

description: genomic DNA from human brain

value: HD


title: HDbrain: genomic DNA from CRBM from Sample280

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample255

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SensoryCortex from Sample252

description: genomic DNA from human brain

value: female


title: HDbrain: genomic DNA from CaudateNucleus from Sample254

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample270

description: genomic DNA from human brain

value: UCLA


title: HDbrain: genomic DNA from Frontal from Sample253

description: genomic DNA from human brain

source_name: Frontal


title: HDbrain: genomic DNA from SensoryCortex from Sample245

description: genomic DNA from human brain

value: Temporal


title: HDbrain: genomic DNA from SuperiorParietal from Sample243

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample246

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SuperiorParietal from Sample244

description: genomic DNA from human brain


title: HDbrain: genomic DNA from InferiorParietal from Sample247

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample241

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample250

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CRBM from Sample248

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CRBM from Sample240

description: genomic DNA from human brain


title: HDbrain: genomic DNA from InferiorParietal from Sample242

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample239

description: genomic DNA from human brain


title: HDbrain: genomic DNA from MotorCortex from Sample238

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample237

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SuperiorParietal from Sample236

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Temporal from Sample235

description: genomic DNA from human brain


title: HDbrain: genomic DNA from VisualCortex from Sample258

description: genomic DNA from human brain

source_name: VisualCortex


title: HDbrain: genomic DNA from CaudateNucleus from Sample231

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Temporal from Sample234

description: genomic DNA from human brain

source_name: Temporal


title: HDbrain: genomic DNA from Occipital from Sample233

description: genomic DNA from human brain


title: HDbrain: genomic DNA from VisualCortex from Sample230

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Hippocampus from Sample228

description: genomic DNA from human brain

value: Limbic


title: HDbrain: genomic DNA from Temporal from Sample251

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CaudateNucleus from Sample249

description: genomic DNA from human brain

source_name: CaudateNucleus


title: HDbrain: genomic DNA from VisualCortex from Sample227

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SensoryCortex from Sample226

description: genomic DNA from human brain


title: HDbrain: genomic DNA from VisualCortex from Sample225

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CingulateGyrus from Sample224

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample223

description: genomic DNA from human brain


title: HDbrain: genomic DNA from MotorCortex from Sample217

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample221

description: genomic DNA from human brain


title: HDbrain: genomic DNA from VisualCortex from Sample215

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SuperiorParietal from Sample222

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Hippocampus from Sample216

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample220

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CaudateNucleus from Sample218

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CRBM from Sample219

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CRBM from Sample214

description: genomic DNA from human brain


title: HDbrain: genomic DNA from VisualCortex from Sample213

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SuperiorParietal from Sample210

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample212

description: genomic DNA from human brain


title: HDbrain: genomic DNA from MotorCortex from Sample211

description: genomic DNA from human brain


title: HDbrain: genomic DNA from MotorCortex from Sample209

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample232

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample206

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample207

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample203

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample229

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample204

description: genomic DNA from human brain


title: HDbrain: genomic DNA from VisualCortex from Sample205

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CRBM from Sample202

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CaudateNucleus from Sample201

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CRBM from Sample199

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Hippocampus from Sample198

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CRBM from Sample200

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Hippocampus from Sample197

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SuperiorParietal from Sample196

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CRBM from Sample208

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Hippocampus from Sample195

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Hippocampus from Sample193

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Hippocampus from Sample194

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Mid from Sample192

description: genomic DNA from human brain

source_name: Mid


title: HDbrain: genomic DNA from Frontal from Sample188

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CingulateGyrus from Sample190

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SuperiorParietal from Sample187

description: genomic DNA from human brain

source_name: SuperiorParietal


title: HDbrain: genomic DNA from MotorCortex from Sample189

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CingulateGyrus from Sample186

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CingulateGyrus from Sample191

description: genomic DNA from human brain


title: HDbrain: genomic DNA from MotorCortex from Sample184

description: genomic DNA from human brain


title: HDbrain: genomic DNA from InferiorParietal from Sample183

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CaudateNucleus from Sample185

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SensoryCortex from Sample181

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample180

description: genomic DNA from human brain


title: HDbrain: genomic DNA from VisualCortex from Sample182

description: genomic DNA from human brain


title: HDbrain: genomic DNA from VisualCortex from Sample178

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CaudateNucleus from Sample176

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Mid from Sample175

description: genomic DNA from human brain


title: HDbrain: genomic DNA from MotorCortex from Sample177

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SuperiorParietal from Sample179

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Hippocampus from Sample173

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CaudateNucleus from Sample171

description: genomic DNA from human brain


title: HDbrain: genomic DNA from MotorCortex from Sample174

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Hippocampus from Sample168

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample172

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SensoryCortex from Sample167

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CingulateGyrus from Sample169

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample170

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SensoryCortex from Sample165

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Mid from Sample166

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Hippocampus from Sample164

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CingulateGyrus from Sample162

description: genomic DNA from human brain


title: HDbrain: genomic DNA from InferiorParietal from Sample163

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Mid from Sample161

description: genomic DNA from human brain


title: HDbrain: genomic DNA from MotorCortex from Sample157

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Mid from Sample159

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample158

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SensoryCortex from Sample160

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Hippocampus from Sample156

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CaudateNucleus from Sample154

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SensoryCortex from Sample153

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CingulateGyrus from Sample152

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CaudateNucleus from Sample151

description: genomic DNA from human brain


title: HDbrain: genomic DNA from InferiorParietal from Sample149

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Temporal from Sample148

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Mid from Sample146

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Mid from Sample147

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SuperiorParietal from Sample150

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Mid from Sample145

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Hippocampus from Sample144

description: genomic DNA from human brain


title: HDbrain: genomic DNA from VisualCortex from Sample140

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Mid from Sample142

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Hippocampus from Sample143

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SuperiorParietal from Sample139

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CingulateGyrus from Sample138

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CRBM from Sample137

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Mid from Sample155

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample136

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SensoryCortex from Sample135

description: genomic DNA from human brain


title: HDbrain: genomic DNA from VisualCortex from Sample133

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SensoryCortex from Sample127

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample130

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CRBM from Sample132

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Hippocampus from Sample129

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CaudateNucleus from Sample131

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Mid from Sample126

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SuperiorParietal from Sample124

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Hippocampus from Sample125

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SuperiorParietal from Sample134

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Temporal from Sample123

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CingulateGyrus from Sample141

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SuperiorParietal from Sample120

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Mid from Sample122

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Mid from Sample118

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample116

description: genomic DNA from human brain


title: HDbrain: genomic DNA from MotorCortex from Sample115

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CingulateGyrus from Sample114

description: genomic DNA from human brain


title: HDbrain: genomic DNA from InferiorParietal from Sample117

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Temporal from Sample128

description: genomic DNA from human brain


title: HDbrain: genomic DNA from InferiorParietal from Sample121

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CaudateNucleus from Sample119

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Mid from Sample111

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CingulateGyrus from Sample112

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample113

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Hippocampus from Sample108

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SensoryCortex from Sample107

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CaudateNucleus from Sample106

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Hippocampus from Sample105

description: genomic DNA from human brain


title: p53_Set_2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

description: Gene Expression 48 hours post transfection

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60ºC and hybridized on to a Agilent Human Gene Expression Microarray 8x60K (AMADID No: 39494) arrays. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D)

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX Version  software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift

source_name: p53_H1299 Cells

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Cells were grown in DMEM, and seeded 14 hours prior to transfection

extract_protocol: RNA was prepared with Qiagen Rneasy kit

treatment_protocol: 500ng of DNA was transfected in cells with Lipofectamine 2000 according to manufacturer's protocol. Cells were harvested 48 hours post transfection and total RNA was isolated with Qiagen Rneasy kit.

value: Lung Carcinoma Cell line H1299

value: plasmid construct expressing p53 alone


title: 14A_Set_2

source_name: 14A_H1299 Cells

value: plasmid construct expressing p53 and p47


title: p53_Set_1


title: HDbrain: genomic DNA from Occipital from Sample110

description: genomic DNA from human brain

source_name: Occipital

value: Occipital

value: Control


title: HDbrain: genomic DNA from Mid from Sample109

description: genomic DNA from human brain


title: 14A_Set_1


title: p47_Set_2

source_name: p47_H1299 Cells

value: plasmid construct expressing p47 alone


title: Irf37d3_205

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

data_processing: The scanned images were analyzed with Feature Extraction Software10.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: lung

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS 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.

extract_protocol: RNA was prepared using Qiagen RNAeasy Kit. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Female mice were intranasally infected with influenza PR8M virus with 20μl virus solution or mock infected (with PBS).

tag: gender

value: Female

tag: infection

value: infected with PR8M virus

tag: strain

value: Irf3/7 mutant


title: GFP_Set_2

source_name: GFP_H1299 Cells

value: plasmid construct expressing GFP


title: p47_Set_1


title: GFP_Set_1


title: Irf37d3_219


title: Irf37d3_220


title: Irf37md3_203

value: mock


title: EpOC from UC patient [154S]

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

institute: IDIBAPS

description: Gene expression data of EpOC; in vitro organoid culture derived from biopsy sample of UC patient.

hyb_protocol: Standard Affymetrix protocol

data_processing: The data were analyzed with Bioconductor tools in R (version 3.1.0; http://www.r-project.org) using GC-RMA as normalization method. Next we employ a probe-filtering step, excluding those probes that showed a lower coefficient of variation or which were non-informative (not annotated).

source_name: EpOC from biopsy sample of UC patient

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

growth_protocol: Crypts from descending/sigmoid colon samples were isolated by EDTA treatment. Crypt units were embedded in Matrigel, expanded for 3-4 days in "stem medium" and dissociated. Single epithelial cells were replated in fresh "stem medium" according to a 1:3 dilution. At day 5 of in vitro expansion, total RNA was isolated from the EpOCs. Part of the EpOCs was induced to differentiate (d-EpOCs) by the addition of fresh "differentiation medium". Total RNA was isolated from d-EpOCs 5 days after differentiation.

extract_protocol: Total RNA was extracted using Trizol+RNA Cleanup protocol by RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

value: ulcerative colitis (UC) patient

value: EpOC

tag: tissue

value: sigmoid colon

tag: uc_evolution_time (years)

tag: age (years)


title: HDbrain: genomic DNA from Temporal from Sample103

description: genomic DNA from human brain

tag: personid

tag: brainbank

value: UCLA

tag: broadbrainregion

tag: Sex

value: male

tag: disease

tag: caglength


title: d-EpOC from UC patient [154D]

description: Gene expression data of d-EpOC; in vitro organoid culture derived from biopsy sample of UC patient.

source_name: d-EpOC from biopsy sample of UC patient

value: d-EpOC


title: HDbrain: genomic DNA from InferiorParietal from Sample104

description: genomic DNA from human brain

source_name: InferiorParietal

value: NewZealand

value: Parietal

tag: age

value: female

tag: dnamage

tag: dnamagewindsorized

tag: postmorteminterval


title: Irf37md3_218

tag: genotype/variation


title: 72h Tet-induction_biological Rep 3

city: Durham

first: Nicole

last: Calakos

state: NC

address: 311 Research Dr

department: Neurology

institute: Duke University

hyb_protocol: Hybridization targets were prepared with a MessageAmp Premier RNA Amplification Kit (Applied Biosystems/Ambion) from total RNA, hybridized to GeneChip U133 Plus 2.0 arrays in Affymetrix GeneChip Hybridization Oven 645, washed in Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned with Affymetrix GeneChip Scanner 7G according to standard Affymetrix GeneChip hybridization, wash, and stain protocols (Affymetrix).

data_processing: The Affymetrix Gene Chip microarray data underwent strict quality control processing using the simpleaffy package in Bioconductor. Log-scale Robust Multiarray Analysis (RMA) from the affy package in Bioconductor was used for normalization to eliminate systematic differences across the arrays. The mas5 algorithm from the affy package was used to make present/absent calls. The MAS5 signal data and presence/absence calls are available in the file MAS5_signal_and_abs_call.txt on the series record.

source_name: Assay cell line 72 h after tetracycline induction of EGFP-∆E302/3-hTorsin1a

label_protocol: Label protocol not provided.

growth_protocol: Flp-In T-REx 293 cells inducibly expressing  ΔE302/3 Torsin1a were maintained in selective media  [DMEM-HG (Thermo Fisher Scientific #11965) + 1x GlutaMax (Thermo Fisher Scientific #35050-061) + 75 µg/mL hygromycin (Thermo Fisher Scientific #10687-010) + 15 µg/mL blasticidin S (Thermo Fisher Scientific #R210-01)  + 10% tetracycline screened FBS (Hyclone #SH30070.03T) + 1% penicillin/streptomycin/amphotericin (Mediatech Inc. #30-004-Cl)].

extract_protocol: Total RNA was extracted using the RNeasy RNA extraction kit (Qiagen #74104) as per manufacturer’s protocol. The quality of the RNA was assessed with an 2100 Bioanalyzer G2939A (Agilent Technologies) and Nanodrop 8000 spectrophotometer (Thermo Scientific).

treatment_protocol: Flp-In T-REx 293 cells inducibly expressing ΔE302/3 Torsin1a were seeded at 2x10^6 cells per 10 cm^2 dish.  Cells were treated with tetracycline (5 µg/mL, Sigma # 87128) or PBS (uninduced control) 24 h after initial plating.  Cells were harvested 72 h after tetracycline induction

tag: cell line

tag: overexpression status

value: Flp-In T-REx 293T cells overexpressing EGFP-deltaE302/3-hTorsin1a


title: EpOC from non-IBD control [155S]

description: Gene expression data of EpOC; in vitro organoid culture derived from surgical sample of non-IBD control.

source_name: EpOC from surgical sample of non-IBD control

value: non-IBD control


title: MYCN siRNA 2 transfected

city: Randwick

first: Chengyuan

last: Xue

state: NSW

address: PO Box 81

department: Molecular Diagnostics

country: Australia

institute: Children's Cancer Institute

description: Gene expression data from neuroblastoma cells with knockdown of MYCN

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray scanner.

data_processing: Images were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Neuroblastoma BE(2)-C cells transfected with N-Myc siRNA

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

extract_protocol: Extraction of total RNA was performed unsing Rneasy Plus Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol:
Cell Culture: Neuroblastoma BE(2)-C cells were cultured in DME medium supplemented with 10% fetal calf serum.
Cells were transfected with control siRNA, MYCN siRNA1, MYCN siRNA2, TFAP4 siRNA1 or TFAP4 siRNA2 for 30 hours.

value: peripheral nervous system tumour cell

value: MYCN-amplified neuroblastoma cells

tag: gene knockdown

value: transfected with MYCN siRNA


title: Irf37md3_201

tag: gender

value: Female

tag: infection

tag: strain

value: Irf3/7 mutant


title: HDbrain: genomic DNA from MotorCortex from Sample99

description: genomic DNA from human brain

source_name: MotorCortex

tag: personid

value: other

value: Control


title: HDbrain: genomic DNA from Frontal from Sample101

description: genomic DNA from human brain

source_name: Frontal

tag: brainbank

value: AD


title: HDbrain: genomic DNA from Mid from Sample102

description: genomic DNA from human brain

tag: broadbrainregion

value: HD


title: HDbrain: genomic DNA from CRBM from Sample100

description: genomic DNA from human brain

source_name: CRBM

value: UCLA

tag: Sex


title: d-EpOC from UC patient [153D]

value: ulcerative colitis (UC) patient

tag: tissue

value: sigmoid colon

tag: uc_evolution_time (years)

tag: age (years)


title: HDbrain: genomic DNA from VisualCortex from Sample98

description: genomic DNA from human brain

source_name: VisualCortex

value: NewZealand

value: Occipital

tag: age

value: male

tag: disease

tag: caglength

tag: dnamage


title: MYCN siRNA 1 transfected

tag: genotype/variation


title: TFAP4 siRNA 2 transfected

description: Gene expression data from neuroblastoma cells with knockdown of TFAP4

source_name: Neuroblastoma BE(2)-C cells transfected with TFAP4 siRNA

value: transfected with TFAP4 siRNA


title: Irf7d3_119

value: infected with PR8M virus

value: Irf7 mutant


title: 72h Tet-induction_biological Rep 2

tag: cell line

tag: overexpression status

value: Flp-In T-REx 293T cells overexpressing EGFP-deltaE302/3-hTorsin1a


title: TL control siRNA transfected

description: Gene expression data from control neuroblastoma cells

source_name: Neuroblastoma BE(2)-C cells transfected with control siRNA

value: peripheral nervous system tumour cell

value: MYCN-amplified neuroblastoma cells

tag: gene knockdown

value: transfected with control siRNA


title: TFAP4 siRNA 1 transfected


title: Irf7d3_106

tag: gender

value: Female

tag: infection


title: Irf7d3_107

tag: strain


title: EpOC from UC patient [153S]

value: EpOC


title: 72h Tet-induction_biological Rep 1


title: HDbrain: genomic DNA from InferiorParietal from Sample97

description: genomic DNA from human brain

tag: personid

tag: brainbank

value: Parietal

value: female

value: Control

tag: dnamagewindsorized

tag: postmorteminterval


title: HDbrain: genomic DNA from Hippocampus from Sample96

description: genomic DNA from human brain

source_name: Hippocampus

value: UCLA

tag: broadbrainregion

value: Limbic

tag: Sex


title: HDbrain: genomic DNA from Frontal from Sample95

description: genomic DNA from human brain

value: other

tag: age

value: AD


title: EpOC from UC patient [136S]

value: ulcerative colitis (UC) patient

tag: tissue

value: sigmoid colon

tag: uc_evolution_time (years)

tag: age (years)


title: EpOC from non-IBD control [149S]

value: non-IBD control


title: Irf7md3_104

value: mock

tag: genotype/variation

value: Irf7 mutant


title: d-EpOC from UC patient [136D]

value: d-EpOC


title: HDbrain: genomic DNA from CingulateGyrus from Sample94

description: genomic DNA from human brain

source_name: CingulateGyrus

value: NewZealand

tag: disease

tag: caglength

tag: dnamage


title: CX control siRNA transfected

value: peripheral nervous system tumour cell

value: MYCN-amplified neuroblastoma cells

tag: gene knockdown

value: transfected with control siRNA


title: HDbrain: genomic DNA from CingulateGyrus from Sample93

description: genomic DNA from human brain

value: male

value: HD


title: Irf7md3_102

tag: gender

value: Female

tag: infection


title: HDbrain: genomic DNA from Frontal from Sample92

description: genomic DNA from human brain

tag: personid

value: Control


title: EpOC from UC patient [134S]

value: EpOC


title: d-EpOC from UC patient [134D]


title: HDbrain: genomic DNA from MotorCortex from Sample91

description: genomic DNA from human brain

tag: brainbank

value: other


title: Irf3md3_41

tag: strain

value: Irf3 mutant


title: 4200270056_D

city: singapore

first: Qiang

last: Yu

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Genespring

label: Biotin

source_name: Normal N31

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with nanodrop

tag: subject status

value: colorectal cancer

value: Colon

tag: tissue type

value: Normal non-cancerous tissue


title: 4200270056_B

source_name: Normal N29


title: Irf3d3_46

source_name: lung

value: infected with PR8M virus


title: Irf3md3_35

value: mock


title: d-EpOC from non-IBD control [117D]

description: Gene expression data of d-EpOC; in vitro organoid culture derived from surgical sample of non-IBD control.

source_name: d-EpOC from surgical sample of non-IBD control

value: non-IBD control

value: d-EpOC

value: sigmoid colon


title: Irf3d3_40


title: d-EpOC from non-IBD control [128D]


title: wtd3_2

value: WT


title: EpOC from non-IBD control [128S]


title: EpOC from UC patient [129S]

source_name: EpOC from biopsy sample of UC patient

value: ulcerative colitis (UC) patient


title: 4200270048_G

source_name: Primary Tumor T28

value: Tumor tissue


title: HDbrain: genomic DNA from Hippocampus from Sample90

description: genomic DNA from human brain

value: UCLA

tag: broadbrainregion

value: Limbic

tag: Sex

value: male

value: HD

tag: dnamagewindsorized

tag: postmorteminterval


title: 4200270056_C

source_name: Primary Tumor T31

tag: tissue


title: EpOC from non-IBD control [117S]

source_name: EpOC from surgical sample of non-IBD control

value: EpOC

tag: age (years)


title: 4200270048_H

source_name: Normal N28


title: HDbrain: genomic DNA from Temporal from Sample89

description: genomic DNA from human brain

source_name: Temporal

value: Temporal

tag: age

tag: disease


title: HDbrain: genomic DNA from Temporal from Sample88

description: genomic DNA from human brain

tag: caglength

tag: dnamage


title: HDbrain: genomic DNA from SuperiorParietal from Sample87

description: genomic DNA from human brain

source_name: SuperiorParietal

value: NewZealand

value: Parietal


title: wtd3_1

tag: gender

value: Female

tag: genotype/variation


title: Irf3d3_52

tag: infection

value: infected with PR8M virus

value: Irf3 mutant


title: HDbrain: genomic DNA from SuperiorParietal from Sample86

description: genomic DNA from human brain

tag: personid

tag: brainbank

value: Control


title: 4200270056_A

source_name: Primary Tumor T29

tag: subject status

value: colorectal cancer

value: Colon


title: 4200270048_E

source_name: Primary Tumor T27

tag: tissue type


title: EpOC from non-IBD control [113S]

description: Gene expression data of EpOC; in vitro organoid culture derived from biopsy sample of non-IBD control.

source_name: EpOC from biopsy sample of non-IBD control

value: non-IBD control

value: sigmoid colon


title: d-EpOC from non-IBD control [115D]

value: d-EpOC


title: HDbrain: genomic DNA from MotorCortex from Sample85

description: genomic DNA from human brain

source_name: MotorCortex

tag: broadbrainregion

value: other

value: female


title: 4200270048_D

source_name: Normal N26

value: Normal non-cancerous tissue


title: 4200270048_F

source_name: Normal N27


title: d-EpOC from UC patient [129D]

source_name: d-EpOC from biopsy sample of UC patient

value: ulcerative colitis (UC) patient

tag: uc_evolution_time (years)


title: d-EpOC from non-IBD control [113D]

description: Gene expression data of d-EpOC; in vitro organoid culture derived from biopsy sample of non-IBD control.

source_name: d-EpOC from biopsy sample of non-IBD control


title: Irf3md3_34

source_name: lung

value: mock

tag: strain


title: HDbrain: genomic DNA from CaudateNucleus from Sample84

description: genomic DNA from human brain

source_name: CaudateNucleus

tag: Sex

value: male

value: HD

tag: dnamagewindsorized

tag: postmorteminterval


title: 4200270048_A

source_name: Primary Tumor T25

tag: tissue

value: Tumor tissue


title: EpOC from non-IBD control [115S]

value: EpOC

tag: age (years)


title: wtmd3_41

value: Female

value: WT


title: HDbrain: genomic DNA from SuperiorParietal from Sample83

description: genomic DNA from human brain

value: NewZealand

value: Parietal

tag: age

tag: disease

value: Control

tag: caglength


title: d-EpOC from non-IBD control [112D]

value: non-IBD control


title: wtmd3_15

tag: gender

tag: genotype/variation


title: HDbrain: genomic DNA from CingulateGyrus from Sample82

description: genomic DNA from human brain

source_name: CingulateGyrus

tag: personid

value: Limbic

tag: dnamage


title: wtmd3_16

tag: infection


title: CD4+ T-cells, + 1% Lys, replicate_2 [MoGene-2_0-st]

hyb_protocol: Following fragmentation, 5-6 micrograms of biotin-labeled targets were hybridized for 16 hr at 45C on an array. Mouse Gene 2.0 ST GeneChips were washed and stained using the Affymetrix Fluidics Station 450.

scan_protocol: Mouse Gene 2.0 ST GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

source_name: CD4+ T cells from DO11.10 TCR transgenic mice, stimulate with macrophages in media containing 1% lysine in normal RPMI (no TCR activation)

label_protocol: For samples analyzed on the Affymetrix Mouse Gene 2.0 ST array, sense target cDNA was prepared from 100ng of total RNA using the Ambion® WT Expression Kit (Life Technologies P/N 4411973). cDNA was fragmented and biotin-labeled using the Affymetrix® GeneChip® WT Terminal Labeling Kit (Affymetrix P/N 900671).

tag: strain/background

value: Balb/c

value: DO11.10 TCR transgenic

tag: cell type

value: CD4+ T cells from axial and cervical lymph nodes (with macrophages from peritoneal cavity present)

tag: treatment

value: 1% Lys


title: HDbrain: genomic DNA from InferiorParietal from Sample81

description: genomic DNA from human brain

source_name: InferiorParietal

tag: brainbank

tag: broadbrainregion

value: female


title: CD4+ T-cells, + 1% Lys, replicate_3 [MoGene-2_0-st]


title: EpOC from non-IBD control [112S]

value: sigmoid colon


title: 4200270047_H

source_name: Normal N24

tag: subject status

value: colorectal cancer

value: Colon

tag: tissue type

value: Normal non-cancerous tissue


title: 4200270048_C

source_name: Primary Tumor T26

tag: tissue

value: Tumor tissue


title: wtd3_5

value: Female

value: infected with PR8M virus

tag: strain


title: 4200270047_G

source_name: Primary Tumor T24


title: 4200270048_B

source_name: Normal N25


title: EpOC from non-IBD control [94S]

source_name: EpOC from surgical sample of non-IBD control

value: EpOC

tag: age (years)


title: HDbrain: genomic DNA from CingulateGyrus from Sample79

description: genomic DNA from human brain

value: NewZealand

tag: age

tag: Sex

tag: disease

value: HD

tag: dnamagewindsorized

tag: postmorteminterval


title: CD4+ T-cells, + 1% Leu, replicate_3 [MoGene-2_0-st]

source_name: CD4+ T cells from DO11.10 TCR transgenic mice, stimulate with macrophages in media containing 1% leucine in normal RPMI (no TCR activation)

tag: genotype/variation

value: 1% Leu


title: EpOC from non-IBD control [92S]

source_name: EpOC from biopsy sample of non-IBD control

value: non-IBD control


title: d-EpOC from non-IBD control [94D]

source_name: d-EpOC from surgical sample of non-IBD control

value: d-EpOC


title: d-EpOC from non-IBD control [92D]


title: HDbrain: genomic DNA from Frontal from Sample78

description: genomic DNA from human brain

source_name: Frontal

tag: personid

value: UCLA

value: other

value: AD

tag: caglength

tag: dnamage


title: CD4+ T-cells, + 1% Lys, replicate_1 [MoGene-2_0-st]

tag: strain/background

value: Balb/c

value: DO11.10 TCR transgenic

tag: cell type

value: CD4+ T cells from axial and cervical lymph nodes (with macrophages from peritoneal cavity present)

tag: treatment

value: 1% Lys


title: d-EpOC from UC patient [91D]

source_name: d-EpOC from biopsy sample of UC patient

value: ulcerative colitis (UC) patient

value: sigmoid colon

tag: uc_evolution_time (years)


title: HDbrain: genomic DNA from Temporal from Sample77

description: genomic DNA from human brain

source_name: Temporal

tag: brainbank

tag: broadbrainregion

value: Temporal

value: female

value: Control


title: CD4+ T-cells, + 1% Leu, replicate_2 [MoGene-2_0-st]


title: 4200270047_E

source_name: Primary Tumor T23

tag: subject status

value: colorectal cancer

tag: tissue

value: Colon

tag: tissue type

value: Tumor tissue


title: d-EpOC from non-IBD control [149D]

value: non-IBD control

tag: age (years)


title: 4200270047_F

source_name: Normal N23

value: Normal non-cancerous tissue


title: HDbrain: genomic DNA from CingulateGyrus from Sample80

description: genomic DNA from human brain

value: NewZealand

value: Limbic

tag: age

tag: Sex

value: male

tag: disease


title: 4200270047_B

source_name: Normal N21


title: 4200270047_D

source_name: Normal N22


title: d-EpOC from non-IBD control [90D]

source_name: d-EpOC from biopsy sample of non-IBD control

value: d-EpOC

value: descending colon


title: CD4+ T-cells, + 1% Arg, replicate_1 [MoGene-2_0-st]

source_name: CD4+ T cells from DO11.10 TCR transgenic mice, stimulate with macrophages in media containing 1% arginine in normal RPMI (no TCR activation)

value: Balb/c

tag: genotype/variation

value: DO11.10 TCR transgenic

value: CD4+ T cells from axial and cervical lymph nodes (with macrophages from peritoneal cavity present)

value: 1% Arg


title: CD4+ T-cells, + 1% Arg, replicate_2 [MoGene-2_0-st]


title: 4200270047_C

source_name: Primary Tumor T22


title: Irf7md3_103

source_name: lung

tag: gender

value: Female

tag: infection

value: mock

tag: strain

value: Irf7 mutant


title: HDbrain: genomic DNA from Mid from Sample76

description: genomic DNA from human brain

source_name: Mid

tag: personid

value: UCLA

value: other

value: female

value: AD

tag: caglength

tag: dnamage

tag: dnamagewindsorized

tag: postmorteminterval


title: CD4+ T-cells, + OVA + 1% Lys, replicate_3 [MoGene-2_0-st]

source_name: CD4+ T cells from DO11.10 TCR transgenic mice, stimulate with cognate peptide on macrophages as antigen presenting cells in media containing 1% of lysine in normal RPMI

tag: strain/background

tag: cell type

tag: treatment

value: OVA + 1% Lys


title: 4200270047_A

source_name: Primary Tumor T21

tag: subject status

value: colorectal cancer

tag: tissue

value: Colon

tag: tissue type

value: Tumor tissue


title: HDbrain: genomic DNA from Frontal from Sample75

description: genomic DNA from human brain

tag: brainbank

tag: broadbrainregion

tag: age

tag: Sex

value: male

value: Control


title: 4200270046_H

source_name: Normal N20

value: Normal non-cancerous tissue


title: CD4+ T-cells, + OVA + 1% Lys, replicate_1 [MoGene-2_0-st]

value: Balb/c

tag: genotype/variation

value: DO11.10 TCR transgenic


title: EpOCs from non-IBD control [90S]

source_name: EpOC from biopsy sample of non-IBD control

value: non-IBD control

value: EpOC

value: descending colon

tag: age (years)