title: HCC Tumor Tissue LCS_560A


title: AS_A8_1-16-0525-3

status: Public on Jun 27 2017

type: RNA

city: Boston

first: Joseph

last: Perez-Rogers

state: MA

address: 72 East Concord St

department: Bioinformatics

country: USA

institute: Boston University

description: Gene expression data from NEC specimen

hyb_protocol: The labeled, fragmented DNA was hybridized to the GeneChip Human Gene 1.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm).  The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: All 505 microarray CEL files were normalized together using the RMA algorithm implemented in the affy Bioconductor R package and the corresponding default Gene 1.0 ST CDF. ComBat (sva Bioconductor package) was used to correct for microarray batch effects. No covariates other than batch were included in the ComBat model.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: NEC specimen

label_protocol: Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).

growth_protocol: not applicable

extract_protocol: Total RNA isolated using miRNeasy kit from Qiagen, quantified using Nanodrop and quality determined using Bioanalyzer 2100 (Life Technologies). RNA was amplified using Ambion WT expression kit (Life Technologies).

treatment_protocol: not applicable

tag: lung cancer status

value: Lung Cancer

tag: smoking status

value: Current Smoker

tag: time since quit

tag: mass size

tag: age

tag: gender

value: Male

tag: rin

tag: batch

tag: pack years


title: CCA Tumor Tissue LCS_616A

city: Bethesda

first: Xin

middle: Wei

last: Wang

state: MD

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures using GeneChip Scanner 3000 and AGCC software

data_processing: Raw gene expression data were analyzed on gene level and normalized using the Robust Multi-array Average (RMA) method and sketch-quantile normalization method on Affymetrix Expression Console Software Build 1.3.1.187.

source_name: CCA Tumor Tissue

label_protocol: Standard Affymetrix procedures

extract_protocol: Total RNA was isolated from frozen tissues using TRIzol (Invitrogen, Carlsbad, CA) according to the manufacturer's protocol. RNA integrity for each sample was confirmed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: tissue

value: Liver Tumor Tissue

tag: disease state

value: Cholangiocarcinoma (CCA)

tag: individual


title: HCC Tumor Tissue LCS_548A

type: genomic

scan_protocol: Standard Affymetrix procedures using GeneChip Scanner 3000 uisng AGCC software

data_processing:
PARTEK Genomic suite (6.6) was used to import allele intensity from the CEL files. Interrogating probes was imported without filtering probes. Adjusmentt for fragment length and probe sequence was performed using the Partek default option. Post import values were corrected for localized GC content using the inbuilt Partek feature based on methods described in Diskin et al. (Nucleic Acids Research. 2008. 36:19). Copy number data was estimated from signal intensity on Affmetrix SNP 6.0 arrays. Copy number ratio values were generated in Partek Genomics Suite (v 6.6) using a paired non-tumor sample as reference following the paired workflow.
Copy number ratio values of tumor sample using a paired non-tumor sample as reference (total 153 columns)

molecule: genomic DNA

source_name: HCC Tumor Tissue

extract_protocol: Total DNA was extracted from frozen tissue using Phenol/Chloroform extraction protocol. Samples with sufficient amount of double-stranded DNA as confirmed by Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific) were included for array studies.

value: Hepatocellular carcinoma (HCC)

tag: sample name matched with transcriptome data


title: CCA Non-Tumor Tissue LCS_614B

source_name: CCA Non-Tumor Tissue

value: Liver Non-Tumor Tissue


title: CCA Non-Tumor Tissue LCS_613B


title: CCA Tumor Tissue LCS_614A


title: CCA Non-Tumor Tissue LCS_612B


title: AS_A3_1-16-0527-3

description: Gene expression data from NEC specimen

value: Female


title: CCA Tumor Tissue LCS_577A


title: HCC Tumor Tissue LCS_562A


title: CCA Tumor Tissue LCS_599A


title: CCA Tumor Tissue LCS_638A


title: CCA Non-Tumor Tissue LCS_610B


title: HCC Tumor Tissue LCS_538A


title: CCA Tumor Tissue LCS_610A


title: AS_B3_7858_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen

value: Former Smoker


title: CCA Tumor Tissue LCS_609A


title: CCA Non-Tumor Tissue LCS_609B


title: AS_B8_7915_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_624A


title: CCA Tumor Tissue LCS_675A


title: AS_D4_7889_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen

value: No Lung Cancer

value: Ill defined infiltrate


title: CCA Tumor Tissue LCS_608A


title: CCA Tumor Tissue LCS_604A


title: AS_B5_1-16-0538-3

description: Gene expression data from NEC specimen


title: AS_A3_1-12-0535-3

description: Gene expression data from NEC specimen


title: HCC Tumor Tissue LCS_549A


title: CCA Tumor Tissue LCS_606A


title: CCA Non-Tumor Tissue LCS_604B


title: AS_E4_1-16-0536-3

description: Gene expression data from NEC specimen


title: AS_F7_7892_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_606B


title: CCA Tumor Tissue LCS_603A


title: CCA Non-Tumor Tissue LCS_603B


title: AS_D3_1-25-0519-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_626A


title: HCC Tumor Tissue LCS_529A


title: AS_A5_1-12-0004-3

description: Gene expression data from NEC specimen


title: AS_A5_7849_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_602B


title: HCC Tumor Tissue LCS_540A


title: CCA Tumor Tissue LCS_602A


title: CCA Non-Tumor Tissue LCS_601B


title: CCA Non-Tumor Tissue LCS_608B


title: CCA Tumor Tissue LCS_575A


title: HCC Tumor Tissue LCS_517A


title: HCC Tumor Tissue LCS_542A


title: AS_E7_1-16-0540-3

description: Gene expression data from NEC specimen


title: AS_F2_7881_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_601A


title: CCA Tumor Tissue LCS_595A


title: HCC Tumor Tissue LCS_541A


title: HCC Tumor Tissue LCS_515A


title: AS_C8_1-6-0019-3

description: Gene expression data from NEC specimen


title: AS_F3_7872_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_600A


title: CCA Tumor Tissue LCS_681A


title: AS_D7_1-25-0502-3

description: Gene expression data from NEC specimen


title: AS_C7_1-15-0514-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_599B


title: AS_C2_1-5-0545-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_598B


title: CCA Tumor Tissue LCS_599A


title: AS_A4_1-11-0501-3

description: Gene expression data from NEC specimen


title: AS_C4_1-7-0018-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_597B


title: CCA Tumor Tissue LCS_597A


title: CCA Tumor Tissue LCS_573A


title: CCA Tumor Tissue LCS_612A


title: CCA Tumor Tissue LCS_637A


title: HCC Tumor Tissue LCS_537A


title: CCA Tumor Tissue LCS_636A


title: AS_C1_1-6-0024-3

description: Gene expression data from NEC specimen


title: HCC Tumor Tissue LCS_513A


title: HCC Tumor Tissue LCS_508A


title: CCA Tumor Tissue LCS_596A


title: HCC Tumor Tissue LCS_512A


title: CCA Tumor Tissue LCS_653A


title: AS_E4_7864_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_628A


title: AS_D6_1-12-0014-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_595B


title: AS_C2_7917_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_F1_7853_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_596B


title: HCC Tumor Tissue LCS_514A


title: CCA Tumor Tissue LCS_618A


title: CCA Non-Tumor Tissue LCS_594B


title: CCA Tumor Tissue LCS_598A


title: CCA Non-Tumor Tissue LCS_592B


title: AS_A7_1-5-0508-3

description: Gene expression data from NEC specimen


title: AS_C7_1-18-0501-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_578A


title: CCA Tumor Tissue LCS_595A


title: AS_F8_7885_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: HCC Tumor Tissue LCS_565A


title: CCA Tumor Tissue LCS_592A


title: CCA Tumor Tissue LCS_594A


title: CCA Non-Tumor Tissue LCS_591B


title: HCC Tumor Tissue LCS_557A


title: AS_C6_5-0036_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_G6_7829_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_B3_1-25-0516-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_591A


title: CCA Non-Tumor Tissue LCS_590B


title: CCA Tumor Tissue LCS_612A


title: AS_A3_7891_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: HCC Tumor Tissue LCS_506A


title: AS_B7_1-5-0031-3

description: Gene expression data from NEC specimen


title: HCC Tumor Tissue LCS_528A


title: HCC Tumor Tissue LCS_505A


title: CCA Tumor Tissue LCS_590A


title: CCA Tumor Tissue LCS_587A


title: HCC Tumor Tissue LCS_504A


title: CCA Non-Tumor Tissue LCS_587B


title: HCC Tumor Tissue LCS_503A


title: AS_D5_1-12-0049-3

description: Gene expression data from NEC specimen


title: AS_E2_1-16-0561-3

description: Gene expression data from NEC specimen


title: AS_G7_7818_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_C1_7913_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_G2_7911_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_B2_1-16-0603-3

description: Gene expression data from NEC specimen


title: HCC Tumor Tissue LCS_501A


title: HCC Tumor Tissue LCS_502A


title: HCC Non-Tumor Tissue LCS_584B

source_name: HCC Non-Tumor Tissue


title: CCA Tumor Tissue LCS_586A


title: CCA Non-Tumor Tissue LCS_585B


title: AS_E8_7842_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_583B


title: CCA Non-Tumor Tissue LCS_674B


title: AS_A8_1-11-0509-3

description: Gene expression data from NEC specimen


title: AS_G5_7828_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_G3_7822_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_664B


title: CCA Non-Tumor Tissue LCS_581B


title: AS_G4_7827_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_B6_1-0138_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_581B


title: CCA Non-Tumor Tissue LCS_642B


title: CCA Non-Tumor Tissue LCS_625B


title: CCA Tumor Tissue LCS_583A


title: CCA Non-Tumor Tissue LCS_668B


title: HCC Tumor Tissue LCS_584A


title: HCC Non-Tumor Tissue LCS_523B


title: HCC Non-Tumor Tissue LCS_567B


title: AS_F2_7852_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_550B


title: CCA Non-Tumor Tissue LCS_609B


title: CCA Non-Tumor Tissue LCS_657B


title: AS_D4_1-14-0008-3

description: Gene expression data from NEC specimen


title: AS_E8_1-25-0501-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_586B


title: HCC Non-Tumor Tissue LCS_535B


title: AS_A8_7854_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_580A


title: AS_B1_1-13-0164-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_581A


title: AS_D1_1-11-0508-3

description: Gene expression data from NEC specimen


title: AS_C3_1-7-0527-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_579A


title: CCA Non-Tumor Tissue LCS_679B


title: CCA Tumor Tissue LCS_578A


title: CCA Non-Tumor Tissue LCS_578B


title: CCA Non-Tumor Tissue LCS_580B


title: AS_E6_7870_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_B8_1-12-0531-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_575B


title: AS_C4_1-16-0502-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_576B


title: CCA Tumor Tissue LCS_575A


title: CCA Non-Tumor Tissue LCS_579B


title: CCA Non-Tumor Tissue LCS_577B


title: CCA Tumor Tissue LCS_577A


title: CCA Non-Tumor Tissue LCS_620B


title: HCC Non-Tumor Tissue LCS_544B


title: CCA Tumor Tissue LCS_585A


title: CCA Non-Tumor Tissue LCS_604B


title: AS_A8_1-22-0516-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_574B


title: CCA Tumor Tissue LCS_574A


title: HCC Non-Tumor Tissue LCS_553B


title: CCA Non-Tumor Tissue LCS_670B


title: CCA Non-Tumor Tissue LCS_615B


title: CCA Non-Tumor Tissue LCS_608B


title: HCC Non-Tumor Tissue LCS_558B


title: AS_A3_1-11-0016-3

description: Gene expression data from NEC specimen


title: AS_E2_1-22-0515-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_678B


title: AS_A4_1-12-0514-3

description: Gene expression data from NEC specimen


title: AS_B6_1-12-0512-3

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_519B


title: AS_A6_1-12-0519-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_572A


title: AS_A3_1-14-0132-3

description: Gene expression data from NEC specimen


title: AS_D8_1-5-0001-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_572B


title: CCA Non-Tumor Tissue LCS_573B


title: CCA Non-Tumor Tissue LCS_571B


title: CCA Non-Tumor Tissue LCS_570B


title: CCA Tumor Tissue LCS_573A


title: CCA Tumor Tissue LCS_570A


title: CCA Tumor Tissue LCS_571A


title: HCC Tumor Tissue LCS_568A


title: AS_G8_7843_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_543B


title: AS_D2_1-6-0014-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_596B


title: HCC Non-Tumor Tissue LCS_518B


title: CCA Non-Tumor Tissue LCS_592B


title: HCC Non-Tumor Tissue LCS_507B


title: CCA Non-Tumor Tissue LCS_585B


title: CCA Non-Tumor Tissue LCS_583B


title: HCC Non-Tumor Tissue LCS_551B


title: AS_D3_7895_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_651B


title: HCC Non-Tumor Tissue LCS_525B


title: AS_B7_1-5-0019-3

description: Gene expression data from NEC specimen


title: AS_D1_7815_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_B5_1-14-0113-3

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_566B


title: HCC Tumor Tissue LCS_567A


title: HCC Non-Tumor Tissue LCS_565B


title: HCC Tumor Tissue LCS_565A


title: AS_D7_7882_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_639B


title: HCC Tumor Tissue LCS_566A


title: AS_B5_1-26-0517-3

description: Gene expression data from NEC specimen


title: AS_D2_1-11-0512-3

description: Gene expression data from NEC specimen


title: AS_A7_1-16-0597-3

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_563B


title: AS_A7_1-7-0522-3

description: Gene expression data from NEC specimen


title: AS_B6_7841_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_562B


title: HCC Non-Tumor Tissue LCS_564B


title: HCC Tumor Tissue LCS_564A


title: HCC Tumor Tissue LCS_563A


title: AS_D8_1-1-0133-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_633B


title: HCC Non-Tumor Tissue LCS_560B


title: CCA Non-Tumor Tissue LCS_648B


title: HCC Non-Tumor Tissue LCS_563B


title: HCC Non-Tumor Tissue LCS_532B


title: HCC Non-Tumor Tissue LCS_527B


title: HCC Non-Tumor Tissue LCS_567B


title: CCA Non-Tumor Tissue LCS_671B


title: HCC Non-Tumor Tissue LCS_520B


title: AS_D4_1-21-0508-3

description: Gene expression data from NEC specimen


title: AS_F7_7883_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_D4_1-12-0005-3

description: Gene expression data from NEC specimen


title: AS_B1_1-12-0024-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_610B


title: HCC Non-Tumor Tissue LCS_559B


title: HCC Tumor Tissue LCS_560A


title: HCC Non-Tumor Tissue LCS_558B


title: HCC Tumor Tissue LCS_559A


title: HCC Tumor Tissue LCS_558A


title: AS_A8_1-14-0115-3

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_557B


title: HCC Non-Tumor Tissue LCS_552B


title: AS_B4_1-13-0119-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_631B


title: HCC Non-Tumor Tissue LCS_509B


title: AS_A4_1-17-0501-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_606B


title: HCC Non-Tumor Tissue LCS_547B


title: AS_B2_7850_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_646B


title: AS_B1_7896_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_B7_1-5-0552-3

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_553B


title: HCC Non-Tumor Tissue LCS_552B


title: HCC Tumor Tissue LCS_553A


title: HCC Non-Tumor Tissue LCS_551B


title: CCA Non-Tumor Tissue LCS_614B


title: AS_D5_1-14-0063-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_621B


title: AS_E4_7898_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_E8_7834_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_B8_1-25-0509-3

description: Gene expression data from NEC specimen


title: AS_E7_7819_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_536B


title: HCC Tumor Tissue LCS_557A


title: CCA Non-Tumor Tissue LCS_616B


title: AS_D7_1-5-0002-3

description: Gene expression data from NEC specimen


title: HCC Tumor Tissue LCS_562A


title: HCC Non-Tumor Tissue LCS_549B


title: HCC Non-Tumor Tissue LCS_550B


title: HCC Tumor Tissue LCS_551A


title: HCC Tumor Tissue LCS_550A


title: HCC Tumor Tissue LCS_552A


title: HCC Tumor Tissue LCS_549A


title: AS_C6_1-12-0505-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_684B


title: CCA Non-Tumor Tissue LCS_667B


title: HCC Non-Tumor Tissue LCS_547B


title: HCC Non-Tumor Tissue LCS_534B


title: CCA Non-Tumor Tissue LCS_658B


title: CCA Non-Tumor Tissue LCS_652B


title: CCA Non-Tumor Tissue LCS_640B


title: CCA Non-Tumor Tissue LCS_600B


title: AS_D2_1-12-0047-3

description: Gene expression data from NEC specimen


title: AS_E3_1-21-0507-3

description: Gene expression data from NEC specimen


title: AS_C7_1-14-0103-3

description: Gene expression data from NEC specimen


title: AS_E8_1-14-0090-3

description: Gene expression data from NEC specimen


title: HCC Tumor Tissue LCS_548A


title: CCA Non-Tumor Tissue LCS_635B


title: HCC Tumor Tissue LCS_547A


title: CCA Non-Tumor Tissue LCS_654B


title: AS_G8_7869_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_C8_1-5-0008-3

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_546B


title: HCC Tumor Tissue LCS_546A


title: AS_E2_7893_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_572B


title: AS_D5_1-22-0507-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_630B


title: CCA Non-Tumor Tissue LCS_587B


title: HCC Non-Tumor Tissue LCS_566B


title: CCA Non-Tumor Tissue LCS_571B


title: AS_E7_1-14-0066-3

description: Gene expression data from NEC specimen


title: AS_C3_7897_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: HCC Tumor Tissue LCS_544A


title: HCC Non-Tumor Tissue LCS_545B


title: HCC Non-Tumor Tissue LCS_544B


title: HCC Tumor Tissue LCS_545A


title: HCC Non-Tumor Tissue LCS_516B


title: HCC Non-Tumor Tissue LCS_559B


title: CCA Non-Tumor Tissue LCS_687B


title: AS_E4_1-15-0509-3

description: Gene expression data from NEC specimen


title: AS_F5_7824_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_B5_1-14-0004-3

description: Gene expression data from NEC specimen


title: AS_C8_1-12-0504-3

description: Gene expression data from NEC specimen


title: AS_A5_1-7-0011-3

description: Gene expression data from NEC specimen


title: AS_B3_1-16-0520-3

description: Gene expression data from NEC specimen


title: AS_C8_7-0006_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_D1_1-14-0095-3

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_541B


title: HCC Tumor Tissue LCS_542A


title: HCC Non-Tumor Tissue LCS_542B


title: HCC Tumor Tissue LCS_543A


title: AS_A6_1-5-0017-3

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_543B


title: HCC Non-Tumor Tissue LCS_548B


title: CCA Non-Tumor Tissue LCS_677B


title: CCA Non-Tumor Tissue LCS_688B


title: HCC Non-Tumor Tissue LCS_510B


title: CCA Non-Tumor Tissue LCS_602B


title: CCA Non-Tumor Tissue LCS_644B


title: CCA Non-Tumor Tissue LCS_634B


title: HCC Tumor Tissue LCS_540A


title: CCA Non-Tumor Tissue LCS_603B


title: HCC Tumor Tissue LCS_541A


title: CCA Non-Tumor Tissue LCS_645B


title: CCA Non-Tumor Tissue LCS_643B


title: AS_E8_1-16-0551-3

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_539B


title: HCC Non-Tumor Tissue LCS_511B


title: AS_D3_1-9-0002-3

description: Gene expression data from NEC specimen


title: AS_C2_14-0018_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_540B


title: HCC Tumor Tissue LCS_539A


title: HCC Non-Tumor Tissue LCS_538B


title: AS_E1_1-1-0131-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_650B


title: HCC Tumor Tissue LCS_538A


title: AS_E6_1-12-0547-3

description: Gene expression data from NEC specimen


title: AS_D8_7901_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_C5_1-5-0540-3

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_530B


title: HCC Tumor Tissue LCS_537A


title: AS_D6_1-6-0029-3

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_537B


title: HCC Non-Tumor Tissue LCS_536B


title: AS_G3_7826_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_597B


title: AS_D1_7890_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: HCC Tumor Tissue LCS_536A


title: HCC Non-Tumor Tissue LCS_535B


title: CCA Non-Tumor Tissue LCS_669B


title: CCA Non-Tumor Tissue LCS_627B


title: CCA Non-Tumor Tissue LCS_685B


title: CCA Non-Tumor Tissue LCS_579B


title: CCA Non-Tumor Tissue LCS_641B


title: HCC Non-Tumor Tissue LCS_584B


title: AS_E7_1-22-0517-3

description: Gene expression data from NEC specimen


title: HCC Tumor Tissue LCS_535A


title: AS_B3_1-21-0517-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_613B


title: AS_B2_1-25-0513-3

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_534B


title: AS_E7_1-16-0600-3

description: Gene expression data from NEC specimen


title: AS_B1_1-2-0018-3

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_545B


title: AS_E1_1-14-0131-3

description: Gene expression data from NEC specimen


title: AS_B5_7845_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: HCC Tumor Tissue LCS_534A


title: HCC Tumor Tissue LCS_532A


title: HCC Non-Tumor Tissue LCS_531B


title: CCA Non-Tumor Tissue LCS_590B


title: HCC Non-Tumor Tissue LCS_533B


title: HCC Tumor Tissue LCS_533A


title: HCC Non-Tumor Tissue LCS_539B


title: AS_D4_1-1-0017-3

description: Gene expression data from NEC specimen


title: AS_C4_1-16-0571-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_574B


title: AS_F1_7887_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_B6_1-7-0519-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_683B


title: HCC Tumor Tissue LCS_531A


title: HCC Non-Tumor Tissue LCS_530B


title: HCC Non-Tumor Tissue LCS_532B


title: HCC Tumor Tissue LCS_530A


title: HCC Non-Tumor Tissue LCS_529B


title: HCC Tumor Tissue LCS_529A


title: CCA Non-Tumor Tissue LCS_601B


title: HCC Non-Tumor Tissue LCS_568B


title: AS_B2_1-19-0508-3

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_528B


title: AS_A3_1-6-0016-3

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_533B


title: HCC Tumor Tissue LCS_528A


title: AS_A7_1-22-0509-3

description: Gene expression data from NEC specimen


title: AS_A2_1-12-0542-3

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_546B


title: HCC Non-Tumor Tissue LCS_524B


title: AS_C3_1-11-0029-3

description: Gene expression data from NEC specimen


title: AS_G7_7838_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_570B


title: CCA Non-Tumor Tissue LCS_586B


title: CCA Non-Tumor Tissue LCS_598B


title: AS_A4_7922_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_527B


title: AS_C3_1-7-0532-3

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_564B


title: HCC Tumor Tissue LCS_525A


title: HCC Tumor Tissue LCS_527A


title: HCC Non-Tumor Tissue LCS_525B


title: HCC Tumor Tissue LCS_524A


title: AS_E6_1-15-0506-3

description: Gene expression data from NEC specimen


title: HCC Tumor Tissue LCS_523A


title: CCA Non-Tumor Tissue LCS_580B


title: HCC Non-Tumor Tissue LCS_520B


title: CCA Non-Tumor Tissue LCS_623B


title: HCC Non-Tumor Tissue LCS_524B


title: CCA Non-Tumor Tissue LCS_682B


title: AS_D8_1-5-0509-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_594B


title: AS_D6_1-12-0511-3

description: Gene expression data from NEC specimen


title: AS_E6_1-5-0507-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_649B


title: HCC Tumor Tissue LCS_520A


title: HCC Non-Tumor Tissue LCS_519B


title: HCC Non-Tumor Tissue LCS_560B


title: HCC Non-Tumor Tissue LCS_548B


title: AS_G1_7877_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_E2_1-14-0088-3

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_562B


title: HCC Non-Tumor Tissue LCS_518B


title: HCC Tumor Tissue LCS_519A


title: AS_A1_1-16-0545-3

description: Gene expression data from NEC specimen


title: AS_C1_1-5-0056-3

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_517B


title: HCC Tumor Tissue LCS_518A


title: CCA Non-Tumor Tissue LCS_680B


title: AS_B1_1-16-0544-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_577B


title: HCC Tumor Tissue LCS_517A


title: AS_D6_1-21-0522-3

description: Gene expression data from NEC specimen


title: AS_A2_1-5-0053-3

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_516B


title: CCA Non-Tumor Tissue LCS_599B


title: AS_C3_1-16-0574-3

description: Gene expression data from NEC specimen


title: AS_B4_1-21-0505-3

description: Gene expression data from NEC specimen


title: AS_B7_1-14-0092-3

description: Gene expression data from NEC specimen


title: AS_E5_1-5-0505-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_638B


title: AS_F6_7876_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_D2_1-16-0566-3

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_514B


title: HCC Tumor Tissue LCS_516A


title: HCC Tumor Tissue LCS_514A


title: HCC Tumor Tissue LCS_515A


title: HCC Non-Tumor Tissue LCS_515B


title: HCC Non-Tumor Tissue LCS_538B


title: CCA Non-Tumor Tissue LCS_675B


title: CCA Non-Tumor Tissue LCS_624B


title: HCC Non-Tumor Tissue LCS_529B


title: CCA Non-Tumor Tissue LCS_626B


title: HCC Non-Tumor Tissue LCS_513B


title: HCC Non-Tumor Tissue LCS_540B


title: AS_D8_1-11-0502-3

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_517B


title: CCA Non-Tumor Tissue LCS_575B


title: HCC Non-Tumor Tissue LCS_542B


title: HCC Non-Tumor Tissue LCS_511B


title: AS_E5_1-13-0148-3

description: Gene expression data from NEC specimen


title: HCC Tumor Tissue LCS_512A


title: AS_C6_1-5-0538-3

description: Gene expression data from NEC specimen


title: AS_E2_1-7-0514-3

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_549B


title: HCC Tumor Tissue LCS_513A


title: CCA Non-Tumor Tissue LCS_637B


title: HCC Non-Tumor Tissue LCS_512B


title: AS_E4_1-14-0099-3

description: Gene expression data from NEC specimen


title: AS_E5_1-13-0147-3

description: Gene expression data from NEC specimen


title: AS_F6_7855_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_A6_1-12-0556-3

description: Gene expression data from NEC specimen


title: HCC Tumor Tissue LCS_508A


title: HCC Non-Tumor Tissue LCS_510B


title: AS_A2_1-14-0125-3

description: Gene expression data from NEC specimen


title: HCC Tumor Tissue LCS_510A


title: HCC Non-Tumor Tissue LCS_515B


title: AS_C3_14-0022_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: HCC Tumor Tissue LCS_509A


title: CCA Non-Tumor Tissue LCS_595B


title: AS_G5_7825_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_A7_1-12-0522-3

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_509B


title: HCC Tumor Tissue LCS_511A


title: HCC Non-Tumor Tissue LCS_508B


title: HCC Non-Tumor Tissue LCS_541B


title: CCA Non-Tumor Tissue LCS_681B


title: HCC Non-Tumor Tissue LCS_537B


title: CCA Non-Tumor Tissue LCS_573B


title: CCA Non-Tumor Tissue LCS_636B


title: HCC Non-Tumor Tissue LCS_513B


title: AS_G2_7848_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_D8_7863_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: HCC Tumor Tissue LCS_507A


title: AS_E6_7868_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_A5_1-11-0537-3

description: Gene expression data from NEC specimen


title: AS_A6_7910_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_A4_1-13-0150-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_653B


title: HCC Non-Tumor Tissue LCS_507B


title: AS_D6_7905_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_D3_1-21-0502-3

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_506B


title: HCC Non-Tumor Tissue LCS_504B


title: HCC Non-Tumor Tissue LCS_505B


title: AS_B5_1-0077_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_508B


title: AS_B2_1-16-0539-3

description: Gene expression data from NEC specimen


title: AS_C5_1-7-0507-3

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_557B


title: HCC Non-Tumor Tissue LCS_565B


title: CCA Non-Tumor Tissue LCS_618B


title: HCC Non-Tumor Tissue LCS_512B


title: AS_F4_7880_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_628B


title: HCC Tumor Tissue LCS_505A


title: HCC Non-Tumor Tissue LCS_501B


title: HCC Non-Tumor Tissue LCS_503B


title: HCC Non-Tumor Tissue LCS_502B


title: CCA Non-Tumor Tissue LCS_578B


title: HCC Tumor Tissue LCS_503A


title: HCC Tumor Tissue LCS_502A


title: HCC Non-Tumor Tissue LCS_505B


title: HCC Tumor Tissue LCS_504A


title: AS_E6_1-14-0021-3

description: Gene expression data from NEC specimen


title: AS_E1_1-25-0506-3

description: Gene expression data from NEC specimen


title: AS_C7_1-18-0505-3

description: Gene expression data from NEC specimen


title: AS_D5_7874_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_514B


title: AS_B5_1-12-0046-3

description: Gene expression data from NEC specimen


title: HCC Tumor Tissue LCS_506A


title: AS_E7_1-5-0058-3

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_502B


title: HCC Non-Tumor Tissue LCS_506B


title: CCA Non-Tumor Tissue LCS_612B


title: HCC Non-Tumor Tissue LCS_528B


title: AS_C5_1-5-0092-3

description: Gene expression data from NEC specimen


title: AS_C4_1-1-0009-3

description: Gene expression data from NEC specimen


title: HCC Tumor Tissue LCS_501A


title: AS_E3_1-2-0007-3

description: Gene expression data from NEC specimen


title: AS_D6_1-7-0518-3

description: Gene expression data from NEC specimen


title: HCC Non-Tumor Tissue LCS_504B


title: HCC Non-Tumor Tissue LCS_503B


title: HCC Non-Tumor Tissue LCS_501B


title: AS_C1_1-14-0015-3

description: Gene expression data from NEC specimen


title: AS_E3_7857_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_C3_1-19-0502-3

description: Gene expression data from NEC specimen


title: AS_D1_1-12-0032-3

description: Gene expression data from NEC specimen


title: AS_A5_1-16-0537-3

description: Gene expression data from NEC specimen


title: Hypothalamus from  POMCMfn1KO 12 week old random fed mice [KO_FED_1045]

city: Barcelona

first: Joan Marc

last: Servitja

state: Catalonia

address: Rosselló, 153

country: Spain

institute: IDIBAPS

description: Hypothalamic gene expression data from  POMCMfn1KO 12 week old random fed mice

hyb_protocol: Following fragmentation, cRNA was hybridized to Affymetrix GeneChip® Mouse HT_MG-430_PM arrays, washed and stained according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol (Affymetrix Genechip Command Console program 3.0.0.1214, scanner GCS 3000-7G)

data_processing: Expression data were normalized with Robust Multi-array Average (RMA)  from the affy package (www.bioconductor.org)

organism: Mus musculus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (150 ng starting total RNA).

growth_protocol: Hypothalami from POMC-specific Mfn1 knockout and control mice were harvested at 12 weeks of age under fed and fasting conditions

extract_protocol: RNA was extracted with Trizol and the RNeasy MiniElute Cleanup kit from Qiagen

treatment_protocol: Random fed versus 16h fasted

tag: background strain

value: mix of C57Bl/6J, FVB/N and 129

value: hypothalamus

tag: genotype

value: 12 weeks


title: Hypothalamus from  POMCMfn1KO 12 week old random fed mice [KO_FED_1047]


title: AS_B6_1-15-0502-3

description: Gene expression data from NEC specimen


title: AS_C4_7840_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_A1_1-12-0541-3

description: Gene expression data from NEC specimen


title: AS_E2_1-1-0089-3

description: Gene expression data from NEC specimen


title: AS_D7_1-1-0005-3

description: Gene expression data from NEC specimen


title: AS_E5_1-21-0512-3

description: Gene expression data from NEC specimen


title: AS_C6_1-5-0530-3

description: Gene expression data from NEC specimen


title: AS_B3_1-0023_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_B8_1-6-0012-3

description: Gene expression data from NEC specimen


title: AS_G1_7924_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_E1_7866_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_D2_7894_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: Hypothalamus from  POMCMfn1KO 12 week old random fed mice [KO_FED_1042]


title: Hypothalamus from  POMCMfn1KO 12 week old fasted mice [KO_FAST_1016]

description: Hypothalamic gene expression data from  POMCMfn1KO 12 week old fasted mice


title: AS_A5_1-7-0503-3

description: Gene expression data from NEC specimen


title: Hypothalamus from  POMCMfn1KO 12 week old random fed mice [KO_FED_1023]


title: AS_E4_1-12-0510-3

description: Gene expression data from NEC specimen


title: AS_B6_1-1-0126-3

description: Gene expression data from NEC specimen


title: AS_B1_7-0014_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_C2_1-11-0019-3

description: Gene expression data from NEC specimen


title: AS_C4_1-9-0019-3

description: Gene expression data from NEC specimen


title: AS_C2_1-6-0002-3

description: Gene expression data from NEC specimen


title: AS_A2_1-22-0502-3

description: Gene expression data from NEC specimen


title: Hypothalamus from  POMCMfn1KO 12 week old fasted mice [KO_FAST_1018]


title: AS_A6_1-5-0504-3

description: Gene expression data from NEC specimen


title: AS_E1_1-12-0545-3

description: Gene expression data from NEC specimen


title: Hypothalamus from  POMCMfn1KO 12 week old fasted mice [KO_FAST_1019]


title: Hypothalamus from control 12 week old random fed mice [CTRL_FED_1046]

description: Hypothalamic gene expression data from control 12 week old random fed mice

value: control


title: Hypothalamus from control 12 week old random fed mice [CTRL_FED_1041]


title: AS_D7_1-21-0509-3

description: Gene expression data from NEC specimen


title: AS_D1_1-12-0524-3

description: Gene expression data from NEC specimen


title: Hypothalamus from control 12 week old fasted mice [CTRL_FAST_1033]

description: Hypothalamic gene expression data from control 12 week old fasted mice


title: Hypothalamus from control 12 week old random fed mice [CTRL_FED_1044]


title: Hypothalamus from control 12 week old random fed mice [CTRL_FED_1043]


title: AS_B1_1-7-0513-3

description: Gene expression data from NEC specimen


title: AS_F3_7899_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_C1_1-14-0054-3

description: Gene expression data from NEC specimen


title: AS_F4_7823_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: Hypothalamus from control 12 week old fasted mice [CTRL_FAST_1034]


title: AS_E6_1-12-0555-3

description: Gene expression data from NEC specimen


title: Hypothalamus from control 12 week old fasted mice [CTRL_FAST_1017]


title: AS_A1_1-12-0523-3

description: Gene expression data from NEC specimen


title: AS_E1_7909_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: RSV & IFNγ sample, rep 1

status: Public on Jun 26 2017

city: London

first: Akul

last: Singhania

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description:
RSV_IFNG_1
IFNγ-primed and RSV-infected AALEB cells, replicate 1.

hyb_protocol: Samples were hybridized to Affymetrix HG U133 Plus 2.0 BeadChips.

scan_protocol: Arrays were scanned.

data_processing: Raw microarray gene expression data was normalized using GC Robust Multi-Array Analysis (GCRMA) and subjected to quality control procedures. Fold changes were calculated by averaging the replicates and subtracting the log2 expression values from control. Only genes with actual fold changes greater than 2 or less than -2 were considered for functional enrichment analysis.

label: Biotin

source_name: AALEB, IFN-gamma treated, RSV infected

label_protocol: RNA was labeled with biotin.

growth_protocol: AALEB were kept in culture in flasks coated with collagen (PureCol, Nutacon, Netherlands ) using Bronchial Epithelial Growth Medium with supplements (BEGM BulletKit, Lonza, Slough, UK). Cells at passage 2 or 3 were then plated in collagen-coated 24-well plates at 1x10^4/well and maintained for 48 h in starvation media (BEGM BulletKit, Lonza, Slough, UK) supplemented with ITS 1X (insulin, transferrin, selenium, Life Biotechnology, Thermo Fisher Scientific Waltham, MA USA) and 0.02% BSA (SIGMA Dorset, England).

extract_protocol: Total RNA was extracted using TriFast as for standard protocol and concentration was determined using a spectrophotometer (NanoDrop 1000; Thermo Fisher Scientific).

treatment_protocol: Where required, 24 h before viral infection, IFNy (10 ng/ml, R&D Systems, Abingdon, UK) was added. Before RSV infection, cells were washed twice with DMEM (SIGMA, Dorset, England) supplemented with 2 mM Glutamine (SIGMA) before RSV subtype A Memphis 37 (Amsbio Abingdon, UK) (Perkins 2005) at MOI 1 was added to the wells required in a volume of 200 ul for 2 h at 37oC with gentle agitation. Then, cells were washed twice with DMEM 2 mM Glutamine and cultured for 48 h in starvation media. Cells were harvested and stored in TriFast (peqGOLD PEQLAB, Southampton, UK) at -80 oC until RNA extraction was performed.

tag: cell line

value: AALEB

tag: treatment

value: interferon-gamma

tag: infection

value: RSV subtype A Memphis 37


title: IFNγ only sample, rep 2

description:
IFNG_2
IFNγ-primed AALEB cells, replicate 2.

source_name: AALEB, IFN-gamma treated


title: 7w_48h_female1

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

country: Japan

institute: National Institutes for Quantum and Radiological Science and Technology

description: Gene expression in 7-week-old mouse liver at 48 hour after 4 Gy Gamma-ray irradiation

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >11.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing Agilent fragmentation buffer and Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse Gene Expression Microarrays (G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014850_D_F_20110819) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

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

extract_protocol: RNA was prepared using the AllPrep DNA/RNA/Protein Mini kit (QIAGEN) following the manufacturer's recommendations.

treatment_protocol: B6C3F1 mice were either sham-irradiated, or irradiated at 1 or 7 weeks of age with 4 Gy gamma rays from a 137Cs source (0.57 Gy/min). Liver tissue from irradiated mice was sampled up to 48 h post-irradiation,

value: female

value: liver

value: 7 week-old


title: Control sample, rep 1

description:
Control_1
Untreated AALEB cells, replicate 1.

source_name: AALEB, control


title: Control sample, rep 2

description:
Control_2
Untreated AALEB cells, replicate 2.


title: AS_A4_1-14-0069-3

description: Gene expression data from NEC specimen

tag: lung cancer status

value: Lung Cancer

tag: smoking status

value: Current Smoker


title: RSV only sample, rep 1

description:
RSV_1
RSV-infected AALEB cells, replicate 1.

source_name: AALEB, RSV infected


title: RSV only sample, rep 2

description:
RSV_2
RSV-infected AALEB cells, replicate 2.


title: RSV & IFNγ sample, rep 2

description:
RSV_IFNG_2
IFNγ-primed and RSV-infected AALEB cells, replicate 2.


title: 7w_48h_female2


title: 7w_48h_male2

value: male


title: 7w_24h_male2

description: Gene expression in 7-week-old mouse liver at 24 hour after 4 Gy Gamma-ray irradiation


title: 7w_24h_male1


title: 7w_24h_female2


title: 7w_0h_female2

description: Gene expression in 7-week-old mouse liver at 0 hour after 4 Gy Gamma-ray irradiation


title: IFNγ only sample, rep 1

description:
IFNG_1
IFNγ-primed AALEB cells, replicate 1.


title: 7w_0h_female1


title: 7w_0h_male2


title: 7w_24h_female1


title: 1w_48h_female2

description: Gene expression in 1-week-old mouse liver at 48 hour after 4 Gy Gamma-ray irradiation

value: 1 week-old


title: 7w_48h_male1


title: 7w_0h_male1


title: 1w_24h_female2

description: Gene expression in 1-week-old mouse liver at 24 hour after 4 Gy Gamma-ray irradiation


title: 1w_0h_female1

description: Gene expression in 1-week-old mouse liver at 0 hour after 4 Gy Gamma-ray irradiation


title: 1w_24h_female1


title: 1w_48h_male1


title: 1w_24h_male2


title: 1w_0h_female2


title: 1w_48h_male2


title: 1w_48h_female1


title: 1w_0h_male1


city: Hefei

first: Ping

last: Gao

state: Anhui

address: Huangshan Road 443

department: Innovation Center for Cell Biology

country: China

institute: School of Life Science, University of Science and Technology of China

description: Gene expression data from HT1080 cells treated with non-target control shRNA.

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit in Hybridization Oven 645 and Fluidics Station 450 followed the manufacturer’s instructions.

scan_protocol: GeneChips were scanned by GeneChip® Scanner 3000 and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by Expression Console.

source_name: Human fibrosarcoma HT1080 cells treated with non-targetting control shRNA

label_protocol: Total RNA were amplified, labeled and purified by using Affymetrix WT Amplication Kit and GeneChip WT Terminal Labeling Kit followed the manufacturer’s instructions to obtain biotin labeled cDNA.

growth_protocol: Human fibrosarcoma HT1080 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM). Cells were maintained in a water-jacketed incubator with 5% CO2 in 37 °C.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Life technologies) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100.Qualified total RNA was further purified by RNeasy micro kit and RNase-Free DNase Set.

treatment_protocol: shRNAs were purchased form Sigma. HT1080 cells were harvested after infecting with viruses containing shRNAs 48 hours.

tag: cell type

value: fibrosarcoma


title: muscle_HiraCKO_animal3_rep1

city: Houston

first: M. David

last: Stewart

state: TX

address: 4800 Calhoun Rd

institute: University of Houston

hyb_protocol: Phalanx Biotech One Array Plus protocol. Each sample was hybridized in triplicate.

scan_protocol: Agilent 0.1 XDR protocol.

data_processing: Normalization was performed using median scaling normalization method.

source_name: tibialis anterior, Hira CKO

label_protocol: 5 micrograms Cy5-labelled total RNA.

extract_protocol: Tibialis anterior muscles were dissected in PBS and flash frozen in liquid nitrogen. RNA was extracted using Trizol reagent.

tag: strain/background

tag: genotype/variation

value: Myf6 cre/+; Hira flox/-

value: muscle, tibialis anterior

tag: age

value: 6 weeks

tag: animal


title: muscle_HiraCKO_animal4_rep3


title: muscle_HiraCKO_animal1_rep3


title: muscle_HiraCKO_animal4_rep1


title: muscle_HiraCKO_animal3_rep3


title: muscle_HiraCKO_animal1_rep2


title: muscle_HiraCKO_animal3_rep2


title: muscle_control_animal4_rep3

source_name: tibialis anterior, control

value: Myf6 cre/+; Hira flox/+


title: muscle_control_animal4_rep2


title: muscle_HiraCKO_animal2_rep1


title: muscle_HiraCKO_animal2_rep2


title: muscle_control_animal4_rep1


title: muscle_control_animal3_rep3


title: muscle_control_animal3_rep1


title: muscle_control_animal2_rep1


title: muscle_HiraCKO_animal4_rep2


title: muscle_control_animal1_rep2


title: 1w_0h_male2

tag: gender


title: muscle_control_animal2_rep3

tag: tissue


title: cells treated with cMyc shRNA

description: Gene expression data from HT1080 cells treated with cMyc shRNA.

source_name: Human fibrosarcoma HT1080 cells treated with cMyc shRNA


title: muscle_control_animal2_rep2


title: muscle_control_animal1_rep1


title: muscle_HiraCKO_animal2_rep3


title: muscle_HiraCKO_animal1_rep1


title: muscle_control_animal3_rep2


title: muscle_control_animal1_rep3


title: muscle_HiraCKO_animal6954_rep2

hyb_protocol: Phalanx Biotech One Array Plus protocol.  Each sample was hybridized in triplicate.

scan_protocol: Agilent 0.1 XDR protocol

data_processing: Normalization was performed using median scaling normalization method

source_name: tibialis anterior

label_protocol: 5 micrograms Cy5-labelled total RNA

extract_protocol: Tibialis anterior muscles were dissected in PBS and flash frozen in liquid nitrogen.  RNA was extracted using Trizol reagent.

tag: strain

value: 6 months old


title: muscle_HiraCKO_animal6954_rep1


title: muscle_HiraCKO_animal6951_rep3


title: muscle_HiraCKO_animal6954_rep3


title: muscle_HiraCKO_animal6475_rep3


title: muscle_HiraCKO_animal6951_rep1


title: muscle_control_animal6953_rep2


title: muscle_control_animal6901_rep3


title: muscle_control_animal6953_rep3


title: muscle_HiraCKO_animal6475_rep1


title: muscle_control_animal6953_rep1


title: muscle_HiraCKO_animal6475_rep2


title: muscle_HiraCKO_animal6477_rep3


title: muscle_HiraCKO_animal6951_rep2


title: muscle_HiraCKO_animal6477_rep2


title: muscle_HiraCKO_animal6477_rep1


title: muscle_control_animal6901_rep1


title: muscle_control_animal6901_rep2


title: muscle_control_animal6480_rep3


title: muscle_control_animal6482_rep3


title: muscle_control_animal6482_rep1


title: muscle_control_animal6482_rep2


title: muscle_control_animal6480_rep2


title: 1vs5-R2

city: Potsdam

first: Christian

last: Kappel

address: Karl-Liebknecht-Str. 24-25, Haus 26

department: Institut für Biochemie und Biologie

country: Germany

institute: Universität Potsdam

description: Vitis vinifera L.

hyb_protocol: Just before hybridization, the oligos were fixed on the chip by exposure to 100 MJ of UV light in a UV Stratalinker 2400 crosslinker (Stratagene, La Jolla, California, USA). The slides were then soaked twice in 0.2% sodium dodecyl sulfate (SDS) for 1 min. The probe solution was denatured at 100 °C for 1 min, cooled on ice for 2 min, stabilized at 37 °C for 5 min and injected into the hybridization chamber of the HS 4800 Hybridization Station (Tecan, Durham, North Carolina, USA). The slides were incubated at 37 °C for 16 h with medium agitation and then washed sequentially at 30 °C in 1X saline-sodium citrate (SSC)/0.1% SDS for 1 min 3 times, in 0.1X SSC/0.1% SDS for 1 min 3 times and finally in 0.1X SSC for 30 s.

scan_protocol: Washed slides were quickly dried with nitrogen and immediately scanned at 532 (Cy3) and 635 (Cy5) nm with GenePix 4000B fluorescence reader (Molecular Devices, Sunnyvale, California, USA) using GenePix 4.0 software. Parameters were fixed as follows: 400 V at 532 nm and 460 V at 635 nm for PTM (photomultiplier), 100% power, 5 for pixel size and 3 lines to average.

data_processing: Spot intensities were quantified with the software MAIA 2.75 (Novikov and Barillot, 2007). After excluding bad quality spots, median intensity gene expression data without background subtraction were normalized by a global lowess method followed by a print-tip median method with a modified version of the Goulphar script version 1.1.2 (Lemoine et al., 2006).

organism: Vitis vinifera

source_name: berry skins, stage 5

label_protocol: Fluorescently (Cy3/Cy5) labelled antisense RNA (aRNA) targets were obtained using the Amino Allyl MessageAmpTM II aRNA Amplification Kit (Ambion, Austin, Texas, USA) according to manufacturer’s instructions. Six hundred pmol Cy3- and Cy5-labelled aRNA were pooled together, fragmented and adjusted to 100 µL with hybridization buffer.

growth_protocol: Berries of the cultivar Moscato Bianco (Vitis vinifera L.) were sampled in 2006 from pre-véraison to over-ripening, for a total of 13 collection dates. At each time point, ten bunches were taken from ten plants out of the ~250 grown in the experimental field “Inferno” of FEM (Fondazione Edmund Mach, San Michele all’Adige, Italy). Care was paid to sample from different vines and positions within each vine. In the lab, berries were pooled in order to minimize environmental effects. Berries were hand-peeled, the skins were immediately frozen in liquid nitrogen and stored at -80 °C until RNA extraction. Five of the 13 time points were used for microarray analysis.

extract_protocol: Total RNA was extracted from grape skins using the SpectrumTM Plant Total RNA Kit (Sigma-Aldrich, St. Louis, Missouri, USA). RNA quantity and quality were evaluated with a NanoDrop ND-8000 spectrophotometer (NanoDrop Technologies, Wilmington, Delaware, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Mississauga, Ontario, Canada).

tag: cultivar

value: Moscato Bianco

value: berry skins

tag: developmental stage

value: 5 (over-ripening, 19.0 °Brix)

source_name: berry skins, stage 1

value: 1 (pre-veraison, 4.4 °Brix)


title: 1vs5-R1

description: Vitis vinifera L.


title: 5vs1-R2

description: Vitis vinifera L.


title: 5vs1-R1

description: Vitis vinifera L.


title: 4vs1-R2

description: Vitis vinifera L.

source_name: berry skins, stage 4

value: 4 (pre-ripening, 17.3 °Brix)


title: muscle_control_animal6480_rep1


title: 1vs4-R2

description: Vitis vinifera L.


title: 1vs3-R2

description: Vitis vinifera L.

source_name: berry skins, stage 3

value: 3 (pre-ripening, 14.9 °Brix)


title: 3vs1-R2

description: Vitis vinifera L.


title: 2vs1-R2

description: Vitis vinifera L.

source_name: berry skins, stage 2

value: 2 (pre-ripening, 11.4 °Brix)


title: 3vs1-R1

description: Vitis vinifera L.


title: 4vs1-R1

description: Vitis vinifera L.


title: Thiamet-G-48hr-rep3

city: Durham

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Drive, DUMC 3382

department: Molecular Genetics and Microbiology

institute: Duke University

description:
OGA-48H-3
3566_13816_43190_OGAin-48hr-3_HG-U133A+2.CEL

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: RMA express was used to generate the RMA file

label_protocol: Affymetrix standard protocol

growth_protocol: MDA-MB-231 cells were grown in 37'C and 5%, CO2, incubated with normal DMEM with 10% FBS

extract_protocol: Immediately washed with cold PBS, scraped, and frozen at -80C. RNA was extracted with QIAGEN's Rneasy Mini Kit

treatment_protocol: cells were treated with DMSO (vechicle), 5SGlcNAc (50uM), or Thiamet-G (25uM) for the inidcated time points

tag: tissue origin

value: Breast cancer

tag: treated with

value: Thiamet for G for 48hr


title: 1vs4-R1

description: Vitis vinifera L.


title: 1vs3-R1

description: Vitis vinifera L.


title: 1vs2-R2

description: Vitis vinifera L.


title: Thiamet-G-24hr

description:
OGA-24H
3566_13661_43090_OGA-24h_HG-U133A+2.rma-Signal

tag: cell line

value: Thiamet for G for 24hr


title: Thiamet-G-0hr

description:
OGA-0H
3566_13661_43075_OGA-0h_HG-U133A+2.rma-Signal

value: Thiamet for G for 0hr


title: Thiamet-G-4hr

description:
OGA-4H
3566_13661_43081_OGA-4h_HG-U133A+2.rma-Signal

value: Thiamet for G for 4hr


title: Thiamet-G-48hr-rep1

description:
OGA-48H-1
3566_13816_43188_OGAin-48hr-1_HG-U133A+2.CEL


title: Thiamet-G-8hr

description:
OGA-8H
3566_13661_43087_OGA-8h_HG-U133A+2.rma-Signal

value: Thiamet for G for 8hr


title: Thiamet-G-2hr

description:
OGA-2H
3566_13661_43078_OGA-2h_HG-U133A+2.rma-Signal

value: Thiamet for G for 2hr


title: 1vs2-R1

description: Vitis vinifera L.


title: Thiamet-G-6hr

description:
OGA-6H
3566_13661_43084_OGA-6h_HG-U133A+2.rma-Signal

value: Thiamet for G for 6hr


title: 5SGlcNAc-48hr-rep3

description:
OGT-48H-3
3566_13816_43187_OGTin-48hr-3_HG-U133A+2.CEL

value: 5SGlcNAc for 48hr


title: 2vs1-R1

description: Vitis vinifera L.


title: 5SGlcNAc-48hr-rep1

description:
OGT-48H-1
3566_13816_43185_OGTin-48hr-1_HG-U133A+2.CEL


title: 5SGlcNAc-48hr-rep2

description:
OGT-48H-2
3566_13816_43186_OGTin-48hr-2_HG-U133A+2.CEL


title: Thiamet-G-48hr-rep2

description:
OGA-48H-2
3566_13816_43189_OGAin-48hr-2_HG-U133A+2.CEL


title: 5SGlcNAc-24hr

description:
OGT-24H
3566_13661_43089_OGT-24h_HG-U133A+2.rma-Signal

value: 5SGlcNAc for 24hr


title: Δclp-1

city: Nanjing

first: Wang

last: Yansheng

address: No.1 Weigang

department: Department of Plant Pathology

institute: Nanjing Agricultural University

description: This sample is of Lysobacter enzymogenes OH11 delta-clp mutant. It is the first of two mutant biological replicates used in this experiment, each from separate cultures.

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

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

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

organism: Lysobacter enzymogenes

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

growth_protocol: Lysobacter enzymogenes OH11 and delta-clp mutant were grown to mid-log phase (O.D.600nm 1.0) at 28°C in 10%TSB

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

tag: genotype

value: delta-clp mutant


title: Lysobacter enzymogenes OH11-2

description: This sample is of wild-type Lysobacter enzymogenes OH11. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Lysobacter enzymogenes OH11 wild-type

value: Wild-type


title: Δclp-2

description: This sample is of Lysobacter enzymogenes OH11 delta-clp mutant. It is the second of two mutant biological replicates used in this experiment, each from separate cultures.


title: 1w_24h_male1

description: Gene expression in 1-week-old mouse liver at 24 hour after 4 Gy Gamma-ray irradiation

value: male

value: liver

value: 1 week-old


title: 5SGlcNAc-6hr

description:
OGT-6H
3566_13661_43083_OGT-6h_HG-U133A+2.rma-Signal

value: 5SGlcNAc for 6hr


title: Lysobacter enzymogenes OH11-1

description: This sample is of wild-type Lysobacter enzymogenes OH11. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures.


title: Brucella suis 1330 DregA study wild-type A

city: Montpellier

first: Veronique

middle: Jubier

last: Maurin

address: 1919 route de Mende

country: France

institute: CNRS

description: ds cDNA

hyb_protocol: Hybridization was performed at the “GeT-Biopuces” platform (Toulouse, France) in the Hybridization System of Roche NimbleGen.

scan_protocol: Scanning was performed by the “GeT-Biopuces” platform (Toulouse, France) with the MS200 Microarray Scanner (TECAN, Männedorf, Switzerland).

data_processing: A RMA (Robust Multi-array Average) analysis was performed to normalize background-subtracted raw data (“GeT-Biopuces” platform, Toulouse, France).

organism: Brucella suis 1330

source_name: Brucella suis 1330 wild-type

label_protocol: labeling of ds cDNA was performed at the “GeT-Biopuces” platform (Toulouse, France) with the One Color DNA Labeling Kit (Roche NimbleGen).

growth_protocol: Bacteria were harvested after 3 days of culture in an in vitro model of persistence, at 37°C in minimal medium.

extract_protocol: Total RNA was extracted with the RNeasy mini kit from Qiagen (Qiagen Inc., Valencia, CA, USA) and DNA was removed by two Dnase digestion (Abdou et al. Infect. Immun 2013;81:2053–61). RNA concentration was determined using the NanoDrop ND-1000 (Labtech), and controlled qualitatively using the Agilent 2100 bioanalyzer.

treatment_protocol: samples were recovered after addition of 1/9 V ethanol / phenol solution (9:1).

tag: phenotype

value: normal

tag: accession


title: Brucella suis 1330 DregA study mutant C

description: ds cDNA

source_name: Brucella suis 1330 DregA

value: deletion mutant DregA

value: non-persistent


title: Brucella suis 1330 DregA study wild-type B

description: ds cDNA


title: 5SGlcNAc-4hr

description:
OGT-4H
3566_13661_43080_OGT-4h_HG-U133A+2.rma-Signal

value: Breast cancer

value: 5SGlcNAc for 4hr


title: 5SGlcNAc-2hr

description:
OGT-2H
3566_13661_43077_OGT-2h_HG-U133A+2.rma-Signal

value: 5SGlcNAc for 2hr


title: 5SGlcNAc-0hr

description:
OGT-0H
3566_13661_43074_OGT-0h_HG-U133A+2.rma-Signal

value: 5SGlcNAc for 0hr


title: 5SGlcNAc-8hr

description:
OGT-8H
3566_13661_43086_OGT-8h_HG-U133A+2.rma-Signal

value: 5SGlcNAc for 8hr


title: DMSO-48hr-rep1

description:
DMSO-48H-1
3566_13816_43182_DMSO-48hr-1_HG-U133A+2.CEL

value: DMSO for 48hr


title: Brucella suis 1330 DregA study mutant B

description: ds cDNA


title: DMSO-2hr

description:
DMSO-2H
3566_13661_43076_DMSO-2h_HG-U133A+2.rma-Signal

value: DMSO for 2hr


title: Brucella suis 1330 DregA study wild-type C

description: ds cDNA


title: DMSO-48hr-rep3

description:
DMSO-48H-3
3566_13816_43184_DMSO-48hr-3_HG-U133A+2.CEL


title: DMSO-8hr

description:
DMSO-8H
3566_13661_43085_DMSO-8h_HG-U133A+2.rma-Signal

value: DMSO for 8hr


title: DMSO-0hr

description:
DMSO-0H
3566_13661_43073_DMSO-0h_HG-U133A+2.rma-Signal

value: DMSO for 0hr


title: DMSO-24hr

description:
DMSO-24H
3566_13661_43088_DMSO-24h_HG-U133A+2.rma-Signal

value: DMSO for 24hr


title: DMSO-4hr

description:
DMSO-4H
3566_13661_43079_DMSO-4h_HG-U133A+2.rma-Signal

value: DMSO for 4hr


title: DMSO-48hr-rep2

description:
DMSO-48H-2
3566_13816_43183_DMSO-48hr-2_HG-U133A+2.CEL


title: Brucella suis 1330 DregA study mutant A

description: ds cDNA


title: DMSO-6hr

description:
DMSO-6H
3566_13661_43082_DMSO-6h_HG-U133A+2.rma-Signal

value: DMSO for 6hr


title: 98

status: Public on Jun 25 2017

city: chapel hill

first: Yunjung

last: Kim

state: North Carolina

address: 120 Mason farm road

institute: UNC at Chapel Hill

description:
gene expression data
MM_100_24h_98_AU18042_Liver_.HT_MG.430_PM._B04.CEL

hyb_protocol: Total RNA was isolated from the median lobe liver tissue of all animals using Trizol reagent (Invitrogen) according to manufacturer’s instructions. The isolated RNA was further purified using the QIAcube automated system (Qiagen). Following purification, the quantity of RNA was determined spectrophotometrically and the integrity of the RNA was evaluated with the Agilent 2100 Bioanalyzer. Double-stranded cDNA was synthesized from 50-150 ng (dependent on RNA yield) of total RNA, then transcribed to biotin-labeled cRNA using the 3’ Express IVT kit (Affymetrix). Fifteen (15) µg of labeled cRNA was fragmented and prepared for hybridization on HT MG430 PM peg arrays. The Gene Titan robotic instrumentation (Affymetrix) was used to perform the hybridization, washing and scanning of the peg arrays.

scan_protocol: standar Affymetrix protocol

data_processing: Robust multiarray average method (RMA) implemented in the Affymetrix gene expression console with default settings (median polish and sketch-quantile normalization) to estimate normalized expression levels of transcripts

label_protocol: standar Affymetrix protocol

extract_protocol: The liver of each animal was excised and weighed. A section of the left and median liver lobes was fixed in 10% neutral buffered formalin and processed for histological analysis. A section of liver tissue encompassing all regions of the median lobe was diced, placed in RNAlater (Ambion), and processed for gene expression analysis.

treatment_protocol: Eight male mice from each 45 genetically different inbred strains of the CC were purchased from the University of North Carolina, Chapel Hill (UNC). Animals were housed in polycarbonate cages, kept on a 12-h light-dark cycle and provided Pelleted PicoLab Rodent Diet 20 (Lab Diet) ad libitum, except during an approximate 18-h period of fasting prior to necropsy. Animals were acclimated for approximately 7 days prior to dosing. At the initiation of dosing, mice were approximately 8-10 weeks of age. Care of mice followed institutional guidelines under a protocol approved by Mispro Biotech Services Institutional Animal Care and Use Committee.

tag: treatment

value: Tolvaptan


title: 97

description:
gene expression data
MM_100_24h_97_AU8042_Liver_.HT_MG.430_PM._D11.CEL


title: 85

description:
gene expression data
MM_100_24h_85_AU8033_Liver_.HT_MG.430_PM._D03.CEL


title: 95

description:
gene expression data
MM_100_24h_95_AU8042_Liver_.HT_MG.430_PM._D09.CEL


title: 88

description:
gene expression data
MM_100_24h_88_AU8033_Liver_.HT_MG.430_PM._B02.CEL


title: 96

description:
gene expression data
MM_100_24h_96_AU8042_Liver_.HT_MG.430_PM._D10.CEL


title: 86

description:
gene expression data
MM_100_24h_86_AU8033_Liver_.HT_MG.430_PM._D04.CEL


title: 68

description:
gene expression data
MM_100_24h_68_AU8024_Liver_.HT_MG.430_PM._A12.CEL


title: 67

description:
gene expression data
MM_100_24h_67_AU8024_Liver_.HT_MG.430_PM._C11.CEL


title: 87

description:
gene expression data
MM_100_24h_87_AU8033_Liver_.HT_MG.430_PM._D05.CEL


title: 57

description:
gene expression data
MM_100_24h_57_AU8021_Liver_.HT_MG.430_PM._C05.CEL


title: 58

description:
gene expression data
MM_100_24h_58_AU8021_Liver_.HT_MG.430_PM._A10.CEL


title: 55

description:
gene expression data
MM_100_24h_55_AU8021_Liver_.HT_MG.430_PM._C03.CEL


title: 488

description:
gene expression data
MM_100_24h_488_OR3415_Liver_.HT_MG.430_PM._H07.CEL


title: 56

description:
gene expression data
MM_100_24h_56_AU8021_Liver_.HT_MG.430_PM._C04.CEL


title: 478

description:
gene expression data
MM_100_24h_478_OR3393_Liver_.HT_MG.430_PM._H05.CEL


title: 475

description:
gene expression data
MM_100_24h_475_OR3393_Liver_.HT_MG.430_PM._G09.CEL


title: 47

description:
gene expression data
MM_100_24h_47_AU8034_Liver_.HT_MG.430_PM._B11.CEL


title: 66

description:
gene expression data
MM_100_24h_66_AU8024_Liver_.HT_MG.430_PM._C10.CEL


title: 46

description:
gene expression data
MM_100_24h_46_AU8034_Liver_.HT_MG.430_PM._B10.CEL


title: 65

description:
gene expression data
MM_100_24h_65_AU8024_Liver_.HT_MG.430_PM._C09.CEL


title: 48

description:
gene expression data
MM_100_24h_48_AU8034_Liver_.HT_MG.430_PM._A08.CEL


title: 468

description:
gene expression data
MM_100_24h_468_OR3252_Liver_.HT_MG.430_PM._H03.CEL


title: 487

description:
gene expression data
MM_100_24h_487_OR3415_Liver_.HT_MG.430_PM._C05.CEL


title: 485

description:
gene expression data
MM_100_24h_485_OR3415_Liver_.HT_MG.430_PM._B05.CEL


title: 476

description:
gene expression data
MM_100_24h_476_OR3393_Liver_.HT_MG.430_PM._H05.CEL


title: 477

description:
gene expression data
MM_100_24h_477_OR3393_Liver_.HT_MG.430_PM._H07.CEL


title: 486

description:
gene expression data
MM_100_24h_486_OR3415_Liver_.HT_MG.430_PM._B07_2.CEL


title: 467

description:
gene expression data
MM_100_24h_467_OR3252_Liver_.HT_MG.430_PM._F07.CEL


title: 466

description:
gene expression data
MM_100_24h_466_OR3252_Liver_.HT_MG.430_PM._F05.CEL


title: 465

description:
gene expression data
MM_100_24h_465_OR3252_Liver_.HT_MG.430_PM._E09.CEL


title: 45

description:
gene expression data
MM_100_24h_45_AU8034_Liver_.HT_MG.430_PM._B09.CEL


title: 446

description:
gene expression data
MM_100_24h_446_OR3609_Liver_.HT_MG.430_PM._B05.CEL


title: 457

description:
gene expression data
MM_100_24h_457_OR773_Liver_.HT_MG.430_PM._D07.CEL


title: 458

description:
gene expression data
MM_100_24h_458_OR773_Liver_.HT_MG.430_PM._H01.CEL


title: 456

description:
gene expression data
MM_100_24h_456_OR773_Liver_.HT_MG.430_PM._D05.CEL


title: 445

description:
gene expression data
MM_100_24h_445_OR3609_Liver_.HT_MG.430_PM._A09.CEL


title: 447

description:
gene expression data
MM_100_24h_447_OR3609_Liver_.HT_MG.430_PM._B07.CEL


title: 455

description:
gene expression data
MM_100_24h_455_OR773_Liver_.HT_MG.430_PM._F05.CEL


title: 425

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