title: IRT5912_T00320471

description: T00320471_2011-2-1_IRT5912 28WK

source_name: Exfoliated colonocytes

value: Sprague Dawley

value: FO/P

value: AOM

value: 28 wk after AOM injection


title: IRT5712_T00245011

status: Public on Feb 20 2012

type: RNA

city: College Station

first: Youngmi

last: Cho

state: TX

address: 2253 TAMU

department: Faculty of Nutrition

country: USA

institute: Texas A&M University

description: T00245011_2011-2-8_IRT 5712 28WK

hyb_protocol: Codelink Gene Expression System: Single-Assay Bioarray Hybridization and Detection according to manufacturer's instructions http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf

scan_protocol: Codelink Gene Expression System: Single-Assay Bioarray Hybridization and Detection according to manufacturer's instructions http://www.appliedmicroarrays.com/application_notes/63005079.pdf

data_processing: Median normalized values derived from Codelink Expression Analysis Version 5.0

label: biotin

molecule: total RNA

organism: Rattus norvegicus

label_protocol: Ambion MessageAmp II aRNA Amplification and Biotin Enhanced kits:  Manual Labelled cRNA Target preparation following manufacturer's instructions http://www.ambion.com/techlib/prot/fm_1751.pdf and http://www.ambion.com/techlib/prot/fm_1791.pdf

growth_protocol: Rats were housed individually in a temperature and humidity controlled animal facility with a 12 h light/dark cycle.

extract_protocol: To enrich the level of eukaryotic mRNA in the fecal samples, poly (A)+ RNA was isolated from total RNA using oligo dT cellulose micro spin columns and the mTRAP Maxi kit.

treatment_protocol: Rats consumed diets containing FO/P or CO/C and were injected with azoxymethane (AOM, 2x, 15 mg/kg BW, s.c.).

tag: strain

tag: diet

tag: injection

tag: time


title: IRT5811_T00320572

description: T00320572_2011-2-1_IRT5811 28WK


title: IRT5303_T00320413

description: T00320413_2011-2-1_IRT5303 28WK


title: hnRNPA2B1 293T splicing array 3

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description: polyA selected RNA

hyb_protocol: Hybridization cocktails containing ~5.5 ug of fragmented and labeled DNA target were prepared and applied to GeneChip Human Splice Junction arrays. Hybridization was performed for 16 hours using the Fluidics 450 station.

scan_protocol: Arrays were scanned using the Affymetrix 3000 7G scanner and GeneChip Operating Software version 1.4 to produce .CEL intensity files.

data_processing: Data processed using Affymetrix package (Affy Power Tools) apt-probeset-summarize. Iter-plier algorithm used to quantify probesets.

molecule: polyA RNA

organism: Homo sapiens

source_name: human 293T cells

label_protocol: WT Terminal Labeling Kit, Affymetrix

growth_protocol: Human 293T cells were obtained from ATCC and cultured in DMEM supplemented with 10% FBS at 37 ̊C and 5% CO2.

extract_protocol: Trizol (Invitrogen) extraction of RNA was performed according to the manufacturer’s instructions.

treatment_protocol: Cells were transfected at 40% confluency using 5μl/ml Lipofectamine-2000 (Invitrogen) and siRNAs at a final concentration of 100nM. For hnRNP A1, A2/B1, H1, M and U, equal mixtures of multiple siRNA sequences were used and for hnRNP F only one siRNA sequence was used. Media was changed 4-6 hrs after the initial transfection, and the transfection was repeated 48 hrs later. Cells intended for RNA analysis were suspended and lysed in TRIzol (Invitrogen) 72 hrs after the first transfection.

tag: treatment

value: HnRNP A2B1 siRNA

tag: cell line


title: hnRNPH1 293T splicing array 3

description: polyA selected RNA

value: HnRNP H1 siRNA


title: IRT5814_T00320421

description: T00320421_2011-2-1_IRT 5814 28WK


title: Normal Uterine Cervix ART2601

type: genomic

city: London

first: Andrew

middle: E

last: Teschendorff

address: 72 Huntley Street

department: UCL Cancer Institute/Institute for Women's Health

country: United Kingdom

institute: University College London

description: Liquid Based Cytology samples from the uterine cervix were collected from 152 women as part of the ARTISTIC trial (A Randomised Trial in Screening to Improve Cytology). All samples were of normal histology at time of sample draw, but 75 women developed a CIN2+ within 3 years of sample collection.

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Biotin

molecule: genomic DNA

source_name: genomic DNA from normal cells of the uterine cervix ART2601

label_protocol: Standard Illumina Protocol for Infinium 27k Chip

extract_protocol: DNA was extracted from liquid based cytology samples of women using the Qiagen DNeasy Blood and Tissue kit (Qiagen Ltd, UK)

tag: cell type

tag: sample type

value: bisulphite converted genomic DNA from a prospective CIN2+

tag: outcome

tag: age

tag: hpv status

tag: pcr

value: Round2Cyt 0

tag: sentrix id

tag: sentrix position

value: C

tag: bisulphite 1

value: BS conversion C1 Grn 852

tag: bisulphite 2

value: BS conversion C2 Grn 900


title: RCT0495_T00245612

description: T00245612_2011-2-8_RCT 495 28WK

value: CO/C


title: RCT0492_T00244986

description: T00244986_2011-2-2_RCT 492 29WK


title: control 293T splicing array 2

description: polyA selected RNA

value: control siRNA


title: hnRNPA2B1 293T splicing array 2

description: polyA selected RNA


title: control 293T splicing array 3

description: polyA selected RNA


title: hnRNPH1 293T splicing array 1

description: polyA selected RNA


title: control 293T splicing array 1

description: polyA selected RNA


title: hnRNPH1 293T splicing array 2

description: polyA selected RNA


title: hnRNPU 293T splicing array 3

description: polyA selected RNA

value: HnRNP U siRNA


title: hnRNPU 293T splicing array 2

description: polyA selected RNA


title: Normal Uterine Cervix ART9983

source_name: genomic DNA from normal cells of the uterine cervix ART9983

value: bisulphite converted genomic DNA from a prospective CIN2-

value: Round2Cyt 1

value: A

value: BS conversion C1 Grn 900

value: BS conversion C2 Grn 926


title: Normal Uterine Cervix ART60419

source_name: genomic DNA from normal cells of the uterine cervix ART60419

value: K

value: BS conversion C1 Grn 920

value: BS conversion C2 Grn 1225


title: Normal Uterine Cervix ART10323

source_name: genomic DNA from normal cells of the uterine cervix ART10323

value: I

value: BS conversion C1 Grn 977

value: BS conversion C2 Grn 916


title: Normal Uterine Cervix ART6314

source_name: genomic DNA from normal cells of the uterine cervix ART6314

value: H

value: BS conversion C1 Grn 740

value: BS conversion C2 Grn 877


title: Normal Uterine Cervix ART1077

source_name: genomic DNA from normal cells of the uterine cervix ART1077

value: bisulphite converted genomic DNA from a prospective CIN2+

value: Round2Cyt 0

value: J

value: BS conversion C1 Grn 830

value: BS conversion C2 Grn 915


title: Normal Uterine Cervix ART12931

source_name: genomic DNA from normal cells of the uterine cervix ART12931

value: L

value: BS conversion C1 Grn 743

value: BS conversion C2 Grn 717


title: RCT0485_T00320463

description: T00320463_2011-2-1_RCT485 28WK

value: Sprague Dawley

value: CO/C

value: AOM

value: 28 wk after AOM injection


title: hnRNPM 293T splicing array 1

description: polyA selected RNA

value: HnRNP M siRNA


title: hnRNPM 293T splicing array 2

description: polyA selected RNA


title: hnRNPU 293T splicing array 1

description: polyA selected RNA

value: HnRNP U siRNA


title: hnRNPA2B1 293T splicing array 1

description: polyA selected RNA

value: HnRNP A2B1 siRNA


title: hnRNPM 293T splicing array 3

description: polyA selected RNA


title: hnRNPF 293T splicing array 2

description: polyA selected RNA

value: HnRNP F siRNA


title: hnRNPF 293T splicing array 1

description: polyA selected RNA


title: RCT0483_T00320415

description: T00320415_2011-2-1_RCT483 28WK


title: Normal Uterine Cervix ART13778

source_name: genomic DNA from normal cells of the uterine cervix ART13778

value: bisulphite converted genomic DNA from a prospective CIN2-

value: F

value: BS conversion C1 Grn 845

value: BS conversion C2 Grn 762


title: RCT0491_T00320430

description: T00320430_2011-2-1_RCT 491 28WK


title: RCT0475_T00245007

description: T00245007_2011-2-8_RCT 475 29WK


title: hnRNPF 293T splicing array 3

description: polyA selected RNA


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1)_M2_Day1_Exp2

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

description: US93503719_251486829760_S01_GE1-v5_95_Feb07_1_3.txt

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505C).

data_processing:
Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol.
Agilent Feature extractor software:
platform       x86_64-redhat-linux-gnu
arch           x86_64
os             linux-gnu
system         x86_64, linux-gnu
R version 2.12.2 (2011-02-25)
bioconductor packages: limma
Information on package 'limma'
Description:
Package:       limma
Version:       3.6.9
Date:          2010/12/01version
For the creation of the normalized data matrix, the limma package was used. Background correction was performed (method=normexp, offset=1).
Data was quantile normalized between arrays with the quantile normalization method and then log2 transformed.

organism: Mus musculus

source_name: lung

growth_protocol: Six- to 8- week old female C57Bl/6 mice were obtained from Jackson Laboratory and kept in a barrier facility. Mice were inoculated with 30 μl of virus (recombinant influenza A/WSN/33 carrying the PB1 gene segment from A/Hong Kong/156/97 (H5N1) or a PB1 mutant recombinant virus resulting in an amino acid change at position 66 in the PB1-F2 protein (N66S)) in phosphate-buffered saline (PBS) containing penicillin-streptomycin and bovine serum albumin (PBS-BA-PS). A total of 10^4 PFU of virus was given in all inoculations. Control mice were given PBS-BA-PS. Lung samples were harvested for microarray at 12hr, 1d, 3d, and 5d post-inoculation.

extract_protocol: All TRIzol lysates were  phase-separated, and RNA was isolated from the aqueous phase using Qiagen RNeasy Mini columns according to the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: Tissue samples were homogenize in Trizol (Invitrogen) for subsequent RNA extraction.

tag: tissue

value: lung

tag: infected

tag: biological replicate within time point for given experiment

tag: sample collection time post-infection

tag: experiment number


title: hnRNPA1 293T splicing array 3

description: polyA selected RNA

tag: treatment

value: HnRNP A1 siRNA


title: Normal Uterine Cervix ART20985

source_name: genomic DNA from normal cells of the uterine cervix ART20985

value: Round2Cyt 1

value: E

value: BS conversion C1 Grn 926

value: BS conversion C2 Grn 1027


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1) containing N66S mutation_M1_Day5_Exp1

description: US93503719_251486829759_S01_GE1-v5_95_Feb07_1_3.txt

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing.

tag: strain


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1) containing N66S mutation_M2_Day3_Exp2

description: US93503719_251486829760_S01_GE1-v5_95_Feb07_1_1.txt


title: Normal Uterine Cervix ART60069

source_name: genomic DNA from normal cells of the uterine cervix ART60069

tag: cell type

value: bisulphite converted genomic DNA from a prospective CIN2+

value: Round2Cyt 0

value: B

value: BS conversion C1 Grn 920

value: BS conversion C2 Grn 1043


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1) containing N66S mutation_M3_Day5_Exp1

description: US93503719_251486829759_S01_GE1-v5_95_Feb07_1_2.txt


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1) containing N66S mutation_M2_12h_Exp2

description: US93503719_251486829758_S01_GE1-v5_95_Feb07_1_3.txt


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1)_M3_Day1_Exp2

description: US93503719_251486829759_S01_GE1-v5_95_Feb07_1_4.txt


title: hnRNPA1 293T splicing array 2

description: polyA selected RNA

tag: cell line


title: hnRNPA1 293T splicing array 1

description: polyA selected RNA


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1) containing N66S mutation_M3_Day1_Exp1

description: US93503719_251486829758_S01_GE1-v5_95_Feb07_1_1.txt


title: RCT0474_T00320582

description: T00320582_2011-2-1_RCT474 28WK

value: Sprague Dawley

tag: diet

value: CO/C

tag: injection

value: AOM

tag: time

value: 28 wk after AOM injection


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1) containing N66S mutation_M2_Day1_Exp2

description: US93503719_251486829757_S01_GE1-v5_95_Feb07_1_4.txt


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1) containing N66S mutation_M3_Day3_Exp1

description: US93503719_251486829757_S01_GE1-v5_95_Feb07_1_2.txt


title: RCT0192_T00320423

description: T00320423_2011-2-1_RCT 192 28WK

value: FO/P


title: Normal Uterine Cervix ART12918

source_name: genomic DNA from normal cells of the uterine cervix ART12918

tag: sample type

value: bisulphite converted genomic DNA from a prospective CIN2-

tag: outcome

tag: age

tag: hpv status

tag: pcr

value: J

value: BS conversion C1 Grn 1884

value: BS conversion C2 Grn 1244


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1)_M1_Day3_Exp2

description: US93503719_251486829750_S01_GE1-v5_95_Feb07_1_4.txt

tag: tissue

value: lung


title: lung_not infected (PBS mock)_M1_Day3_Exp1

description: US93503719_251486829750_S01_GE1-v5_95_Feb07_1_3.txt

tag: infected

value: not infected (PBS mock)


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1) containing N66S mutation_M1_Day1_Exp2

description: US93503719_251486829705_S01_GE1-v5_95_Feb07_1_3.txt

tag: biological replicate within time point for given experiment


title: RCT0183_T00245591

description: T00245591_2011-2-2_RCT 183 28WK


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1)_M2_Day3_Exp1

description: US93503719_251486829705_S01_GE1-v5_95_Feb07_1_4.txt

tag: sample collection time post-infection


title: RCT0475_T00245030

description: T00245030_2011-2-2_RCT 475 29WK


title: RCT0471_T00320432

description: T00320432_2011-2-1_RCT471 28WK


title: RCT0183_T00244976

description: T00244976_2011-2-2_RCT 183 28WK


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1) containing N66S mutation_M3_12h_Exp2

description: US93503719_251486829750_S01_GE1-v5_95_Feb07_1_1.txt

tag: experiment number


title: Normal Uterine Cervix ART2270

source_name: genomic DNA from normal cells of the uterine cervix ART2270

tag: sentrix id

tag: sentrix position

value: K

tag: bisulphite 1

value: BS conversion C1 Grn 1881

tag: bisulphite 2

value: BS conversion C2 Grn 1176


title: Normal Uterine Cervix ART14109

source_name: genomic DNA from normal cells of the uterine cervix ART14109

tag: cell type

value: bisulphite converted genomic DNA from a prospective CIN2+

value: Round2Cyt 0

value: L

value: BS conversion C1 Grn 1163

value: BS conversion C2 Grn 661


title: Normal Uterine Cervix ART17165

source_name: genomic DNA from normal cells of the uterine cervix ART17165

value: Round2Cyt 1

value: C

value: BS conversion C1 Grn 802

value: BS conversion C2 Grn 927


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1)_M2_Day1_Exp1

description: US93503719_251486829704_S01_GE1-v5_95_Feb07_1_1.txt

tag: strain


title: RCT0181_T00245597

description: T00245597_2011-2-2_RCT 181 29WK

source_name: Exfoliated colonocytes

value: Sprague Dawley

tag: diet

value: FO/P

tag: injection

value: AOM

tag: time

value: 28 wk after AOM injection


title: Normal Uterine Cervix ART6874

source_name: genomic DNA from normal cells of the uterine cervix ART6874

tag: sample type

value: bisulphite converted genomic DNA from a prospective CIN2-

tag: outcome

tag: age

value: I

value: BS conversion C1 Grn 1651

value: BS conversion C2 Grn 1250


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1)_M3_12h_Exp2

description: US93503719_251486829704_S01_GE1-v5_95_Feb07_1_2.txt

tag: tissue

value: lung


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1) containing N66S mutation_M1_12h_Exp2

description: US93503719_251486829703_S01_GE1-v5_95_Feb07_1_1.txt

tag: infected


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1)_M2_Day3_Exp2

description: US93503719_251486829704_S01_GE1-v5_95_Feb07_1_3.txt

tag: biological replicate within time point for given experiment


title: RCT0182_T00244982

description: T00244982_2011-2-2_RCT 182 29WK


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1)_M1_12h_Exp2

description: US93503719_251486829703_S01_GE1-v5_95_Feb07_1_4.txt

tag: sample collection time post-infection


title: Normal Uterine Cervix ART8269

description: Liquid Based Cytology samples from the uterine cervix were collected from 152 women as part of the ARTISTIC trial (A Randomised Trial in Screening to Improve Cytology). All samples were of normal histology at time of sample draw, but 75 women developed a CIN2+ within 3 years of sample collection.

source_name: genomic DNA from normal cells of the uterine cervix ART8269

tag: hpv status

tag: pcr

value: H

value: BS conversion C1 Grn 1864

value: BS conversion C2 Grn 1525


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1)_M1_Day1_Exp2

description: US93503719_251486829702_S01_GE1-v5_95_Feb07_1_1.txt

tag: experiment number


title: RCT0172_T00320465

description: T00320465_2011-2-1_RCT172 28WK


title: Normal Uterine Cervix ART9185

source_name: genomic DNA from normal cells of the uterine cervix ART9185

value: bisulphite converted genomic DNA from a prospective CIN2+

value: Round2Cyt 0

tag: sentrix id

tag: sentrix position

value: G

tag: bisulphite 1

value: BS conversion C1 Grn 1776

value: BS conversion C2 Grn 1283


title: lung_not infected (PBS mock)_M2_Day1_Exp1

description: US93503719_251486829618_S01_GE1-v5_95_Feb07_1_2.txt

tag: strain

value: not infected (PBS mock)


title: lung_not infected (PBS mock)_M1_Day3_Exp2

description: US93503719_251486829618_S01_GE1-v5_95_Feb07_1_3.txt


title: RCT0171_T00320414

description: T00320414_2011-2-1_RCT171 28WK

value: Sprague Dawley

tag: diet

value: FO/P


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1)_M1_Day1_Exp1

description: US93503719_251486829618_S01_GE1-v5_95_Feb07_1_1.txt


title: Normal Uterine Cervix ART20241

source_name: genomic DNA from normal cells of the uterine cervix ART20241

tag: cell type

value: Round2Cyt 1

value: E

value: BS conversion C1 Grn 1851

tag: bisulphite 2

value: BS conversion C2 Grn 1087


title: lung_not infected (PBS mock)_M1_Day5_Exp1

description: US93503719_251486829617_S01_GE1-v5_95_Feb07_1_4.txt


title: Normal Uterine Cervix ART23845

source_name: genomic DNA from normal cells of the uterine cervix ART23845

tag: sample type

value: F

value: BS conversion C1 Grn 2103

value: BS conversion C2 Grn 1794


title: Normal Uterine Cervix ART7352

source_name: genomic DNA from normal cells of the uterine cervix ART7352

tag: outcome

value: D

value: BS conversion C1 Grn 1772

value: BS conversion C2 Grn 1294


title: IRT8915_T00245608

description: T00245608_2011-2-2_IRT 8915 7WK

value: CO/C

tag: injection

value: AOM

tag: time

value: 7 wk after AOM injection


title: Normal Uterine Cervix ART1386

source_name: genomic DNA from normal cells of the uterine cervix ART1386

value: bisulphite converted genomic DNA from a prospective CIN2+

tag: age

value: Round2Cyt 0

value: A

value: BS conversion C1 Grn 1727

value: BS conversion C2 Grn 1259


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1)_M2_Day5_Exp1

description: US93503719_251486829617_S01_GE1-v5_95_Feb07_1_3.txt

tag: tissue

value: lung

tag: infected

tag: biological replicate within time point for given experiment


title: lung_not infected (PBS mock)_M2_12h_Exp2

description: US93503719_251486829593_S01_GE1-v5_95_Feb07_1_4.txt

value: not infected (PBS mock)

tag: sample collection time post-infection


title: Normal Uterine Cervix ART15114

source_name: genomic DNA from normal cells of the uterine cervix ART15114

value: bisulphite converted genomic DNA from a prospective CIN2-

tag: hpv status

tag: pcr

value: Round2Cyt 1

value: C

value: BS conversion C1 Grn 1995

value: BS conversion C2 Grn 2380


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1) containing N66S mutation_M2_Day3_Exp1

description: US93503719_251486829592_S01_GE1-v5_95_Feb07_1_4.txt

tag: experiment number


title: Normal Uterine Cervix ART1827

source_name: genomic DNA from normal cells of the uterine cervix ART1827

tag: sentrix id

tag: sentrix position

value: B

tag: bisulphite 1

value: BS conversion C1 Grn 1730

value: BS conversion C2 Grn 1750


title: lung_not infected (PBS mock)_M1_Day1_Exp1

description: US93503719_251486829594_S01_GE1-v5_95_Feb07_1_3.txt

source_name: lung

tag: strain


title: IRT8712_T00245026

description: T00245026_2011-2-8_IRT 8712 7WK

value: Sprague Dawley

tag: diet

value: CO/C

value: AOM


title: lung_not infected (PBS mock)_M2_Day5_Exp1

description: US93503719_251486829590_S01_GE1-v5_95_Feb07_1_2.txt


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1)_M3_Day3_Exp2

description: US93503719_251486829512_S01_GE1-v5_95_Feb07_1_4.txt


title: lung_not infected (PBS mock)_M2_Day3_Exp1

description: US93503719_251486829591_S01_GE1-v5_95_Feb07_1_1.txt


title: IRT5914_T00244999

description: T00244999_2011-2-8_IRT 5914 7WK

value: FO/P

value: 7 wk after AOM injection


title: IRT8814_T00244998

description: T00244998_2011-2-8_IRT 8814 7WK


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1)_M1_Day5_Exp1

description: US93503719_251486829760_S01_GE1-v5_95_Feb07_1_4.txt


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1)_M2_12h_Exp2

description: US93503719_251486829512_S01_GE1-v5_95_Feb07_1_1.txt


title: IRT8712_T00245017

description: T00245017_2011-2-8_IRT 8712 7WK


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1) containing N66S mutation_M2_Day1_Exp1

description: US93503719_251486829594_S01_GE1-v5_95_Feb07_1_1.txt


title: lung_not infected (PBS mock)_M2_Day1_Exp2

description: US93503719_251486829591_S01_GE1-v5_95_Feb07_1_4.txt


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1) containing N66S mutation_M1_Day3_Exp2

description: US93503719_251486829592_S01_GE1-v5_95_Feb07_1_2.txt


title: Normal Uterine Cervix ART357

description: Liquid Based Cytology samples from the uterine cervix were collected from 152 women as part of the ARTISTIC trial (A Randomised Trial in Screening to Improve Cytology). All samples were of normal histology at time of sample draw, but 75 women developed a CIN2+ within 3 years of sample collection.

source_name: genomic DNA from normal cells of the uterine cervix ART357

tag: cell type

tag: sample type

value: bisulphite converted genomic DNA from a prospective CIN2+

value: Round2Cyt 0

value: K

value: BS conversion C1 Grn 2009

tag: bisulphite 2

value: BS conversion C2 Grn 1627


title: IRT8813_T00245594

description: T00245594_2011-2-2_IRT 8813 8WK

tag: injection

tag: time


title: lung_not infected (PBS mock)_M1_Day1_Exp2

description: US93503719_251486829511_S01_GE1-v5_95_Feb07_1_1.txt

tag: tissue

value: lung

value: not infected (PBS mock)


title: Normal Uterine Cervix ART5441

source_name: genomic DNA from normal cells of the uterine cervix ART5441

tag: outcome

tag: age

value: J

value: BS conversion C1 Grn 1922

value: BS conversion C2 Grn 1462


title: IRT5911_T00245002

description: T00245002_2011-2-8_IRT5911 7WK


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1) containing N66S mutation_M1_Day3_Exp1

description: US93503719_251486829510_S01_GE1-v5_95_Feb07_1_3.txt

tag: infected

tag: biological replicate within time point for given experiment

tag: sample collection time post-infection


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1) containing N66S mutation_M2_Day5_Exp1

description: US93503719_251486829510_S01_GE1-v5_95_Feb07_1_4.txt

tag: experiment number


title: lung_not infected (PBS mock)_M1_12h_Exp2

description: US93503719_251486829510_S01_GE1-v5_95_Feb07_1_2.txt


title: Normal Uterine Cervix ART61019

source_name: genomic DNA from normal cells of the uterine cervix ART61019

tag: hpv status

tag: pcr

tag: sentrix id

value: L

value: BS conversion C1 Grn 1854

value: BS conversion C2 Grn 1212


title: IRT5814_T00245013

description: T00245013_2011-2-2_IRT 5814 7WK

tag: strain

value: Sprague Dawley


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1)_M1_Day3_Exp1

description: US93503719_251486829493_S01_GE1-v5_95_Feb07_1_4.txt


title: IRT5913_T00245025

description: T00245025_2011-2-8_IRT 5913 8WK

tag: diet

value: AOM


title: Normal Uterine Cervix ART60247

source_name: genomic DNA from normal cells of the uterine cervix ART60247

tag: cell type

value: bisulphite converted genomic DNA from a prospective CIN2-

value: Round2Cyt 1

tag: sentrix position

value: H

tag: bisulphite 1

value: BS conversion C1 Grn 2089

value: BS conversion C2 Grn 1467


title: lung_not infected (PBS mock)_M2_Day3_Exp2

description: US93503719_251486829492_S01_GE1-v5_95_Feb07_1_2.txt


title: Mx+/+_uninf_lung_8h_A_IFN

description: US93503719_251486830896_S01_GE1-v5_95_Feb07_1_1.txt

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing.

data_processing:
Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.
Agilent Feature extractor software:
platform       x86_64-redhat-linux-gnu
arch           x86_64
os             linux-gnu
system         x86_64, linux-gnu
R version 2.12.2 (2011-02-25)
bioconductor packages: limma
Information on package 'limma'
Description:
Package:       limma
Version:       3.6.9
Date:          2010/12/01version
For the creation of the normalized data matrix, the limma package was used. Background correction was performed (method=normexp, offset=1).
Data was quantile normalized between arrays with the quantile normalization method and then log2 transformed.

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation. cRNA probes were generated from each sample by the use of an Agilent one-color Low Input Quick Amp Labeling Kit (Agilent Technologies, Santa Clara CA).

growth_protocol: Balb/c and Balb.A2F-Mx1 mice were divided equally into interferon treatment (10,000 unit recombinant human IFN-α A/D administered intranasally [R&D Systems, Minneapolis, MN]) or no-treatment groups. Animals were anesthetized by IP injection and half of the animals from each genetic background and treatment group inoculated intranasally with 3.2 × 10^5 PFU (100 50% lethal dose (LD50)) of the reconstructed 1918 infectious virus diluted in 50 μl phosphate-buffered saline (PBS) and the other half of the animals from each genetic background and treatment group mock infected with PBS alone.  Lungs samples were harvested for microarray analysis at 12, 24 and 72 hr post-infection.

extract_protocol: RNA was isolated using Qiagen RNeasy Mini kits with RNA-Later solution according to the manufacturer’s recommended protocol and purified using RNasy columns (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: Lung lobes from each animal were harvested, placed in Solution D (4 M guanidinium thiocyanate, 25 mM sodium citrate, 0.5% sarcosyl, 0.1 M B-mercaptoethanol) and frozen at -80 degrees C prior to RNA isolation.

tag: background strain

tag: genotype/variation

tag: virus infection

value: uninfected

tag: sample collection time post infection

tag: biological replicate

value: A

tag: treatment

value: IFN


title: Normal Uterine Cervix ART9038

source_name: genomic DNA from normal cells of the uterine cervix ART9038

tag: sample type

value: bisulphite converted genomic DNA from a prospective CIN2+

tag: outcome

tag: age

value: Round2Cyt 0

value: I

value: BS conversion C1 Grn 2015

tag: bisulphite 2

value: BS conversion C2 Grn 1599


title: lung_A/WSN/33 with PB1 from A/Hong Kong/156/97 (H5N1) containing N66S mutation_M1_Day1_Exp1

description: US93503719_251486829493_S01_GE1-v5_95_Feb07_1_1.txt

tag: tissue

value: lung

tag: infected

tag: biological replicate within time point for given experiment

tag: sample collection time post-infection

tag: experiment number


title: IRT5712_T00245000

description: T00245000_2011-2-8_IRT 5712 7WK

tag: strain

tag: diet

value: FO/P

tag: injection

tag: time

value: 7 wk after AOM injection


title: ira8903_T00320394

description: T00320394_2011-2-1_IRA8903 7WK

value: Sprague Dawley

value: CO/C

value: AOM


title: Normal Uterine Cervix ART4090

source_name: genomic DNA from normal cells of the uterine cervix ART4090

tag: cell type

tag: hpv status

tag: pcr

tag: sentrix id

tag: sentrix position

value: G

tag: bisulphite 1

value: BS conversion C1 Grn 1944

value: BS conversion C2 Grn 1391


title: IRT5814_T00244980

description: T00244980_2011-2-2_IRT5814 7WK

source_name: Exfoliated colonocytes


title: Mx+/+_uninf_lung_8h_C_IFN

description: US93503719_251486830898_S01_GE1-v5_95_Feb07_1_1.txt

tag: background strain

tag: genotype/variation

tag: virus infection

value: uninfected

tag: sample collection time post infection

tag: biological replicate

value: C

tag: treatment


title: Normal Uterine Cervix ART11913

source_name: genomic DNA from normal cells of the uterine cervix ART11913

tag: sample type

value: bisulphite converted genomic DNA from a prospective CIN2-

tag: outcome

tag: age

value: Round2Cyt 1

value: E

value: BS conversion C1 Grn 2151

tag: bisulphite 2

value: BS conversion C2 Grn 2023


title: Mx+/+_uninf_lung_24h_C_IFN

description: US93503719_251486830895_S01_GE1-v5_95_Feb07_1_4.txt

value: IFN


title: Mx+/+_uninf_lung_8h_B_IFN

description: US93503719_251486830897_S01_GE1-v5_95_Feb07_1_2.txt

value: B


title: Mx+/+_uninf_lung_24h_B_IFN

description: US93503719_251486830898_S01_GE1-v5_95_Feb07_1_3.txt


title: Normal Uterine Cervix ART17828

source_name: genomic DNA from normal cells of the uterine cervix ART17828

value: Round2Cyt 0

value: F

value: BS conversion C1 Grn 2169

value: BS conversion C2 Grn 1767


title: Balb/c_uninf_lung_8h_A_IFN

description: US93503719_251486830896_S01_GE1-v5_95_Feb07_1_4.txt

value: Balb/c

value: A


title: Mx+/+_uninf_lung_24h_A_IFN

description: US93503719_251486830897_S01_GE1-v5_95_Feb07_1_1.txt


title: ira8902_T00320386

description: T00320386_2011-2-1_IRA8902 7WK

tag: strain

value: Sprague Dawley

tag: diet

value: CO/C

tag: injection

value: AOM

tag: time

value: 7 wk after AOM injection


title: Normal Uterine Cervix ART7874

source_name: genomic DNA from normal cells of the uterine cervix ART7874

tag: cell type

value: bisulphite converted genomic DNA from a prospective CIN2-

tag: hpv status

tag: pcr

tag: sentrix id

value: C

value: BS conversion C1 Grn 2270

value: BS conversion C2 Grn 1802


title: ira8605_T00320397

description: T00320397_2011-2-1_IRA8605 7WK


title: ira8901_T00320585

description: T00320585_2011-2-1_IRA8901 7WK


title: Balb/c_uninf_lung_24h_C_IFN

description: US93503719_251486830897_S01_GE1-v5_95_Feb07_1_3.txt

tag: background strain

tag: genotype/variation

value: uninfected


title: Balb/c_uninf_lung_8h_C_IFN

description: US93503719_251486830895_S01_GE1-v5_95_Feb07_1_3.txt

tag: virus infection

tag: sample collection time post infection

value: IFN


title: Balb/c_uninf_lung_8h_B_IFN

description: US93503719_251486830895_S01_GE1-v5_95_Feb07_1_1.txt

tag: biological replicate

value: B

tag: treatment


title: Balb/c_uninf_lung_24h_B_IFN

description: US93503719_251486830898_S01_GE1-v5_95_Feb07_1_2.txt


title: Normal Uterine Cervix ART5306

description: Liquid Based Cytology samples from the uterine cervix were collected from 152 women as part of the ARTISTIC trial (A Randomised Trial in Screening to Improve Cytology). All samples were of normal histology at time of sample draw, but 75 women developed a CIN2+ within 3 years of sample collection.

source_name: genomic DNA from normal cells of the uterine cervix ART5306

tag: sample type

value: bisulphite converted genomic DNA from a prospective CIN2+

tag: outcome

value: Round2Cyt 0

tag: sentrix position

value: D

tag: bisulphite 1

value: BS conversion C1 Grn 2045

value: BS conversion C2 Grn 1971


title: ira5905_T00321150

description: T00321150_2011-2-8_IRA5905 7WK

tag: strain

tag: diet

value: FO/P


title: Normal Uterine Cervix ART16319

source_name: genomic DNA from normal cells of the uterine cervix ART16319

tag: age

value: Round2Cyt 1

value: A

value: BS conversion C1 Grn 1892

tag: bisulphite 2

value: BS conversion C2 Grn 1428


title: ira5902_T00320384

description: T00320384_2011-2-1_IRA5902 7WK

value: Sprague Dawley

tag: injection

value: AOM

tag: time

value: 7 wk after AOM injection


title: Mx+/+_Mock_lung_D3_B_Untreated

description: US93503719_251486829637_S01_GE1-v5_95_Feb07_1_3.txt

value: Mock infected (PBS)

value: Untreated


title: Balb/c_uninf_lung_24h_A_IFN

description: US93503719_251486830896_S01_GE1-v5_95_Feb07_1_3.txt

value: Balb/c

value: uninfected

value: IFN


title: Mx+/+_Mock_lung_D3_A_Untreated

description: US93503719_251486829633_S01_GE1-v5_95_Feb07_1_3.txt


title: Normal Uterine Cervix ART13767

source_name: genomic DNA from normal cells of the uterine cervix ART13767

tag: cell type

value: bisulphite converted genomic DNA from a prospective CIN2-

tag: hpv status

tag: pcr

tag: sentrix id

value: L

value: BS conversion C1 Grn 2287

value: BS conversion C2 Grn 2575


title: ira5901_T00320389

description: T00320389_2011-2-8_IRA5901 7WK

value: FO/P


title: Mx+/+_Mock_lung_D3_C_Untreated

description: US93503719_251486829637_S01_GE1-v5_95_Feb07_1_1.txt

tag: background strain

tag: genotype/variation

tag: virus infection

tag: sample collection time post infection

value: C


title: Mx+/+_Mock_lung_D1_C_Untreated

description: US93503719_251486829636_S01_GE1-v5_95_Feb07_1_3.txt

tag: biological replicate

tag: treatment


title: Mx+/+_Mock_lung_D1_A_Untreated

description: US93503719_251486829634_S01_GE1-v5_95_Feb07_1_1.txt

value: A


title: ira5604_T00320597

description: T00320597_2011-2-3_IRA5604 7WK


title: Normal Uterine Cervix ART16109

source_name: genomic DNA from normal cells of the uterine cervix ART16109

tag: sample type

tag: outcome

value: Round2Cyt 1

tag: sentrix position

value: B

tag: bisulphite 1

value: BS conversion C1 Grn 2113

value: BS conversion C2 Grn 2095


title: Mx+/+_Mock_lung_12h_C_Untreated

description: US93503719_251486829636_S01_GE1-v5_95_Feb07_1_1.txt


title: Normal Uterine Cervix ART61199

source_name: genomic DNA from normal cells of the uterine cervix ART61199

value: bisulphite converted genomic DNA from a prospective CIN2+

tag: age

value: Round2Cyt 0

value: K

value: BS conversion C1 Grn 2391

tag: bisulphite 2

value: BS conversion C2 Grn 2365


title: Normal Uterine Cervix ART6595

source_name: genomic DNA from normal cells of the uterine cervix ART6595

value: J

value: BS conversion C1 Grn 2123

value: BS conversion C2 Grn 2025


title: Normal Uterine Cervix ART1013

source_name: genomic DNA from normal cells of the uterine cervix ART1013

value: G

value: BS conversion C1 Grn 2395

value: BS conversion C2 Grn 2186


title: Normal Uterine Cervix ART7248

source_name: genomic DNA from normal cells of the uterine cervix ART7248

value: bisulphite converted genomic DNA from a prospective CIN2-

value: I

value: BS conversion C1 Grn 2275

value: BS conversion C2 Grn 1952


title: Normal Uterine Cervix ART8372

source_name: genomic DNA from normal cells of the uterine cervix ART8372

value: Round2Cyt 1

value: H

value: BS conversion C1 Grn 2371

value: BS conversion C2 Grn 2196


title: RCT0492_T00245592

description: T00245592_2011-2-2_RCT 492 8WK

tag: strain

value: Sprague Dawley

tag: diet

value: CO/C

tag: injection

value: AOM

tag: time

value: 7 wk after AOM injection


title: Mx+/+_Mock_lung_D1_B_Untreated

description: US93503719_251486829634_S01_GE1-v5_95_Feb07_1_4.txt

source_name: lung

value: Mock infected (PBS)

value: B

value: Untreated


title: Mx+/+_18inf_lung_72h_C_Untreated

description: US93503719_251486829692_S01_GE1-v5_95_Feb07_1_1.txt

value: r1918 virus

value: C


title: Mx+/+_Mock_lung_12h_B_Untreated

description: US93503719_251486829634_S01_GE1-v5_95_Feb07_1_2.txt


title: Normal Uterine Cervix ART584

source_name: genomic DNA from normal cells of the uterine cervix ART584

tag: cell type

value: bisulphite converted genomic DNA from a prospective CIN2-

tag: hpv status

tag: pcr

value: Round2Cyt 0

tag: sentrix id

value: F

value: BS conversion C1 Grn 1910

value: BS conversion C2 Grn 1251


title: Mx+/+_18inf_lung_12h_B_Untreated

description: US93503719_251486829635_S01_GE1-v5_95_Feb07_1_4.txt

tag: background strain

tag: genotype/variation

tag: virus infection

tag: sample collection time post infection


title: RCT0495_T00244996

description: T00244996_2011-2-3_RCT 495 7WK


title: Mx+/+_18inf_lung_24h_C_Untreated

description: US93503719_251486829693_S01_GE1-v5_95_Feb07_1_4.txt

tag: biological replicate

tag: treatment


title: Mx+/+_18inf_lung_72h_B_Untreated

description: US93503719_251486829690_S01_GE1-v5_95_Feb07_1_1.txt


title: RCT0475_T00244994

description: T00244994_2011-2-3_RCT 475 7WK


title: Normal Uterine Cervix ART2497

source_name: genomic DNA from normal cells of the uterine cervix ART2497

tag: sample type

value: bisulphite converted genomic DNA from a prospective CIN2+

tag: outcome

tag: sentrix position

value: E

tag: bisulphite 1

value: BS conversion C1 Grn 2396

value: BS conversion C2 Grn 1852


title: Mx+/+_18inf_lung_24h_A_Untreated

description: US93503719_251486829690_S01_GE1-v5_95_Feb07_1_2.txt

value: A


title: Mx+/+_18inf_lung_72h_A_Untreated

description: US93503719_251486829690_S01_GE1-v5_95_Feb07_1_4.txt


title: Mx+/+_18inf_lung_24h_B_Untreated

description: US93503719_251486829693_S01_GE1-v5_95_Feb07_1_2.txt


title: Mx+/+_18inf_lung_72h_C_IFN

description: US93503719_251486829693_S01_GE1-v5_95_Feb07_1_1.txt

value: IFN


title: Mx+/+_Mock_lung_12h_A_Untreated

description: US93503719_251486829557_S01_GE1-v5_95_Feb07_1_2.txt


title: Mx+/+_18inf_lung_72h_B_IFN

description: US93503719_251486829694_S01_GE1-v5_95_Feb07_1_3.txt


title: RCT0491_T00244997

description: T00244997_2011-2-8_RCT 491 7WK

tag: strain

value: Sprague Dawley

tag: diet

value: CO/C

value: AOM

value: 7 wk after AOM injection


title: Mx+/+_18inf_lung_72h_A_IFN

description: US93503719_251486829692_S01_GE1-v5_95_Feb07_1_3.txt

value: r1918 virus


title: RCT0492_T00245584

description: T00245584_2011-2-2_RCT 492 8WK

tag: injection

tag: time


title: Normal Uterine Cervix ART15986

description: Liquid Based Cytology samples from the uterine cervix were collected from 152 women as part of the ARTISTIC trial (A Randomised Trial in Screening to Improve Cytology). All samples were of normal histology at time of sample draw, but 75 women developed a CIN2+ within 3 years of sample collection.

source_name: genomic DNA from normal cells of the uterine cervix ART15986

tag: cell type

tag: age

tag: hpv status

value: Round2Cyt 1

value: D

value: BS conversion C1 Grn 1614

tag: bisulphite 2

value: BS conversion C2 Grn 1069


title: RCT0471_T00244992

description: T00244992_2011-2-2_RCT 471 8WK

source_name: Exfoliated colonocytes


title: Mx+/+_18inf_lung_12h_C_Untreated

description: US93503719_251486829557_S01_GE1-v5_95_Feb07_1_4.txt

tag: background strain

tag: genotype/variation

value: C

value: Untreated


title: RCT0183_T00245018

description: T00245018_2011-2-2_RCT 183 7WK

value: FO/P


title: Normal Uterine Cervix ART12244

source_name: genomic DNA from normal cells of the uterine cervix ART12244

value: bisulphite converted genomic DNA from a prospective CIN2-

tag: pcr

tag: sentrix id

value: BS conversion C1 Grn 2645

value: BS conversion C2 Grn 2392


title: Mx+/+_18inf_lung_24h_C_IFN

description: US93503719_251486829479_S01_GE1-v5_95_Feb07_1_1.txt

tag: virus infection

tag: sample collection time post infection

tag: biological replicate

tag: treatment


title: Normal Uterine Cervix ART15599

source_name: genomic DNA from normal cells of the uterine cervix ART15599

tag: sample type

tag: outcome

tag: sentrix position

value: L

tag: bisulphite 1

value: BS conversion C1 Grn 2170

value: BS conversion C2 Grn 2214


title: Mx+/+_18inf_lung_12h_C_IFN

description: US93503719_251486829479_S01_GE1-v5_95_Feb07_1_3.txt

value: IFN


title: RCT0182_T00245022

description: T00245022_2011-2-2_RCT 182 7WK

tag: strain

value: Sprague Dawley

tag: diet

tag: injection

value: AOM

tag: time


title: Mx+/+_18inf_lung_12h_B_IFN

description: US93503719_251486829691_S01_GE1-v5_95_Feb07_1_4.txt

value: r1918 virus

value: B


title: Balb/c_Mock_lung_72h_A_Untreated

description: US93503719_251486829555_S01_GE1-v5_95_Feb07_1_3.txt

value: Balb/c

value: Mock infected (PBS)

value: A


title: Normal Uterine Cervix ART16563

source_name: genomic DNA from normal cells of the uterine cervix ART16563

tag: cell type

value: bisulphite converted genomic DNA from a prospective CIN2+

tag: age

tag: hpv status

value: Round2Cyt 0

value: J

value: BS conversion C1 Grn 2206

tag: bisulphite 2

value: BS conversion C2 Grn 2191


title: Mx+/+_18inf_lung_24h_B_IFN

description: US93503719_251486829694_S01_GE1-v5_95_Feb07_1_2.txt

tag: background strain

tag: genotype/variation


title: Mx+/+_18inf_lung_12h_A_Untreated

description: US93503719_251486829637_S01_GE1-v5_95_Feb07_1_2.txt

tag: virus infection

tag: sample collection time post infection

value: Untreated


title: Normal Uterine Cervix ART571

source_name: genomic DNA from normal cells of the uterine cervix ART571

tag: pcr

tag: sentrix id

value: BS conversion C1 Grn 2514

value: BS conversion C2 Grn 2318


title: Normal Uterine Cervix ART16928

source_name: genomic DNA from normal cells of the uterine cervix ART16928

tag: sample type

tag: outcome

value: BS conversion C1 Grn 2032

value: BS conversion C2 Grn 1524


title: rca0481_T00320584

description: T00320584_2011-2-1_RCA481 7WK

value: Sprague Dawley

value: CO/C

value: 7 wk after AOM injection


title: RCT0181_T00244970

description: T00244970_2011-2-2_RCT 181 7WK

value: FO/P

value: AOM


title: Balb/c_Mock_lung_72h_B_Untreated

description: US93503719_251486829556_S01_GE1-v5_95_Feb07_1_1.txt

value: Balb/c

value: Mock infected (PBS)

tag: biological replicate

value: B

tag: treatment


title: Mx+/+_18inf_lung_24h_A_IFN

description: US93503719_251486829692_S01_GE1-v5_95_Feb07_1_2.txt

value: r1918 virus

value: A

value: IFN


title: Mx+/+_18inf_lung_12h_A_IFN

description: US93503719_251486829479_S01_GE1-v5_95_Feb07_1_2.txt


title: Balb/c_Mock_lung_24h_B_Untreated

description: US93503719_251486829689_S01_GE1-v5_95_Feb07_1_1.txt


title: Balb/c_Mock_lung_12h_B_Untreated

description: US93503719_251486829554_S01_GE1-v5_95_Feb07_1_2.txt


title: Balb/c_18inf_lung_72h_B_Untreated

description: US93503719_251486829554_S01_GE1-v5_95_Feb07_1_3.txt


title: Normal Uterine Cervix ART17887

source_name: genomic DNA from normal cells of the uterine cervix ART17887

value: bisulphite converted genomic DNA from a prospective CIN2+

value: Round2Cyt 0

tag: sentrix position

value: K

tag: bisulphite 1

value: BS conversion C1 Grn 2321

value: BS conversion C2 Grn 2520


title: Balb/c_Mock_lung_24h_A_Untreated

description: US93503719_251486829555_S01_GE1-v5_95_Feb07_1_1.txt

value: Untreated


title: RCT0182_T00244991

description: T00244991_2011-2-2_RCT 182 7WK

tag: strain

value: Sprague Dawley

tag: diet

tag: injection

tag: time


title: RCT0172_T00245603

description: T00245603_2011-2-2_RCT 172 8WK


title: RCT0171_T00244993

description: T00244993_2011-2-3_RCT 171 7WK


title: Balb/c_18inf_lung_72h_C_Untreated

description: US93503719_251486829635_S01_GE1-v5_95_Feb07_1_1.txt

value: C


title: Balb/c_Mock_lung_12h_A_Untreated

description: US93503719_251486829689_S01_GE1-v5_95_Feb07_1_2.txt


title: Normal Uterine Cervix ART11552

description: Liquid Based Cytology samples from the uterine cervix were collected from 152 women as part of the ARTISTIC trial (A Randomised Trial in Screening to Improve Cytology). All samples were of normal histology at time of sample draw, but 75 women developed a CIN2+ within 3 years of sample collection.

source_name: genomic DNA from normal cells of the uterine cervix ART11552

tag: cell type

value: bisulphite converted genomic DNA from a prospective CIN2-

tag: age

tag: hpv status

value: Round2Cyt 1

value: I

value: BS conversion C1 Grn 2234

tag: bisulphite 2

value: BS conversion C2 Grn 1732


title: Balb/c_18inf_lung_72h_A_Untreated

description: US93503719_251486829555_S01_GE1-v5_95_Feb07_1_2.txt

tag: background strain

value: Balb/c

tag: genotype/variation

tag: virus infection

tag: sample collection time post infection


title: rca0435_T00320398

description: T00320398_2011-2-1_RCA435 7WK

value: CO/C

value: AOM

value: 7 wk after AOM injection


title: Normal Uterine Cervix ART5458

source_name: genomic DNA from normal cells of the uterine cervix ART5458

tag: sample type

value: bisulphite converted genomic DNA from a prospective CIN2+

tag: outcome

tag: pcr

tag: sentrix id

value: H

value: BS conversion C1 Grn 2179

value: BS conversion C2 Grn 1525


title: Normal Uterine Cervix ART12118

source_name: genomic DNA from normal cells of the uterine cervix ART12118

tag: sentrix position

value: G

tag: bisulphite 1

value: BS conversion C1 Grn 2023

value: BS conversion C2 Grn 1348


title: Normal Uterine Cervix ART189

source_name: genomic DNA from normal cells of the uterine cervix ART189

value: Round2Cyt 0

value: F

value: BS conversion C1 Grn 2189

value: BS conversion C2 Grn 1455


title: Balb/c_18inf_lung_24h_A_Untreated

description: US93503719_251486829555_S01_GE1-v5_95_Feb07_1_4.txt

value: r1918 virus

tag: biological replicate

value: A

tag: treatment

value: Untreated


title: rca0434_T00321151

description: T00321151_2011-2-8_RCA434 7WK

tag: strain

value: Sprague Dawley

tag: diet

value: CO/C

tag: injection

tag: time


title: Balb/c_18inf_lung_24h_B_Untreated

description: US93503719_251486829689_S01_GE1-v5_95_Feb07_1_3.txt

value: Balb/c

value: B


title: rca0134_T00320393

description: T00320393_2011-2-1_RCA134 7WK

value: FO/P

value: AOM

value: 7 wk after AOM injection


title: Normal Uterine Cervix ART18749

source_name: genomic DNA from normal cells of the uterine cervix ART18749

tag: cell type

value: bisulphite converted genomic DNA from a prospective CIN2-

tag: age

tag: hpv status

value: Round2Cyt 1

value: E

value: BS conversion C1 Grn 2036

tag: bisulphite 2

value: BS conversion C2 Grn 1826


title: Balb/c_18inf_lung_12h_B_Untreated

description: US93503719_251486829554_S01_GE1-v5_95_Feb07_1_1.txt

tag: background strain

tag: genotype/variation

tag: virus infection

tag: sample collection time post infection


title: rca0195_T00320405

description: T00320405_2011-2-1_RCA195 7WK


title: Balb/c_18inf_lung_12h_C_Untreated

description: US93503719_251486829556_S01_GE1-v5_95_Feb07_1_2.txt

value: C


title: Normal Uterine Cervix ART6305

source_name: genomic DNA from normal cells of the uterine cervix ART6305

tag: sample type

value: bisulphite converted genomic DNA from a prospective CIN2+

tag: outcome

tag: pcr

value: Round2Cyt 0

tag: sentrix id

value: D

value: BS conversion C1 Grn 2176

value: BS conversion C2 Grn 1612


title: rca0135_T00320400

description: T00320400_2011-2-1_RCA135 7WK

value: Sprague Dawley


title: Balb/c_18inf_lung_24h_C_Untreated

description: US93503719_251486829556_S01_GE1-v5_95_Feb07_1_4.txt

source_name: lung

value: Balb/c

value: r1918 virus

tag: biological replicate

tag: treatment

value: Untreated


title: Balb/c_18inf_lung_72h_B_IFN

description: US93503719_251486829635_S01_GE1-v5_95_Feb07_1_2.txt

value: B

value: IFN


title: ir894_T00317422

description: T00317422_2011-2-1_IR894 24h

tag: strain

tag: diet

value: CO/C

value: AOM

value: 24 h after AOM injection


title: Balb/c_18inf_lung_72h_C_IFN

description: US93503719_251486829633_S01_GE1-v5_95_Feb07_1_4.txt


title: Balb/c_18inf_lung_12h_A_Untreated

description: US93503719_251486829556_S01_GE1-v5_95_Feb07_1_3.txt

value: A


title: Normal Uterine Cervix ART2337

source_name: genomic DNA from normal cells of the uterine cervix ART2337

value: bisulphite converted genomic DNA from a prospective CIN2-

value: Round2Cyt 1

tag: sentrix position

tag: bisulphite 1

value: BS conversion C1 Grn 2431

value: BS conversion C2 Grn 2403


title: Balb/c_18inf_lung_24h_A_IFN

description: US93503719_251486829635_S01_GE1-v5_95_Feb07_1_3.txt


title: Balb/c_18inf_lung_24h_B_IFN

description: US93503719_251486829636_S01_GE1-v5_95_Feb07_1_2.txt


title: Balb/c_18inf_lung_72h_A_IFN

description: US93503719_251486829634_S01_GE1-v5_95_Feb07_1_3.txt


title: rca0194_T00320586

description: T00320586_2011-2-1_RCA194 7WK

value: FO/P

tag: injection

tag: time

value: 7 wk after AOM injection


title: Normal Uterine Cervix ART519

source_name: genomic DNA from normal cells of the uterine cervix ART519

tag: cell type

value: bisulphite converted genomic DNA from a prospective CIN2+

tag: age

tag: hpv status

value: Round2Cyt 0

value: BS conversion C1 Grn 2690

tag: bisulphite 2

value: BS conversion C2 Grn 2111


title: Balb/c_18inf_lung_24h_C_IFN

description: US93503719_251486829633_S01_GE1-v5_95_Feb07_1_2.txt

tag: background strain

value: Balb/c

tag: genotype/variation

tag: virus infection

value: r1918 virus

tag: sample collection time post infection

value: C


title: Balb/c_18inf_lung_12h_C_IFN

description: US93503719_251486829557_S01_GE1-v5_95_Feb07_1_1.txt

value: IFN


title: Balb/c_18inf_lung_12h_A_IFN

description: US93503719_251486829633_S01_GE1-v5_95_Feb07_1_1.txt


title: ir834_T00320360

description: T00320360_2011-2-1_IR834 24h

value: Sprague Dawley

value: CO/C

value: AOM


title: Balb/c_18inf_lung_12h_B_IFN

description: US93503719_251486829637_S01_GE1-v5_95_Feb07_1_4.txt

value: B


title: Male 2 vs pooled reference

city: Pacific Grove

first: Luke

last: Gardner

state: California

address: 120 Ocean View Blvd, Hopkins Marine Station

institute: Stanford University

description: Male biological replicate 2 of 4 compared to pooled reference

hyb_protocol: Hybridization of the microarrays followed the Two-Color Microarray-Based Gene Expression Analysis protocol with reagents from the Gene Expression Hybridization Kit (Agilent Technologies, Santa Clara, CA, USA)

scan_protocol: Axon GenePix® 4000B microarray scanner (Molecular Devices, Sunnyvale, CA, USA).

data_processing: Feature Extraction 9.5.3 image analysis software (Agilent Technologies, Santa Clara, CA, USA) was used to extract and process these raw microarray images using protocol GE2-v5_95_Feb07 protocol.

organism: Thunnus thynnus

source_name: Male 2

label_protocol: Target preparation including, reverse transcription of total RNA, RNA amplification by in vitro transcription and aRNA labeling was conducted using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Applied Biosystems, Foster City, CA, USA) according to manufacturer’s instruction.

extract_protocol:
tissue collection: Gonad tissue samples were collected from mature T. thynnus by observers as part of the Pelagic Longline Observer Program coordinated by the National Oceanic and Atmospheric Administration (NOAA). Gonad tissue was sampled from the fish in a sterile manner and fixed immediately in RNAlater
Total RNA extracted using Trizol following manufacturer's instructions

tag: tissue

value: Testes

tag: Sex

value: Male

tag: sexual maturity

value: Mature

source_name: Pooled reference of total RNA from all 8 gonad samples (pooled equally)

value: combined testes and ovary


title: Male 4 vs pooled reference

description: Male biological replicate 4 of 4 compared to pooled reference

source_name: Male 4


title: posttreatment-T9

city: shanghai

first: lei

last: ye

address: 197#, second ruijin road

country: China

institute: ruijin hospital

description: peripheral blood mononuclear- six months posttreatment-patient 9

hyb_protocol: Following fragmentation, 200 ug of cRNA were hybridized for 16 hr at 4°C onAffymetrix Human Genome U133 Plus 2.0 microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using  Affymetrix Scanner 3000 7G.

data_processing: Gene expression levels were normalized using the robust multiarray average (RMA) procedure using Partek GS 6.5.

source_name: peripheral blood mononuclear at six months posttreatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ug total RNA.

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

treatment_protocol: PBMC was isolated within six hours by LymphoprepTm gradient purification according to the manufacturer’s instructions (Axis-Shield PoC AS, Oslo, Norway) and stored in liquid nitrogen until use.

value: peripheral blood mononuclear cell

value: at six months posttreat


title: posttreatment-T8

description: peripheral blood mononuclear- six months posttreatment-patient 8


title: ir884_T00316332

description: T00316332_2011-2-1_IR884 24h

source_name: Exfoliated colonocytes

tag: strain

value: 24 h after AOM injection


title: Rag-/-, Day0

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

institute: Montana State University

data_processing:
CT values were gathered using 7500 Fast System SDS software. Comparative data analysis was performed using the DDCT method and the PCR-Array Data analysis web portal http://www.sabioscinece.com/pcrarraydataanalysis.php. Data from RAG-/- mice at day 0 were used as the comparison group.
(1) AVG Ct, (2) AVG Ct STDEV, (3) AVG Delta(Ct)*, (4) 2^(-AVG(Delta(Ct))  *AVG Delta(Ct) = Ct(gene of interest) - AVG Ct(housekeeping gene)

label: SYBR Green

source_name: total bone marrow cells

label_protocol:
reverse_transcription_protocol:100 ng of RNA per sample were used with three replicates in each comparison group. RT2 first strand reagents from SAbioscience were used according to the manufacturer's protocol.
qPCR_protocol: Real time PCR was performed using reagents and protocol provided in the RT2 PCR Pathway focused Array system from SAbioscience. An Applied Biosystems 7500 Fast Real-Time PCR machine was used.

extract_protocol: RNA was harvested from total bone marrow cells using a RNeasy Plus mini kit from Qiagen. DNA was removed from samples using DNA-eliminator columns as provided in the kit. In addition a DNase treatment was performed using genomic DNA elimination mixture from SAbioscience.

treatment_protocol: bone marrow of IFrag-/-, and RAG-/- mice was harvested at day 0 and 7 post PC lung infection

value: Rag-/-

tag: treatment

value: uninfected


title: ir824_T00317400

description: T00317400_2011-2-1_IR824 24h

tag: diet


title: Normal Uterine Cervix ART10742

description: Liquid Based Cytology samples from the uterine cervix were collected from 152 women as part of the ARTISTIC trial (A Randomised Trial in Screening to Improve Cytology). All samples were of normal histology at time of sample draw, but 75 women developed a CIN2+ within 3 years of sample collection.

source_name: genomic DNA from normal cells of the uterine cervix ART10742

tag: sample type

value: bisulphite converted genomic DNA from a prospective CIN2-

tag: outcome

tag: pcr

value: Round2Cyt 1

tag: sentrix id

tag: sentrix position

tag: bisulphite 1

value: BS conversion C1 Grn 2414

value: BS conversion C2 Grn 1939


title: ir874_T00317429

description: T00317429_2011-2-1_IR874 24h

value: Sprague Dawley

tag: injection

tag: time


title: posttreatment-T7

description: peripheral blood mononuclear- six months posttreatment-patient 7


title: ir844_T00320367

description: T00320367_2011-2-1_IR844 24h

value: CO/C


title: Female 4 vs pooled reference

description: Female biological replicate 4 of 4 compared to pooled reference

source_name: Female 4

value: Ovary

value: Female


title: Female 3 vs pooled reference

description: Female biological replicate 3 of 4 compared to pooled reference

source_name: Female 3


title: Male 3 vs pooled reference

description: Male biological replicate 3 of 4 compared to pooled reference

source_name: Male 3

value: Testes


title: Male 1 vs pooled reference

description: Male biological replicate 1 of 4 compared to pooled reference

source_name: Male 1

value: Male


title: ir594_T00317416

description: T00317416_2011-2-1_IR594 24h

value: FO/P

value: AOM


title: IFRag-/- +NAC, Day7

tag: genotype/variation

value: IFRag-/- +NAC

value: day 7 post PC lung infection mice treated with N-Acetylcystein


title: ir584_T00317391

description: T00317391_2011-2-1_IR 584 24h

value: 24 h after AOM injection


title: Female 1 vs pooled reference

description: Female biological replicate 1 of 4 compared to pooled reference

source_name: Female 1

value: Mature

value: combined testes and ovary


title: posttreatment-T6

description: peripheral blood mononuclear- six months posttreatment-patient 6

value: peripheral blood mononuclear cell

value: at six months posttreat


title: TGF_5/Pool-2; biol. Rep. 2; tech. Rep. 2

city: São Paulo

first: Katia

middle: Cristina Pereira

last: Oliveira

state: O

address: Av Prof lineu prestes 748

department: Centro de Parasitologia e Micologia

country: Brazil

institute: Instituto Adolfo Lutz

hyb_protocol: Samples were combined and hybridize on a custom oligoarray with 4 x 44k elements produced by Agilent Technologies (GPL8606), the hybridization and washing steps were perfomed according to agilent instructions

scan_protocol: The washed slides were scanned using the equipament GenePix4000B (molecular devices)

data_processing: Data was extracted using Feature Extraction software (Agilent Technologies), the intensities were LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

organism: Schistosoma mansoni

label_protocol: All samples were linearly amplified and labeled using Agilent protocol with Low input RNA amplification kit

growth_protocol: Adult worms were obtained by portal perfusion in 45-days infected hamsters

extract_protocol: RNA from all samples was extract using Trizol reagent (invitrogen)  followed by DNAse treatment using RNeasy kit (QIAGEN) according to manufacturer´s instructions. The two non-treated smaples were pooled together (using the same amount from each sample)

treatment_protocol: Adult worms were kept in culture overnight with TGF-beta (1nM) or the veicule solution

tag: development stage

value: adult

value: TGF-beta treated adult worms kept in culture overnight

value: Non-treated adult worms kept in culture overnight (pooled two biological replicas)


title: Rag-/-, Day7

value: Rag-/-

value: day 7 post PC lung infection


title: ir574_T00317396

description: T00317396_2011-2-1_IR574 24h

value: Sprague Dawley


title: IFRag-/-, Day7

value: IFRag-/-


title: posttreatment-T5

description: peripheral blood mononuclear- six months posttreatment-patient 5


title: Female 2 vs pooled reference

description: Female biological replicate 2 of 4 compared to pooled reference

source_name: Female 2

value: Ovary

value: Female


title: posttreatment-T4

description: peripheral blood mononuclear- six months posttreatment-patient 4


title: IFRag-/-, Day0

value: uninfected


title: posttreatment-T2

description: peripheral blood mononuclear- six months posttreatment-patient 2


title: TGF_5/Pool-3; biol. Rep. 2; tech. Rep. 3


title: TGF_5/Pool-4; biol. Rep. 2; tech. Rep. 4


title: TGF_5/Pool-1; biol. Rep. 3; tech. Rep. 1


title: posttreatment-T3

description: peripheral blood mononuclear- six months posttreatment-patient 3


title: pretreatment-D8

description: peripheral blood mononuclear- pretreatment-patient 8

source_name: peripheral blood mononuclear before treatment

value: before treatment


title: ir524_T00316334

description: T00316334_2011-2-1_IR524 24h

value: FO/P

value: AOM


title: TGF_4/Pool-4; biol. Rep. 2; tech. Rep. 4


title: pretreatment-D9

description: peripheral blood mononuclear- pretreatment-patient 9


title: ir534_T00317410

description: T00317410_2011-2-1_IR534 24h

value: 24 h after AOM injection


title: TGF_4/Pool-2; biol. Rep. 2; tech. Rep. 2


title: rc494_T00320374

description: T00320374_2011-2-1_RC494 24h

value: CO/C


title: ir544_T00320369

description: T00320369_2011-2-1_IR544 24h


title: TGF_1/Pool-4; biol. Rep. 1; tech. Rep. 4


title: rc434_T00317421

description: T00317421_2011-2-1_2RC434 24h


title: TGF_4/Pool-1; biol. Rep. 2; tech. Rep. 1


title: posttreatment-T1

description: peripheral blood mononuclear- six months posttreatment-patient 1

value: peripheral blood mononuclear cell


title: TGF_4/Pool-3; biol. Rep. 2; tech. Rep. 3


title: TGF_1/Pool-2; biol. Rep. 1; tech. Rep. 2


title: rc484_T00320372

description: T00320372_2011-2-1_RC484 24h


title: pretreatment-D5

description: peripheral blood mononuclear- pretreatment-patient 5


title: pretreatment-D7

description: peripheral blood mononuclear- pretreatment-patient 7


title: TGF_1/Pool-3; biol. Rep. 1; tech. Rep. 3


title: pretreatment-D4

description: peripheral blood mononuclear- pretreatment-patient 4


title: rc194_T00317395

description: T00317395_2011-2-1_RC 194 24h


title: rc474_T00316353

description: T00316353_2011-2-1_RC 474 24h


title: rc174_T00316331

description: T00316331_2011-2-1_RC174 24h


title: pretreatment-D3

description: peripheral blood mononuclear- pretreatment-patient 3


title: pretreatment-D6

description: peripheral blood mononuclear- pretreatment-patient 6


title: rc134_T00320365

description: T00320365_2011-2-1_2RC134 24h


title: rc424_T00320368

description: T00320368_2011-2-1_2RC424 24h


title: pretreatment-D1

description: peripheral blood mononuclear- pretreatment-patient 1


title: pretreatment-D2

description: peripheral blood mononuclear- pretreatment-patient 2


title: Pro_B_1

status: Public on Feb 19 2012

city: Oxford

first: Sten Eirik

last: Jacobsen

address: Headington

department: Weatherall Institute

institute: University of Oxford

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array MOE430A 2.0, using a  Genechip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (performed at the PAN Facility, Stanford)

scan_protocol: Chips were scanned using the Genechip Scanner 3000 7G

data_processing: Cel files were processed in R using RMA normalisation

label_protocol: Nugen kit WT-Ovation Pico RNA Amplifications System for total RNA amplification. Uesd WT Ovation cDNA Biotin Module V2 for cDNA labeling and fragmentation.

tag: age

value: 1 week

value: Male/Female

tag: developmental stage

value: Normal

tag: cell type

value: Hematopoietic

value: B-cell progenitor


title: ETPFlt3hi_4

tag: Sex

value: early thymic progenitors


title: i-OSKM-ESC_-Dox_rep1

city: Omaha

first: Angie

last: Rizzinio

state: NE

address: 986805 Nebraska Medical Center

department: Eppley Institute for Research in Cancer and Allied Diseases

institute: University of Nebraska Medical Center

description: Gene expression data from i-OSKM-ESC

hyb_protocol: Hybridization for 16 hours at 45C using the GeneChip® WT Terminal Labeling and Hybridization on Affymetrix GeneChip Mouse Gene 1.0 ST. Washing and staining were performed with the Affymetrix Fluidics Station 450.

scan_protocol: The gene chips were scanned using the Affymetrix GeneChip Scanner 3000 7G by the University of Nebraska Medical Center DNA Microarray Core Facility.

data_processing: Data was analyzed with Affymetrix Expression Console software (Affymetrix, Santa Clara, CA) using Robust Multichip Analysis (RMA) for normalization.

source_name: i-OSKM-ESC (Control)

label_protocol: Sense-strand cDNA was generated from 300ng total RNA using the Ambion WT Expression kit for Affymetrix Whole Transcript Expression Arrays. This cDNA was fragmented and labeled using the GeneChip® WT Terminal Labeling and Hybridization.

growth_protocol: Stock cultures of i-OSKM-ESC (engineered from KH2 ESC, obtained from K.Hochedlinger, K.Hochedlinger, 2005, PMID: 15882627) were cultured as described previously (Kopp,J.L., 2008, PMID: 18238855).

extract_protocol: RNA isolation has been described previously (Kopp,J.L., 2008, PMID: 18238855).

treatment_protocol: i-OSKM-ESC were subculture onto gelatin coated tissue culture plastic at a density of 4x10^4 cells per cm^2. Twenty-four hours after subculture, doxycycline was added to the culture medium (4 µg/mL) of the +Dox sample. The -Dox sample was refed fresh medium without doxycycline. Twenty-four hours after the addition of doxycycline, RNA was isolated from i-OSKM-ESC.

tag: strain

value: i-OSKM-ESC


title: Pro_B_2


title: ETPFlt3hi_6


title: LSKFlt3hi IL7R+_5

source_name: LSKFlt3hi IL7R+

value: thymic seeding progenitors


title: LSKFlt3hi IL7R+_4


title: i-OSKM-ESC_+Dox_rep1

description: Gene expression data from i-OSKM-ESC treated with doxycycline (4 µg/mL) for 24 hours


title: LSKFlt3-CD48-CD150+_4

value: Hematopoietic Stem Cell


title: CLP_2

source_name: CLP

value: putative thymus seeding progenitor


title: LSKFlt3hi IL7R+_6


title: CLP_3


title: LSKFlt3-CD48-CD150+_6


title: Pro_B_3


title: ETPFlt3hi_5


title: DN3_6


title: DN3_5


title: DN3_4


title: TGF_1/Pool-1, biol. Rep. 1; tech. Rep. 1

value: adult

value: Non-treated adult worms kept in culture overnight (pooled two biological replicas)

value: TGF-beta treated adult worms kept in culture overnight


title: CLP_1


title: Adult_ETP_2

value: adult early thymic progenitor


title: Adult_ETP_1


title: DN2Kit+_3

description: each sample is acutally from a pool derived from several mice

tag: tissue

value: Thymus


title: CLP


title: ETPFlt3hi_3


title: DN2Kit+_1


title: LSKFlt3-CD48-CD150+_3

value: Bone Marrow


title: LSKFlt3-CD48-CD150+_5


title: ETPFlt3hi_1


title: DN2Kit+_2


title: ETPFlt3hi_2


title: LSKFlt3-CD48-CD150+_1


title: LSKFlt3hi IL7R+_2


title: LSKFlt3hi IL7R+_3


title: LSKFlt3-CD48-CD150+_2


title: DN3_3


title: LSKFlt3hi IL7R+_1


title: DN3_1


title: Zhonghua_6D, biological rep1

city: Shanghai

first: Hong-Wei

last: Xue

address: 300 Fenglin Road

institute: Institute of Plant Physiology and Ecology,Shanghai Institutes of Biological Sciences

description: Gene expression data from rice seed of Zhonghua at 6DAF

hyb_protocol: Affymetrix® GeneChip® Operating Software Version 1.0 was used for washing, staining as described in the supplier’s protocol.  (Expression Analysis Technical Manual, 2004, Affymetrix).

scan_protocol: Affymetrix® GeneChip® Operating Software Version 1.0 was used for  scanning as described in the supplier’s protocol.

data_processing: The data was analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Oryza sativa

source_name: Rice seed of Zhonghua at 6DAF

label_protocol: RNA was labeled with biotin for use with the Affymetrix GeneChip Rice Genome array according to the manufactures protocol.

growth_protocol: Growth protocol Rice (Oryza sativa, japonica cultivar Zhonghua 11 and Hanfeng), was cultivated at day/night temperatures (28/22 °C) in phytotron.

extract_protocol: RNA was extracted using the TRIzol method (Invitrogen).

treatment_protocol: For the low temperature treatment, rice plants were transfer to 14°C for two days at 4 or 10 Days after fertilization(DAF) respectively.

value: seed

tag: cultivar

value: Zhonghua 11

tag: treatment


title: Zhonghua_6D, biological rep2


title: Zhonghua_4D, biological rep1

description: Gene expression data from rice seed of Zhonghua at 4DAF

source_name: Rice seed of Zhonghua at 4DAF


title: mcs6-as2_cdk9-as_CAK1_rep4

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

description: biological replicate 2 of 2

hyb_protocol: 750 ng of labeled cRNA was hybridized per sample, according to standard Agilent protocols.

scan_protocol: Microarrays were scanned using an Agilent Microarray Scanner G2565CA (Agilent Technologies)

data_processing: Spot quantification was carried out using Feature Extraction software v9.5 (Agilent Technologies). Following quantification, the microarray data was lowess-normalized and an expression ratio was calculated for each microarray feature by dividing the signal intensity of the treatment channel (analog inhibitor) by the control channel (no inhibitor).

organism: Schizosaccharomyces pombe

source_name: total RNA from an mcs6 and cdk9 analog-sensitive double-mutant in a CAK1::ura4 background grown in the presence of 30 μM 3-MB-PP1 ATP analog

label_protocol: For each sample, 500 µg of total RNA was converted into labeled cRNA with nucleotides coupled to a fluorescent dye using the Low RNA Input Linear Amplification Kit (Agilent Technologies).

growth_protocol: A culture of 100ml was grown at 32°C in YES medium until mid-log phase, pelleted and snap-frozen in liquid nitrogen.

extract_protocol: RNA was prepared by acidic phenol extraction at 65°C for 1 hour with brief vortexing every 10 minutes. The water phase was re-extracted with acidic phenol-chloroform-IAA (24:24:1) and the RNA precipitated. About 250 µg of RNA were purified on Qiagen RNeasy column and eluted with 30 µl H20.

treatment_protocol: 30 μM 3-MB-PP1 ATP analog was added to the specified treatment conditions

value: 30 μM 3-MB-PP1 in DMSO

tag: genotype

source_name: total RNA from an mcs6 and cdk9 analog-sensitive double-mutant in a CAK1::ura4 background grown without ATP analog

value: DMSO only (control)


title: DN3_2

value: 1 week

value: Male/Female

value: Normal

value: Hematopoietic

tag: sample type


title: mcs6-as2_rep1

description: biological replicate 1 of 2

source_name: total RNA from an mcs6-as analog-sensitive mutant grown without ATP analog

value: mcs6-as analog-sensitive mutant

source_name: total RNA from an mcs6-as analog-sensitive mutant grown in the presence of 30 μM 3-MB-PP1 ATP analog


title: Zhonghua_4D, biological rep2


title: Zhonghua_4D_2DC, biological rep2

description: Gene expression data from rice seed of Zhonghua at 4DAF with 2 day low temperature treatment

source_name: Rice seed of Zhonghua at 4DAF with 2 day low temperature treatment

value: low temperature


title: mcs6-as2_CAK1_rep4

description: biological replicate 2 of 2

source_name: total RNA from an mcs6 analog-sensitive mutant in a CAK1::ura4 background grown in the presence of 30 μM 3-MB-PP1 ATP analog

source_name: total RNA from an mcs6 analog-sensitive mutant in a CAK1::ura4 background grown without ATP analog


title: Zhonghua_4D_2DC, biological rep1


title: mcs6-as2_rep4

description: biological replicate 2 of 2


title: mcs6-as2_rep3

description: biological replicate 1 of 2


title: mcs6-as2_rep2

description: biological replicate 2 of 2


title: mcs6-as2_cdk9-as_CAK1_rep2

description: biological replicate 2 of 2

value: mcs6 and cdk9 analog-sensitive double-mutant in a CAK1::ura4 background


title: mcs6-as2_cdk9-as_CAK1_rep1

description: biological replicate 1 of 2


title: Zhonghua_12D, biological rep2

description: Gene expression data from rice seed of Zhonghua at 12DAF

source_name: Rice seed of Zhonghua at 12DAF


title: Zhonghua_10D, biological rep2

description: Gene expression data from rice seed of Zhonghua at 10DAF

source_name: Rice seed of Zhonghua at 10DAF


title: mcs6-as2_CAK1_rep3

description: biological replicate 1 of 2

value: mcs6 analog-sensitive mutant in a CAK1::ura4 background


title: Zhonghua_10D_2DC, biological rep1

description: Gene expression data from rice seed of Zhonghua at 10DAF with 2 day low temperature treatment

source_name: Rice seed of Zhonghua at 10DAF with 2 day low temperature treatment


title: mcs6-as2_cdk9-as_CAK1_rep3

description: biological replicate 1 of 2


title: Zhonghua_12D, biological rep1


title: Zhonghua_10D, biological rep1


title: Zhonghua_10D_2DC, biological rep2


title: mcs6-as2_CAK1_rep2

description: biological replicate 2 of 2


title: cdk9-as_rep4

description: biological replicate 2 of 2

source_name: total RNA from a cdk9 analog-sensitive mutant grown in the presence of 30 μM 3-MB-PP1 ATP analog

value: cdk9 analog-sensitive mutant

source_name: total RNA from a cdk9 analog-sensitive mutant grown without ATP analog


title: mcs6-as2_CAK1_rep1

description: biological replicate 1 of 2


title: Hanfeng_4D_2DC, biological rep2

description: Gene expression data from rice seed of Hanfeng at 4DAF with 2 day low temperature treatment

source_name: Rice seed of Hanfeng at 4DAF with 2 day low temperature treatment

value: Hanfeng


title: cdk9-as_rep3

description: biological replicate 1 of 2


title: Hanfeng_4D, biological rep1

description: Gene expression data from rice seed of Hanfeng at 4DAF

source_name: Rice seed of Hanfeng at 4DAF


title: cdk9-as_rep1

description: biological replicate 1 of 2


title: Hanfeng_4D, biological rep2


title: cdk9-as_rep2

description: biological replicate 2 of 2


title: Hanfeng_4D_2DC, biological rep1


title: Breast cancer_1,25(OH)2D3_34_Post

status: Public on Feb 18 2012

first: Maria Lucia

middle: Hirata

last: Katayama

state: São Paulo

address: Av Dr Arnaldo

department: Radiology and Oncology

institute: Faculty of Medicine University São Paulo

hyb_protocol: After hybridization cocktails preparation, the Affymetrix Human Genome U133 Plus 2.0 GeneChip array was hybridized with 15 mg of biotin-labeled cRNA for 16 h at 45°C as described in the Affymetrix Technical Analysis Manual (2005-2006)

scan_protocol: GeneChips, bound to streptavidin-biotin, were processed using the Affymetrix GeneChip Fluidics Station 400 and scanned with an Affymetrix GeneChip Scanner 3000 G7

data_processing: Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).

source_name: tissue, breast cancer, calcitriol

label_protocol: Beginning with 100 ng total RNA, two-round linear amplification was carried out according to Affymetrix protocol (Two Cycle Target Labeling Kit, Affymetrix, Santa Clara, CA, USA). Afterwards, biotin-labeled cRNA was synthesized from double strand cDNA, using IVT labeling kit (Affymetrix) and 20 µg of biotinylated were fragmented cRNA.

growth_protocol: Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed

extract_protocol: Tissue specimens were pulverized (Bio-PulverizerTM BioSpec Products Inc., Oklahoma, USA) under liquid nitrogen and total RNA was isolated using RNeasy kit (Qiagen, Valencia, CA, USA), according to the manufacturer's protocol. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.

tag: gender

value: female

tag: histologic type

value: CDI

tag: tissue type

value: breast cancer


title: Breast cancer_1,25(OH)2D3_36_Post


title: Breast cancer_1,25(OH)2D3_29_Post


title: Breast cancer_Control_41_Pre

source_name: tissue, breast cancer, control


title: Breast cancer_Control_36_Pre


title: Breast cancer_1,25(OH)2D3_41_Post


title: Breast cancer_1,25(OH)2D3_35_Post


title: Breast cancer_1,25(OH)2D3_42_Post


title: Breast cancer_Control_29_Pre


title: Breast cancer_Control_34_Pre

value: CDICLI


title: Breast cancer_Control_35_Pre


title: Breast cancer_1,25(OH)2D3_33_Post

value: CDI/CLI


title: Breast cancer_Control_42_Pre


title: Breast cancer_1,25(OH)2D3_43_Post


title: Breast cancer_Control_33_Pre


title: Breast cancer_Control_43_Pre


title: Breast cancer_Control_30_Pre


title: Breast cancer_1,25(OH)2D3_26_Post

value: CLI


title: Breast cancer_Control_26_Pre


title: Breast cancer_1,25(OH)2D3_16_Post


title: Breast cancer_1,25(OH)2D3_30_Post


title: Breast cancer_1,25(OH)2D3_15_Post

value: metaplastic


title: Breast cancer_Control_17_Pre


title: Breast cancer_1,25(OH)2D3_27_Post


title: Breast cancer_Control_15_Pre


title: Breast cancer_Control_21_Pre


title: Breast cancer_Control_27_Pre


title: Breast cancer_1,25(OH)2D3_21_Post


title: Breast cancer_Control_16_Pre


title: Breast cancer_1,25(OH)2D3_17_Post


title: Picea mariana_xylem_rep13

city: Québec

first: John

last: MacKay

state: Québec

address: 1030, avenue de la Médecine, Pavillon C.-E. Marchand

department: Centre d'étude de la forêt

country: Canada

institute: Université Laval

description: Raw data represented in 'ch1' columns of raw file after the Begin Data tag.

hyb_protocol: Each microarray was hybridized with one sample labelled with one dye. The samples were mixed and the volume was reduced to ~10 µl by evaporating excess water in a DNA 120 speedvac (Thermo Fisher Scientific). Labelled aRNAs were fragmented for 15 minutes at 70°C using Ambion’s ”RNA Fragmentation Reagents“, placed on ice for 1 minute, denatured for 2 minutes at 95°C, put on ice for 2 min and resuspended in 120 µl hybridization buffer (50% formamide, 5X SSC, 0,1% SDS, 0,1 mg/mL Herring sperm DNA) preheated to 55°C. Samples were kept in a heating block at 50°C until hybridization. Hybridizations were performed in HS400Pro hybridization stations (Tecan Group Ltd., Männedorf, Switzerland). The slides were heated at 80°C for 10 minutes, then washed once at 37°C with 0.5X SSC, 0.1% SDS for 20 seconds and once at 50°C with 2X SSC, 0.5% SDS for 20 seconds, and prehybridized for 1 hour at 65°C in 5X SSC, 0.1% SDS, 0.1 mg/ml BSA, 0.1 mg/ml Herring Sperm DNA. Next the slides were washed at 55°C with 2X SSC, 0.5% SDS for 1 minute with a 30 seconds soak and washed again at 45°C for 1 minute with the same solution. The resuspended labelled targets were injected into the chambers and hybridized for 16 hours at 45°C with sample agitation. The slides were then washed as follows: 2 times 1 minute 30 seconds at 45°C with 30 seconds soaking in 2X SSC, 0.5% SDS, 1 time 1 minute at 45° in 2X SSC, 0.5% SDS, 2 times 1 minute 30 seconds at 45°C with 30 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute at 37°C with 20 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute at 23°C with 20 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute 30 seconds at 23°C with 30 seconds soaking in 0.1X SSC, 1 time 30 seconds at 23°C in 0.1X SSC and 2 times 30 seconds at 23°C in milliQ filtered water. Finally slides were dried for 2 minutes 30 seconds with nitrogen gaz.

scan_protocol: Slide scanning was performed at 5 micron resolution on a ScanArray Express (Perkin Elmer, Waltham MA, USA) microarray scanner and image analysis was carried out using QuantArray v3.0 (Packard BioChip Technologies, Billerica, MA, USA).

data_processing: Data (spot intensity means) analyses were performed using customized scripts for R and Bioconductor (http://www.r-project.org and http://www.bioconductor.org). Spots that were flagged as presenting abnormal morphology during the image processing were replaced by mean value of the remaining spots of the same probe from the other slides from the same sample type. Background intensities were subtracted from the foreground intensities. Background-subtracted data were log2-transformed and normalized using quantile correction approach.   A filtering step was applied to select positive genes to be used for further analysis. The mean intensity of spots containing buffer only was calculated for each row of sub-grids, and was taken as the minimum intensity of probes for that subgrid. A probe was called positive (detected above background) when its signal intensity was above the buffer intensity on at least 50% of slides within a given sample type. When determining differential expression, positive probes were probes that were detected according to this criterion in at least one of the tissues (e.g. phelloderm and xylem). Mean probe intensity was determined for genes represented by more than one positive probe.   The average signal intensity was determined from all of the slides available for a sample type. The genes were then ranked based on their average signal intensities within a tissue type and equally divided into 10 separate classes according to their signal intensity. Genes from class 1 or class 10 were the 10% with lowest and highest signal intensities, respectively.

label: Alexa 555

organism: Picea mariana

source_name: Picea mariana, xylem

label_protocol: Total RNA (1 µg) was transcribed in-vitro by using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion by Life Technologies, Austin, TX, USA), following the manufacturer’s instructions. The aaRNA (5 ug per sample) was labeled using Alexa Fluor 555 dyes (Invitrogen, Carlsbad, CA, USA), and purified as per the manufacturer’s instructions. Dye incorporation efficiency was determined by using a Nanodrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer’s instructions.

growth_protocol: Nursery planting stock (from open-pollinated seed lots) were obtained as 3-year-old seedlings of Picea glauca, Picea sitchensis and Picea mariana, were transferred to 8-inch pots and grown in a greenhouse under natural light conditions. Sampling of tissues was timed with the ending of primary shoot elongation, i.e. after 6 to 8 weeks of growth, and was as described (Pavy et al. 2008). For each tissue type five biological samples were prepared by pooling 6 independent trees.

extract_protocol: All of the tissue samples were frozen in liquid nitrogen immediately after removal from the trees and stored at -80°C. Tissues were ground under liquid nitrogen and total RNA was extracted following Chang et al. (1993) as described in Pavy et al. (2008) for all of the sample types.

value: xylem

tag: time of collection

value: am

tag: replicate

tag: slide batch


title: Picea mariana_phelloderm_rep13

source_name: Picea mariana, phelloderm

value: phelloderm


title: Picea mariana_xylem_rep14


title: Picea mariana_phelloderm_rep12


title: Picea mariana_xylem_rep12


title: Picea mariana_phelloderm_rep15


title: Picea mariana_xylem_rep15


title: Picea mariana_xylem_rep9


title: AML1-before treatment

city: Hong Kong

first: Cheuk Him

last: Man

address: L816, LAB BLK, FMB, HKU

country: Hong Kong

institute: HKU

description: SAMPLE 1

hyb_protocol: According to standard Affymetrix protocol

data_processing: Data was analysed by GeneSpring GX version 11, affymetrix-algorithm-name = rma-gene-default, affymetrix-algorithm-version = 1.0

growth_protocol: Bone marrow was aspirated from patients

extract_protocol: TRIZOL extration of total RNA and purfied by QIAGEN RNeasy MinElute Cleanup Kit

treatment_protocol: Sorafenib 200-400mg twice daily was prescribed to patients

value: blood cells

value: CD33+CD34+ myeloblast


title: Picea mariana_xylem_rep11


title: Picea mariana_xylem_rep7


title: AML4-after treatment

description: SAMPLE 6

scan_protocol: According to standard Affymetrix protocol


title: Picea mariana_phelloderm_rep14


title: Picea mariana_xylem_rep8


title: Picea mariana_xylem_rep10


title: Picea mariana_phelloderm_rep10


title: AML10-after treatment

description: SAMPLE 8

label_protocol: According to standard Affymetrix protocol


title: AML4-before treatment

description: SAMPLE 5


title: AML1-after treatment

description: SAMPLE 2


title: AML3-before treatment

description: SAMPLE 3


title: Picea mariana_phelloderm_rep8


title: AML10-before treatment

description: SAMPLE 7


title: Med13 WT WAT

city: Dallas

first: Chad

last: Grueter

state: Texas

address: 6000 Harry Hines Blvd

institute: UT Southwestern Medical Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Med13 WT WAT

label_protocol: cRNA were prepared for Illumina arrays

growth_protocol: RNA from liver, WAT and BAT of 3, 4 week old Med13 alpha MHC TG mice and wild-type littermates

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Bioanalyser.

treatment_protocol: Mice were fasted over night

value: 4 week-old

value: male

value: wild type

value: gonadal white adipose tissue


title: Picea mariana_xylem_rep6


title: AML3-after treatment

description: SAMPLE 4


title: Med13 WT Liver

source_name: Med13 WT Liver

value: liver


title: Picea mariana_phelloderm_rep9


title: Med13 WT BAT

source_name: Med13 WT BAT

value: brown adipose tissue


title: Picea mariana_phelloderm_rep6


title: Picea mariana_phelloderm_rep7


title: Picea mariana_phelloderm_rep5


title: Med13 TG Liver

source_name: Med13 TG Liver

value: Med13 alphaMHC transgenic


title: Picea mariana_xylem_rep4


title: Picea mariana_xylem_rep3


title: Picea mariana_phelloderm_rep4


title: wild-type zebrafish, biological rep2

city: Camden

first: Xiaoxin

middle: Luke

last: Chen

state: NJ

address: 403 Haddon Avenue

institute: Coriell Institute for Medical Research

description: Gene expression data from upper digestive tract tissue of 3 wild-type zebrafish

hyb_protocol: After purification of cRNAs by GeneChip Sample Cleanup Module (Affymetrix), 15 µg of cRNA was fragmented at 94°C for 35 min. Approximately 12.5 µg of fragmented cRNA was used in a 250-µl hybridization mixture containing herring-sperm DNA (0.1 mg/ml; Promega), plus bacterial and phage cRNA controls (1.5 pM BioB, 5 pM BioC, 25 pM BioD, and 100 pM Cre) to serve as internal controls for hybridization efficiency. Aliquots (200 µl) of the mixture were hybridized to arrays for 16 h at 45°C in a GeneChip Hybridization Oven 640 (Affymetrix). Each array was washed and stained with streptavidin–phycoerythrin (Invitrogen) and amplified with biotinylated anti-streptavidin antibody (Vector Laboratories) on the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned with the GeneArray G7 scanner (Affymetrix) to obtain image and signal intensities

data_processing: Data analysis was performed using the Affymetrix MAS5 algorithm.

organism: Danio rerio

source_name: upper digestive tract tissue from 3 wild-type zebrafish

label_protocol: Biotinylated cRNAs were generated from cDNAs by in vitro transcription and amplified by using the BioArray T7 RNA polymerase labeling kit (Enzo Diagnostics).

growth_protocol: Zebrafish were obtained from the Zebrafish International Resource Center (Eugene, OR). To generate zCdx1b transgenic fish, AB* line was used. Fish were housed in an automatic fish housing system (Aquaneering, San Diego, CA) at 28.5°C and maintained according to the established procedures

extract_protocol: The upper digestive tract tissue from 3 adult zebrafish (3 months old) was dissected and pooled as one sample. Three zCdx1b transgenic samples were used for microarray, and 2 wild type samples were used for control. The total RNA was extracted using TRIzol according to the manufacturer's instructions.

treatment_protocol: Transgenic zebrafish were generated by microinjection of one cell stage fertilized AB* zebrafish eggs with a mixture of pmini Tol2-zK5p-zCdx1b-EGFP (80µg/ml) and Tol2 transposase RNA (4 µg/ml)

value: upper digestive tract

tag: genetic background

value: AB

value: 3 months

value: wild-type


title: Picea mariana_phelloderm_rep3


title: Med13 TG BAT

source_name: Med13 TG BAT

tag: age


title: Med13 WT heart

source_name: Med13 WT heart

growth_protocol: RNA from hearts of 3, 4 week old Med13 alpha MHC TG mice and wild-type littermates

value: heart


title: zCdx1b transgenic zebrafish, biological rep2

description: Gene expression data from upper digestive tract tissue of 3 zCdx1b transgenic zebrafish

source_name: upper digestive tract tissue from 3 zCdx1b transgenic zebrafish


title: Picea mariana_xylem_rep5

value: xylem


title: zCdx1b transgenic zebrafish, biological rep3