title: Embryo_ptpn6-morpholino_SL1027-infected_rep2

city: Leiden

first: Annemarie

middle: H.

last: Meijer

address: Einsteinweg 55

department: Animal Sciences and Health

institute: Institute of Biology, Leiden University

description:
Raw data file:
US22502421_252162610076_S01_GE2_105_Jan09_1_1.txt
Biological replicate 1 of 3: ptpn6 knockdown embryos infected with S. typhimurium SL1027.
Injected with ptpn6 morpholino  at the 1-2 cell stage and injected with 200-250 CFU of S. typhimurium SL1027 bacteria into the caudal vein at 28 hpf; RNA isolated at 8 h post infection

hyb_protocol: The dual colour hybridization of the microarray chips was performed at the Microarray Department (MAD) of the University of Amsterdam (Amsterdam, The Netherlands) using the standard Agilent protocol.

scan_protocol: The arrays were scanned with DNA Microarray Scanner G2565CA from Agilent Technologies. The arrays were scanned twice with 10% PMT and 100% PMT laser power.

data_processing: Microarray data was processed from raw data image files with Feature Extraction Software 9.5.3.1 (Agilent Technologies). The XDR function was used to extend the dynamic range. Processed data were subsequently imported into Rosetta Resolver 7.0 (Rosetta Biosoftware, Seattle, Washington) and subjected to default ratio error modelling. The Agilent Feature Extraction files contain the final log ratio data. The algorithms that were used to normalize the feature signal and calculate the log ratios are described in the Reference Guide for Agilent Feature Extraction Software v9.5. The standard settings as described for the GE2-v5_95 protocol in the Reference Guide were used. In order to calculate the normalized signal, the Rank Consistency Probes method was used and the Linear&LOWESSDyeNormFactor (= DyeNormalSignal/(BGSubSignal x LinearDyeNormFactor) was calculated as described on page 231 of the Reference Guide. The dye normalized signal was calculated as follows (page 232): DyeNormSignal = BGSubSignal x DyeNormFactor. The log10 ratio was subsequently calculated as follows (page 232): LogRatio = Log(rProcessedSignal/gProcessedSignal), where rProcessedSignal and gProcessedSignal are signals post dye normalization and post surrogate processing in the red and green channels, respectively. The surrogate values are calculated and used as the lowest limit of detection to replace the dye normalized signal when either the mean feature signal is less than the background signal or not significant when compared to the background signal, or when the mean signal is less than its background standard deviation (page 226).

organism: Danio rerio

label_protocol: Amino Allyl modified aRNA was synthesized in one amplification round from 1 ug of total RNA using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion). Subsequently, 6 ug of Amino Allyl modified aRNA was used for coupling of monoreactive Cy3 or Cy5 dye (GE Healthcare) and column purified.

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol: Embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Embryos were homogenized in 1 ml of TRIZOL® Reagent (Invitrogen) and subsequently total RNA was extracted according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Zebrafish embryos were injected at the 1-2 cell stage with 1 nl of an 0.0625 mM solution of ptpn6 splice-blocking morpholino (5’actcattccttacccgatgcggagc3’) in 1× Danieau buffer (58mM NaCl, 0.7mM KCl, 0.4mM MgSO4, 0.6mM Ca(NO3)2, 5.0mM N-2-hydroxyethylpiperazine-N ́-2-ethanesulfonic acid; pH 7.6) containing 1% phenol red (Sigma-Aldrich). The control group was mock-injected with  Danieau buffer/phenol red. Embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro-injected into the caudal vein with 200-250 CFU of S. typhimurium SL1027 bacteria suspended in PBS (phosphate-buffered saline), or were mock-injected with PBS as a control. At 36 hpf (8 h post infection)  pools of 15-20 embryos per treatment group were snap-frozen in liquid nitrogen.

tag: reference

value: The CR (common reference) was a mixture of all 12 RNA samples from this microarray study.

value: ptpn6 knockdown

tag: infection

value: 36 hpf (8 h post infection)


title: C.elegans fed with E.coli OP50 3 days rep1

status: Public on Dec 31 2012

type: RNA

city: Montevideo

first: Tamara

last: Fernandez-Calero

state: Montevideo

address: Mataojo 2020

department: Bioinfomatics Unit

country: Uruguay

institute: Institut Pasteur de Montevideo

description: Gene expression data from C.elegans fed with E.coli OP50 for 3 days

hyb_protocol: Hybridization was performed as described by the manufacturer (Affymetrix, SantaClara, CA). The complementary RNA hybridization cocktail was incubated overnight at 45C while rotating in a hybridization oven. After 16 h of hybridization, the cocktail was removed and the arrays were washed and stained in an Affymetrix GeneChip Fluidics Station 450, according to the Affymetrix-recommended protocol.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, CA, USA)

data_processing: Data analysis was accomplished in “R” (R Foundation for Statistical Computing, Vienna, Austria; http://www.R-project.org) mainly through packages in the “Bioconductor” suite. Normalization was performed using rma (robust multi-array average expression measure) in “affy”.

label: biotin

molecule: total RNA

organism: Caenorhabditis elegans

label_protocol: Total RNA (300 ng per sample) was labeled using the Affymetrix GeneChip 3´GeneChip®3’ IVT Express Kit protocol.

growth_protocol: Synchronized populations were obtained from embryos isolated from gravid adults in the different feeding conditions. After feeding period (3 or 10 days) of worms were collected with M9 buffer, washed three times and collected in eppendorf tubes for worm disruption by sonication (3 pulses at 10 W, 20 s/pulse).

extract_protocol: Total RNA isolation was performed with RNAasy Kit (Qiagen, Barcelona, Spain).

tag: strain

tag: diet

value: E. coli OP50 (control condition)

tag: time

value: 3 days


title: Embryo_ptpn6-morpholino_SL1027-infected_rep1

country: Netherlands

description:
Raw data file:
US22502421_252162610075_S01_GE2_105_Jan09_1_1.txt
Biological replicate 1 of 3: ptpn6 knockdown embryos infected with S. typhimurium SL1027.
Injected with ptpn6 morpholino  at the 1-2 cell stage and injected with 200-250 CFU of S. typhimurium SL1027 bacteria into the caudal vein at 28 hpf; RNA isolated at 8 h post infection

tag: genotype/variation


title: C.elegans fed with E.coli OP50 3 days rep2

source_name: C.elegans fed with E.coli OP50 for 3 days


title: OSCC methylation 139

status: Public on Jan 01 2013

type: genomic

city: Houston

first: Jiexin

last: Zhang

state: TX

address: 1515 Holcombe Blvd

department: Bioinformatics & Computational Biology

country: USA

institute: UT MD Anderson Cancer Center

description: Tongue

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: GenomeStudio software V2010.3 with GenomeStudio Methylation Version 1.8.5.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: OSCC

label_protocol: Standard Illumina protocol

growth_protocol: not applicable

extract_protocol: Tri-reagent (Sigma)

treatment_protocol: not applicable

tag: gender

value: M

tag: source tissue

value: Tongue

tag: tissue

value: Oral cavity squamous cell carcinoma tumor

tag: case


title: OSCC methylation 447

description: Tongue


title: Embryo_ptpn6-morpholino_uninfected_rep3

description:
Raw data file:
US22502421_252162610077_S01_GE2_105_Jan09_1_2.txt
Biological replicate 3 of 3: ptpn6 knockdown embryos uninfected.
Injected with ptpn6 morpholino at the 1-2 cell stage and mock-injected with buffer into the caudal vein at 28 hpf; RNA isolated at 8 h post injection

value: uninfected


title: Embryo_ptpn6-morpholino_SL1027-infected_rep3

description:
Raw data file:
US22502421_252162610077_S01_GE2_105_Jan09_1_1.txt
Biological replicate 1 of 3: ptpn6 knockdown embryos infected with S. typhimurium SL1027.
Injected with ptpn6 morpholino  at the 1-2 cell stage and injected with 200-250 CFU of S. typhimurium SL1027 bacteria into the caudal vein at 28 hpf; RNA isolated at 8 h post infection


title: Twin 686 fat

status: Public on Dec 10 2012

city: Copenhagen

first: Rasmus

last: Ribel-Madsen

address: Universitetsparken 1

country: Denmark

institute: University of Copenhagen

description: bisulfite treated

hyb_protocol: DNA bisulfite converted by the EZ DNA Methylation Kit 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 setting

data_processing: Illumina GenomeStudio v.2011.1

source_name: subcutaneous adipose tissue

extract_protocol: Genomic DNA was extracted and purified from skeletal muscle and adipose tissue samples using Qiagen DNeasy Kit according to standard instructions

tag: type 2 diabetes status

value: non-diabetic


title: OSCC methylation 91

description: Tongue


title: Embryo_ptpn6-morpholino_uninfected_rep1

description:
Raw data file:
US22502421_252162610075_S01_GE2_105_Jan09_1_2.txt
Biological replicate 1 of 3: ptpn6 knockdown embryos uninfected.
Injected with ptpn6 morpholino at the 1-2 cell stage and mock-injected with buffer into the caudal vein at 28 hpf; RNA isolated at 8 h post injection


title: Embryo_control_SL1027-infected_rep3

description:
Raw data file:
US22502421_252162610077_S01_GE2_105_Jan09_1_3.txt
Biological replicate 3 of 3: control embryos infected with S. typhimurium SL1027.
Mock-injected with buffer at the 1-2 cell stage and injected with 200-250 CFU of S. typhimurium SL1027 bacteria into the caudal vein at 28 hpf; RNA isolated at 8 h post infection

value: control


title: OSCC methylation 367

description: Tongue


title: Embryo_control_uninfected_rep3

description:
Raw data file:
US22502421_252162610077_S01_GE2_105_Jan09_1_4.txt
Biological replicate 3 of 3: control embryos uninfected.
Mock-injected with buffer at the 1-2 cell stage and mock-injected with buffer into the caudal vein at 28 hpf; RNA isolated at 8 h post injection


title: Embryo_control_SL1027-infected_rep1

description:
Raw data file:
US22502421_252162610075_S01_GE2_105_Jan09_1_3.txt
Biological replicate 1 of 3: control embryos infected with S. typhimurium SL1027.
Mock-injected with buffer at the 1-2 cell stage and injected with 200-250 CFU of S. typhimurium SL1027 bacteria into the caudal vein at 28 hpf; RNA isolated at 8 h post infection


title: Embryo_control_SL1027-infected_rep2

description:
Raw data file:
US22502421_252162610076_S01_GE2_105_Jan09_1_3.txt
Biological replicate 2 of 3: control embryos infected with S. typhimurium SL1027.
Mock-injected with buffer at the 1-2 cell stage and injected with 200-250 CFU of S. typhimurium SL1027 bacteria into the caudal vein at 28 hpf; RNA isolated at 8 h post infection


title: Twin 530 fat

description: bisulfite treated


title: Embryo_control_uninfected_rep2

description:
Raw data file:
US22502421_252162610076_S01_GE2_105_Jan09_1_4.txt
Biological replicate 2 of 3: control embryos uninfected.
Mock-injected with buffer at the 1-2 cell stage and mock-injected with buffer into the caudal vein at 28 hpf; RNA isolated at 8 h post injection


title: C.elegans fed with CNCM I-3690 3 days rep3

description: Gene expression data from C.elegans fed with CNCM I-3690 for 3 days

value: Lactobacillus rhamnosus CNCM I-3690


title: Embryo_control_uninfected_rep1

description:
Raw data file:
US22502421_252162610075_S01_GE2_105_Jan09_1_4.txt
Biological replicate 1 of 3: control embryos uninfected.
Mock-injected with buffer at the 1-2 cell stage and mock-injected with buffer into the caudal vein at 28 hpf; RNA isolated at 8 h post injection


title: Embryo_ptpn6-morpholino_uninfected_rep2

description:
Raw data file:
US22502421_252162610076_S01_GE2_105_Jan09_1_2.txt
Biological replicate 1 of 3: ptpn6 knockdown embryos uninfected.
Injected with ptpn6 morpholino at the 1-2 cellstage and mock-injected with buffer into the caudal vein at 28 hpf; RNA isolated at 8 h post injection


title: Twin 658 fat

description: bisulfite treated


title: Twin 529 fat

description: bisulfite treated

value: type 2 diabetic


title: Twin 30 fat

description: bisulfite treated


title: Twin 29 fat

description: bisulfite treated


title: Twin 2048 muscle

description: bisulfite treated

source_name: vastus lateralis muscle

tag: Sex

value: Male

tag: age


title: Twin 658 muscle

description: bisulfite treated


title: Twin 686 muscle

description: bisulfite treated

value: Female


title: C.elegans fed with CNCM I-4317 10 days rep3

description: Gene expression data from C.elegans fed with CNCM I-4317 for 10 days

value: Lactobacillus rhamnosus CNCM I-4317

value: 10 days


title: Twin 398 fat

description: bisulfite treated


title: Twin 685 muscle

description: bisulfite treated


title: Twin 397 muscle

description: bisulfite treated


title: Twin 529 muscle

description: bisulfite treated


title: Twin 2047 muscle

description: bisulfite treated


title: Twin 398 muscle

description: bisulfite treated


title: Twin 41B muscle

description: bisulfite treated


title: Twin 35A muscle

description: bisulfite treated


title: Twin 657 fat

description: bisulfite treated


title: Twin 41A muscle

description: bisulfite treated


title: Twin 15A muscle

description: bisulfite treated


title: Twin 13B muscle

description: bisulfite treated


title: Twin 657 muscle

description: bisulfite treated


title: Twin 20A muscle

description: bisulfite treated


title: Twin 20B muscle

description: bisulfite treated


title: Twin 22A muscle

description: bisulfite treated


title: Twin 35B muscle

description: bisulfite treated


title: Twin 15B muscle

description: bisulfite treated


title: Twin 530 muscle

description: bisulfite treated


title: Twin 22B muscle

description: bisulfite treated


title: Twin 13A muscle

description: bisulfite treated


title: THPOK-CD8a+_1_TR

city: New York

first: Bernardo

last: Reis

state: NY

address: 1234 York Avenue

institute: Rockefeller University

description:
replicate 1
Illumina.SingleColor.MouseRef-8_V2_0_R2_11278551_A

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Gene SpringGX software version 11.5.1 was used to do percentile shift normalization. 1.Transforms the signal values to the log base 2. 2.Arranges the log transformed signal values in increasing order. 3.Computes the rank of the required percentile (Pth percentile)The data were normalised using quantile normalisation with IlluminaGUI in R

organism: Mus musculus

source_name: TR CD4 T-cell sIEL

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

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

value: B6-ThPOK-GFP reporter

value: 10-12 weeks

value: small intestine

tag: cell type

value: CD4 intraepithelial T lymphocytes

tag: cell sub-type


title: THPOK-CD8a-_2_TR

description:
replicate 2
Illumina.SingleColor.MouseRef-8_V2_0_R2_11278551_A


title: THPOK+CD8a-_2_TR


title: THPOK-CD8a+_1_WT

source_name: WT CD4 T-cell sIEL


title: THPOK-CD8a+_2_TR


title: THPOK-CD8a-_1_TR


title: THPOK-CD8a+_2_WT


title: THPOK-CD8a-_1_WT


title: THPOK+CD8a-_1_TR


title: THPOK-CD8a-_2_WT


title: THPOK+CD8a-_1_WT


title: THPOK+CD8a-_2_WT


title: pCR+npCR mamma breast cancer BC_5342587027_C

status: Public on Dec 01 2012

city: Amsterdam

first: Jelle

middle: Johannes

last: ten Hoeve

address: Plesmanlaan 121

department: Molecular Biology

institute: Netherlands Cancer Institute

data_processing: The data were between-array normalised using simple scaling (SSN) subsequently log2 transformed

label: Biotin

source_name: 14G core needle breast tumor biopsy

label_protocol: Total RNA was amplified and biotin labeled using the Illumina® TotalPrep™-96 RNA kit. All steps were performed according to standard protocol.

extract_protocol: From the frozen biopsies approximately 30 sections of 30-μm thickness were used for total RNA isolation with RNABee (Campro Scientific, Amersfoort, The Netherlands). Isolated total RNA was subsequently DNase-treated by using the Qiagen RNase-free DNase kit and RNeasy spin columns (Qiagen, West Sussex, U.K.) and dissolved in RNase-free H2O.

tag: response breast

value: pCR+npCR mamma

tag: response

value: CR+kl

tag: ihc er percentage

tag: ihc pr percentage

tag: intrinsic molecular subtype

value: Basal

tag: treatment

value: AC

tag: clinical subtype

value: TN

value: breast cancer tumor


title: MR-VP_rep1

status: Public on Dec 04 2012

city: Ghent

first: Wannes

last: Dermauw

address: Coupure Links 653

department: Crop Protection

country: Belgium

institute: University Ghent

description: Biological replicate 1 of 6, MR-VP vs. London

hyb_protocol: Cy3 and Cy5 labeled cRNAs were pooled and hybridized using the Gene Expression Hybridization Kit (Agilent Technologies) for 17h in a rotating hybridization oven at 20 r.p.m. and 65°C; Slides were washed using the Gene Expression Wash Buffer Kit (Agilent Technologies)

scan_protocol: Hybridized arrays were scanned using an Agilent Microarray High Resolution Scanner.

data_processing: Data were extracted and normalized using Agilent Feature Extraction Software 10.5 with default parameter settings for gene expression two-color microarrays (protocol GE2_105_Dec08). Further processed 'fold change' data are generated using Genespring.

organism: Tetranychus urticae

source_name: MR-VP

label_protocol: 100 ng of total RNA (+ RNA-spike in control) was used to generate Cy3 or Cy5 labeled cRNAs, using the Agilent Low Input Quick Amp Labeling Kit (version 6.5 Agilent Technologies)

growth_protocol: T. urticae strains, London, MAR-AB and MR-VP, were grown on potted kidney bean (Phaseolus vulgaris cv. "Prelude") plants at 26+-0.5°C and a 16/8h light/dark photoperiod. For the host change experiment, female adut mites from the London strain were grown for 2h, 12h, and 5 generations on tomato (Solanum lycopersicon cv. "Moneymaker") at 26°+-0.5°C and a 16/8 light/dark photoperiod.

extract_protocol: Total RNA was extracted from about 100 adult female spider mites using RNEasy Mini Kit (Qiagen) following manufacturer's instructions.

value: adult

source_name: London


title: pCR+npCR mamma breast cancer BC_5342587013_B

value: CR


title: pCR+npCR mamma breast cancer BC_5357957009_A


title: PR+NR breast cancer BC_5357957042_A

value: PR+NR

value: NOCR


title: MR-VP_rep2

description: Biological replicate 2 of 6, MR-VP vs. London


title: PR+NR breast cancer BC_5357957043_B


title: pCR+npCR mamma breast cancer BC_5342587013_E


title: MR-VP_rep3

description: Biological replicate 3 of 6, MR-VP vs. London


title: PR+NR breast cancer BC_5357957042_D


title: NA breast cancer BC_5357957052_C

value: NE


title: PR+NR breast cancer BC_5357957044_F


title: pCR+npCR mamma breast cancer BC_5357957053_D


title: PR+NR breast cancer BC_4753042046_A


title: pCR+npCR mamma breast cancer BC_5357957053_F


title: pCR+npCR mamma breast cancer BC_5357957053_C


title: pCR+npCR mamma breast cancer BC_5357957044_D


title: pCR+npCR mamma breast cancer BC_5357957009_D


title: pCR+npCR mamma breast cancer BC_5357957044_E


title: PR+NR breast cancer BC_5357957044_C


title: PR+NR breast cancer BC_5357957053_B


title: pCR+npCR mamma breast cancer BC_5357957045_B


title: Twin 397 fat

description: bisulfite treated

value: type 2 diabetic


title: PR+NR breast cancer BC_5357957043_C

value: LumB


title: pCR+npCR mamma breast cancer BC_5342587009_C


title: PR+NR breast cancer BC_5357957054_B

value: LumA


title: pCR+npCR mamma breast cancer BC_4560224015_E


title: pCR+npCR mamma breast cancer BC_4560224015_F


title: pCR+npCR mamma breast cancer BC_4560224064_F


title: pCR+npCR mamma breast cancer BC_4560224073_E


title: PR+NR breast cancer BC_4560224089_D


title: PR+NR breast cancer BC_4560224045_F

value: Normal


title: PR+NR breast cancer BC_4560224027_F


title: PR+NR breast cancer BC_4560224053_F


title: PR+NR breast cancer BC_4560224035_F


title: PR+NR breast cancer BC_4560224064_C


title: PR+NR breast cancer BC_4560224066_F


title: PR+NR breast cancer BC_4560224015_D


title: Twin 685 fat

description: bisulfite treated


title: pCR+npCR mamma breast cancer BC_4560224073_B


title: pCR+npCR mamma breast cancer BC_4560224035_D


title: pCR+npCR mamma breast cancer BC_4560224073_F


title: PR+NR breast cancer BC_4520679065_D

value: PD


title: pCR+npCR mamma breast cancer BC_4560224089_F


title: pCR+npCR mamma breast cancer BC_4560224084_C


title: pCR+npCR mamma breast cancer BC_4560224088_E


title: pCR+npCR mamma breast cancer BC_4560224073_A


title: pCR+npCR mamma breast cancer BC_4520679065_E


title: pCR+npCR mamma breast cancer BC_4531933083_C


title: pCR+npCR mamma breast cancer BC_4531933077_A


title: PR+NR breast cancer BC_4520679065_C


title: pCR+npCR mamma breast cancer BC_4560224074_D


title: PR+NR breast cancer BC_4531933059_B


title: pCR+npCR mamma breast cancer BC_4531933045_B


title: pCR+npCR mamma breast cancer BC_4560224089_E


title: pCR+npCR mamma breast cancer BC_4531933043_F


title: pCR+npCR mamma breast cancer BC_4531933044_D


title: PR+NR breast cancer BC_4531933072_B


title: pCR+npCR mamma breast cancer BC_4531933045_D


title: PR+NR breast cancer BC_4531933044_C


title: PR+NR breast cancer BC_5357957045_D

value: LUM


title: PR+NR breast cancer BC_5342587008_D


title: PR+NR breast cancer BC_5342587009_D


title: pCR+npCR mamma breast cancer BC_5342587008_E

value: pCR+npCR mamma


title: PR+NR breast cancer BC_5342587013_D


title: PR+NR breast cancer BC_5342587009_F


title: pCR+npCR mamma breast cancer BC_4531933045_A


title: PR+NR breast cancer BC_5342587013_C


title: pCR+npCR mamma breast cancer BC_5342587014_D


title: pCR+npCR mamma breast cancer BC_5342587014_F


title: pCR+npCR mamma breast cancer BC_5342587013_A


title: pCR+npCR mamma breast cancer BC_5342587015_C

value: CR+kl


title: PR+NR breast cancer BC_5342587015_E


title: PR+NR breast cancer BC_5342587014_C


title: PR+NR breast cancer BC_5342587014_B


title: PR+NR breast cancer BC_5357957045_F

value: Basal


title: WoundSkin_FullyOccluded_5D_rep4

city: Chicago

first: Wei

last: Xu

state: IL

address: 303 E Chicago Ave, Tarry 4-714

department: Surgery

institute: Northwestern University, Feinberg School of Medicine

hyb_protocol: For each array, 1650 ng of Cy3 labeled was fragmented and hybridized with rotation at 65°C for 17 hours. Samples were hybridized to rabbit custom design 4X44k arrays (Agilent Technologies, Inc).

scan_protocol: The arrays were washed according to the manufacturer’s protocol and then scanned on an Agilent G2505B scanner. Data were extracted using Feature Extraction 10.1.1.1 software (Agilent Technologies, Inc.).

data_processing: Using Limma software package in R environment (R386 2.15.2), the background of extracted microarray data was corrected by ‘normexp’ with offset 50. After normalized within and between arrays, the data was fit in a linear model with the empirical Bayes to moderate the standard errors. The p values of output data were adjusted with Benjamini and Hochberg's method to control the false discovery rate.

organism: Oryctolagus cuniculus

source_name: Wounded skin_Fully-occluded_day 5

label_protocol: RNA concentration was determined on a NanoDrop Spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE) and sample quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA). cDNA was synthesized from 400 ng of total RNA using the Quick-Amp labeling Kit (Agilent Technologies, Inc.) according the manufacturer’s protocol. Briefly, the cDNA was used as a template for in vitro transcription (IVT) in the presence of T7 RNA Polymerase and cyanine labeled CTP’s.  The amplified, labeled mRNA was purified using the RNeasy Mini Kit (Qiagen).

growth_protocol: One half of the each harvested wound was incubated with 0.5M ammonium thiocyanate at room temperature for 30 min. The epidermis of the wounding area was separated from the dermis and rinsed with PBS solution.

extract_protocol: The epidermis was immediately put into Tri Reagent® for RNA isolation (Sigma-Aldrich, St. Louis, MO) following the manufacture instruction. The TurboTM DNase (Life Technologies, Carlsberg, CA) was used to remove the genomic DNA from the total RNA followed by a RNA clean-up step with RNeasy® Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: The superficial incisional grids on rabbit ear were created by using a double blade scalpel with 1 mm space between the two blades (Fig.1A and 1B). A single layer of Tegaderm was used to cover the wounding areas on both right and left ears until the wounding areas were fully re-epithelialized (two days post wounding, POE0). Thereafter, the Tegaderm on right ear was completely removed (NOW) while four more layers of Tegaderms were applied on left ear wounds (FOW). Rabbit ear samples were harvested at POE0, POE3 and POE5.

tag: breed

value: New Zealand White rabbit

value: female

value: wounded skin epithelium with full occlusion

tag: samples harvested on

value: day 5 post epithelialization


title: PR+NR breast cancer BC_5342587027_D

value: AC

value: breast cancer tumor


title: WoundSkin_FullyOccluded_5D_rep5

tag: gender


title: WoundSkin_FullyOccluded_5D_rep1

tag: tissue


title: WoundSkin_NonOccluded_5D_rep3

source_name: Wounded skin_Non-occluded_day 5

value: wounded skin epithelium without occlusion


title: PR+NR breast cancer BC_5342587027_A

value: PR+NR

value: NOCR


title: WoundSkin_NonOccluded_5D_rep6


title: WoundSkin_FullyOccluded_5D_rep3


title: PR+NR breast cancer BC_5357957009_B

value: LumB


title: WoundSkin_FullyOccluded_5D_rep2


title: PR+NR breast cancer BC_5357957009_C

value: LumA


title: PR+NR breast cancer BC_5357957008_C


title: pCR+npCR mamma breast cancer BC_5357957008_D


title: PR+NR breast cancer BC_5342587027_B


title: WoundSkin_NonOccluded_5D_rep2


title: WoundSkin_NonOccluded_5D_rep4


title: PR+NR breast cancer BC_5357957009_F


title: WoundSkin_NonOccluded_5D_rep5


title: WoundSkin_NonOccluded_5D_rep1


title: WoundSkin_FullyOccluded_3D_rep5

source_name: Wounded skin_Fully-occluded_day 3

value: day 3 post epithelialization


title: PR+NR breast cancer BC_5357957008_A


title: PR+NR breast cancer BC_5357957042_C


title: WoundSkin_FullyOccluded_3D_rep2


title: WoundSkin_FullyOccluded_3D_rep4


title: WoundSkin_FullyOccluded_3D_rep3


title: PR+NR breast cancer BC_5357957042_B


title: PR+NR breast cancer BC_4560224074_C

value: TN


title: WoundSkin_NonOccluded_3D_rep6

source_name: Wounded skin_Non-occluded_day 3


title: WoundSkin_NonOccluded_3D_rep4


title: WoundSkin_FullyOccluded_3D_rep1


title: pCR+npCR mamma breast cancer BC_5357957052_F

value: Normal

value: LUM


title: WoundSkin_NonOccluded_3D_rep5


title: pCR+npCR mamma breast cancer BC_5357957045_E

value: pCR+npCR mamma

value: CR+kl


title: PR+NR breast cancer BC_5357957045_A


title: PR+NR breast cancer BC_5357957058_F


title: PR+NR breast cancer BC_5357957043_A


title: PR+NR breast cancer BC_5357957044_A


title: PR+NR breast cancer BC_5357957052_E


title: PR+NR breast cancer BC_5357957052_A


title: PR+NR breast cancer BC_5357957052_B


title: WoundSkin_NonOccluded_3D_rep1

value: New Zealand White rabbit


title: WoundSkin_NonOccluded_3D_rep3

value: female


title: PR+NR breast cancer BC_5357957058_B


title: PR+NR breast cancer BC_5357957058_A


title: PR+NR breast cancer BC_4560224064_A


title: WoundSkin_NonOccluded_3D_rep2


title: pCR+npCR mamma breast cancer BC_5357957054_D

value: CR


title: PR+NR breast cancer BC_4753042046_C


title: PR+NR breast cancer BC_4560224064_B


title: pCR+npCR mamma breast cancer BC_4560224064_E


title: pCR+npCR mamma breast cancer BC_4560224015_A


title: PR+NR breast cancer BC_4560224029_F


title: PR+NR breast cancer BC_4560224015_C


title: PR+NR breast cancer BC_4560224043_F


title: PR+NR breast cancer BC_4560224035_B


title: PR+NR breast cancer BC_4560224029_E


title: pCR+npCR mamma breast cancer BC_4560224043_E


title: PR+NR breast cancer BC_4560224035_A


title: PR+NR breast cancer BC_4560224027_E


title: PR+NR breast cancer BC_4560224043_B


title: pCR+npCR mamma breast cancer BC_4560224045_E


title: PR+NR breast cancer BC_4560224027_D


title: PR+NR breast cancer BC_4560224066_C


title: PR+NR breast cancer BC_4560224045_D


title: PR+NR breast cancer BC_4560224066_A


title: PR+NR breast cancer BC_4560224029_B


title: PR+NR breast cancer BC_4560224045_B


title: PR+NR breast cancer BC_4560224043_D


title: PR+NR breast cancer BC_4560224073_C


title: PR+NR breast cancer BC_4560224035_E


title: PR+NR breast cancer BC_4560224045_C


title: PR+NR breast cancer BC_4560224074_F


title: PR+NR breast cancer BC_4560224078_B


title: PR+NR breast cancer BC_4560224078_A


title: PR+NR breast cancer BC_4560224084_E


title: pCR+npCR mamma breast cancer BC_4560224088_D


title: PR+NR breast cancer BC_4560224066_E


title: PR+NR breast cancer BC_4520679065_F


title: PR+NR breast cancer BC_4560224066_D


title: pCR+npCR mamma breast cancer BC_4531933041_F


title: PR+NR breast cancer BC_4531933064_D


title: PR+NR breast cancer BC_4531933064_E


title: PR+NR breast cancer BC_4531933059_C


title: PR+NR breast cancer BC_5357957008_F


title: pCR+npCR mamma breast cancer BC_4560224073_D


title: pCR+npCR mamma breast cancer BC_4560224045_A


title: PR+NR breast cancer BC_4531933070_B


title: PR+NR breast cancer BC_4531933083_E


title: PR+NR breast cancer BC_4531933044_E


title: PR+NR breast cancer BC_4531933064_B


title: pCR+npCR mamma breast cancer BC_4531933070_E


title: PR+NR breast cancer BC_4531933083_B


title: PR+NR breast cancer BC_4531933045_E


title: PR+NR breast cancer BC_4531933064_F


title: PR+NR breast cancer BC_4531933044_F


title: PR+NR breast cancer BC_5357957043_E


title: PR+NR breast cancer BC_4531933044_B


title: PR+NR breast cancer BC_4531933070_F


title: PR+NR breast cancer BC_4531933077_E


title: PR+NR breast cancer BC_4531933044_A


title: PR+NR breast cancer BC_4531933045_F


title: PR+NR breast cancer BC_4531933077_F


title: PR+NR breast cancer BC_4544460088_F


title: PR+NR breast cancer BC_4531933077_B


title: PR+NR breast cancer BC_4531933045_C


title: pCR+npCR mamma breast cancer BC_4560224008_F


title: PR+NR breast cancer BC_4531933077_D


title: PR+NR breast cancer BC_4560224007_E


title: PR+NR breast cancer BC_4544460088_C


title: PR+NR breast cancer BC_4560224007_F


title: pCR+npCR mamma breast cancer BC_4560224008_D


title: PR+NR breast cancer BC_4531933072_E


title: pCR+npCR mamma breast cancer BC_4544460088_A


title: PR+NR breast cancer BC_4560224008_C


title: PR+NR breast cancer BC_4531933041_C


title: PR+NR breast cancer BC_4531933041_B


title: PR+NR breast cancer BC_4531933041_D


title: PR+NR breast cancer BC_4544460088_B


title: PR+NR breast cancer BC_4531933043_C


title: PR+NR breast cancer BC_4531933041_A


title: pCR+npCR mamma breast cancer BC_4560224007_C


title: pCR+npCR mamma breast cancer BC_4531933077_C


title: pCR+npCR mamma breast cancer BC_4531933046_B


title: PR+NR breast cancer BC_4560224007_A


title: pCR+npCR mamma breast cancer BC_4531933069_E


title: newborn (P0) Krt1+/+ skin_replicate 3

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description: replicate 3

data_processing: The data were normalised using quantile normalisation in R

source_name: mouse full-thickness skin

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

value: full-thickness skin

value: newborn (P0)

tag: genotype/variation

tag: strain


title: Input DNA

status: Public on Nov 22 2012

city: London

first: Rahul

last: Thadani

address: 44 Lincoln's Inn Fields

country: United Kingdom

institute: Cancer Research UK

description:
Supernatant DNA
1466_BrdU_UB_210909

hyb_protocol: Hybridization was performed as previously described (Katou et al. 2003). Samples were hybridized in buffer containing SSPE, TritonX-100, denatured salmon sperm DNA and biotin-labelled control oligonucleotide, oligo B2. Samples were denatured at 95ºC for 10 minutes before being hybridized to the arrays for 16 hours at 42C in a GeneChip Hybridization Oven 640.

scan_protocol: The washing and scanning protocol (FlexMidi_euk2v3_450), provided by Affymetrix, was performed automatically on a GeneChip Fluidics Station 450. Arrays were scanned using the GeneChip Scanner 3000 7G, and primary analysis of tiling chip data was performed using the Affymetrix GeneChip Operating Software (GCOS).

data_processing:
Signal intensities between the ChIP and supernatant samples were normalized across all probe sets. Changes and change p-values were called as detailed in the Affymetrix Statistical Algorithms Reference Guide (http://www.affymetrix.com/support/technical/technotes/statistical_reference_guide.pdf). Probe sets and changes were averaged within adjacent 100 bp windows for graphical depiction. DETECTION P-VALUE = Reliability of raw signal intensity
DETECTION P-VALUE = Reliability of raw signal intensity, VALUE=Normalized signal intensity against SUPernatant fraction

organism: Saccharomyces cerevisiae

source_name: input DNA from yeast cells

label_protocol: 10 ng of amplified DNA was digested with DNase I and end-labeled using biotin-N6-ddATP using terminal transferase TdT (Roche, 400 U/µl) and Biotin-N6-ddATP (Enzo Life Sciences).

growth_protocol: Cells were grown in YP + 2% Glucose to an OD600 of 0.3. Cells were then arrested in G1 by adding a-factor to a final concentration of 0.5mg/ml during 2h. Cells were released into YP + 2% Glucose + 200 mM HU + 0.4 M BrdU for 1h.

extract_protocol: Chromatin Immunoprecipitation followed by hybridization to a high-density oligonucleotide microarray (ChIP on chip) were performed as previously described (Katou et al. 2003; Lengronne et al. 2004; Lengronne et al. 2006). Briefly, cross-linked cells were disrupted using a Multi-Beads Shocker, and whole cell extracts were sonicated to obtain 400-600 bp genomic DNA fragments. Chromatin immunoprecipitation (ChIP) was performed with anti-PK monoclonal antibody (clone SV5-Pk1, Serotec) coupled to protein A Dynabeads. Immunoprecipates were eluted and incubated overnight at 65ºC to reverse the cross-link. An aliquot of the supernatant fraction of the immunoprecipitation was treated in parallel to provide a whole genome DNA sample for comparison.  The ChIP and supernatant samples were then incubated with proteinase K, extracted twice with phenol/chloroform/isoamylalcohol, precipitated, resuspended in TE and incubated with RNaseA. The DNA was purified, concentrated by ethanol precipitation and amplified by PCR after random priming.

treatment_protocol: HU arrested cells were cross-linked with 1% Formaldehide for 30 minutes at room temperature. The reaction was stopped with 0.125 M Glycine for 10 minutes.


title: PR+NR breast cancer BC_4531933092_D

value: AC

value: breast cancer tumor


title: newborn (P0) Krt1-/- epidermis_replicate 2

description: replicate 2

source_name: mouse epidermis

value: epidermis


title: PR+NR breast cancer BC_4531933092_E

value: PR+NR

value: NOCR


title: PR+NR breast cancer BC_4531933069_D

value: LumA


title: newborn (P0) Krt1-/- epidermis_replicate 1

description: replicate 1


title: PR+NR breast cancer BC_4531933092_C

value: LumB


title: newborn (P0) Krt1+/+ skin_replicate 2

description: replicate 2


title: newborn (P0) Krt1+/+ epidermis_replicate 2

description: replicate 2


title: newborn (P0) Krt1-/- epidermis_replicate 3

description: replicate 3


title: BrdU incorporation in WT cells

description:
Inmunoprecipitated DNA
1466_BrdU_B_210909

source_name: ChIP DNA from yeast cells

tag: chip antibody

value: anti-BrdU Clone 2B1

tag: chip antibody vendor

value: MBL


title: BrdU incorporation in wapl∆ cells

description:
Inmunoprecipitated DNA
1466_Dwapl_BrdU_B_210909

value: MATa, URA3::GPD1pr-TK, aur1::ADH1pr-hENT1, wpl1∆::HIS3


title: newborn (P0) Krt1-/- skin_replicate 1

description: replicate 1

tag: age


title: newborn (P0) Krt1+/+ epidermis_replicate 1

description: replicate 1


title: Rat liver HW 100 TCDD 240 hours rep 5

status: Public on Oct 18 2012

city: Toronto

first: Stephenie

last: Prokopec

state: Ontario

address: 661 University Avenue, Suite 510

country: Canada

institute: Ontario Institute for Cancer Research

description: Treated

data_processing: Raw OpenArray PCR data (Ct values) were loaded into the R statistical environment (v2.12.2). Data was normalized using reference genes Eef1a1, Gapdh, Hprt1, Pgk1, Ppia and Sdha and fold-changes calculated using the mean of the biological replicates (Treated - Control, in log2 space). Matrix non-normalized contains the mean of the raw Ct values. Matrix normalized contains values normalized to the  housekeeping genes (delta Ct). Fold Change contains values of treated animals compared to untreated animals (Ct[treated] - Ct[untreated]).

label: FAM

organism: Rattus norvegicus

source_name: liver, Han/Wistar, 100 TCDD, 240 hours exposure

label_protocol: RNA was reverse-transcribed using High Capacity cDNA Reverse Transcription Kits (Applied Biosystems, Carlsbad, CA) following the manufacturer’s instructions, with the thermal cycler set to run at 25°C for 10 minutes, 37°C for 2 hours, 85°C for 5 minutes followed by a rapid cooling to 4°C. cDNA was sent to Life Technologies (Applied Biosystems, Carlsbad, CA) for PCR on the OpenArray system.

growth_protocol: Animals were housed in suspended, stainless-steel wire-mesh cages in groups of 4 rats with a 12h/12h light/dark cycle and with pelleted R36 feed and tap water. The temperature was maintained at  21 +/- 1 degree Celcius with relative humidity 50% +/- 10%.

extract_protocol: Total RNA was extracted using Qiagen RNeasy Mini kits according to the manufacturer’s instructions (Qiagen, Mississauga, Canada). RNA was quantified using a NanoDrop UV spectrophotometer (Thermo Scientific, Mississauga, ON) and RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Animals were treated with either TCDD or corn oil vehicle alone by oral gavage.

value: Male

value: Liver

value: Han/Wistar

value: 10-12 weeks

value: 100 ug/kg TCDD

tag: exposure

value: 240 hours


title: newborn (P0) Krt1-/- skin_replicate 3

description: replicate 3

value: full-thickness skin

value: newborn (P0)


title: newborn (P0) Krt1+/+ skin_replicate 1

description: replicate 1


title: newborn (P0) Krt1+/+ epidermis_replicate 3

description: replicate 3


title: Rat liver HW 100 TCDD 240 hours rep 4

description: Treated


title: Liver_Ad-shHnf1b 3

status: Public on Nov 10 2012

city: Cologne

first: Jan-Wilhelm

last: Kornfeld

address: Zülpicher Strasse 47a

department: Department of Mouse Genetics and Metabolism

institute: Institute for Genetics

hyb_protocol: After fragmentation, cDNAs were hybridized for 17h at 45°C on Affymetrix Mouse Gene 1.0 ST Arrays.

scan_protocol: The Arrays were washed and stained in the GeneChip Fluidics Station 450 and scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Data intensities were log transformed and normalized with a quantile normalization method using Affymetrix Power Tools (APT), using the command "apt-probeset-summarize", with the option "-a rma" ("rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish").
i.e. full quantile normalization", and "probeset summarization"  including "median polish" (Irizarry et al. 2003)
http://www.affymetrix.com/partners_programs/programs/developer/tools/powertools.affx
http://media.affymetrix.com/support/developer/powertools/changelog/apt-probeset-summarize.html
Differentially expressed genes were identified according to statistical evidence indicated by Student's t-test and fold change statistics.

source_name: Liver, Ad-shHnf1b  1x10E VP/g BW

label_protocol: Biotin-labeled cDNA was synthesized using GeneChip Whole Transcript Sense Labeling Assay (Affymetrix) according to vendor’s instructions.

extract_protocol: Trizol total RNA extraction

value: male

tag: injected with

value: Adenoviruses (Ad5) encoding shHnf1b (Ad-shHnf1b 1-4)

tag: injection dose

value: 1x10E10 viral particles (VP) per gram bodyweight

value: knockdown of hepatic Hnf1b (Ad-shHnf1b)

value: liver


title: Rat liver HW 100 TCDD 240 hours rep 3

description: Treated


title: Liver_Ad-shHnf1b 2


title: Rat liver HW Corn oil 240 hours rep 5

description: Control

source_name: liver, Han/Wistar, Corn oil treated, 240 hours exposure

value: Corn Oil vehicle


title: Rat liver HW 100 TCDD 240 hours rep 2

description: Treated


title: Rat liver HW Corn oil 240 hours rep 4

description: Control


title: Rat liver HW 100 TCDD 240 hours rep 1

description: Treated


title: Liver_Ad-Ctrl 3

source_name: Liver, Ad-Ctrl  1x10E VP/g BW

value: Adenoviruses (Ad5) encoding GFP (Ad-Ctrl 1-3)

value: control


title: Rat liver HW Corn oil 240 hours rep 2

description: Control


title: Rat liver HW Corn oil 240 hours rep 1

description: Control


title: Rat liver HW Corn oil 240 hours rep 3

description: Control


title: newborn (P0) Krt1-/- skin_replicate 2

description: replicate 2


title: Liver_Ad-shHnf1b 1


title: Liver_Ad-Ctrl 1


title: Liver_Ad-shHnf1b 4


title: ir-hspro_14d_Pindica_rep1

status: Public on Nov 06 2012

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

institute: Max-Planck-Institute for Chemical Ecology

description: Gene expression after 14 days of inoculation with P. indica

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent platform GPL13527 for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and at 37°C with GE Wash buffer 2 (Agilent) as outlined in the One-Color Microarray-Based Gene Expression Analysis manual (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Data was acquired with the Agilent Scan Control software (version A.7.0.1 for the B scanner) and extracted using the Agilent Feature Extraction software (version 9.5). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. 75 percentile normalization was performed for all probes including all controls and replicate probes. Controls were removed from the list. All replicated probes were averaged.

organism: Nicotiana attenuata

source_name: ir-hspro roots, 14 days, P. indica inoculation, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp labeling kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Hilden, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Seeds from N. attenuata wild type and ir-hspro plants were grown in the glasshouse under high-pressure sodium lamps (200-300 µmol s-1 m-2 light) with a day/night cycle of 16 h(26-28°C)/8 h(22-24°C) and 45 to 55% humidity.

extract_protocol: Total RNA was extracted from leaves using the Plant RNeasy kit (Qiagen, Hilden, Germany) and its quality checked by spectrophotometry (NanoDrop, Wilmington, DE). Genomic DNA was removed by DNAse treatment following commercial instructions (Turbo DNase; Ambion, Europe), RNA was cleaned up with RNeasy MinElute columns (Qiagen) and the RNA quality was checked with the RNA 6000 Nano kit (Agilent, Santa Clara, CA) using an Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: For the treatment, two 7-day old seedlings of the same genotype were placed on a polyamide membrane covering the surface of an agar plate. In equal distance to each seedling ( 1 cm) either a sterile agar plug (control) or an agar plug containing P. indica was placed. The lid and the plate were sealed with Parafilm and incubated for 14 days at a light intensity of 80 µmol m–2 s–1.

value: ir-hspro

value: roots


title: WT_14d_Pindica_rep2

source_name: wild type roots, 14 days, P. indica inoculation, replicate 2

value: wild type


title: Liver_Ad-Ctrl 2


title: Rat liver HW 100 TCDD 240 hours rep 2

description: Treated

data_processing: Raw qPCR data (Ct values) were loaded into the R statistical environment (v2.12.2). Wells flagged with Non-Amplified Well were removed prior to downstream analysis. Data was normalized using reference genes Gapdh and Pgk1 and fold-changes calculated using the mean of the biological replicates (Treated - Control, in log2 space). Matrix non-normalized contains the mean of the raw Ct values. Matrix normalized contains values normalized to the  housekeeping genes (delta Ct). Fold Change contains values of treated animals compared to untreated animals (Ct[treated] - Ct[untreated]).

label_protocol: RNA was reverse-transcribed using High Capacity cDNA Reverse Transcription Kits (Applied Biosystems, Carlsbad, CA) following the manufacturer’s instructions, with the thermal cycler set to run at 25°C for 10 minutes, 37°C for 2 hours, 85°C for 5 minutes followed by a rapid cooling to 4°C. qPCR was performed using the 7900HT Fast Real-Time PCR System (Applied Biosystems, Carlsbad, CA) using the ΔΔCT standard 384-well PCR plate settings; an initial 2-minute hold at 50°C was performed to ensure that any UTP-containing contaminants from previous PCR reactions were fully digested by the AmpErase UNG nuclease. Polymerase was activated by a 10-minute hold at 95°C and reactions carried out by 40 cycles of 15 seconds at 95°C and 1 minute at 60°C

value: Male

value: Liver

value: Han/Wistar


title: Rat liver HW 100 TCDD 240 hours rep 3

description: Treated

value: 10-12 weeks

value: 100 ug/kg TCDD

value: 240 hours


title: Rat liver HW Corn oil 240 hours rep 1

description: Control


title: Rat liver HW Corn oil 240 hours rep 4

description: Control


title: Rat liver HW Corn oil 240 hours rep 5

description: Control


title: Rat liver HW Corn oil 240 hours rep 2

description: Control


title: Rat liver HW 100 TCDD 240 hours rep 4

description: Treated


title: Rat liver HW 100 TCDD 240 hours rep 5

description: Treated


title: WT_14d_Pindica_rep1

source_name: wild type roots, 14 days, P. indica inoculation, replicate 1


title: ir-hspro_14d_Pindica_rep2

source_name: ir-hspro roots, 14 days, P. indica inoculation, replicate 2


title: WT_14d_Pindica_rep3

source_name: wild type roots, 14 days, P. indica inoculation, replicate 3


title: Rat liver HW 100 TCDD 240 hours rep 1

description: Treated


title: HSMM_B1

status: Public on Aug 29 2012

city: Rensselaer

first: Sridar

middle: V

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

description: .bed file contains gene-level normalized expression values

data_processing: Probesets flagged as cross-hybridizing were removed. Probesets were assigned to genes based on the GENCODE v10 annotation (July 2011). To normalize, we first classified each exon as constitutive, meaning present in all annotated isoforms, or not constitutive for each gene, reasoning these would be the most robust across celltypes. For genes with at least 4 constitutive probesets, only constitutive probesets were used to normalize. For all other genes, including all non-protein-coding genes, we sused all probesets that mapped to the gene. To normalize, we used Affymetrix Power Tools (APT) with the chipstream command “rma-bg, med-norm, pm-gcbg, med-polish”. This chipstream calls for an RMA normalization with gc-background correction using antigenomic background probes. We used an ComBat to correct for batch effects.

source_name: skeletal muscle myoblasts

label_protocol: 1ug of total RNA was labeled according to Standard Affymetrix WT protocol for Exon 1.0 ST arrays

growth_protocol: Cells were grown according to the approved ENCODE cell culture protocols.Specific protocol descriptions can be found at http://genome.ucsc.edu/ENCODE/cellTypes.html.

extract_protocol: total RNA was extracted from cell pellets using Trizol protocol

tag: cell type

value: skeletal muscle myoblasts


title: HSMMtube_B1

hyb_protocol: Standard Affymetrix WT protocol for Exon 1.0 ST arrays

source_name: skeletal muscle myotubes differentiated from the HSMM cell line


title: Dataset 48

status: Public on Jul 31 2012

city: Eggenstein-Leopoldshafen

first: Jessica

last: Legradi

state: Baden-Wuerttemberg

address: Hermann-von-Helmholtz-Platz 1

department: Institute of Toxicology and Genomics ITG

institute: Karlsruhe Institute of Technology

description:
biological repeat
252232610017_b2: CY5

hyb_protocol: The hybridistaion of labelled probes was performed following Agilent Microarray hyridisation Kit.

scan_protocol: Samples were scanned on Axon 4000B scanner and the images analysed used GenePix Pro 61

data_processing: The data was analysed using Matlab R2009b, data is background substracted, log2-values calculated and Quantile normalization was perfomed.

source_name: 48 hpf

label_protocol: 2 µg of total RNA from each sample (exposure and control embryos) was labelled with Cyanine3 and Cyanine 5-CTP according to Agilent Low RNA Input Linear Amplification Kit.

growth_protocol: Adult fish were maintained in fish water at 28.5 °C, subjected to a photoperiod of 10 hours light and 14 hours dark, and fed with dry flake food and brine shrimp. Embryos were kept in embryo medium.

extract_protocol: Was extracted with Trizol (Invitrogen) using a tissue homogenizer (Ultra-Turrax, Janke&Kunkel, IKA-Werk) according to the manufacturer´s protocol followed by a second round of extraction with phenol-chloroform and precipitation as described previously (Gohlke et al., 2008)

treatment_protocol: Embryos were raised in embryo medium at 28 °C

tag: stage/tissue

value: 48 hpf

value: wild type AB, Tübingen


title: HSMMtube_B3

scan_protocol: Standard Affymetrix WT protocol for Exon 1.0 ST arrays

value: skeletal muscle myotubes differentiated from the HSMM cell line


title: HSMMtube_B2


title: Rat liver HW Corn oil 240 hours rep 3

description: Control


title: Dataset 44

description:
biological repeat
252232610016_b3: CY5

source_name: Tail

value: Tail


title: Dataset 46

description:
biological repeat
252232610017_b1: CY5

source_name: 24 hpf

value: 24 hpf


title: HSMM_B3


title: Dataset 47

description:
biological repeat
252232610017_b2: CY3


title: Dataset 45

description:
biological repeat
252232610017_b1: CY3


title: Dataset 42

description:
biological repeat
252232610016_b2: CY5

source_name: Head

value: Head


title: Dataset 43

description:
biological repeat
252232610016_b3: CY3


title: Dataset 39

description:
biological repeat
252232610016_b1: CY3


title: Dataset 35

description:
biological repeat
252232610015_b3: CY3

source_name: Telencephalon

value: Telencephalon


title: Dataset 38

description:
biological repeat
252232610015_b4: CY5


title: Dataset 41

description:
biological repeat
252232610016_b2: CY3


title: Dataset 34

description:
biological repeat
252232610015_b2: CY5

source_name: Diecephalon

value: Diecephalon


title: Dataset 40

description:
biological repeat
252232610016_b1: CY5


title: Dataset 36

description:
biological repeat
252232610015_b3: CY5


title: Dataset 37

description:
biological repeat
252232610015_b4: CY3


title: Dataset 33

description:
biological repeat
252232610015_b2: CY3


title: Dataset 26

description:
biological repeat
252232610014_b2: CY5


title: Dataset 24

description:
biological repeat
252232610014_b1: CY5


title: Dataset 32

description:
biological repeat
252232610015_b1: CY5


title: Dataset 20

description:
biological repeat
252232610013_b2: CY5


title: Dataset 27

description:
biological repeat
252232610014_b3: CY3


title: Dataset 21

description:
biological repeat
252232610013_b3: CY3


title: Dataset 29

description:
biological repeat
252232610014_b4: CY3


title: Dataset 22

description:
biological repeat
252232610013_b3: CY5


title: Dataset 31

description:
biological repeat
252232610015_b1: CY3


title: Dataset 28

description:
biological repeat
252232610014_b3: CY5


title: Dataset 16

description:
biological repeat
252232610012_b4: CY5


title: Dataset 23

description:
biological repeat
252232610014_b1: CY3


title: Dataset 17

description:
biological repeat
252232610013_b1: CY3


title: Dataset 15

description:
biological repeat
252232610012_b4: CY3


title: Dataset 14

description:
biological repeat
252232610012_b3: CY5


title: Dataset 25

description:
biological repeat
252232610014_b2: CY3


title: Dataset 11

description:
biological repeat
252232610012_b2: CY3

source_name: 1-6 somites

value: 1-6 somites


title: Dataset 13

description:
biological repeat
252232610012_b3: CY3


title: Dataset 19

description:
biological repeat
252232610013_b2: CY3


title: Dataset 18

description:
biological repeat
252232610013_b1: CY5


title: Dataset 10

description:
biological repeat
252232610012_b1: CY5


title: Dataset 5

description:
biological repeat
252232610011_b3: CY3

source_name: 30% epiboly

value: 30% epiboly


title: Dataset 7

description:
biological repeat
252232610011_b4: CY3


title: ir-hspro_14d_Pindica_rep3

source_name: ir-hspro roots, 14 days, P. indica inoculation, replicate 3

value: ir-hspro

value: roots


title: Dataset 6

description:
biological repeat
252232610011_b3: CY5


title: HSMM_B2


title: Dataset 12

description:
biological repeat
252232610012_b2: CY5


title: Dataset 9

description:
biological repeat
252232610012_b1: CY3


title: Dataset 8

description:
biological repeat
252232610011_b4: CY5


title: Dataset 3

description:
biological repeat
252232610011_b2: CY3


title: Salmonella_enterica_serovar_Typhimurium_UK1_delta_raoN_mutant_5mM hydrogen peroxide_wild-type_rep2

status: Public on Jul 01 2012

city: Seoul

first: Yong Keun

last: Park

address: Anam-dong 5Ga, Seoungbuk-Gu

department: School of Life Sciences and Biotechnology

country: South Korea

institute: Korea University

description: This sample is of wild-type Salmonella enterica serovar Typhimurium UK1 delta-rsiM. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Labeled cDNAs were hybridized to a NimbleGen 4-plex array which was designed based on S. Typhimurium strain LT2 (Roche NimbleGen) for 12 h at 42 °C using MAUI system (Biomicro systems).

scan_protocol: Arrays were washed and scanned using an Axon GenePix 4000B scanner (Molecular Devices).

data_processing: Gene expression levels were calculated with NimbleScan software version 2.4 (Roche NimbleGen) using the median polish normalization method and relative signal intensities were generated using the robust multi-array average algorithm. Data analysis was performed using GeneSpring GX 7.3.1 (Agilent Technologies).

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. UK-1

source_name: Salmonella enterica serovar Typhimurium UK1 delta-raoN

label_protocol: Each total RNA sample was labeled with Cyanine 3 (Cy3)-conjugated dCTP by a reverse transcription reaction, and then was resuspended in 10 µl of hybridization solution (GenoCheck, Korea).

growth_protocol: Salmonellal enterica serovar Typhimurium UK1 and ∆raoN mutant were grown upto O.D.600nm 0.6 in LB broth. then, 5.0 mM hydroperoxide was treated and bacteria were grown and stressed for 30 minutes.

extract_protocol: Total RNA was extracted from Hot phenol method and concentration was measured by analysis with a Nano drop.

treatment_protocol: 5.0mM hydrogen peroxide were treated in LB media after grown until O.D.600nm 0.6 and incubated for 30 min.

tag: genotype

value: deletion mutant delta-raoN

tag: phenotype

value: sensitive to oxidative stress

tag: accession


title: Salmonella_enterica_serovar_Typhimurium_UK1_delta_raoN_mutant_5mM hydrogen peroxide_wild-type_rep1

description: This sample is of wild-type Salmonella enterica serovar Typhimurium UK1 delta-raoN. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: Dataset 30

description:
biological repeat
252232610014_b4: CY5


title: Dataset 1

description:
biological repeat
252232610011_b1: CY3


title: WT_2h_Wound +Os elicitation_rep3

status: Public on Jul 12 2012

description: Gene expression after 1hr of elicitation with oral secretions from Manduca sexta larvae

source_name: wild type leaves, 2h, oral secretion elicitation, replicate 3

growth_protocol: Seeds from N. attenuata Utah wild type and ir-JAZh plants were grown in the glasshouse under high-pressure sodium lamps (200-300 µmol s-1 m-2 light) with a day/night cycle of 16 h(26-28°C)/8 h(22-24°C) and 45 to 55% humidity.

treatment_protocol: For elicitation treatment, leaves were wounded by rolling a fabric-pattern wheel three times on each side of the midvein and the wounds were supplemented with 20 microliters of Manduca sexta oral secretions diluted 1/5 (v/v) in water.

value: leaves

value: wild type

tag: stress

value: 2h, oral secretion elicitation from Manduca sexta larvae


title: irJAZh_2h_Wound+Os elicitation_rep2

source_name: irJAZh leaves, 2h, oral secretion elicitation, replicate 2

value: irJAZh


title: Dataset 2

description:
biological repeat
252232610011_b1: CY5

value: wild type AB, Tübingen


title: JAK1-3 shRNA, Exp2

status: Public on Jun 28 2012

city: Essen

first: Stefan

last: Heinrichs

address: Virchowstr. 179

department: Institute of Transfusion Medicine

institute: University Hospital Essen

hyb_protocol: The fragmented cDNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C.  The chips were then transferred to a fluidics instrument that performed washes to remove cDNA that has not hybridized to its complementary oligonucleotide probe. The bound cDNA was subsequently fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cDNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured. These measures provided the raw expression data of subsequent biostatistical analysis.

data_processing: Raw data were processed in Expression Console (Affymetrix) using RMA normalization. Meta probe sets (Probeset-Annotation.txt) for each gene were annotated by mapping all probe sets to the human genome version hg19 and expression values were obtained. Data complexity was reduced to one canonical transcript per gene, resulting in a single identifier per gene (customized annotation, 17982 individual genes total).

source_name: JAK1-3 shRNA

label_protocol: The cDNA was generated according to manufacturer's instructions (Affymetrix). The fragmented cDNA was end-labeled with a biotinylated nucleotide analog.

growth_protocol: exponentially growing cells

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

tag: cell line

value: expressing the JAK1-specific shRNA JAK1-3


title: irJAZh_2h_Wound+Os elicitation_rep1

source_name: irJAZh leaves, 2h, oral secretion elicitation, replicate 1


title: WT_2h_Wound +Os elicitation_rep1

source_name: wild type leaves, 2h, oral secretion elicitation, replicate 1


title: control shRNA, Exp2

source_name: control shRNA

value: expressing a control shRNA


title: parental cells, Exp2

source_name: parental cells


title: control shRNA, Exp1


title: JAK1-1 shRNA, Exp2

source_name: JAK1-1 shRNA

value: expressing the JAK1-specific shRNA JAK1-1


title: WT_2h_Wound +Os elicitation_rep2

source_name: wild type leaves, 2h, oral secretion elicitation, replicate 2


title: parental cells, Exp1


title: irJAZh_2h_Wound+Os elicitation_rep3

source_name: irJAZh leaves, 2h, oral secretion elicitation, replicate 3


title: BDEsp Tumor-Derived Epithelial cells rep3

status: Public on Jun 23 2012

city: Jacksonville

first: Catherine

last: Dumur

state: FL

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GC3000 scanner.

data_processing: After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries was performed using the log-scale Robust Multiarray Analysis (RMA) method.

source_name: BDEsp Tumor-Derived Epithelial cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: Tissues were snap-frozen immediately after extirpation from the animal.

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

treatment_protocol: BDEsp tumor-derived cells lines were grown in a rat tail type I collagen gel matrix, alone or in co-culture. For the co-cultures, cholangiocarcinoma (Epithelial) cells were plated at a density of  1 x 105 cells/mL and with a-SMA positive CAF (Fibroblasts) at various plating densities, ranging 0–8 x 105 cells/gel.

tag: sample type

value: BDEsp Tumor-Derived Epithelial cell line, clone H10 genetic background:Fischer 344


title: JAK1-3 shRNA, Exp1


title: BDEsp Tumor-Derived Fibroblastic cells rep1

description: BDEsp Tumor-Derived Fibroblastic cell line

source_name: BDEsp Tumor-Derived Fibroblastic cells

value: BDEsp Tumor-Derived Fibroblastic cell, clone E4

tag: genetic background

value: Fischer 344


title: BDEsp Tumor-Derived Fibroblastic cells rep2

value: BDEsp Tumor-Derived Fibroblastic cell line


title: BDEsp Tumor-Derived Fibroblastic cells rep4


title: JAK1-1 shRNA, Exp1

tag: genotype/variation


title: DGM-00433_lg

status: Public on Jun 20 2012

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

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

source_name: large airway epithelium brushing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: smoking status

value: nonsmoker


title: BDEsp Tumor-Derived Epithelial cells rep2

description: BDEsp Tumor-Derived Epithelial cell line


title: BDEsp Tumor-Derived Fibroblastic cells rep3


title: Colon Tissue, Normal, RT-608

status: Public on Jan 31 2012

city: Honolulu

first: Lenora

middle: WM

last: Loo

state: HI

address: 1236 Lauhala St #407

department: Epidemiology Program

institute: University of Hawaii Cancer Center

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials according to the manufacturer’s recommendations

scan_protocol: The GeneChip® Scanner 3000 7G

data_processing:
Partek Genomics Suite software was used for analysis.  Gene-level expression values (Core Meta Probe-set) were log2-transformed and normalized using Robust Multi-array Analysis (RMA).
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: Colon Tissue, Normal

label_protocol: DNA is labeled by terminal deoxynucleotidyl transferase (TdT) with the Affymetrix® proprietary DNA Labeling Reagent that is covalently linked to biotin.  transferase (TdT) with the Affymetrix® proprietary DNA Labeling Reagent that is  covalently linked to biotin.

extract_protocol: Total RNA was extracted from these tissue samples using the QIAGEN AllPrep DNA/RNA Mini kit (QIAGEN, Valencia, CA) following manufacturer’s recommendations.

tag: disease state

value: Normal

tag: 1q41 genotype rs11579490

value: GT

tag: 1q41 genotype rs6691195

value: TT

tag: 3q26 genotype rs12638862

value: CT

tag: 8q23 genotype rs16892766

tag: 8q24 genotype rs6983267

value: GG

tag: 8q24 genotype rs10505477

tag: 8q24 genotype rs7014346

tag: 9q24 genotype rs10975552

value: AG

tag: 10p14 genotype rs706771

tag: 11q23 genoptype rs3802840

tag: 12q13 genotype rs7136702

value: AA

tag: 15q13 genotype rs4779584

value: CC

tag: 16q22 genotype rs2059254

tag: 18q21 genotype rs7226855

tag: 20q13 genotype rs4925386


title: Mammary Gland-rtTA/Cyclin D1- Rep3

status: Public on Feb 10 2012

city: PHILADELPHIA

first: Adam

last: Ertel

state: PA

address: 233 S 10TH ST

department: Cancer Biology

institute: Thomas Jefferson University

hyb_protocol: Mouse Gene 1.0 ST arrays were hybridized with fragmented and biotin-labeled target (2.5 µg) in 110 µl of hybridization cocktail. Target denaturation was performed a 99oc for 2 min. and then 45oc for 5 min., followed by hybridization for 18 hrs. Arrays then were washed and stained using Genechip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).  For the Mouse 430A v2.0 arrays, 15µg of cRNA was fractionated to produce fragments between 35–200 bp using 5x Fragmentation buffer provided in the Cleanup Module, followed by hybridization for 18 hrs. Arrays then were washed and stained using Genechip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.

data_processing: Affymetrix Expression Console 1.1 was used to compute Robust Multichip average (RMA) expression values.  For the Mouse Gene 1.0 ST microarrays. The core set of probe set clusters was used with annotation version na30, dated December 2009. The dataset was imported into Matlab version R2010b (The Mathworks, Natick, MA) and one-way ANOVA was used to evaluate the significance of differential expression between biological conditions. Genes with differential expression p-value ≤ 0.01 and absolute fold change ≥ 1.25 were clustered and visualized using a clustergram heatmap.

source_name: Mouse Mammary gland 8 week old females

label_protocol: Labeling for Mouse Gene 1.0 ST arrays was performed by the WT-Ovation Pico RNA amplification system (NuGen Technologies, Inc.).   For 430A v2.0 arrays, the double stranded cDNA was used as a template to generate biotinylated cRNA using Bioarray HighYield RNA.Transcription Labeling Kit (Enzo) and the labeled cRNA purified by GeneChip Sample Cleanup Module (Affymetrix).

growth_protocol: No specific growth protocol

extract_protocol: Total RNA extracted using Trizol reagent (Invitrogen) as per manufacturers' guidelines.

treatment_protocol: rtTA/CCND1 KE mutant samples underwent 7 days of doxycycline treatment

tag: strain

value: FvB/N

tag: tissue

value: mammary gland

tag: transgenic mouse


title: Mammary Gland-rtTA/Cyclin D1- Rep2


title: Colon Tissue, Tumor, RT-677

source_name: Colon Tissue, Tumor

tag: disease state

value: Tumor

tag: 1q41 genotype rs11579490

tag: 1q41 genotype rs6691195

value: AT


title: Colon Tissue, Normal, RT-677

tag: 3q26 genotype rs12638862

tag: 8q23 genotype rs16892766

tag: 8q24 genotype rs6983267


title: Colon Tissue, Tumor, RT-606

tag: 8q24 genotype rs10505477

tag: 8q24 genotype rs7014346

tag: 9q24 genotype rs10975552


title: Colon Tissue, Tumor, RT-608

tag: 10p14 genotype rs706771

tag: 11q23 genoptype rs3802840

tag: 12q13 genotype rs7136702


title: Colon Tissue, Normal, RT-87

tag: 15q13 genotype rs4779584

tag: 16q22 genotype rs2059254

tag: 18q21 genotype rs7226855


title: Colon Tissue, Normal, RT-58

tag: 20q13 genotype rs4925386


title: BDEsp Tumor-Derived Epithelial cells rep1

tag: sample type

value: BDEsp Tumor-Derived Epithelial cell line, clone H10 genetic background:Fischer 344

tag: cell type


title: Colon Tissue, Tumor, RT-567

tag: disease state

tag: 1q41 genotype rs11579490


title: Colon Tissue, Normal, RT-721

tag: 1q41 genotype rs6691195

tag: 3q26 genotype rs12638862


title: Colon Tissue, Tumor, RT-721

tag: 8q23 genotype rs16892766

tag: 8q24 genotype rs6983267


title: Colon Tissue, Tumor, RT-87

tag: 8q24 genotype rs10505477

tag: 8q24 genotype rs7014346


title: Mammary Gland-rtTA Control- Rep1

tag: strain

tag: tissue

tag: transgenic mouse

value: rtTA


title: Mammary Gland-rtTA Control- Rep2


title: Colon Tissue, Tumor, RT-483

tag: 9q24 genotype rs10975552

tag: 10p14 genotype rs706771

tag: 11q23 genoptype rs3802840

tag: 12q13 genotype rs7136702

tag: 15q13 genotype rs4779584


title: Colon Tissue, Normal, RT-606

tag: 16q22 genotype rs2059254

tag: 18q21 genotype rs7226855

tag: 20q13 genotype rs4925386


title: Colon Tissue, Tumor, RT-465

tag: disease state

tag: 1q41 genotype rs11579490

tag: 1q41 genotype rs6691195


title: Colon Tissue, Tumor, RT-58

tag: 3q26 genotype rs12638862

tag: 8q23 genotype rs16892766

tag: 8q24 genotype rs6983267


title: Colon Tissue, Normal, RT-483

tag: 8q24 genotype rs10505477

tag: 8q24 genotype rs7014346


title: Colon Tissue, Normal, RT-465


title: Mammary Gland-rtTA/Cyclin D1- Rep1

tag: strain

tag: tissue

tag: transgenic mouse


title: Colon Tissue, Tumor, RT-455

tag: 9q24 genotype rs10975552

tag: 10p14 genotype rs706771

tag: 11q23 genoptype rs3802840


title: Colon Tissue, Normal, RT-567

tag: 12q13 genotype rs7136702

tag: 15q13 genotype rs4779584

tag: 16q22 genotype rs2059254


title: Colon Tissue, Tumor, RT-432

tag: disease state

tag: 18q21 genotype rs7226855

tag: 20q13 genotype rs4925386


title: Colon Tissue, Normal, RT-432

tag: 1q41 genotype rs11579490

tag: 1q41 genotype rs6691195

tag: 3q26 genotype rs12638862


title: Colon Tissue, Normal, RT-434

tag: 8q23 genotype rs16892766

tag: 8q24 genotype rs6983267

tag: 8q24 genotype rs10505477


title: Colon Tissue, Tumor, RT-434

tag: 8q24 genotype rs7014346


title: Colon Tissue, Normal, RT-294


title: Colon Tissue, Normal, RT-380


title: Colon Tissue, Tumor, RT-122


title: Colon Tissue, Normal, RT-329


title: Colon Tissue, Normal, RT-158


title: Colon Tissue, Tumor, RT-380


title: Colon Tissue, Normal, RT-340


title: Colon Tissue, Tumor, RT-158


title: Colon Tissue, Tumor, RT-312


title: Colon Tissue, Tumor, RT-272


title: Colon Tissue, Tumor, RT-329


title: Colon Tissue, Tumor, RT-340


title: Colon Tissue, Tumor, RT-358

value: ND


title: Colon Tissue, Tumor, RT-294


title: Colon Tissue, Normal, RT-122


title: Colon Tissue, Normal, RT-272


title: Colon Tissue, Normal, RT-116


title: Colon Tissue, Normal, RT-312


title: Colon Tissue, Tumor, RT-116


title: Colon Tissue, Normal, RT-358


title: Colon Tissue, Normal, RT-203


title: Colon Tissue, Tumor, RT-203


title: Colon Tissue, Tumor, 832


title: Colon Tissue, Normal, RT-455


title: Colon Tissue, Normal, 832


title: Colon Tissue, Tumor, 809


title: Colon Tissue, Normal, 756


title: Colon Tissue, Normal, 788


title: Colon Tissue, Tumor, 746


title: Colon Tissue, Normal, 746


title: Colon Tissue, Tumor, 788


title: Colon Tissue, Normal, 736


title: Colon Tissue, Tumor, 723


title: Colon Tissue, Tumor, 687


title: Colon Tissue, Normal, 723


title: Replication timing of GM06999 lymphoblastoid cells, replicate 2

status: Public on May 16 2012

city: Tallahassee

first: Tyrone

last: Ryba

address: 319 Stadium Dr.

department: Biological Science

institute: Florida State University

description: submitted as of 5/12/12

hyb_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, Cy3 and Cy5 labeled DNA samples (34 ug each) were co-hybridized to Nimblegen CGH arrays containing one oligonucleotide probe every 2.5 kb across the human genome.

scan_protocol: NimbleGen MS200 microarray scanner (Roche NimbleGen, Inc.) and MS200 data collection software were used per NimbleGen's standard protocol (www.nimblegen.com/products/lit/index.html).

data_processing: NimbleScan software was used to obtain .pair raw data per manufacturer's instructions. Raw early/late data (i.e. from .pair files) from two independent biological replicates in which early and late replicating DNA were differentially labeled were loess-normalized to remove signal intensity-dependent bias, then scaled to a reference data set to have the same median absolute deviation (limma package, R/Bioconductor).The early/late ratios were used to generate a smoothed profile (i.e. processed data) using local polynomial smoothing (loess, 300-kb span) for each chromosome using the loess function in the statistical language R. Processed data sets can be graphically displayed (and are also downloadable) on our web site (http://www.replicationdomain.org). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].

source_name: Early-replicating DNA of GM06999 lymphoblastoid cells

label_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, randomly-amplified BrdU-immunoprecipitated DNA samples (1 ug each) were Cy3- or Cy5-labeled by Klenow reaction using end-labeled Cy3- or Cy5-random 9-mers.

extract_protocol: Replication timing data were obtained by hybridizing early and late replication intermediates to NimbleGen oligonucleotide arrays, as described in Hiratani et al [PLoS Biology (2008) 6: e245]. Briefly, replication intermediates are prepared from cells that are first pulse-labeled with BrdU and then sorted into early (1st half of S) and late (2nd half of S) stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. Samples were labeled after unbiased amplification of recovered DNA by whole-genome amplification (WGA; Sigma, GenomePlex). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].

tag: gender

value: F

tag: disease stage

tag: karyotype

source_name: Late replicating DNA of GM06999 lymphoblastoid cells

tag: age (yrs)


title: Colon Tissue, Normal, 809

tag: 9q24 genotype rs10975552

tag: 10p14 genotype rs706771

tag: 11q23 genoptype rs3802840

tag: 12q13 genotype rs7136702


title: Colon Tissue, Tumor, 756

tag: disease state

tag: 15q13 genotype rs4779584

tag: 16q22 genotype rs2059254

tag: 18q21 genotype rs7226855


title: Colon Tissue, Tumor, 762

tag: 1q41 genotype rs11579490

tag: 1q41 genotype rs6691195

tag: 3q26 genotype rs12638862

tag: 20q13 genotype rs4925386


title: Colon Tissue, Tumor, 736

tag: 8q23 genotype rs16892766

tag: 8q24 genotype rs6983267

tag: 8q24 genotype rs10505477

tag: 8q24 genotype rs7014346


title: Colon Tissue, Normal, 615


title: Colon Tissue, Normal, 616


title: Colon Tissue, Tumor, 615


title: Colon Tissue, Normal, 687


title: Colon Tissue, Tumor, 552


title: Dataset 4

description:
biological repeat
252232610011_b2: CY5

tag: stage/tissue

tag: genotype/variation

value: wild type AB, Tübingen


title: Colon Tissue, Tumor, 499696

tag: 9q24 genotype rs10975552

tag: 10p14 genotype rs706771


title: Colon Tissue, Tumor, 616

tag: 11q23 genoptype rs3802840

tag: 12q13 genotype rs7136702


title: Colon Tissue, Normal, 499696

tag: disease state

value: Normal

tag: 15q13 genotype rs4779584


title: Colon Tissue, Normal, 552

value: GT

tag: 16q22 genotype rs2059254

tag: 18q21 genotype rs7226855


title: Colon Tissue, Tumor, 475

tag: 1q41 genotype rs11579490

tag: 1q41 genotype rs6691195

value: TT


title: Colon Tissue, Normal, 762

tag: 3q26 genotype rs12638862

value: CT

tag: 20q13 genotype rs4925386


title: Colon Tissue, Tumor, 444667

value: GG

tag: 8q23 genotype rs16892766

tag: 8q24 genotype rs6983267


title: Colon Tissue, Normal, 475

tag: 8q24 genotype rs10505477

tag: 8q24 genotype rs7014346

value: AG


title: Colon Tissue, Tumor, 462

value: AA


title: Colon Tissue, Normal, 462

value: CC


title: Colon Tissue, Normal, 444667


title: Colon Tissue, Tumor, 407593


title: Colon Tissue, Normal, 407593


title: WT_17h_Water-treatment_Treated leaves_Rep2

status: Public on Dec 29 2011

description: wild type source leaves, 6am, 1h after water-treatment

data_processing: Data was acquired with the Agilent Scan Control software (version A.7.0.1 for the B scanner) and extracted using the Agilent Feature Extraction software (version 9.5). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. All controls and replicated probes are averaged. Log transformation was done. 75 percentile normalization was performed (keeping the controls in the list). BASELINE transformation was done. Controls were removed from the list.

source_name: WT_17h_Water-treatment_Treated leaves

growth_protocol: Early elongated stage of WT, Nicotiana attenuata plants were used. Wild type, Nicotiana attenuata seedlings were transferred to 1L pots with sand to facilitate sampling of roots. Plants were watered by flood irrigation system with 200 g CaNO34H2O, 200 g Flory B1 in 400 L water and grown in the glasshouse at 26 - 28oC under 16 h supplemental light from Master Sun-T PIA Agro 400 or Master Sun-T PIA Plus 600 W Na lights (Philips, Turnhout, Belgium)

treatment_protocol: Diluted OS (1:5 dilution with distilled water) from larvae of the specialist herbivore, M. sexta, were applied to puncture wounds in leaves created with a pattern wheel (OS-elicitation) to mimic herbivory at 1 pm. We also treated wounds with water (Water-treatment) to distinguish OS-specific responses from wound-induced responses.

tag: genotype/variation

value: wild type

tag: Stage

value: Early elongated stage

tag: tissue

value: source leaf


title: WT_17h_Water-treatment_Treated leaves_Rep1


title: WT_5h_Water-treatment_Roots_Rep3

description: wild type roots, 6pm, 1h after water-treatment

value: root


title: WT_1h_Water-treatment_Roots_Rep3

description: wild type roots, 2pm, 1h after water-treatment


title: WT_5h_Water-treatment_Systemic leaves_Rep3

description: wild type sink leaves, 6pm, 1h after water-treatment

source_name: WT_5h_Water-treatment_Systemic leaves

value: sink leaf


title: WT_17h_Water-treatment_Systemic leaves_Rep1

description: wild type sink leaves, 6am, 1h after water-treatment

source_name: WT_17h_Water-treatment_Systemic leaves


title: WT_5h_Water-treatment_Roots_Rep2


title: WT_17h_Water-treatment_Roots_Rep3

description: wild type roots, 6am, 1h after water-treatment


title: WT_17h_Water-treatment_Roots_Rep1


title: WT_17h_Water-treatment_Roots_Rep2


title: WT_5h_Water-treatment_Roots_Rep1


title: WT_17h_Water-treatment_Systemic leaves_Rep2


title: WT_17h_Water-treatment_Treated leaves_Rep3


title: WT_5h_Water-treatment_Treated leaves_Rep2

description: wild type source leaves, 6pm, 1h after water-treatment

source_name: WT_5h_Water-treatment_Treated leaves


title: WT_5h_Water-treatment_Treated leaves_Rep3


title: WT_5h_Water-treatment_Treated leaves_Rep1


title: WT_5h_Water-treatment_Systemic leaves_Rep2


title: WT_1h_Water-treatment_Roots_Rep2


title: WT_1h_Water-treatment_Roots_Rep1


title: WT_5h_Water-treatment_Systemic leaves_Rep1


title: WT_1h_Water-treatment_Systemic leaves_Rep1

description: wild type sink leaves, 2pm, 1h after water-treatment

source_name: WT_1h_Water-treatment_Systemic leaves


title: WT_1h_Water-treatment_Systemic leaves_Rep3


title: WT_1h_Water-treatment_Systemic leaves_Rep2


title: WT_21h_OS-elicitation_Roots_Rep3

description: wild type roots, 10am, 1h after OS-elicitation


title: WT_21h_OS-elicitation_Roots_Rep1


title: WT_1h_Water-treatment_Treated leaves_Rep2

description: wild type source leaves, 2pm, 1h after water-treatment

source_name: WT_1h_Water-treatment_Treated leaves


title: WT_1h_Water-treatment_Treated leaves_Rep3


title: WT_13h_OS-elicitation_Systemic leaves_Rep2

description: wild type sink leaves, 2am, 1h after OS-elicitation

source_name: WT_13h_OS-elicitation_Systemic leaves


title: WT_13h_OS-elicitation_Roots_Rep1

description: wild type roots, 2am, 1h after OS-elicitation


title: WT_17h_OS-elicitation_Treated leaves_Rep3

description: wild type source leaves, 6am, 1h after OS-elicitation

source_name: WT_17h_OS-elicitation_Treated leaves


title: WT_13h_OS-elicitation_Roots_Rep3


title: WT_1h_Water-treatment_Treated leaves_Rep1


title: WT_13h_OS-elicitation_Systemic leaves_Rep1


title: WT_17h_OS-elicitation_Treated leaves_Rep2


title: WT_17h_OS-elicitation_Systemic leaves_Rep1

description: wild type sink leaves, 6am, 1h after OS-elicitation

source_name: WT_17h_OS-elicitation_Systemic leaves


title: WT_17h_OS-elicitation_Systemic leaves_Rep3


title: WT_21h_OS-elicitation_Systemic leaves_Rep2

description: wild type sink leaves, 10am, 1h after OS-elicitation

source_name: WT_21h_OS-elicitation_Systemic leaves


title: WT_17h_OS-elicitation_Roots_Rep2

description: wild type roots, 6am, 1h after OS-elicitation


title: WT_17h_OS-elicitation_Treated leaves_Rep1


title: WT_21h_OS-elicitation_Treated leaves_Rep3

description: wild type source leaves, 10am, 1h after OS-elicitation

source_name: WT_21h_OS-elicitation_Treated leaves


title: WT_13h_OS-elicitation_Roots_Rep2


title: WT_21h_OS-elicitation_Roots_Rep2


title: WT_17h_OS-elicitation_Roots_Rep1


title: WT_17h_OS-elicitation_Systemic leaves_Rep2


title: WT_21h_OS-elicitation_Systemic leaves_Rep3


title: WT_13h_OS-elicitation_Treated leaves_Rep2

description: wild type source leaves, 2am, 1h after OS-elicitation

source_name: WT_13h_OS-elicitation_Treated leaves


title: WT_21h_OS-elicitation_Treated leaves_Rep2


title: WT_21h_OS-elicitation_Systemic leaves_Rep1


title: WT_17h_OS-elicitation_Roots_Rep3


title: WT_13h_OS-elicitation_Systemic leaves_Rep3


title: WT_9h_OS-elicitation_Roots_Rep1

description: wild type roots, 10pm, 1h after OS-elicitation


title: WT_9h_OS-elicitation_Treated leaves_Rep3

description: wild type source leaves, 10pm, 1h after OS-elicitation

source_name: WT_9h_OS-elicitation_Treated leaves


title: WT_13h_OS-elicitation_Treated leaves_Rep3


title: WT_21h_OS-elicitation_Treated leaves_Rep1


title: WT_9h_OS-elicitation_Systemic leaves_Rep1

description: wild type sink leaves, 10pm, 1h after OS-elicitation

source_name: WT_9h_OS-elicitation_Systemic leaves


title: WT_9h_OS-elicitation_Treated leaves_Rep2


title: WT_17h_Water-treatment_Systemic leaves_Rep3

description: wild type sink leaves, 6am, 1h after water-treatment


title: WT_13h_OS-elicitation_Treated leaves_Rep1


title: WT_9h_OS-elicitation_Roots_Rep2


title: WT_5h_OS-elicitation_Systemic leaves_Rep3

description: wild type sink leaves, 6pm, 1h after OS-elicitation

source_name: WT_5h_OS-elicitation_Systemic leaves


title: WT_9h_OS-elicitation_Systemic leaves_Rep3


title: WT_9h_OS-elicitation_Roots_Rep3


title: WT_5h_OS-elicitation_Roots_Rep2

description: wild type roots, 6pm, 1h after OS-elicitation


title: WT_9h_OS-elicitation_Treated leaves_Rep1


title: WT_1h_OS-elicitation_Roots_Rep3

description: wild type roots, 2pm, 1h after OS-elicitation


title: WT_5h_OS-elicitation_Treated leaves_Rep3

description: wild type source leaves, 6pm, 1h after OS-elicitation

source_name: WT_5h_OS-elicitation_Treated leaves


title: WT_9h_OS-elicitation_Systemic leaves_Rep2


title: WT_5h_OS-elicitation_Roots_Rep1


title: WT_5h_OS-elicitation_Systemic leaves_Rep1


title: WT_5h_OS-elicitation_Systemic leaves_Rep2


title: WT_5h_OS-elicitation_Roots_Rep3


title: WT_1h_OS-elicitation_Systemic leaves_Rep1

description: wild type sink leaves, 2pm, 1h after OS-elicitation

source_name: WT_1h_OS-elicitation_Systemic leaves


title: WT_1h_OS-elicitation_Roots_Rep2


title: WT_5h_OS-elicitation_Treated leaves_Rep1


title: WT_5h_OS-elicitation_Treated leaves_Rep2


title: WT_1h_OS-elicitation_Roots_Rep1


title: WT_1h_OS-elicitation_Systemic leaves_Rep3


title: WT_1h_OS-elicitation_Treated leaves_Rep3

description: wild type source leaves, 2pm, 1h after OS-elicitation

source_name: WT_1h_OS-elicitation_Treated leaves


title: WT_1h_OS-elicitation_Treated leaves_Rep1


title: WT_21h_Control_Roots_Rep2

description: wild type roots, 10am


title: WT_21h_Control_Systemic leaves_Rep3

description: wild type sink leaves, 10am

source_name: WT_21h_Control_Systemic leaves


title: WT_1h_OS-elicitation_Treated leaves_Rep2


title: WT_21h_Control_Treated leaves_Rep2

description: wild type source leaves, 10am

source_name: WT_21h_Control_Treated leaves


title: WT_21h_Control_Roots_Rep3

description: wild type roots, 10am


title: WT_21h_Control_Treated leaves_Rep3

description: wild type source leaves, 10am


title: WT_1h_OS-elicitation_Systemic leaves_Rep2


title: WT_21h_Control_Treated leaves_Rep1

description: wild type source leaves, 10am


title: WT_21h_Control_Systemic leaves_Rep2

description: wild type sink leaves, 10am


title: WT_17h_Control_Roots_Rep3

description: wild type roots, 6am


title: WT_21h_Control_Roots_Rep1

description: wild type roots, 10am


title: WT_17h_Control_Systemic leaves_Rep2

description: wild type sink leaves, 6am

source_name: WT_17h_Control_Systemic leaves


title: WT_17h_Control_Systemic leaves_Rep1

description: wild type sink leaves, 6am


title: WT_21h_Control_Systemic leaves_Rep1

description: wild type sink leaves, 10am


title: WT_17h_Control_Systemic leaves_Rep3

description: wild type sink leaves, 6am


title: WT_13h_Control_Roots_Rep2

description: wild type roots, 2am


title: WT_13h_Control_Treated leaves_Rep3

description: wild type source leaves, 2am

source_name: WT_13h_Control_Treated leaves


title: WT_17h_Control_Treated leaves_Rep2

description: wild type source leaves, 6am

source_name: WT_17h_Control_Treated leaves


title: WT_13h_Control_Roots_Rep1

description: wild type roots, 2am


title: WT_13h_Control_Systemic leaves_Rep2

description: wild type sink leaves, 2am

source_name: WT_13h_Control_Systemic leaves


title: WT_13h_Control_Treated leaves_Rep1

description: wild type source leaves, 2am


title: WT_13h_Control_Roots_Rep3

description: wild type roots, 2am


title: WT_17h_Control_Treated leaves_Rep3

description: wild type source leaves, 6am


title: WT_13h_Control_Systemic leaves_Rep1

description: wild type sink leaves, 2am


title: WT_13h_Control_Systemic leaves_Rep3

description: wild type sink leaves, 2am


title: WT_13h_Control_Treated leaves_Rep2

description: wild type source leaves, 2am


title: WT_9h_Control_Roots_Rep2

description: wild type roots, 10pm


title: WT_9h_Control_Treated leaves_Rep1

description: wild type source leaves, 10pm

source_name: WT_9h_Control_Treated leaves


title: WT_5h_Control_Roots_Rep1

description: wild type roots, 6pm


title: WT_9h_Control_Roots_Rep3

description: wild type roots, 10pm


title: WT_9h_Control_Roots_Rep1

description: wild type roots, 10pm


title: WT_9h_Control_Treated leaves_Rep3

description: wild type source leaves, 10pm


title: WT_9h_Control_Systemic leaves_Rep1

description: wild type sink leaves, 10pm

source_name: WT_9h_Control_Systemic leaves


title: WT_9h_Control_Systemic leaves_Rep2

description: wild type sink leaves, 10pm


title: WT_9h_Control_Systemic leaves_Rep3

description: wild type sink leaves, 10pm


title: WT_5h_Control_Roots_Rep3

description: wild type roots, 6pm


title: WT_9h_Control_Treated leaves_Rep2

description: wild type source leaves, 10pm


title: WT_17h_Control_Treated leaves_Rep1

description: wild type source leaves, 6am


title: WT_5h_Control_Systemic leaves_Rep2

description: wild type sink leaves, 6pm

source_name: WT_5h_Control_Systemic leaves


title: WT_5h_Control_Treated leaves_Rep3

description: wild type source leaves, 6pm

source_name: WT_5h_Control_Treated leaves


title: WT_5h_Control_Roots_Rep2

description: wild type roots, 6pm


title: WT_5h_Control_Systemic leaves_Rep3

description: wild type sink leaves, 6pm


title: WT_5h_Control_Treated leaves_Rep1

description: wild type source leaves, 6pm


title: WT_5h_Control_Systemic leaves_Rep1

description: wild type sink leaves, 6pm


title: WT_5h_Control_Treated leaves_Rep2

description: wild type source leaves, 6pm


title: WT_1h_Control_Roots_Rep3

description: wild type roots, 2pm


title: WT_1h_Control_Roots_Rep2

description: wild type roots, 2pm


title: WT_1h_Control_Roots_Rep1

description: wild type roots, 2pm


title: WT_17h_Control_Roots_Rep2

description: wild type roots, 6am


title: WT_1h_Control_Systemic leaves_Rep2

description: wild type sink leaves, 2pm

source_name: WT_1h_Control_Systemic leaves


title: WT_1h_Control_Systemic leaves_Rep3

description: wild type sink leaves, 2pm


title: 8 dpi in vitro Bradyzoites a

status: Public on Oct 01 2011

city: Stanford

first: Kerry

middle: R

last: Buchholz

state: California

address: Fairchild Bld, 299 Campus Drive D305

department: Microbiology and Immunology

institute: Stanford University

description: 8 dpi bradyzoites, infected MOI 3 in HFF cells. Grown  in RPMI media, no sodium bicarbonate, 1% FCS, 10 mg/ml HEPES, pH 8.0, 37°C without supplemented CO2

hyb_protocol: Affymetrix GeneChip Hybridization Oven 640, Affymetrix GeneChip Fluidics Station 450

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: Software: Affymetrix Genechip Command Console (AGCC) Data were converted from .cel files and averaged across probes within each probeset using the Bioconductor package affy (version 1.22.1) within the statistical software system R (version 2.10.1), then transformed via a generalized logarithm transformation using the Bioconductor package LMGene (version 2.4.0). Data was transformed via generalized logarithm transformation (glog) and normalized between chips with LOWESS (locally weighted scatterplot smoothing) algorithm using the Bioconductor package LMGene (version 2.4.0, Rocke et al 2010.) A one-way analysis of variance (ANOVA) model was fitted to the data one probeset at a time. For probeset for which the global F test was significant at the 5% level, indicating significant differences between at least two levels of the factor, Tukey HSD post-hoc tests were conducted to test for significant differences among the comparisons of interest.

organism: Toxoplasma gondii

source_name: Toxoplasma bradyzoite

label_protocol: 3’ IVT express kit (Affymetrix ) was used to biotin label 250 ng of total RNA.

extract_protocol: TRIzol (Invitrogen) extraction of total RNA

tag: developmental stage

value: bradyzoite 8 dpi

tag: strain


title: WT_1h_Control_Treated leaves_Rep3

description: wild type source leaves, 2pm

source_name: WT_1h_Control_Treated leaves


title: 4 dpi in vitro Bradyzoites b

description: 4 dpi bradyzoites, infected MOI 3 in HFF cells. Grown  in RPMI media, no sodium bicarbonate, 1% FCS, 10 mg/ml HEPES, pH 8.0, 37°C without supplemented CO2

value: bradyzoite 4 dpi


title: WT_1h_Control_Treated leaves_Rep1

description: wild type source leaves, 2pm


title: WT_1h_Control_Systemic leaves_Rep1

description: wild type sink leaves, 2pm


title: In vivo Bradyzoites b (21 dpi)

description: isolated from mouse brains 21 dpi

source_name: Toxoplasma in vivo bradyzoite

value: bradyzoite 21 dpi


title: ir-lecRK1_1h_Oselicitation_rep3

status: Public on Nov 25 2011

description: Gene expression after 1hr of elicitation with oral secretions from Manduca sexta larvae

source_name: ir-lecRK1 leaves_1hr after oral secretion elicitation

growth_protocol: Seeds from N. attenuata wild type and ir-lecRK1 plants were grown in the glasshouse under high-pressure sodium lamps (200-300 µmol s-1 m-2 light) with a day/night cycle of 16 h(26-28°C)/8 h(22-24°C) and 45 to 55% humidity.

value: leaves


title: 4 dpi in vitro Bradyzoites a


title: WT_1h_Oselicitation_rep3

source_name: wild type leaves_1h after oral secretion elicitation


title: WT_1h_Control_Treated leaves_Rep2

description: wild type source leaves, 2pm


title: 2 dpi in vitro Tachyzoite b

description: 2 dpi tachyzoites grown in HFF, infected at MOI 3 in DMEM supplemented with 10% fetal calf serum 2 mM glutamine 100 U/ml penicillin and 100 µg/ml streptomycin at 37°C with 5% CO2.

source_name: Toxoplasma tachyzoite

value: tachyzoite 2 dpi


title: ir-lecRK1_1h_Oselicitation_rep1


title: WT_1h_Oselicitation_rep1


title: 8 dpi in vitro Bradyzoites b


title: Oocyst d10a (sporulated 10 days)

description: Prior to RNA extraction, oocysts samples in Trizol were passed through a French Pressure cell at 20,000 p.s.i. to crack open oocysts.

source_name: Toxoplasma oocyst

value: oocyst sporulated 10d


title: 2 dpi in vitro Tachyzoite a

description: 2 dpi tachyzoites grown in HFF, infected at MOI3 in DMEM supplemented with 10% fetal calf serum 2 mM glutamine 100 U/ml penicillin and 100 µg/ml streptomycin at 37°C with 5% CO2.


title: Oocyst d0b (unsporulated)

value: oocyst unsporulated 0d


title: Oocyst d4a (sporulated 4 days)

value: oocyst sporulated 4d


title: In vivo Bradyzoites a (21 dpi)

description: isolated from mouse brains 21 dpi


title: Oocyst d4b (sporulated 4 days)


title: 41_4_expTreg + RAPA +CD3/28

status: Public on Aug 16 2011

description: replicate 4

data_processing: The data were normalised using quantile normalisation in R

source_name: expanded CD4+CD25+ Treg cell (isolated from peripheral blood)

growth_protocol: Freshly isolated CD4+CD25low/intCD127+ T cells; CD4+ T cells were cultured for 12 hrs followed by 8 hrs treatment as indicated. CD4+CD25+ Treg cells were expanded in cell culture.

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

treatment_protocol: Immediately after isolation or after described treatment, cells were lysed in Trizol reagent.

tag: cell type

value: CD4+ T cell

tag: cell type subpopulation

value: CD25+ Treg

tag: treatment protocol

value: expanded in cell culture with Rapamycin with short-term CD3CD28 stimulation


title: 40_4_expTreg + CD3/28

description: replicate 4

value: expanded CD4+CD25+ Treg

value: CD3CD28 short-time activation


title: 30_4_CD4+CD25low-int

description: replicate 4

source_name: peripheral blood


title: Oocyst d0a (unsporulated)


title: 39_4_expTreg + RAPA

description: replicate 4

value: expanded in cell culture with Rapamycin


title: 36_4_aCD4+CD25+ Treg

description: replicate 4

source_name: activated CD4+CD25+ Treg (isolated from peripheral blood)

growth_protocol: freshly isolated CD4+ T cells, separated into CD25 negativ and positiv subpopulation

treatment_protocol: immediately after isolation, cells were lysed in Trizol reagent or activated with CD3IL2

value: activated via CD3IL2


title: Oocyst d10b (sporulated 10 days)


title: 22_5_CD4+ 0h

description: replicate 5

growth_protocol: Freshly isolated CD4+ T cells as well as CD4+ T cells further separated into CD25 negativ and positiv subpopulation. Furthermore, CD4+CD25+ Treg cells were expanded in cell culture.

treatment_protocol: Immediately after isolation, cells were lysed in Trizol reagent. Expanded Treg cells were CD3CD28 activated for a short time period and then lysed in Trizol reagent.


title: 33_4_CD4+CD25highCD127low Treg

description: replicate 4

source_name: buffy coats of peripheral blood

growth_protocol: Freshly isolated CD4+ T cells and CD4+ T cells separated into CD25 negativ and positiv subpopulation activated with variuos conditions

treatment_protocol: Immediately after isolation, cells were lysed in Trizol reagent or activated with CD3CD28 and either TGFb1 or PGE2

value: CD4+CD25high-CD127 low

value: freshly isolated


title: 23_4_CD4+CD25- Tconv

description: replicate 4

treatment_protocol: immediately after isolation, cells were lysed in Trizol reagent

value: CD4+CD25- non-Treg


title: 20_6_Tconv 20h

description: replicate 6

treatment_protocol: immediately after described treatment, cells were lysed in Trizol reagent.

value: 20 hrs culture


title: 37_4_aCD4+CD25+ Treg CLL

description: replicate 4

tag: disease state

value: B-cell chronic lymphocytic leukemia (B-CLL)


title: 9_4_aCD4+CD25-

description: replicate 4

growth_protocol: freshly isolated CD4+ T cells, CD4+CD25- as well as CD4+CD25+ Treg cells were treated as indicated.

value: CD4+CD25- Tconv cell

value: 24 hrs culture with CD3 and IL2


title: 32_4_CD4+CD25+ Treg

description: replicate 4

value: CD4+CD25+ Treg


title: 14_4_20h+10ng TGF

description: replicate 4

value: 20 hrs culture with TGFb1


title: 20_5_Tconv 20h

description: replicate 5


title: 20_4_Tconv 20h

description: replicate 4