title: Nasal cells from smoker volunteer 2 treated with kaempferol

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

description: Gene expression data from untreated nasal epithelial cells

hyb_protocol: Following fragmentation, cRNA was hybridized on Affymetrix Human Gene 1.0 ST array

scan_protocol: GeneChips were scanned using Affymetrix scanner

data_processing: Data were analyzed with robust multichip analysis in Partek® Genomics SuiteTM software (version 6.5)

source_name: Primary human nasal epithelial cells treated with 14 uM kaempferol

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

growth_protocol: Human nasal epithelial cells were extracted from healthy smoking volunteers and cultured in bronchial epithelial growth medium

extract_protocol: TRIzol extraction protocol

treatment_protocol: Expanded cells were treated with 14 uM kaempferol for 6 hours

value: Primary human nasal epithelial cells


title: CTRL8879_21_Cy5

status: Public on Apr 01 2016

type: RNA

city: Iowa City

first: Rolf

last: Turk

state: IA

address: 285 Newton Road, 4283CBRB

department: Molecular Physiology and Biophysics

country: USA

institute: University of Iowa

hyb_protocol: Hybmix: 50% Formamide, 5x SSC, 0.5%SDS

scan_protocol: GenePix 4000B

data_processing: Hybridizations were performed in a dye-swap fashion. Microarrays were analyzed by GenePix Pro 6 (Axon). Local background corrected, median spot intensities were normalized using VSN in R. Oligonucleotides were considered expressed when at least 36 out of 48 replicates per array showed intensity higher than the background. Fold-changes were calculated on a linear scale by subtraction of averaged normalized intensities of control samples from FSHD samples, followed by returning e raised to the power of the difference.

molecule: total RNA

organism: Homo sapiens

source_name: Differentiated myoblast from CTRL8879

label_protocol: Small transcripts were isolated and amplified from 1 µg of total RNA using the Global MiRNA Amplification Kit (SBI System Biosciences, RA400A-1). The transcripts contain a T7 promotor sequence which was used for a second round of amplification using the T7 MEGAscript kit according to the manufacturer’s protocol (Ambion, AM1333). Aminoallyl-UTP (Ambion, AM8436) was incorporated during the in vitro transcription. Run-off transcripts were chemically labeled with either Cy3 or Cy5.

growth_protocol: Primary myoblasts were cultured in DMEM (Gibco) supplemented with 2mM L-Glutamine (Gibco), 1% Pen Strep (Gibco) and 20% Fetal Bovine Serum (HyClone). Primary myoblasts were forced into differentiation by switching to differentiation media, which contains DMEM (Gibco), 2mM L-Glutamine (Gibco), 1% Pen Strep (Gibco) and 2% Fetal Bovine Serum (HyClone).

extract_protocol: Total RNA was isolated according to the manufacturer’s protocol (TRIzol, Invitrogen).

treatment_protocol: The samples were not treated.

tag: Differentiated myoblast from CTRL8879


title: glu-24h-1

city: Tsukuba

first: Hiroshi

last: Takatsuji

state: Ibaraki

address: 2-1-2 Kannondai

department: Division of Plant Sciences

country: Japan

institute: National Institute of Agrobiological Sciences

description: SAMPLE 7

hyb_protocol: Agilent protocol G4140-90040

scan_protocol: Slides were scanned immediately after washing on Agilent Scanner model G2505B and software G2565BA using default parameters

data_processing: The scanned images were analyzed with Feature Extraction software (version 9.1; Agilent Technologies)  using default parameters.

organism: Oryza sativa

source_name: glu 24h

label_protocol: The RNAs (400-ng aliquots) were labeled with a Low RNA Input Linear Amplification/Labeling Kit (Agilent Technologies)

extract_protocol: Total RNA was isolated using Trizol and cleaned up with an RNeasy plant mini kit (Qiagen).

treatment_protocol: 10 mM glutamate from roots

tag: cultivar

value: Nipponbare

tag: tissue

value: 4th leaves at 4-leaf stage


title: FSHD8891_22_Cy5

source_name: Differentiated myoblast from FSHD8891

tag: Differentiated myoblast from FSHD8891


title: FSHD8891_21_Cy3


title: CTRL8655_19_Cy5

source_name: Differentiated Myoblast from CTRL8655

tag: Differentiated Myoblast from CTRL8655


title: CTRL8655_20_Cy3

source_name: Differentiated myoblast from CTRL8655

tag: Differentiated myoblast from CTRL8655


title: glu-24h-2

description: SAMPLE 8


title: mock-24h-2

description: SAMPLE 6

source_name: mock 24h


title: glu-9h-2

description: SAMPLE 4

source_name: glu 9h


title: Nasal cells from smoker volunteer 1 treated with kaempferol

city: Chapel Hill

label: Biotin

tag: cell type


title: Sphere-cultured CRC#21 (Cy3/Cy5)

city: Sapporo city

first: TADASHI

last: OGAWA

state: Hokkaido

address: S-1 W-17, Chuo-ku

department: Pathology

institute: Sapporo medical University School of Medicine

description: Cancer stem cells from colorectal cancer cell line (CRC#21) using sphere culture method.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scaned on an Agilent Technologies Scanner G2505C

data_processing: Images were analyzed using  Agilent’s feature extraction software (version 10.7.1.1, protocol GE2_107_Sep09)

source_name: Sphere-cultured cells

label_protocol: 3 µg of total RNA were primed with 2 µl of 100 µM T7 promoter DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: The cells were cultured in two conditions: one was an adherent culture using DMEM with 10% FBS and 1% Penicillin-Streptomycin-Amphotericin B Suspension, and the other was a sphere culture using DMEM/F12 with 20 ng/ml recombinant human FGF basic, 20 ng/ml recombinant human EGF, x100 sodium pyruvate and x100 N2 supplement in an ultra-low attachment plate.

extract_protocol: Total RNA extracted using RNeasy Mini Kit following manufacturer's instructions

tag: cell line

value: colon

source_name: Adherent-cultured cells


title: Untreated nasal cells from smoker volunteer 2

source_name: Untreated primary human nasal epithelial cells

treatment_protocol: Expanded cells were mock-treated with the vehicle control, dimethyl sulfoxide, for 6 hours


title: mock-24h-1

description: SAMPLE 5


title: Untreated nasal cells from smoker volunteer 1


title: NSCL61shRNA No.2

city: Sapporo

first: Toru

last: Kondo

address: Kita-15, Nishi-7, Kita-ku,

department: Institute for Genetic Medicine

institute: Hokkaido University

description: TORAY 3D gene mouse 24K DNA chip

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

organism: Mus musculus

source_name: mouse NSC

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: NSCL61 were made and cultured as previosly described (Hide et al., Stem Cells 2011, 29, 590-599). Eva1shRNA expressing NSCL61 were established by hygromycin selection for 2 weeks .

extract_protocol: Total RNA was prepared using a RNeasy Mini Kit (QIAGEN).

treatment_protocol: After transfection of the expression vectors, the transformants were selected in the presence of hygromycin for 1 week.

tag: strain

value: brain

tag: developmental stage


title: glu-9h-1

description: SAMPLE 3


title: mock-9h-2

description: SAMPLE 2

source_name: mock 9h


title: Aldefluor of CRC#21(Cy3/Cy5)

description: Cancer stem cells, sorted out from colorectal cancer cell line (CRC#21) using ALDEFLUOR assay.

source_name: ALDH-high cells

source_name: ALDH-low cells


title: Aldefluor of CRC#21(Cy5/Cy3)


title: Sphere-cultured CRC#21 (Cy5/Cy3)


title: mock-9h-1

description: SAMPLE 1


title: NSCL61shRNA No.1

description: TORAY 3D gene mouse 24K DNA chip


title: NSCL61 No.1

description: TORAY 3D gene mouse 24K DNA chip


title: HUVECs treated with MAP4K4 siRNA and serum starved overnight, biological rep 3

city: worcester

first: Michael

last: Czech

state: MA

address: 373 plantation st

department: PMM

institute: UMASS Medical Scool

description: Gene expression data from human endothelial cells with siRNA to Map4k4

hyb_protocol: 3.5 ug of cDNA were hybridized overnight at 45C for 16-18hrs to Affymetrix Human Gene 1.0 ST arrays. GeneChips were washed and stained on Affymetrix Fluidics 450 using FS450_0002 protocol.

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

data_processing: Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package affy

label: biotin

label_protocol: Targets were prepared using Ambion WT Expression Kit and Affymetrix GeneChip WT Terminal Labeling and Hybridization Mix according to the manufacturer's instructions

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were obtained from Lonza and cultured in EGM-2 media.

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

treatment_protocol: Cells were transfected with siRNA using RNAi max in EGM-2 overnight and switched to EBM-2 for serum starvation overnight.

tag: genotype/variation

value: Map4k4 KD


title: VCaP_siOct1-Veh

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

institute: Tokyo Metropolitan Institute of Gerontology

description:
Gene expression data from VCaP cells treated with vehicle (ethanol) after trasfected with siOct1
3-VCaP-siOCT1-Et

hyb_protocol: The samples were hybridized to Human Gene 1.0 ST microarrays according to standardized protocols from Affymetrix.

scan_protocol: The samples were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The microarray data were preprocessed with Affymetrix Expression Console software using Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow.

source_name: prostate cancer

label_protocol: Total RNA was labeled employing the Affymetrix GeneChip Whole Transcript (WT) Terminal Labeling kit according to the manufacturer’s instructions

growth_protocol: LNCaP cells were cultured in RPMI 1640 containing 10% FBS.  VCaP cells were cultured in DMEM containing 10% FBS. Before hormone treatment, cells were incubated in Phenol red-free RPMI 1640 or DMEM containing 2.5% charcoal/dextran treated FBS for three days.

extract_protocol: Total RNAs were extracted using ISOGEN (Nippon gene) according to the manufacturer's instructions.

treatment_protocol: Cells were transfected with each siRNA or polyamide 48 h before hormone treatment. Cells were treated with vehicle or DHT (10 nM).

value: AR-positive prostate cancer cell line VCaP

tag: treatment (pre-hormone)

tag: hormone treatment

value: vehicle (ethanol)


title: HUVECs treated with scrambled siRNA and serum starved overnight, biological rep 1

description: Gene expression data from human endothelial cells with siRNA control

value: Human umbilical vein endothelial cells (HUVECs)

value: control


title: VCaP_siControl-DHT

description:
Gene expression data from VCaP cells treated with DHT 10 nM after transfected with siControl
2-VCaP-DHT

value: siControl

value: DHT 10 nM


title: HUVECs treated with scrambled siRNA and serum starved overnight, biological rep 3


title: HUVECs treated with scrambled siRNA and serum starved overnight, biological rep 2


title: LNCaP_PI-1-DHT

description:
Gene expression data from LNCaP cells  treated with DHT 10 nM 48h after polyamide Oct1-1 addition.
PI-1 DHT

value: AR-positive prostate cancer cell line LNCaP

value: PI polyamide Oct1-1


title: VCaP_siOct1-DHT

description:
Gene expression data from VCaP cells  treated with DHT 10 nM after trasfected with siOct1
4-VCaP-siOCT1-DHT


title: HUVECs treated with MAP4K4 siRNA and serum starved overnight, biological rep 1


title: LNCaP_siOct1-DHT

description:
Gene expression data from LNCaP cells  treated with DHT 10 nM after trasfected with siOct1
4-siOCT1-DHT


title: LNCaP_siControl-Veh

description:
Gene expression data from LNCaP cells treated with vehicle (ethanol) after transfected with siControl
1-siCont-Et


title: LNCaP_siControl-DHT

description:
Gene expression data from LNCaP cells treated with DHT 10 nM after transfected with siControl
2-siCont-DHT


title: NSCL61 No.2

description: TORAY 3D gene mouse 24K DNA chip


title: LNCaP_PI-3-DHT

description:
Gene expression data from LNCaP cells  treated with DHT 10 nM 48h after polyamide Oct1-3 addition.
PI-3 DHT

value: PI polyamide Oct1-3


title: VCaP_siControl-Veh

description:
Gene expression data from VCaP cells treated with vehicle (ethanol) after transfected with siControl
1-VCaP-Et


title: LNCaP_siOct1-Veh

description:
Gene expression data from LNCaP cells treated with vehicle (ethanol) after trasfected with siOct1
3-siOCT1-Et


title: HUVECs treated with MAP4K4 siRNA and serum starved overnight, biological rep 2


title: MKN1

type: genomic

city: Yufu-city

first: Yoshiyuki

last: Tsukamoto

state: Oita

address: hasamacho idaigaoka 1-1

department: Molecular Pathology

institute: Oita university, Faculty of Medicine

hyb_protocol: dissolved in hybridization buffer (Agilent Oligo aCGH Hybridization Kit; Agilent Technologies), denatured and hybridized to the CGH array at 65℃ for 40 h

scan_protocol: A microarray was scanned using Microarray acanner (Agilrny Technologies) at a pixel resolution size of 5μm

data_processing: Microarray images were analyzed by using FEATURE EXTRACTION v.9.5.3.1 (Agilent Technologies) with linear normalization (protocol CGH-v4_95_Feb07), and the resulting data were subsequently imported into the DNA Analytics v.4.0.81 software package (Agilent Technologies).Microarray images were analyzed using FEATURE EXTRACTION v.9.5.3.1 (Agilent Technologies) with linear normalization (protocol CGH-v4_95_Feb07), and the resulting data were imported into the DNA Analytics v.4.0.81 software package (Agilent Technologies). Following normalization of the raw data, the log2ratio of Cy3 (tumor) to Cy5 (Control) was calculated. Aberrant regions were determined by the ADM-2 algorithm at a threshold of 12.0 in DNA Analytics. To detect gains and losses, we set the values of parameters for aberration filters as: minimum number of probes in region 2, minimum absolute average log2ratio for region 0.263034, maximum number of aberrant regions 10000, and percentage penetrance per feature 0. We set the value of the minimum absolute average log2ratio at 0.263034 to detect regions showing a change in the averaged copy number equal to or more than 1.2-fold (log2(1.2)=0.263034).

molecule: genomic DNA

source_name: gastric cancer cell line

label_protocol: Agilent Genomic DNA Labeling Kit Plus(Agilent)

growth_protocol: 10%FCS-RPMI (SNU638, NUGC4, SNU484, HSC44, AGS, SH101P4, MKN74, MKN1), 10%FCS-DMEM (IM95, OCUM1, FU97)

extract_protocol: standard proteinase K-digestion method. Two µg of genomic DNA.

tag: copy number increase of chromosome 20q13

value: yes

source_name: peripheral blood cells from eight healthy volunteers

value: peripheral blood cells

value: no


title: MKN74


title: SH101P4


title: HSC44


title: AGS

value: AGS


title: OCUM1


title: FU97


title: LNCaP_PI-1-Veh

description:
Gene expression data from LNCaP cells treated with vehicle (ethanol) 48h after polyamide Oct1-1 addition.
PI-1Et


title: LNCaP_PI-3-Veh

description:
Gene expression data from LNCaP cells treated with vehicle (ethanol) 48h after polyamide Oct1-3 addition.
PI-3 Et


title: LNCaP_Control-DHT

description:
Gene expression data from LNCaP cells treated with DHT 10 nM 48h after vehicle addition.
Cont DHT

value: vehicle control


title: LNCaP_Control-Veh

description:
Gene expression data from LNCaP cells treated with vehicle (ethanol) 48h after vehicle addition.
Cont Et


title: Rev2

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

description: Human umbilical vein endothelial cells (HUVECs), condition reversed replicate 2

hyb_protocol: Total RNA was extracted using the using the PureLink total RNA purification system (Life Tehcnologies). RNA concentration and purity was confirmed with a NanoDrop spectrophotometer for RT-PCR and by Agilent Bioanalyzer (XX). Each replicate was run under the three conditions simultaneously.

data_processing: Data extraction, QC, and RMA normalization were performed with BioConductor software. Probes were annotated using the Bioconductor annotate package. Probesets not mapping to an Entrez ID were removed.  Differential expression was assessed with moderated ANOVA, using the BioConductor limma package; false discovery rate (FDR) estimates were calculated using the Benjamini-Hochberg method.

source_name: RNA from reversed

growth_protocol: Human umbilical vein endothelial cells (HUVECs) purchased from Cell Applications Inc., VEC Technologies Inc. (Rensselaer, NY), and Lonza were unthawed and maintained on 0.1% gelatin coated flasks in M-199 medium (Lonza), supplemented with 10%  fetal bovine serum (Life Technologies, Inc. Grand Island, NY),  100U/mL penicillin-G + 100ug/ml streptomyocin (Life Technologies) , 2mmol/L  L-glutamine (Life Technologies), 5ug/ml endothelial cell growth supplement (Biomedical Technologies, Stoughton, MA), and 10ug/ml heparin (Sigma). For each set of experimental comparisons, cells were used from the same company and cell line, in their third subculture passage.

treatment_protocol: HUVECs were plated on cell culture grade plastic dishes coated with 0.1% gelatin and grown to confluence. A cone and plate flow apparatus (Blackman, García-Cardeña, & Gimbrone, 2002), which maintains cells at 5% CO2 and 37oC, was used to induce a shear stress protocol. The applied shear stress protocol consisted of a 24 hour preconditioning period at a steady 15dyne/cm2  and was then either increased to 30 dynes/cm2 (non-reveresed), increased to 30 dynes/cm2 and reversed in direction (reversed), or held constant at 15 dynes/cm2 (control) (Figure XX).  Fresh culture media consisting of M199 with 4% dextran from Leuconostoc spp (Sigma, Mr ~500,000), 2% fetal bovine serum, 100U/mL penicillin-G + 100ug/ml streptomyocin, 2mmol/L  L-glutamine, 5ug/ml endothelial cell growth supplement, and 10ug/ml heparin was added to cells before exposure to shear stress and was continuously exchanged throughout the duration in the cone and plate apparatus.


title: NUGC4


title: H1299 Negative Control

city: Atlanta

first: Peng

last: Jin

state: GA

address: Whitehead Research Building, 615 Michael Street

department: Department of Human Genetics

institute: Emory University School of Medicine

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

source_name: H1299 Negative Control

label_protocol: standard Affymetrix protocol

extract_protocol: Trizol

tag: treatment

value: negative control


title: Rev4

description: Human umbilical vein endothelial cells (HUVECs), condition reversed replicate 4

scan_protocol: Total RNA was extracted using the using the PureLink total RNA purification system (Life Tehcnologies). RNA concentration and purity was confirmed with a NanoDrop spectrophotometer for RT-PCR and by Agilent Bioanalyzer (XX). Each replicate was run under the three conditions simultaneously.


title: Rev3

description: Human umbilical vein endothelial cells (HUVECs), condition reversed replicate 3

label_protocol: Total RNA was extracted using the using the PureLink total RNA purification system (Life Tehcnologies). RNA concentration and purity was confirmed with a NanoDrop spectrophotometer for RT-PCR and by Agilent Bioanalyzer (XX). Each replicate was run under the three conditions simultaneously.


title: IM95


title: NoRev1

description: Human umbilical vein endothelial cells (HUVECs), condition nonreversed replicate 1

source_name: RNA from nonreversed

extract_protocol: Total RNA was extracted using the using the PureLink total RNA purification system (Life Tehcnologies). RNA concentration and purity was confirmed with a NanoDrop spectrophotometer for RT-PCR and by Agilent Bioanalyzer (XX). Each replicate was run under the three conditions simultaneously.


title: Rev1

description: Human umbilical vein endothelial cells (HUVECs), condition reversed replicate 1


title: H1299 + p53


title: NoRev3

description: Human umbilical vein endothelial cells (HUVECs), condition nonreversed replicate 3


title: C1

description: Human umbilical vein endothelial cells (HUVECs), condition control replicate 1

source_name: RNA from control


title: C2

description: Human umbilical vein endothelial cells (HUVECs), condition control replicate 2


title: NoRev4

description: Human umbilical vein endothelial cells (HUVECs), condition nonreversed replicate 4


title: C4

description: Human umbilical vein endothelial cells (HUVECs), condition control replicate 4


title: NoRev2

description: Human umbilical vein endothelial cells (HUVECs), condition nonreversed replicate 2


title: C3

description: Human umbilical vein endothelial cells (HUVECs), condition control replicate 3


title: SNU638


title: WT/rerj1_Wound_120min_rep2

city: Tokyo

first: Kazunori

last: Okada

address: 1-1-1, Yayoi, Bunkyo-ku

department: Biotechnology Research Center

institute: The University of Tokyo

description: Biological replicate 2 of 2

scan_protocol: Agilent scanner model G2565

data_processing: Data was analyzed by Fearure Extraction software (Agilent)

source_name: WT rice leaves

label_protocol: Low RNA input Linear Amplification/Labeling Kit (Agilent)

growth_protocol: Two week-old rice plants (Oryza sativa L. cv. Nipponbare) were grown under 14 h light 10 h dark conditions at 28°C in a light/temperature regulated growth chamber.

extract_protocol: RNeasy Plant Mini Kit (Qiagen)

treatment_protocol: Plantlets were wound treated by adding pressure on the second leaf blade with a pin holder.

value: wild type

tag: cultiver

value: Nipponnbare

value: wound

tag: time

value: 120 min

source_name: rerj1 mutant leaves wound

value: rerj1 mutant


title: SNU484


title: WT/rerj1_Wound_0min_rep1

description: Biological replicate 1 of 2

value: 0 min


title: WT_Wound_120min_rep2

description: Biological replicate 2 of 2

source_name: Untreated rice leaves

value: Control(untreated)

source_name: Rice leaves wounded 120min


title: WT/rerj1_Wound_120min_rep1

description: Biological replicate 1 of 2


title: WT/rerj1_Wound_0min_rep2

description: Biological replicate 2 of 2


title: WT/rerj1_Wound_60min_rep2

description: Biological replicate 2 of 2

value: 60 min


title: WT/rerj1_Wound_30min_rep1

description: Biological replicate 1 of 2

value: 30 min


title: WT_Wound_240min_rep2

description: Biological replicate 2 of 2

source_name: Rice leaves wounded 240min

value: 240 min


title: WT_Wound_60min_rep2

description: Biological replicate 2 of 2

source_name: Rice leaves wounded 60min


title: Liver Uninfected_Day 3 rep 4_experiment_3

city: London

first: Krzysztof

last: Potempa

address: The Ridgeway

country: United Kingdom

institute: National Institute for Medical Research (NIMR)

description:
replicate 4
8762536103_C

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with GeneSpring GX12.1

source_name: Mouse Liver_Uninfected_Day 3

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

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

tag: genotype

value: wildtype

tag: gender

value: Female

value: Liver

value: Uninfected_Day 3

tag: experiment


title: WT/rerj1_Wound_60min_rep1

description: Biological replicate 1 of 2

tag: cultivar


title: WT_Wound_30min_rep2

description: Biological replicate 2 of 2

source_name: Rice leaves wounded 30min


title: WT_Wound_120min_rep1

description: Biological replicate 1 of 2


title: Liver Uninfected_Day 3 rep 5_experiment_3

description:
replicate 5
8762536148_D

tag: tissue


title: WT/rerj1_Wound_30min_rep2

description: Biological replicate 2 of 2


title: Liver Uninfected_Day 3 KO rep 1_experiment_3

description:
replicate 1
8762536073_B

value: B6 IFNAR-/-

value: IFNAR-/-


title: WT_Wound_30min_rep1

description: Biological replicate 1 of 2


title: Liver Uninfected_Day 3 KO rep 4_experiment_3

description:
replicate 4
8762536148_A


title: WT_Wound_60min_rep1

description: Biological replicate 1 of 2


title: Liver Uninfected_Day 3 rep 1_experiment_3

description:
replicate 1
8762536073_A


title: Liver Uninfected_Day 3 KO rep 3_experiment_3

description:
replicate 3
8762536103_D


title: Liver Uninfected_Day 3 rep 2_experiment_3

description:
replicate 2
8762536073_F


title: Liver Infected_Day 3 rep 4_experiment_3

description:
replicate 4
8762536103_B

source_name: Mouse Liver_Infected_Day 3

value: Infected_Day 3


title: Liver Uninfected_Day 3 rep 3_experiment_3

description:
replicate 3
8762536075_B


title: Liver Uninfected_Day 3 KO rep 5_experiment_3

description:
replicate 5
8762536148_E


title: Liver Infected_Day 3 KO rep 4_experiment_3

description:
replicate 4
8762536103_F


title: Liver Infected_Day 3 KO rep 2_experiment_3

description:
replicate 2
8762536075_E


title: Liver Infected_Day 3 rep 1_experiment_3

description:
replicate 1
8762536073_D


title: Liver Infected_Day 3 KO rep 3_experiment_3

description:
replicate 3
8762536103_A


title: Liver Infected_Day 3 rep 3_experiment_3

description:
replicate 3
8762536075_F


title: Liver Infected_Day 3 KO rep 5_experiment_3

description:
replicate 5
8762536148_F


title: Liver Infected_Day 3 rep 2_experiment_3

description:
replicate 2
8762536075_A


title: Liver Uninfected_Day 3 KO rep 2_experiment_3

description:
replicate 2
8762536075_C


title: Liver Infected_Day 3 rep 5_experiment_3

description:
replicate 5
8762536148_C


title: Spleen Uninfected_Day 3 rep 4_experiment_3

description:
replicate 4
8784170046_C

source_name: Mouse Spleen_Uninfected_Day 3

value: Spleen


title: WT_Wound_240min_rep1

description: Biological replicate 1 of 2

value: Nipponnbare


title: Spleen Uninfected_Day 3 rep 1_experiment_3

description:
replicate 1
8762536098_A


title: Spleen Uninfected_Day 3 rep 3_experiment_3

description:
replicate 3
8762536099_B


title: Spleen Uninfected_Day 3 KO rep 5_experiment_3

description:
replicate 5
8784170081_E


title: Spleen Uninfected_Day 3 rep 2_experiment_3

description:
replicate 2
8762536098_F


title: Spleen Infected_Day 3 rep 3_experiment_3

description:
replicate 3
8762536099_F

source_name: Mouse Spleen_Infected_Day 3


title: Spleen Uninfected_Day 3 KO rep 1_experiment_3

description:
replicate 1
8762536098_B


title: Spleen Uninfected_Day 3 KO rep 2_experiment_3

description:
replicate 2
8762536099_C


title: Spleen Uninfected_Day 3 KO rep 4_experiment_3

description:
replicate 4
8784170081_A


title: Spleen Infected_Day 3 rep 4_experiment_3

description:
replicate 4
8784170046_B


title: Spleen Uninfected_Day 3 KO rep 3_experiment_3

description:
replicate 3
8784170046_D


title: Spleen Infected_Day 3 rep 5_experiment_3

description:
replicate 5
8784170081_C


title: Spleen Infected_Day 3 KO rep 5_experiment_3

description:
replicate 5
8784170081_F


title: Spleen Infected_Day 3 rep 1_experiment_3

description:
replicate 1
8762536098_D


title: Spleen Infected_Day 3 KO rep 4_experiment_3

description:
replicate 4
8784170046_F


title: Spleen Infected_Day 3 KO rep 1_experiment_3

description:
replicate 1
8762536098_C


title: Spleen Infected_Day 3 KO rep 2_experiment_3

description:
replicate 2
8762536099_E


title: Blood Uninfected_Day 3 rep 5_experiment_3

description:
replicate 5
8762536092_A

source_name: Mouse Blood_Uninfected_Day 3

value: Blood


title: Spleen Infected_Day 3 KO rep 3_experiment_3

description:
replicate 3
8784170046_A


title: Blood Uninfected_Day 3 rep 3_experiment_3

description:
replicate 3
8762536041_F


title: Blood Uninfected_Day 3 rep 4_experiment_3

description:
replicate 4
8762536077_E


title: Spleen Infected_Day 3 rep 2_experiment_3

description:
replicate 2
8762536099_A


title: Blood Uninfected_Day 3 rep 2_experiment_3

description:
replicate 2
8762536048_C


title: Blood Uninfected_Day 3 KO rep 4_experiment_3

description:
replicate 4
8762536077_C


title: Blood Uninfected_Day 3 KO rep 3_experiment_3

description:
replicate 3
8762536041_E


title: GCT94NG

city: Chuo-ku

first: Shintaro

last: Fukushima

address: 5-1-1 Tsukiji

institute: National Cancer Center Research Institute

description:
Germ cell tumor tissues obtained by surgical procedure
Control sample of non-germinoma component

hyb_protocol: Hybridization was preformed using Illumina Infinium HumanMethylation450 Beadchip according to the standard Illumina protocol.

scan_protocol: Array was scanned with an iScan System (Illumina).

data_processing: Data were analyzed using GenomeStudio Methylation Module Software (Illumina).

label: Cy5 and Cy3

source_name: Yolk sac tumor

label_protocol: Labeling was performed according to the standard Illumina protocol.

extract_protocol:
Genomic DNA was extracted using a DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.
bisulfite conversion protocol: Bisulfite modification was performed using EZ DNA Methylation Kit (Zymo Research Corporation, Irvine, CA) according to the manufacturer’s protocol.

value: Yolk sac tumor

value: Male

tag: location

value: Central nervous system

tag: disease state

value: Tumor

tag: sample type

value: FFPE


title: Blood Uninfected_Day 3 KO rep 5_experiment_3

description:
replicate 5
8762536092_F

tag: strain


title: Blood Uninfected_Day 3 KO rep 2_experiment_3

description:
replicate 2
8762536048_A


title: Blood Uninfected_Day 3 rep 1_experiment_3

description:
replicate 1
8762536028_E


title: Blood Uninfected_Day 3 KO rep 1_experiment_3

description:
replicate 1
8762536028_B


title: GCT86G

description:
Germ cell tumor tissues obtained by surgical procedure
Germinoma component in mixed-GCT after microdissection

source_name: Germinoma component

value: Germinoma component


title: Blood Infected_Day 3 rep 5_experiment_3

description:
replicate 5
8762536092_C

source_name: Mouse Blood_Infected_Day 3


title: GCT86NG

description:
Germ cell tumor tissues obtained by surgical procedure
Non-germinoma component (mature teratoma, yolk sac tumor, embryonal carcinoma) in mixed-GCT after microdissection

source_name: Non-germinoma component

value: Non-germinoma component


title: Blood Infected_Day 3 rep 3_experiment_3

description:
replicate 3
8762536048_F

value: wildtype


title: Spleen Uninfected_Day 3 rep 5_experiment_3

description:
replicate 5
8784170081_D

value: Female


title: GCT58G


title: Liver Infected_Day 3 KO rep 1_experiment_3

description:
replicate 1
8762536073_C

value: Liver


title: GCT51NG

description:
Germ cell tumor tissues obtained by surgical procedure
Non-germinoma component (immature teratoma, yolk sac tumor) in mixed-GCT after microdissection


title: GCT51G


title: GCT58NG

description:
Germ cell tumor tissues obtained by surgical procedure
Non-germinoma component (mature teratoma) in mixed-GCT after microdissection


title: GCT43NG

description:
Germ cell tumor tissues obtained by surgical procedure
Non-germinoma component (immature teratoma, choriocarcinoma, embryonal carcinoma) in mixed-GCT after microdissection


title: GCT49G

description:
Germ cell tumor tissues obtained by surgical procedure
Control sample of germinoma component

source_name: Germinoma

value: Germinoma


title: Blood Infected_Day 3 rep 1_experiment_3

description:
replicate 1
8762536028_A


title: Blood Infected_Day 3 KO rep 4_experiment_3

description:
replicate 4
8762536077_D

value: B6 IFNAR-/-


title: GCT84G


title: Blood Infected_Day 3 KO rep 5_experiment_3

description:
replicate 5
8762536092_E

value: IFNAR-/-


title: Pineal gland

description: Normal sample obtained from autopsied body

source_name: Pineal gland

value: Pineal gland

value: Normal

value: Fresh frozen


title: Blood Infected_Day 3 KO rep 3_experiment_3

description:
replicate 3
8762536041_D

value: Blood

value: Infected_Day 3


title: Neural stem cell

description: Normal sample obtained from cultured cell

source_name: Neural stem cell

value: Neural stem cell

value: Cultured cell


title: Liver Infected_Day 3 rep 4_experiment_2

description:
replicate 4
9482913090_F


title: Blood Infected_Day 3 KO rep 2_experiment_3

description:
replicate 2
8762536048_B


title: Blood Infected_Day 3 rep 2_experiment_3

description:
replicate 2
8762536048_D


title: Testis

source_name: Testis

value: Testis

value: Male

value: Gonad


title: Ovary

source_name: Ovary

value: Ovary


title: tGCT13

description: Germ cell tumor tissues obtained by surgical procedure

source_name: Seminoma

value: Seminoma

value: Tumor


title: Blood Infected_Day 3 KO rep 1_experiment_3

description:
replicate 1
8762536028_F

value: Female


title: GCT43G

value: Germinoma component

value: Central nervous system

value: FFPE


title: Liver Infected_Day 3 rep 3_experiment_2

description:
replicate 3
9481416080_D

value: wildtype

value: Liver


title: Liver Infected_Day 3 rep 2_experiment_2

description:
replicate 2
9371989056_B


title: tGCT7

value: Fresh frozen


title: Cerebral cortex

source_name: Cerebral cortex

value: Cerebral cortex

value: Normal


title: GCT96

value: Germinoma


title: tGCT2


title: Liver Infected_Day 3 rep 1_experiment_2

description:
replicate 1
9371989032_B

value: Infected_Day 3


title: Liver Infected_Day 3 KO rep 2_experiment_2

description:
replicate 2
9371989056_A

value: B6 IFNAR-/-

value: IFNAR-/-


title: Liver Infected_Day 3 KO rep 4_experiment_2

description:
replicate 4
9482913087_F


title: Liver Infected_Day 3 KO rep 3_experiment_2

description:
replicate 3
9371989039_F


title: Blood Infected_Day 3 rep 4_experiment_3

description:
replicate 4
8762536041_A

value: Blood


title: GCT94

value: Yolk sac tumor

value: Male


title: GCT100

value: Tumor


title: GCT95


title: Liver Infected_Day 3 KO rep 1_experiment_2

description:
replicate 1
9371989066_C

value: Female


title: GCT113

source_name: Embryonal carcinoma, Germinoma

value: Embryonal carcinoma, Germinoma


title: Liver Infected_Day 2 rep 4_experiment_2

description:
replicate 4
9482913090_C

source_name: Mouse Liver_Infected_Day 2

value: Infected_Day 2


title: Liver Infected_Day 2 rep 3_experiment_2

description:
replicate 3
9481416080_B


title: Liver Infected_Day 2 KO rep 4_experiment_2

description:
replicate 4
9482913087_C


title: Liver Infected_Day 2 rep 2_experiment_2

description:
replicate 2
9371989056_F


title: GCT85

value: Central nervous system


title: Liver Infected_Day 2 rep 1_experiment_2

description:
replicate 1
9371989032_A

value: wildtype


title: Liver Infected_Day 2 KO rep 3_experiment_2

description:
replicate 3
9482913090_D

value: Liver


title: GCT86

source_name: Mature teratoma, Germinoma, Yolk sac tumor, Embryonal carcinoma

value: Fresh frozen


title: Liver Infected_Day 2 KO rep 1_experiment_2

description:
replicate 1
9371989066_A


title: Liver Infected_Day 2 KO rep 2_experiment_2

description:
replicate 2
9371989056_C


title: GCT73

source_name: Choriocarcinoma, Germinoma, Immature teratoma


title: GCT84


title: Liver UnInfected_Day 1 rep 4_experiment_2

description:
replicate 4
9482913090_E

source_name: Mouse Liver_UnInfected_Day 1

value: UnInfected_Day 1


title: Liver UnInfected_Day 1 rep 2_experiment_2

description:
replicate 2
9371989056_D


title: GCT77

source_name: Germinoma, Yolk sac tumor

value: Germinoma, Yolk sac tumor


title: GCT65

source_name: Yolk sac tumor


title: Liver UnInfected_Day 1 rep 1_experiment_2

description:
replicate 1
9371989032_E


title: Liver UnInfected_Day 1 rep 3_experiment_2

description:
replicate 3
9371989039_A


title: Liver UnInfected_Day 1 KO rep 4_experiment_2

description:
replicate 4
9482913087_A


title: GCT67

source_name: Mature teratoma, Germinoma

value: Mature teratoma, Germinoma


title: GCT69

source_name: Immature teratoma, Germinoma

value: Immature teratoma, Germinoma


title: Liver UnInfected_Day 1 KO rep 3_experiment_2

description:
replicate 3
9481416080_C

value: B6 IFNAR-/-


title: GCT62

source_name: Mature teratoma

value: Mature teratoma


title: GCT83

source_name: Germinoma

value: Germinoma


title: GCT70

source_name: Mature teratoma, Germinoma, hemangioma

value: Mature teratoma, Germinoma, hemangioma


title: GCT63

value: Male


title: GCT60

source_name: Germinoma, Embryonal carcinoma

value: Germinoma, Embryonal carcinoma

value: Tumor


title: GCT81

source_name: Choriocarcinoma

value: Choriocarcinoma

value: Female


title: Liver UnInfected_Day 1 KO rep 2_experiment_2

description:
replicate 2
9371989066_D

value: IFNAR-/-


title: GCT66

source_name: Immature teratoma

value: Immature teratoma

value: Central nervous system


title: GCT61

value: Fresh frozen


title: Liver Infected_Day 1 rep 4_experiment_2

description:
replicate 4
9482913087_B

source_name: Mouse Liver_Infected_Day 1

value: wildtype

value: Liver

value: Infected_Day 1


title: Liver UnInfected_Day 1 KO rep 1_experiment_2

description:
replicate 1
9371989032_C

value: UnInfected_Day 1


title: Liver Infected_Day 1 rep 2_experiment_2

description:
replicate 2
9371989066_F


title: GCT58

value: Mature teratoma, Germinoma


title: Liver Infected_Day 1 rep 3_experiment_2

description:
replicate 3
9371989039_B


title: Liver Infected_Day 1 KO rep 4_experiment_2

description:
replicate 4
9482913087_D

value: B6 IFNAR-/-


title: GCT56

value: Germinoma


title: GCT59

value: Immature teratoma, Germinoma


title: Liver Infected_Day 1 rep 1_experiment_2

description:
replicate 1
9371989032_F


title: GCT57

source_name: Mature teratoma, Yolk sac tumor, Embryonal carcinoma, Germinoma

value: Male


title: GCT52

value: Mature teratoma


title: Liver Infected_Day 1 KO rep 3_experiment_2

description:
replicate 3
9481416080_A


title: GCT44

value: Tumor


title: Liver Infected_Day 1 KO rep 1_experiment_2

description:
replicate 1
9371989066_E


title: Liver Infected_Day 1 KO rep 2_experiment_2

description:
replicate 2
9371989056_E


title: GCT51

source_name: Immature teratoma, Germinoma, polyembryoma, Yolk sac tumor


title: Spleen Infected_Day 3 rep 2_experiment_2

description:
replicate 2
9423642056_B

source_name: Mouse Spleen_Infected_Day 3

value: Spleen

value: Infected_Day 3


title: Spleen Infected_Day 3 rep 3_experiment_2

description:
replicate 3
9423642056_F

value: Female


title: Spleen Infected_Day 3 rep 4_experiment_2

description:
replicate 4
9402708002_A


title: GCT49


title: GCT43

source_name: Germinoma, Immature teratoma, Choriocarcinoma, Embryonal carcinoma


title: GCT42

source_name: Embryonal carcinoma

value: Embryonal carcinoma


title: GCT37

value: Central nervous system


title: GCT40

value: Yolk sac tumor

value: Fresh frozen


title: GCT39


title: GCT41

source_name: Yolk sac tumor, Germinoma

value: Yolk sac tumor, Germinoma


title: GCT34


title: Spleen Infected_Day 2 rep 1_experiment_2

description:
replicate 1
9423642099_D

source_name: Mouse Spleen_Infected_Day 2

value: wildtype

value: Infected_Day 2


title: GCT38


title: Spleen Infected_Day 3 KO rep 1_experiment_2

description:
replicate 1
9423642104_D

value: IFNAR-/-


title: GCT35


title: Spleen Infected_Day 3 KO rep 3_experiment_2

description:
replicate 3
9423642075_A

value: B6 IFNAR-/-


title: Spleen Infected_Day 2 rep 2_experiment_2

description:
replicate 2
9423642056_D


title: Spleen Infected_Day 3 KO rep 4_experiment_2

description:
replicate 4
9423642056_C


title: Spleen Infected_Day 2 rep 4_experiment_2

description:
replicate 4
9402708002_F


title: GCT31


title: Spleen Infected_Day 3 KO rep 2_experiment_2

description:
replicate 2
9423642060_A


title: GCT36

value: Immature teratoma


title: Spleen Infected_Day 3 rep 1_experiment_2

description:
replicate 1
9423642060_E


title: GCT33


title: GCT32


title: Spleen Infected_Day 2 KO rep 3_experiment_2

description:
replicate 3
9402708011_F


title: Spleen Infected_Day 2 KO rep 2_experiment_2

description:
replicate 2
9423642075_B


title: Spleen Infected_Day 2 KO rep 4_experiment_2

description:
replicate 4
9402708002_E


title: Spleen UnInfected_Day 1 rep 4_experiment_2

description:
replicate 4
9402708002_D

source_name: Mouse Spleen_UnInfected_Day 1

value: UnInfected_Day 1


title: Spleen UnInfected_Day 1 rep 2_experiment_2

description:
replicate 2
9402708011_C


title: GCT25

value: Germinoma


title: Spleen Infected_Day 2 KO rep 1_experiment_2

description:
replicate 1
9423642104_A


title: Spleen UnInfected_Day 1 rep 3_experiment_2

description:
replicate 3
9402708011_E


title: Spleen UnInfected_Day 1 KO rep 2_experiment_2

description:
replicate 2
9423642099_F


title: GCT24

value: Male


title: Spleen UnInfected_Day 1 KO rep 3_experiment_2

description:
replicate 3
9423642075_F


title: Spleen UnInfected_Day 1 rep 1_experiment_2

description:
replicate 1
9423642060_F


title: GCT20

value: Tumor


title: Spleen Infected_Day 2 rep 3_experiment_2

description:
replicate 3
9402708011_B

value: Spleen


title: GCT19


title: Spleen UnInfected_Day 1 KO rep 4_experiment_2

description:
replicate 4
9402708002_C


title: GCT28


title: GCT29


title: GCT16


title: GCT23

value: Mature teratoma


title: Spleen UnInfected_Day 1 KO rep 1_experiment_2

description:
replicate 1
9423642104_E

value: Female


title: GCT26


title: GCT8


title: Spleen Infected_Day 1 KO rep 4_experiment_2

description:
replicate 4
9402708002_B

source_name: Mouse Spleen_Infected_Day 1

value: Infected_Day 1


title: Spleen Infected_Day 1 KO rep 2_experiment_2

description:
replicate 2
9423642075_E


title: GCT14

value: Central nervous system


title: GCT1

source_name: Yolk sac tumor

value: Yolk sac tumor


title: Spleen Infected_Day 1 KO rep 3_experiment_2

description:
replicate 3
9402708011_D


title: GCT18

source_name: Mature teratoma, Germinoma

value: Mature teratoma, Germinoma

value: Fresh frozen


title: Spleen Infected_Day 1 rep 4_experiment_2

description:
replicate 4
9423642099_E

value: wildtype


title: GCT9

source_name: Immature teratoma, Germinoma

value: Immature teratoma, Germinoma


title: GCT6


title: Spleen Infected_Day 1 rep 3_experiment_2

description:
replicate 3
9423642060_C


title: Spleen Infected_Day 1 rep 2_experiment_2

description:
replicate 2
9423642060_B


title: GCT4

source_name: Yolk sac tumor, Embryonal carcinoma, Immature teratoma, Germinoma


title: KO20_1

city: Copenhagen

first: Jesper

middle: B

last: Andersen

address: Ole Maaloes Vej 5

department: Biotech Research and Innovation Centre

country: Denmark

institute: Copenhagen University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iSCAN using standard recommended Illumina scanner setting

data_processing: Data was preprocessed by means of Genome Studio v2011 from illumina, Inc.

label: Cy3 and Cy5

source_name: isolated hepatocytes

label_protocol: Standard Illumina Protocol (humanmethylation450v1_15017482

extract_protocol: Qiagen mini kit for genomic DNA

value: DNMT1 knockout

tag: week


title: Blood Infected_Day 3 rep 4_experiment_2

description:
replicate 4
3999936012_A

source_name: Mouse Blood_Infected_Day 3

value: Blood

value: Infected_Day 3


title: KO20_3

tag: genotype/variation


title: Spleen Infected_Day 1 KO rep 1_experiment_2

description:
replicate 1
9423642099_B

value: B6 IFNAR-/-

value: IFNAR-/-


title: Spleen Infected_Day 1 rep 1_experiment_2

description:
replicate 1
9423642104_B


title: FL20_3

value: control


title: Blood Infected_Day 3 rep 2_experiment_2

description:
replicate 2
3999936008_B


title: Blood Infected_Day 3 rep 1_experiment_2

description:
replicate 1
10012449025_E


title: Blood Infected_Day 3 rep 3_experiment_2

description:
replicate 3
3999936008_F


title: KO20_2


title: Blood Infected_Day 3 KO rep 3_experiment_2

description:
replicate 3
3999936008_C


title: Blood Infected_Day 3 KO rep 1_experiment_2

description:
replicate 1
10012449025_A


title: FL20_1


title: Blood Infected_Day 2 KO rep 3_experiment_2

description:
replicate 3
3999936012_E

source_name: Mouse Blood_Infected_Day 2

value: Infected_Day 2


title: root_light_rep1

city: Pozuelo de Alracon

first: Juan

middle: Carlos

last: del Pozo

state: Madrid

address: Campus de Montegancedo, UPM

department: Biotechnology

country: Spain

institute: Centro de Biotecnología y Genómica de Plantas

description:
SAMPLE 4
This sample is of roots grown in presence of light. It is the first of three  biological replicates used in this experiment, each from independent in vitro cultured plates.

hyb_protocol: Each microarray was hybridized with the NimbleGen hybridization kit, washed using the NimbleGen wash buffer kit (both from Roche)

scan_protocol: Microarrays were scanned at 2-μm double-pass at 16-bit resolution

data_processing:
Data were analyzed through robust multiarray analysis with NimbleGen Scan software v.2.60 (Roche).
Differential expression analysis was performed with the Bayes t-statistics from the linear models for Microarray data (Limma). P values were corrected for multiple testing using the Benjamini-Hochberg method (false discovery rate) (Reiner et al., 2003).

organism: Arabidopsis thaliana

source_name: Light grown roots

label_protocol: cDNA was generated with 10 μg RNA using the double-stranded cDNA synthesis kit (Invitrogen), and cDNA was Cy3-labeled with the NimbleGen one-color DNA labeling kit (Roche).

growth_protocol: Arabidopsis seedlings were grown in half strench MS medium for 12 days.

extract_protocol: Total RNA was isolated from roots using the Trizol (Lifetechnologies) following the company procedure. This isolated RNA was then purified using the Quiagen RNA isolation kit.

treatment_protocol: Control: seedlings were grown with the shoot and root in presence of white light (75 umoles/m2 seg). Treatment: seedlings were grown with the shoot in presence of white light (75 umoles/m2 seg) but the roots in darksness.

tag: growth condition

value: roots


title: KO8_3


title: root_dark_rep3

description:
SAMPLE 3
This sample is of roots grown in darkness. It is the third of three  biological replicates used in this experiment, each from independent in vitro cultured plates.

source_name: Drak grown roots

value: in darksness


title: root_dark_rep2

description:
SAMPLE 2
This sample is of roots grown in darkness. It is the second of three  biological replicates used in this experiment, each from independent in vitro cultured plates.


title: Blood Infected_Day 3 KO rep 2_experiment_2

description:
replicate 2
3999926058_A

value: Female


title: root_light_rep2

description:
SAMPLE 5
This sample is of roots grown in presence of light. It is the second of three  biological replicates used in this experiment, each from independent in vitro cultured plates.

value: in presence of white light (75 umoles/m2 seg)


title: Blood Infected_Day 2 rep 3_experiment_2

description:
replicate 3
3999936012_F


title: KO8_2


title: root_light_rep3

description:
SAMPLE 6
This sample is of roots grown in presence of light. It is the third of three  biological replicates used in this experiment, each from independent in vitro cultured plates.


title: Blood Infected_Day 2 rep 1_experiment_2

description:
replicate 1
3999936008_D


title: FL8_2


title: KO8_1


title: Blood Infected_Day 1 rep 1_experiment_2

description:
replicate 1
10012449025_B

source_name: Mouse Blood_Infected_Day 1

value: Infected_Day 1


title: Blood Infected_Day 2 KO rep 2_experiment_2

description:
replicate 2
3999889009_F


title: KO4_3


title: FL8_3


title: Blood Infected_Day 1 rep 3_experiment_2

description:
replicate 3
10012449024_E


title: Blood Infected_Day 2 rep 2_experiment_2

description:
replicate 2
3999889009_B


title: Blood Infected_Day 1 rep 4_experiment_2

description:
replicate 4
10012449024_D


title: Blood Infected_Day 1 rep 2_experiment_2

description:
replicate 2
10012449025_C


title: Blood Infected_Day 1 KO rep 4_experiment_2

description:
replicate 4
3999936012_B


title: Blood Uninfected_Day 3 rep 4_experiment_2

description:
replicate 4
3999936012_D

source_name: Mouse Blood_Uninfected_Day 1

value: Uninfected_Day 1


title: Blood Infected_Day 1 KO rep 2_experiment_2

description:
replicate 2
3999926058_E


title: FL8_1


title: KO4_2


title: FL4_2


title: FL4_1


title: Blood Uninfected_Day 3 rep 3_experiment_2

description:
replicate 3
3999889009_E


title: KO4_1


title: Blood Infected_Day 1 KO rep 3_experiment_2

description:
replicate 3
3999889009_D


title: Blood Uninfected_Day 3 rep 1_experiment_2

description:
replicate 1
10012449025_F


title: FL20_2


title: Blood Uninfected_Day 3 KO rep 3_experiment_2

description:
replicate 3
3999936012_C


title: Blood Uninfected_Day 3 KO rep 1_experiment_2

description:
replicate 1
10012449024_F


title: FL4_3


title: Spleen Uninfected_Day 3 rep 2_experiment_1

description:
replicate 2
8615616060_D

source_name: Mouse Spleen_Uninfected_Day 3

value: Spleen

value: Uninfected_Day 3


title: Spleen Uninfected_Day 3 rep 6_experiment_1

description:
replicate 6
8650489050_A

value: wildtype


title: Blood Infected_Day 2 KO rep 1_experiment_2

description:
replicate 1
3999926058_B


title: Spleen Uninfected_Day 3 rep 9_experiment_1

description:
replicate 9
8697771074_B


title: Spleen Uninfected_Day 3 rep 1_experiment_1

description:
replicate 1
8615616051_F


title: Spleen Uninfected_Day 3 rep 3_experiment_1

description:
replicate 3
8615616062_E


title: Spleen Uninfected_Day 3 rep 4_experiment_1

description:
replicate 4
8650489043_C


title: Spleen Uninfected_Day 3 rep 5_experiment_1

description:
replicate 5
8650489045_D


title: root_dark_rep1

description:
SAMPLE 1
This sample is of roots grown in darkness. It is the first of three  biological replicates used in this experiment, each from independent in vitro cultured plates.


title: Blood Uninfected_Day 3 rep 2_experiment_2

description:
replicate 2
3999889009_C


title: Spleen Uninfected_Day 3 rep 7_experiment_1

description:
replicate 7
8650489076_E


title: Spleen Uninfected_Day 3 rep 8_experiment_1

description:
replicate 8
8650489084_C


title: Blood Uninfected_Day 3 KO rep 2_experiment_2

description:
replicate 2
3999926058_F


title: Spleen Infected_Day 3 rep 8_experiment_1

description:
replicate 8
8650489057_C

source_name: Mouse Spleen_Infected_Day 3


title: Spleen Infected_Day 3 rep 9_experiment_1

description:
replicate 9
8650489076_B


title: Spleen Infected_Day 3 rep 6_experiment_1

description:
replicate 6
8650489045_E


title: Spleen Infected_Day 3 rep 2_experiment_1

description:
replicate 2
8615616060_A


title: Spleen Infected_Day 3 rep 7_experiment_1

description:
replicate 7
8650489050_F


title: Spleen Infected_Day 3 rep 10_experiment_1

description:
replicate 10
8650489084_D


title: Blood Uninfected_Day 3 rep 9_experiment_1

description:
replicate 9
8697771054_F

source_name: Mouse Blood_Uninfected_Day 3


title: Blood Uninfected_Day 3 rep 7_experiment_1

description:
replicate 7
8650489059_E


title: Blood Uninfected_Day 3 rep 5_experiment_1

description:
replicate 5
8650489023_B


title: Spleen Infected_Day 3 rep 5_experiment_1

description:
replicate 5
8650489043_E


title: WT IRI Kidneys-rep2

city: Sendai

first: Masahiro

last: Nezu

state: Miyagi

address: 2-1 Seiryo-cho, Aoba-ku

department: Medical Biochemistry

institute: Tohoku University School of Medicine

description: Gene expression of WT IRI kidneys

hyb_protocol: 1.65 ug of Cy3-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 17 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model US82800151.

data_processing: The data were analyzed and normalized with GeneSpring software. After normalization, the data was baseline transformed to the median of all samples.

source_name: WT IRI mouse kidney

label_protocol: 300 ng of total RNA was amplified and labeled using the Low Input Quick Amp Labeling kit (Agilent Technologies) according to the manufacturer's protocol.

extract_protocol: For IRI kidneys, kidneys were harvested at 1 day after unilateral IRI. (right kidney was not clamped). For normal kidneys,left kidneys were just harvested.

treatment_protocol: For IRI kidneys, left renal vein and artery was clamped for 45 minutes and then released.  (right kidney was not clamped). For normal kidneys, left kidneys did not undergo IRI.

value: Kidney

value: male

tag: age

value: 16 weeks

value: Wild type


title: Spleen Infected_Day 3 rep 4_experiment_1

description:
replicate 4
8650489009_A

value: Infected_Day 3


title: Control vs. Failing heart

city: Kamakura

first: Satoshi

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

organism: Rattus norvegicus

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

extract_protocol: Total RNA was extracted from left ventricular samples at the stage of heart failure using mirVana (Applied Biosystems) according to the manufacturer’s instructions

value: Dahl

value: Left ventricle

tag: diet

value: high salt

value: normal salt


title: Blood Uninfected_Day 3 rep 3_experiment_1

description:
replicate 3
8615616065_A

value: Blood

tag: treatment


title: Blood Uninfected_Day 3 rep 4_experiment_1

description:
replicate 4
8615616066_C

value: Female


title: Keap1 KD IRI Kidneys-rep2

description: Gene expression of KKD IRI kidneys

source_name: Keap1 KD mouse IRI kidney

value: Keap1 knockdown


title: Blood Infected_Day 1 KO rep 1_experiment_2

description:
replicate 1
10012449024_B

value: B6 IFNAR-/-

value: IFNAR-/-

value: Infected_Day 1


title: Blood Uninfected_Day 3 rep 10_experiment_1

description:
replicate 10
8784129100_B

value: Uninfected_Day 3


title: Blood Uninfected_Day 3 rep 1_experiment_1

description:
replicate 1
8615616046_F

value: wildtype


title: Spleen Infected_Day 3 rep 11_experiment_1

description:
replicate 11
8697771074_C

value: Spleen


title: Spleen Infected_Day 3 rep 1_experiment_1

description:
replicate 1
8615616051_B


title: Chaetocin treatment vs. Failing heart

source_name: Failing heart_left_ventricle_high salt_diet_with chaetocin treatment


title: Blood Uninfected_Day 3 rep 8_experiment_1

description:
replicate 8
8650489074_B


title: Keap1 KD IRI Kidneys-rep1

description: Gene expression of KKD IRI kidneys

value: Kidney

value: male


title: Blood Infected_Day 3 rep 10_experiment_1

description:
replicate 10
8615616024_F


title: Keap1 KD Normal Kidneys-rep1

description: Gene expression of KKD Normal kidneys

source_name: Keap1 KD mouse Normal kidney

value: 16 weeks


title: Blood Uninfected_Day 3 rep 2_experiment_1

description:
replicate 2
8615616049_C


title: Blood Infected_Day 3 rep 9_experiment_1

description:
replicate 9
7964419099_A

value: Infected_Day 3


title: Blood Uninfected_Day 3 rep 6_experiment_1

description:
replicate 6
8650489048_D


title: Spleen Infected_Day 3 rep 3_experiment_1

description:
replicate 3
8615616062_D


title: Keap1 KD Normal Kidneys-rep2

description: Gene expression of KKD Normal kidneys


title: WT Normal Kidneys-rep2

description: Gene expression of WT Normal kidneys

source_name: WT Normal mouse kidney

value: Wild type


title: Blood Infected_Day 3 rep 7_experiment_1

description:
replicate 7
8697771054_D


title: Blood Infected_Day 3 rep 8_experiment_1

description:
replicate 8
8784129100_A


title: Cd117-Cd27+Cd11b+NK_rep1

city: Regensburg

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

country: Germany

institute: University Hospital Regensburg

description: SAMPLE 6

hyb_protocol: Labeling efficiency was controlled using the NanoDrop spectrophotometer and labeled cRNA were fragmented and hybridized on whole mouse genome expression arrays (4 × 44 K Agilent). Microarrays were washed and subsequently scanned with an Agilent scanner.

data_processing: Raw data were extracted with Feature Extraction 9.5.1 software and analyzed using GeneSpring GX 11 (Agilent).

label_protocol: High-quality RNA were amplified and Cyanine 3-CTP-labelled with the one colour low RNA input linear amplification kit (Agilent).

growth_protocol: Prior to MoFlo sorting, single cell suspensions were stained with the following antibodies: FITC-conjugated anti-CD11b (M1/70) (Miltenyi, Bergisch Gladbach, Germany), PerCP-conjugated anti-CD3ε (145-2C11) and  PerCP-conjugated anti-CD19 (1D3) were purchased from BioLegend (San Diego, CA, USA), APC-conjugated anti-CD117 (c-kit) (2B8), PE-conjugated anti-CD27 (LG.3A11), PE-Cy7-conjugated anti-NK1.1 (PK136) and BD Horizon V450 conjugated anti-CD45.1 (A20) were purchased from BD Biosciences (Heidelberg, Germany). NK cell purity, functional properties and subset distribution was analyzed by FACS Canto II (BD Biosciences, Heidelberg, Germany) and use of the FlowJo Software (Treestar, Ashland, Oregon, USA).

extract_protocol: RNA was isolated from freshly sorted NK subsets using the RNAeasy Micro Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions. RNA quality was checked using the Agilent 2100 Bioanalyzer.

value: female

value: spleen

tag: cell type

value: NK cells

tag: cell subtype


title: Cd117-Cd27-Cd11b+NK_rep1

description: SAMPLE 9

scan_protocol: Microarrays were washed and subsequently scanned with an Agilent scanner.


title: Blood Infected_Day 3 rep 5_experiment_1

description:
replicate 5
8650489059_B

tag: genotype

value: Blood


title: Cd117-Cd27-Cd11b+NK_rep3

description: SAMPLE 11

tag: gender


title: Blood Infected_Day 3 rep 1_experiment_1

description:
replicate 1
8615616049_A

value: Female

tag: experiment


title: Blood Infected_Day 3 rep 4_experiment_1

description:
replicate 4
8650489023_D


title: Cd117-Cd27-Cd11b+NK_rep2

description: SAMPLE 10


title: Blood Infected_Day 3 rep 2_experiment_1

description:
replicate 2
8615616065_C


title: Cd117-Cd27+Cd11b+NK_rep3

description: SAMPLE 8


title: Blood Infected_Day 3 rep 6_experiment_1

description:
replicate 6
8650489074_E


title: Cd117-Cd27+Cd11b-NK_rep2

description: SAMPLE 4


title: Cd117-Cd27+Cd11b-NK_rep3

description: SAMPLE 5


title: mTEC_HDAC3cKO

city: Rehovot

first: Jakub

last: Abramson

address: Herzl 234

department: Immunology

country: Israel

institute: Weizmann Institute

description: Gene expression data from sorted MHC-II mTEC isolated from KO mice

hyb_protocol: 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mo1ST. GeneChips were washed and stained in the Affymetrix Fluidics Station

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

data_processing: Raw data were processed with the RMA algorithm for probe-level normalization and analyzed using GenePattern software

source_name: mTEC, HDAC3cKO

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

growth_protocol: Mice were maintained under specific-pathogen-free conditions at the Weizmann Institute’s animal facility and sacrificed at 6weeks of age by CO2.

treatment_protocol: Thymi were surgically removed from mice and placed into cold 1× PBS supplemented with 2% Fetal Bovine Serum (FBS, Invitrogen). Thymi were trimmed of fat and connective tissues, chopped into small pieces and then disintegrated by sequential enzymatic digestion using Collagenase D (Roche #1088858) and Collagenase-Dispase cocktail (Roche #269638). Thymic stroma, containing the TEC fraction, was enriched using a Percoll gradient (Sigma #P1644) and was subjected to staining with the appropriate antibodies. All types of cells were then stained in 100µl MACS buffer, with the specific fluorophore-labeled antibodies for 20-60 minutes on ice. Cells were then washed, re-suspended in MACS buffer, filtered through a 50mm mesh and sorted on BD FACS Aria III cell sorter into Trizol reagent

value: HDAC3fl/fl Foxn1-Cre (HDAC3cKO)

value: mTEClo (EpCAM+, CD45-, Ly51low, MHC-II low)


title: WT Normal Kidneys-rep1

description: Gene expression of WT Normal kidneys


title: mTEC_WT

description: Gene expression data from sorted MHC-II mTEC isolated from WT mice

source_name: mTEC, WT

value: HDAC3fl/fl (WT)


title: Cd117+Cd27+Cd11b-NK_rep2

description: SAMPLE 2


title: Cd117+Cd27+Cd11b-NK_rep1

description: SAMPLE 1


title: Blood Infected_Day 3 rep 3_experiment_1

description:
replicate 3
8615616065_F


title: gbf1 mutant, biological replicate 2

city: New Delhi

first: Sudip

last: Chattopadhyay

state: Delhi

address: Aruna Asaf Ali Marg, JNU Campus

department: Development Biology

country: India

institute: National Institute of Plant Genome Research

description:
gbf1_Rep2
Gene expression data from 4-day-old constant white light grown gbf1 mutant seedlings.

hyb_protocol: 12.5 micrograms fragmented and labelled aRNA were hybridised for 16 hr at 45 degrees Celsius to Arabidopsis Affymetrix ATH1 Arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Stained and washed arrays were scanned using GeneChip Scanner 3000 7G (Affymetrix) controlled by GeneChip Operating Software (GCOS).

data_processing: The data were analyzed with GeneSpring software version 11.5.1 using RMA (Robust Multichip Averaging) with quantile normalization method. Baseline was set to median for all samples. The other parameters were left as default. Probe intensity values are represented in log scale.

source_name: Whole Arabidopsis seedling, gbf1 mutant

label_protocol: Biotinylated labelled aRNA were prepared from total RNA using the GeneChip 3' IVT Express kit (Affymetrix) according to the manufacturer's instructions.

growth_protocol: Wild-type and various mutant Arabidopsis seeds were surface sterilized and plated on Murashige and Skoog medium supplemented with 0.8% Bactoagar (Difco) and 1% sucrose. The plates were then cold treated at 4 degrees Celsius for 4 days and transferred to light chambers maintained at 22 degrees Celsius with 20 micromol per meter square per second light intensities.

extract_protocol: Total RNA was extracted from the harvested seedlings using the RNeasy Plant Mini Kit (Quiagen, CA) according to the manufacturer's instructions.

value: gbf1 mutant

value: whole seedling

value: 4 days

tag: growth conditions

value: constant white light - 20 micromol/meter square/second


title: gbf1 hy5 mutant, biological replicate 1

description:
gbf1hy5_Rep1
Gene expression data from 4-day-old constant white light grown gbf1 hy5 double mutant seedlings.

source_name: Whole Arabidopsis seedling, gbf1 hy5 double mutant

value: gbf1 hy5 double mutant

tag: tissue


title: Wild-type (Col-0), biological replicate 2

description:
col_Rep2
Gene expression data from 4-day-old constant white light grown wild-type seedlings.

source_name: Whole Arabidopsis seedling, wild-type

tag: ecotype

value: wild-type


title: gbf1 hyh mutant, biological replicate 2

description:
gbf1hyh_Rep2
Gene expression data from 4-day-old constant white light grown gbf1 hyh double mutant seedlings.

source_name: Whole Arabidopsis seedling, gbf1 hyh double mutant

value: gbf1 hyh double mutant


title: gbf1 hy5 mutant, biological replicate 2

description:
gbf1hy5_Rep2
Gene expression data from 4-day-old constant white light grown gbf1 hy5 double mutant seedlings.


title: Wild-type (Col-0), biological replicate 1

description:
col_Rep1
Gene expression data from 4-day-old constant white light grown wild-type seedlings.


title: gbf1 hyh mutant, biological replicate 1

description:
gbf1hyh_Rep1
Gene expression data from 4-day-old constant white light grown gbf1 hyh double mutant seedlings.


title: gbf1 mutant, biological replicate 1

description:
gbf1_Rep1
Gene expression data from 4-day-old constant white light grown gbf1 mutant seedlings.


title: Cd117-Cd27+Cd11b-NK_rep1

description: SAMPLE 3


title: IMCD cultivated at 900 mosmol/kg challenged for 24h with 300 mosmol/kg rep.2

city: Halle

first: Bayram

last: Edemir

address: Ernst-Grube-Str. 20

institute: University Hospital Halle (Saale)

hyb_protocol: Samples were hybridized with GeneChip Rat Gene 1.0 ST Arrays (Affymetrix) and scanned at the University Hospital Muenster IFG Microarray Core Facility.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using RMA-Express software. Background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized and log transformed.
RaGene-1_0-st-v1.r3.pgf
RaGene-1_0-st-v1.r3.mps

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Rat primary cultured inner medullary collecting duct cells kultivated at different osmolalities

extract_protocol: extraction of total RNA was performed using Qiagen Rneasy kit according to the manufacturer's instructions.

treatment_protocol: treated with 5 µM Cyclosporin A for time as indicated

value: Renal inner medulla


title: IMCD cultivated at 900 mosmol/kg challenged for 24h with 300 mosmol/kg rep.1

source_name: Rat primary cultured inner medullary collecting duct cells


title: IMCD cultivated at 900 mosmol/kg challenged for 24h with 300 mosmol/kg rep.9


title: IMCD cultivated at 600 mosmol/kg challenged for 12h with 900 mosmol/kg rep.9


title: IMCD cultivated at 300 mosmol/kg challenged for 48h with 600 mosmol/kg rep.2


title: MCF7 DexEst Rep1

city: Chicago

first: Suzanne

middle: Daniela

last: Conzen

state: IL

address: 5841 S. Maryland Ave, SBRI J301, MC 2115

department: Medicine

institute: The University of Chicago

description: 100 nM dexamethasone dissolved in ethanol + 10 nM estradiol dissolved in ethanol

hyb_protocol: 10 µg of biotin labeled and fragmented  target cRNA was hybridized to Human U133+2.0 array for 16 h at 45°C and 60 rpm in an Affymetrix Hybridization Oven 640 according to the 3 Genechip 3' IVT Express Kit manual (Affymetrix, Inc).

scan_protocol: After hybridization, arrays were washed and stained on a GeneChip Fluidics Station 450 (Affymetrix, Inc.) and scanned using the Gene Chip Scanner 3000 7G to extract CEL. intensity expression data by Affymetrix GeneChip Command Console Software.

data_processing: CEL files were processed and RMA normalized using the “rma-sketch” analysis from the Affymetrix Power Tools v1.10.2 software package.  CEL files were processed and RMA normalized using the “rma-sketch” analysis from the Affymetrix Power Tools v1.10.2 software package.

source_name: MCF7 breast cancer,DEXE2,4h,Rep1

label_protocol: 250 ng of  total RNA was processed for biotin labeled target preparation according to The 3' IVT PLUS Reagent Kit manual (Affymetrix, Inc).

growth_protocol: MCF-7 cells were grown at 37°C in 5% CO2 in Dulbecco’s Modified Eagle’s Medium (DMEM, Lonza) supplemented with 10% fetal bovine serum (FBS, Gemini Bio-Products), and 1% penicillin/streptomycin (Lonza).

extract_protocol: Cells were lysed in a RNA lysis buffer (Ambion, Invitrogen) and total RNA was isolated using an PureLink ® RNA extraction kit (Ambion, Invitrogen)

treatment_protocol: MCF-7 cells were incubated in phenol red-free DMEM containing 2.5% charcoal-stripped serum for 4 days total (with a media change after 48h), MCF-7 cells were treated with either vehicle, Dex (100 nM), E2 (10 nM) or Dex/E2 for 4 h

tag: condition

value: Dexamethasone and Estradiol

tag: cell line


title: IMCD cultivated at 300 mosmol/kg challenged for 48h with 600 mosmol/kg rep.3


title: IMCD cultivated at 600 mosmol/kg challenged for 24h with 900 mosmol/kg rep.1


title: IMCD cultivated at 600 mosmol/kg challenged for 24h with 900 mosmol/kg rep.9


title: MCF7 Dex Rep3

description: 100 nM dexamethasone dissolved in ethanol

source_name: MCF7 breast cancer,DEX,4h,Rep3

value: Dexamethasone


title: IMCD cultivated at 600 mosmol/kg challenged for 12h with 900 mosmol/kg rep.2


title: MCF7 DexEst Rep3

source_name: MCF7 breast cancer,DEXE2,4h,Rep3


title: IMCD cultivated at 600 mosmol/kg challenged for 24h with 900 mosmol/kg rep.2


title: MCF7 DexEst Rep2

source_name: MCF7 breast cancer,DEXE2,4h,Rep2


title: IMCD cultivated at 300 mosmol/kg challenged for 48h with 600 mosmol/kg rep.1


title: IMCD cultivated at 600 mosmol/kg challenged for 12h with 900 mosmol/kg rep.1


title: IMCD cultivated at 300 mosmol/kg challenged for 24h with 600 mosmol/kg rep.1


title: IMCD cultivated at 300 mosmol/kg challenged for 12h with 600 mosmol/kg rep.3


title: IMCD cultivated at 300 mosmol/kg challenged for 12h with 600 mosmol/kg rep.2


title: IMCD cultivated at 300 mosmol/kg challenged for 24h with 600 mosmol/kg rep.3


title: MCF7 Dex Rep1

source_name: MCF7 breast cancer,DEX,4h,Rep1


title: MCF7 Est Rep2

description: 10 nM b-estradiol dissolved in ethanol

source_name: MCF7 breast cancer,E2,4h,Rep2

value: Estradiol


title: IMCD cultivated at 300 mosmol/kg challenged for 12h with 600 mosmol/kg rep.1


title: MCF7 Dex Rep2

source_name: MCF7 breast cancer,DEX,4h,Rep2


title: MCF7 Veh Rep3

description: ethanol

source_name: MCF7 breast cancer,Veh,4h,Rep3

value: Vehicle


title: MCF7 Est Rep1

description: 10 nM b-estradiol dissolved in ethanol

source_name: MCF7 breast cancer,E2,4h,Rep1


title: MCF7 Est Rep3

description: 10 nM b-estradiol dissolved in ethanol

source_name: MCF7 breast cancer,E2,4h,Rep3


title: IMCD cultivated at 300 mosmol/kg challenged for 24h with 600 mosmol/kg rep.2


title: IMCD cultivated at 300 mosmol/kg challenged for 3h with 600 mosmol/kg rep.3


title: WT IRI Kidneys-rep1

description: Gene expression of WT IRI kidneys

source_name: WT IRI mouse kidney

value: Kidney

value: male

value: 16 weeks

value: Wild type


title: Lactation_3

city: Parkville

first: christophe

last: lefevre

state: VIC

address: 1 G Royal Parade

department: Bioinformatics Division

country: Australia

institute: Walter Eliza Hall Institute of Medical Research

description: human milk cell mRNA @ Lactation

hyb_protocol: AGRF

scan_protocol: AGRF

data_processing: Data was normalised using the Affy package of Bioconductor (Gautier et al. 2004), and standard RMA technique (Irizarry et al. 2003).

molecule: polyA RNA

source_name: human milk

label_protocol: Total RNA (3 μg) was used to generate biotin-labeled cRNA for each individual sample which was hybridized to Human genome 2.0 Affymetrix genechips.

extract_protocol: Milk collection and isolation of mammary cells  Human milk was from volunteer mothers at various stages of lactation (Table 1). Milk was collected 24 hours pre-partum during the colostrum period, (n=2), at peak lactation 24, 48, 62, 94and 101 days (n=5), involution at day 7 and day 14 (n=2) and during mastitic infection at day 23 of lactation (n=1). Total cell populations from collected milk were isolated from either fresh or frozen (-80oC) milk samples by centrifugation at 2000g, 5 min at 4oC. Pelleted milk cells were subjected to RNA isolation protocols. Cells from fresh milk (<3 hours) were purified by centrifugation at 2000g, 5 min at 4oC and grown in cell culture for morphology analysis.  RNA purification and Human Affymetrix array  Cells isolated from milk collected at 24 hours pre-partum during the colostrum period (n=2), at peak lactation 24, 48 and 101 days (n=3), involution at day 7 and day 14 (n=2) and during mastitic infection at day 23 of lactation (n=1) (see Table 1 for details) were resuspended in Buffer 1 of the QIAGEN RNeasy Micro kit (Sydney Australia) following the manufacturer’s instructions for isolation of purified total RNA.

tag: Stage

value: Lactation

value: milk


title: Colostrum_1

description: human milk cell mRNA @ Colostrum

value: Colostrum


title: IMCD cultivated at 900 mosmol/kg rep.2


title: IMCD cultivated at 300 mosmol/kg challenged for 3h with 600 mosmol/kg rep.1


title: MCF7 Veh Rep2

description: ethanol

source_name: MCF7 breast cancer,Veh,4h,Rep2


title: IMCD cultivated at 600 mosmol/kg rep.1


title: MCF7 Veh Rep1

description: ethanol

source_name: MCF7 breast cancer,Veh,4h,Rep1


title: Involution_5

description: human milk cell mRNA @ Involution

value: Involution


title: IMCD cultivated at 900 mosmol/kg rep.1


title: Involution_3

description: human milk cell mRNA @ Involution


title: IMCD cultivated at 300 mosmol/kg rep.1


title: IMCD cultivated at 600 mosmol/kg rep.2


title: IMCD cultivated at 300 mosmol/kg rep.3


title: Involution_1

description: human milk cell mRNA @ Involution


title: Colostrum_2

description: human milk cell mRNA @ Colostrum


title: IMCD cultivated at 900 mosmol/kg rep.3


title: ASC KO Replicate 4

city: Brisbane

first: Glen

middle: M

last: Boyle

state: Queensland

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

institute: QIMR Berghofer Medical Research Insitute

hyb_protocol: Labelled cRNA was hybridized to MouseRef-8 v2.0 BeadChip Arrays (Illumina Inc, San Diego, CA, USA), and then washed and scanned according to standard Illumina protocols.

data_processing: Data were extracted in GenomeStudio (Illumina) using default analysis settings and no normalization method.  Resulting data were imported into GeneSpring GX v12.5 (Agilent Technologies, Santa Clara, CA, USA).  Expression values were normalized using quantile normalization with default settings. The GeneSpring software calculates a "control" value for generation of the log2 ratios.  According to the user guide, the "normalised ratios" are the "value generated after thresholding, log transformation and normalization (Quantile here) and Baseline Transformation".

source_name: CD8+ T cell from ASC KO mice

label_protocol: Biotinylated cRNA was prepared with the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX, USA).

extract_protocol: RNA was extracted using Qiagen RNeasy mini kit as per manufacturer’s instructions, then DNase treated and purified.  RNA concentration was determined using the NanoDrop 2000 (Thermo Scientific, Wilmington, DE, USA).

tag: strain

value: knock out


title: IMCD cultivated at 600 mosmol/kg rep.3


title: IMCD cultivated at 300 mosmol/kg challenged for 3h with 600 mosmol/kg rep.2


title: Lactation_2

description: human milk cell mRNA @ Lactation


title: Mastitis

description: human milk cell mRNA @ Mastitis

value: Mastitis


title: Involution_4

description: human milk cell mRNA @ Involution


title: Lactation_1

description: human milk cell mRNA @ Lactation


title: Involution_2

description: human milk cell mRNA @ Involution


title: IMCD cultivated at 300 mosmol/kg rep.2


title: Cd117-Cd27+Cd11b+NK_rep2

first: Michael

description: SAMPLE 7

value: female

value: spleen

value: NK cells


title: ASC KO Replicate 3

scan_protocol: Labelled cRNA was hybridized to MouseRef-8 v2.0 BeadChip Arrays (Illumina Inc, San Diego, CA, USA), and then washed and scanned according to standard Illumina protocols.

tag: genotype/variation


title: CD4+CD25+ T cells

city: Bunkyo-ku

first: Shuji

last: Sumitomo

state: Tokyo

department: Allergy and Rheumatology

hyb_protocol: Following fragmentation, biotinylated cDNA was hybridized  for 18 hours at 45℃ and 60rpm on GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix) using Hybridization, Wash and Stain Kit (Affymetrix).

scan_protocol: Affymetrix Scanning Protocol

data_processing: The data were preprocessed with Robust Multi-array Average (RMA)   algorithm using Bioconductor statistical software R (version 3.1.2).

source_name: Freshly isolated human tonsillar CD4+ T cell subset

label_protocol: Biotinylated cDNA was prepared with in vitro amplification using WT-Ovation Pico RNA Amplification System (NuGEN) and FL-Ovation cDNA Biotin Module V2 (NuGEN).

growth_protocol: Human tonsil was obtained from a patient undergoing routine tonsillectomy. The tonsil samples were cut into pieces, and the lymphoid cells in the tissue were pushed through a 40-μm metal sieve using a plastic syringe plunger. A cell suspension was obtained by rinsing the sieve with HBSS and slowly layered over Ficoll-Paque PLUS (GE Healthcare). Tonsillar mononuclear cells were isolated by density centrifugation at 1800 rpm for 20 min.

extract_protocol: Total RNA was extracted with RNeasy Micro Kit (QIAGEN) and quality was estimated with Bioanalyzer (Agilent Technologies Genomics) prior to gene expression profiling.

treatment_protocol: For sorting human tonsillar CD4+ T cell subsets, human tonsillar cells　were stained with anti-human CD4 mAb, anti-human　CD25 mAb, anti-human CD45RO mAb, anti-human LAG3 mAb, anti-human CXCR5 mAb, anti-human PD-1 mAb after Fc-blocking (Human Fc Receptor Binding Inhibitor). 1 x 10^5 human tonsillar CD4+ T cell subsets (CD4+CD25-LAG3+ T cells, CD4+CD25-CXCR5+PD-1+ follicular helper T cells (TFH), CD4+CD25+ T cells, CD4+CD25-LAG3-CD45RO+ cells and CD4+CD25-LAG3-CD45RO- cells) were sorted with FACSAriaII (BD Biosciences).

value: Tonsil

value: CD4+CD25+ T cells


title: CD4+CD25-LAG3-CD45RO- cells

value: CD4+CD25-LAG3-CD45RO- cells


title: ASC KO Replicate 1


title: ASC WT Replicate 2

source_name: CD8+ T cell from WT mice

value: wild type


title: Leukemic Tp53-/-Lnk-/- B-ALL cells, biological replicate 2

city: Philadelphia

first: Wei

last: Tong

state: PA

address: 316A Abramson Bldg., 3615 Civic Center Blvd.

department: Pediatrics

institute: Children's Hospital of Philadelphia, and University of Pennsylvania School of Medicine

description:
LDKO_2
Gene expression data from Leukemic BM cells of Tp53-/-Lnk-/- B-Acute Lymphoblastic Leukemia mice
Bone marrow B-ALL blasts

hyb_protocol: Following fragmentation, cRNA were hybridized on Mouse Gene 2.0ST Array. GeneChips were washed and stained in the Tecan HS400 Hyb Station.

scan_protocol: GeneChips were scanned using the Axon GenePix 4000B scanner.

data_processing: The data were analyzed using Partek software.

source_name: Leukemic Tp53-/-Lnk-/- B-ALL cells

label_protocol: Biotinylated cRNA were prepared according to NuGEN Pico protocol from 50 ng total RNA.

growth_protocol: None. Freshly isolated bone marrow proB cells or leukemic cells.

extract_protocol: Trizol extraction of total RNA was performed according to QIAGEN miRNeasy instructions

value: bone marrow

value: B-ALL leukemic blasts

tag: disease state

value: leukemia


title: Leukemic Tp53-/-Lnk-/- B-ALL cells, biological replicate 3

description:
LDKO_3
Gene expression data from Leukemic BM cells of Tp53-/-Lnk-/- B-Acute Lymphoblastic Leukemia mice
Bone marrow B-ALL blasts

treatment_protocol: None. Freshly isolated bone marrow proB cells or leukemic cells.


title: ANAC046_knockout_seedling_5days_after_dark_rep3

city: Tsukuba

first: Nobutaka

last: Mitsuda

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology

hyb_protocol: Hybridized using Gene Expression Hybridization kit (Agilent) and washed by Gene Expression wash pack (Agilent).

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing:
Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction. After that, signal of each probe was divided by median value of filter-passed probes.
Normalization was done with quantile normalization method using all in-house microarray data after division by median value of all filter-passed probes.

source_name: ANAC046-knockout Arabidopsis Col0 seedling, 5 days after dark treatment

label_protocol: 200 ng of total RNA was used for labeling procedure using Low Input Quick Amp Labeling kit (One-color) (Agilent).

growth_protocol: All plants for harvesting leaf were grown on soil in green house. All plants for harvesting seedling were grown in MS agar media. All plants were grown at 23 Celsius degree in 16h/8h day/night cycle.

extract_protocol: Plant RNeasy Mini kit (QIAGEN) was used to isolate total RNA.

treatment_protocol: Seedlings in agar media were covered with aluminum foil and left for 5 days as dark treatment.

tag: ecotype/background

value: seedling

value: dark treatment


title: CD4+CD25-LAG3-CD45RO+ cells

value: CD4+CD25-LAG3-CD45RO+ cells


title: SK11_Control Antibody replicate 2

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

description: SK11_Cont Ab_02)

hyb_protocol: The hybridization cocktail containing the fragmented and Biotin labeled cRNAs was hybridized to The Affymetrix Human Genome U133 Plus 2.0 GeneChip. The chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described by Affymetrix. The probe arrays were stained with streptavidin phycoerythrin solution (Molecular Probes, Carlsbad, CA) and enhanced by using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA).

scan_protocol: Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing:
Gene expression intensities were calculated using GeneChip® Command Console® Software (AGCC) and Expression Console™ Software.
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.1.187

source_name: MDA-231_suspension_Control Antibody

label_protocol: Per RNA labeling, 500 nanograms of total RNA was used in conjunction with the Affymetrix GeneChip 3’ IVT Express Kit cat# 901228.

growth_protocol: MDA-MB-231 cells were cultured using complete RPM1 medium up to 90% confluence, gently washed with Ix PBS and  by gentle shaking, viable, floating single cells were collected by centrifugation at 1,200 rpm for 5 minutes and plated in the RPMI 1640 growth medium  with 2%FBS as described in  {Cioce, 2010 #23}{Ponti, 2005 #21}.  CD44high and CD24low bCSCs were isolated using flow cytometry sorting {Gupta, 2011 #22}.  The sorted bCSCs cells were cultured using Premium Cancer Stem Cell Media from ProMab.

extract_protocol: Total RNAs from cells was extracted using miRNeasy Mini kit (Qiagen). (cat. no. 217004)

treatment_protocol: differentiated MDA-MB-231 cells and bCSCs (breast cancer stem cells) in the presence of B6H12 (Abcam, Cambridge, MA), or an isotype-matched control IgG  (1ug/ml) for 36 h.

value: Triple Negative breast cancer cell line

value: suspension cells (breast cancer stem cells; bCSC)

tag: incubated with


title: Leukemic Tp53-/-Lnk-/- B-ALL cells, biological replicate 4

description:
LDKO_4
Gene expression data from Leukemic BM cells of Tp53-/-Lnk-/- B-Acute Lymphoblastic Leukemia mice
Bone marrow B-ALL blasts


title: CD4+CD25-CXCR5+PD-1+ follicular helper T cells (TFH)

institute: The University of Tokyo


title: ASC WT Replicate 3


title: ANAC046_knockout_seedling_5days_after_dark_rep2

tag: treatment


title: Tp53-/-Lnk-/- proB cells, biological replicate 2

description:
DKO_3
Gene expression data from preleukemic healthy Tp53-/-Lnk-/- BM proB cells
B220+CD19+CD43+AA4.1+IgM-NK1.1-Ly6c- bone marrow proB cells

source_name: Tp53-/-Lnk-/- proB cells

tag: developmental stage

value: Adult

tag: cell type

value: proB cells (B220+CD19+CD43+AA4.1+IgM-NK1.1-Ly6c- )

value: control


title: ASC WT Replicate 1


title: ANAC046_knockout_seedling_5days_after_dark_rep1


title: Leukemic Tp53-/-Lnk-/- B-ALL cells, biological replicate 1

description:
LDKO_1
Gene expression data from Leukemic BM cells of Tp53-/-Lnk-/- B-Acute Lymphoblastic Leukemia mice
Bone marrow B-ALL blasts


title: KO20_4

data_processing: Data was processed by means of  Genome Studio v2011 from illumina, Inc. The background noise was substrated and quantile normalization was applied.

source_name: liver

label_protocol: Biotinylated cRNA were prepared using Ambion Totalprep RNA Amplification kit for Illumina arrays

extract_protocol: Total RNA was extracted using Qiagen mini kit. Quality control and measurement were performed using NanoDrop and Agilent Bioanalyser.

value: DNMT1 knockout

tag: week


title: Tp53-/-Lnk-/- proB cells, biological replicate 1

description:
DKO_2
Gene expression data from preleukemic healthy Tp53-/-Lnk-/- BM proB cells
B220+CD19+CD43+AA4.1+IgM-NK1.1-Ly6c- bone marrow proB cells


title: Lnk-/- proB cells, biological replicate 3

description:
Lnk_4
Gene expression data from Lnk-/- BM proB cells
B220+CD19+CD43+AA4.1+IgM-NK1.1-Ly6c- bone marrow proB cells

source_name: Lnk-/- proB cells

value: Lnk-/-


title: KO20_2


title: ASC WT Replicate 4


title: SK08_B6H12 Antibody replicate 2

description: SK08_B6H12 Ab_02

source_name: MDA-231_suspension_B6H12 Antibody

tag: cell subtype

value: B6H12 antibdody for 36hrs


title: SK10_Control Antibody replicate 1

description: SK10_Cont Ab_01

value: an isotype-matched control IgG  (1ug/ml) for 36 h


title: SK09_B6H12 Antibody replicate 3

description: SK09_B6H12 Ab_03


title: ANAC046-SRDX_seedling_5days_after_dark_rep3

source_name: ANAC046-SRDX-overexpression Arabidopsis Col0 seedling, 5 days after dark treatment


title: KO20_3


title: SK07_B6H12 Antibody replicate 1

description: SK07_B6H12 Ab_01


title: ASC KO Replicate 2

value: knock out


title: Lnk-/- proB cells, biological replicate 2

description:
Lnk_3
Gene expression data from Lnk-/- BM proB cells
B220+CD19+CD43+AA4.1+IgM-NK1.1-Ly6c- bone marrow proB cells


title: col0_seedling_5days_after_dark_rep3

source_name: wild type Arabidopsis Col0 seedling, 5 days after dark treatment

value: wt


title: SK04_attached replicate 1

value: attached cells (differentiated)


title: KO8_4


title: Lnk-/- proB cells, biological replicate 1

description:
Lnk_1
Gene expression data from Lnk-/- BM proB cells
B220+CD19+CD43+AA4.1+IgM-NK1.1-Ly6c- bone marrow proB cells

value: bone marrow


title: ANAC046-SRDX_seedling_5days_after_dark_rep2


title: KO20_1


title: KO8_1


title: Tp53-/- proB cells, biological replicate 3

description:
p53_4
Gene expression data from Tp53-/- BM proB cells
B220+CD19+CD43+AA4.1+IgM-NK1.1-Ly6c- bone marrow proB cells

source_name: Tp53-/- proB cells


title: ANAC046ox_leaf_50days_after_seed_sawing_rep3

source_name: ANAC046-overexpression Arabidopsis Col0 leaf, 50 days after seed sawing

value: leaf


title: Tp53-/- proB cells, biological replicate 1

description:
P53_1
Gene expression data from Tp53-/- BM proB cells
B220+CD19+CD43+AA4.1+IgM-NK1.1-Ly6c- bone marrow proB cells


title: KO4_5


title: SK06_attached replicate 3


title: col0_seedling_5days_after_dark_rep1

value: seedling


title: SK01_suspension replicate 1


title: KO8_3


title: SK05_attached replicate 2


title: WT proB cells, biological replicate 3

description:
WT_4
Gene expression data from WT BM proB cells
B220+CD19+CD43+AA4.1+IgM-NK1.1-Ly6c- bone marrow proB cells

source_name: WT proB cells

value: WT


title: SK02_suspension replicate 2


title: SK03_suspension replicate 3


title: KO4_4


title: Tp53-/- proB cells, biological replicate 2

description:
p53_3
Gene expression data from Tp53-/- BM proB cells
B220+CD19+CD43+AA4.1+IgM-NK1.1-Ly6c- bone marrow proB cells


title: ANAC046-SRDX_seedling_5days_after_dark_rep1

value: dark treatment


title: KO8_2


title: col0_seedling_5days_after_dark_rep2


title: ANAC046ox_leaf_50days_after_seed_sawing_rep2


title: WT proB cells, biological replicate 2

description:
WT_3
Gene expression data from WT BM proB cells
B220+CD19+CD43+AA4.1+IgM-NK1.1-Ly6c- bone marrow proB cells


title: WT proB cells, biological replicate 1

description:
WT_2
Gene expression data from WT BM proB cells
B220+CD19+CD43+AA4.1+IgM-NK1.1-Ly6c- bone marrow proB cells


title: FL20_4


title: KO4_3


title: col0_leaf_50days_after_seed_sawing_rep3

source_name: wild type Arabidopsis Col0 leaf, 50 days after seed sawing


title: ANAC046ox_leaf_50days_after_seed_sawing_rep1


title: FA_8

city: Pamplona

first: Jose

last: Hermida

address: Pio XII, 55

institute: CIMA

description: Gene expression data from AF patient without stroke

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133Plus2 chip according to the protocols provided by the manufacturer.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.

data_processing: Data were normalized with Bioconductor software using RMA algorithm.

source_name: Peripheral blood cells of a patient with AF and without stroke

label_protocol: The cDNA was prepared from 2 microg total RNA using the One –Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthezising the cRNA using the IVT labeling kit (Affymetrix). The synthezised cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).

growth_protocol: It does not applied

extract_protocol: Whole blood (2.5 mL) was collected from each subject into a PAXgene tube (BD). PAXgene tubes were frozen at -80ºC after 2 hours at room temperature. Total RNA was isolated according to the manufacturer´s protocol using the PAXgene blood RNA kit (Pre-AnalytiX).

treatment_protocol: Whole blood from stroke (n=8) and non-stroke (n=8) atrial fibrillation patients

value: peripheral blood cells


title: KO4_1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol


title: FL20_3


title: FA_3


title: FA_5


title: col0_leaf_50days_after_seed_sawing_rep1


title: TB mouse liver, ZT 20, replicate 1

city: Irvine

first: Paolo

last: Sassone-Corsi

state: CALIFORNIA

address: Sprague Hall

institute: University of California, Irvine

description:
TB 20-8
Gene expression data from mouse liver at indicated ZT.

hyb_protocol: 3.3ug of the labeled, fragmented single-stranded cDNA is hybridized at 45oC with rotation for 17 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix Mouse GeneChip 2.0 ST array.

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G and Command Console Software v. 3.2.3 to produce .CEL intensity files.

data_processing:
The probe cell intensity files (*.CEL) were analyzed in Affymetrix Expression Console software v1.1.1 using the PLIER algorithm to generate probe level summarization files (*.CHP).
The settings used were algorithm-PLIER v2.0; quantification scale-Linear; quantification type-signal and detection p-value; background-PM-GCBG; normalization method-sketch-quantile.

source_name: TB mouse liver, ZT 20

label_protocol: Labeling using a recombinant terminal deoxynucleotidyl transferase (TdT) and an Affymetrix proprietary DNA labeling reagent was done to covalently link to biotin.

growth_protocol: Animals were housed in 12 hour Light/Dark conditions and harvested over the circadian cycle.

extract_protocol: Total RNA was prepared by Trizol extraction, and RNA was cleaned-up prior to array analysis with Qiagen RNeasy clean-up kit.

treatment_protocol: WT and TB mice were harvested every 4 hours over the circadian cycle and livers were flash frozen in liquid nitrogen after sacrifice.

tag: strain/background

tag: disease status

value: lung adenocarcinoma

value: liver

tag: circadian cycle time point

value: ZT 20


title: FA_6


title: FL20_2

city: Copenhagen

first: Jesper

institute: Copenhagen University

value: control


title: col0_leaf_50days_after_seed_sawing_rep2

tag: tissue


title: TB mouse liver, ZT 20, replicate 2

description:
TB 20-9
Gene expression data from mouse liver at indicated ZT.


title: TB mouse liver, ZT 16, replicate 3

description:
TB 16-8
Gene expression data from mouse liver at indicated ZT.

source_name: TB mouse liver, ZT 16

value: ZT 16


title: FA_7


title: TB mouse liver, ZT 20, replicate 3

description:
TB 20-10
Gene expression data from mouse liver at indicated ZT.


title: TB mouse liver, ZT 16, replicate 2

description:
TB 16-7
Gene expression data from mouse liver at indicated ZT.


title: FA_4


title: FL20_1


title: TB mouse liver, ZT 16, replicate 1

description:
TB 16-6
Gene expression data from mouse liver at indicated ZT.


title: PALLSD

city: Randwick

first: Duohui

last: Jing

state: NSW

address: Lowy Cancer Research Centre, UNSW

department: Leukaemia Biology

institute: Children’s Cancer Institute Australia

description:
TGT161, Acute lymphoblastic leukemia established by the Therapeutically Applicable Research to Generate Effective Treatments (TARGET)
PALLSD

data_processing: The matrix non-normalized was generated using IlluminaExpressionFileCreator module in GenePattern. The data were then normalised using quantile normalisation with NormalizeColumns module in Genepattern

organism:
Homo sapiens
Mus musculus

source_name: Patient-derived xenograft cells

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA kit for Illumina arrays

growth_protocol: ALL xenograft cells were inoculated by tail-vein injection into NOD/SCID mice, and engraftment was monitored weekly.

extract_protocol: RNA was extracted with a combination of Trizol reagent and QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: NOD/SCID

tag: age

value: xenograft cells Injected at 6-10 weeks

value: Xenograft cells (>95% hCD45+ cells) from mouse spleens

tag: dexamethasone response


title: PAMDRM

description:
TGT258, Acute lymphoblastic leukemia established by the Therapeutically Applicable Research to Generate Effective Treatments (TARGET)
PAMDRM


title: SK12_Control Antibody replicate 3

description: SK12_Cont Ab_03

tag: cell line

value: Triple Negative breast cancer cell line

value: suspension cells (breast cancer stem cells; bCSC)

value: an isotype-matched control IgG  (1ug/ml) for 36 h


title: FL8_5

last: Andersen

address: Ole Maaloes Vej 5


title: CD4+CD25-LAG3+ T cells

source_name: Freshly isolated human tonsillar CD4+ T cell subset

value: Tonsil

value: CD4+CD25-LAG3+ T cells


title: FA_2


title: FL4_5


title: PAKRSL

description:
TGT047, Acute lymphoblastic leukemia established by the Therapeutically Applicable Research to Generate Effective Treatments (TARGET)
PAKRSL

tag: strain


title: FA_1


title: TB mouse liver, ZT 8, replicate 3

description:
TB 8-9
Gene expression data from mouse liver at indicated ZT.

source_name: TB mouse liver, ZT 8

tag: genotype/variation

value: ZT 8


title: TB mouse liver, ZT 12, replicate 2

description:
TB 12-7
Gene expression data from mouse liver at indicated ZT.

source_name: TB mouse liver, ZT 12

value: ZT 12


title: FAIC_8

description: Gene expression data from AF patient with stroke

source_name: Peripheral blood cells of a patient with AF and stroke


title: TB mouse liver, ZT 12, replicate 1

description:
TB 12-6
Gene expression data from mouse liver at indicated ZT.


title: TB mouse liver, ZT 12, replicate 3

description:
TB 12-8
Gene expression data from mouse liver at indicated ZT.


title: PAKSWW

description:
TGT052, Acute lymphoblastic leukemia established by the Therapeutically Applicable Research to Generate Effective Treatments (TARGET)
PAKSWW


title: TB mouse liver, ZT 8, replicate 2

description:
TB 8-8
Gene expression data from mouse liver at indicated ZT.


title: T1D-2-SC-B-REPLICATE1

city: Cambridge

first: Jeffrey

middle: Robert

last: Millman

state: Massachusetts

address: 7 Divinity Ave

department: HSCRB

institute: Harvard University

hyb_protocol: 750 ng cRNA from each sample was hybridized to Human HT-12 Expression BeadChips (Illumina). The Whole- Genome Expression Direct Hybridization kit (Illumina) was used according to manufacturer's instructions.

scan_protocol: Illumina Beadstation 500

data_processing: GenomeStudio (Illumina, V2011.1). Raw data were adjusted by background subtraction and quantile normalization. The p- values for differences between mean signals were calculated in GenomeStudio by t-test and corrected for multiple hypotheses testing by the Benjamini-Hochberg method in combination with the Illumina custom false discovery rate (FDR) model.

label_protocol: The Illumina TotalPrep RNA Amplification kit (Ambion) was using according to manufacturer's instructions.

growth_protocol: hiPS cells were grown in suspension in mTesr prior to differentiation.

extract_protocol: MARIS was used to extract total RNA after flow cytometry sorting. Detailed protocol is described in the paper: Generation of functional human pancreatic β cells in vitro

treatment_protocol: Differentiation methods are available in the paper: Generation of functional human pancreatic β cells in vitro

tag: disease status of patient source

value: Type 1 diabetic

value: stage 6 Nkx6.1+/Ins+ cells


title: FAIC_6

value: peripheral blood cells


title: FAIC_7


title: FL8_2

source_name: liver


title: FL8_4


title: FL8_3


title: FL4_4


title: PAKHZT

description:
TGT020, Acute lymphoblastic leukemia established by the Therapeutically Applicable Research to Generate Effective Treatments (TARGET)
PAKHZT


title: T1D-2-PH-REPLICATE2

value: PH INS+ cells


title: PALNTB

description:
TGT174, Acute lymphoblastic leukemia established by the Therapeutically Applicable Research to Generate Effective Treatments (TARGET)
PALNTB


title: FAIC_5


title: TB mouse liver, ZT 8, replicate 1

description:
TB 8-7
Gene expression data from mouse liver at indicated ZT.

value: lung adenocarcinoma

value: liver


title: FL4_1

value: control


title: FAIC_3


title: T1D-2-PH-REPLICATE3


title: FAIC_4


title: FL4_3