title: human primary keratinocytes [PK]

city: La Jolla

first: Masakazu

last: KURITA

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Laboratoy

institute: Salk Institute for Biological Studies

description: PK (Normalized)

hyb_protocol: Hybridization was done with GeneExpression hybridization kit <5188-5242> from Agilent technologies, as described by manufacturer.

scan_protocol: Using scanner <G2539A> from Agilent Technologies, scanned as described by manufacturer

data_processing: Data was processed with GeneSpring GX <version 12.5.0> from Agilent technologies. Flag import: [Detected], [Compromised],[Not Detected] were adjust as Default. Normalization: [Percentile Shift=75] Baseline Options: [Do not perform baseline transformation]. Grouping: PF and PK for each group. Interpretation: PF vs PK. Dta Filtering=[Controltype=0], 2 sample within 2 sample. Fold change: Fold change=[Standard sample:PK] Fold change cut off=1.0.

source_name: Cultured primary keratinocytes

label_protocol: Labeling was done with Low Input Quick Amp labeling kit, one-color <5190-2305> from Agilent technologies, as described by manufacturer

growth_protocol: Primary keratinocytes are cultured in non-serum culture medium (Epilife) with HKGS growth supplement, while primary dermal fibroblasts are cultured in 10% FBS DMEM medium.

extract_protocol: total RNA was obtained with Rneasy Mini Kit (Qiagen) as described by manufactureler

treatment_protocol: No specific treatment. Obtained on growth phase.

tag: subject status

value: healthy

tag: subject gender

value: male

value: Cultured primary keratinocytes


title: S08-0285

status: Public on Sep 01 2016

type: RNA

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

hyb_protocol: Samples that pass the QC for specific activity were taken for hybridization. 600ng of labeled cRNA were hybridized on the array using the Hi-RPM large Hybridization Kit (Part No: 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression Wash Buffers Set (Part No: 5188-5327).  The hybridized, washed microarray slides were then scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D) at 5 micron resolution.

scan_protocol: scanned using the Agilent Microarray Scanner (Agilent Technologies)

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

molecule: total RNA

organism: Homo sapiens

source_name: Punch biopsies from psoriatic lesions

label_protocol: The samples were labeled using Agilent Low Input Quick Amp Labeling Kit one color (Part number: 5190-02305).30ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using  RNeasy Mini Kit(Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop. Samples that pass the QC for specific activity were taken for hybridization.

growth_protocol: Skin biopsies from clinical trial

extract_protocol: RNA isolation was performed using Qiagen RNeasy Mini Kit (CAT# 74106 ) following the manufacturer's recommendations.

treatment_protocol: Punch biopsies were collected in RNA later stored at 2-8 degree C. The tissues were cut and frozen at -80 degree C for microarray analysis.

tag: group

value: Responder

tag: tissue

value: skin

tag: disease state

value: psoriasis

tag: time


title: fibroblast_ERT2-TRF2dB_12hr_rep1

city: Nankang

first: Liuh-Yow

last: Chen

state: Taipei

address: 128, Section 2, Academia Rd,

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

description:
Gene expression after 12hr in 1 µM of  4-hydroxytamoxifen in immortalized fibroblast transduced with ERT2-TRF2dB
EXP-12

hyb_protocol: The fluorochrome-labeled cDNAs were hybridized on Agilent human GE array 8x60K using Agilent Gene Expression Hybridization Kit. After hybridization, sildes were wased sequential.

scan_protocol: Scanned on an Agilent G2565CA Microarray Scanner. Images were then quantified using Agilent Feature Extraction Software (version A.10.5.1.1, protocol GE1_105_Dec08)

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.5.11 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 039494_D__F20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Raw intensity is normalized at 75th percentile and  log2 transformed to untreated samples of corresponding cells.

label_protocol: The cDNAs of vector control and ERT2-TRF2dB cells were reverse transcribed from 10 microgram of total RNAs and labeled with Alexa Fluor 555 647, respectively, by SuperScript® Indirect cDNA Labeling System (Life Technologies) following manufacturer's instructions.

growth_protocol: All human cell lines were maintained in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum, 2.5 mM of L-glutamine and 5 U/ml of penicillin/streptomycin (Life Technology) at 37°C with 5% CO2.

extract_protocol: Total RNA was isolated from 4-OHT-treated and non-treated BJTL/ERT2-TRF2dB or BJTL/Vec cells using RNeasy Mini Kit (QIAGEN, Germany). RNA quality was determined using Agilent RNA 6000 Nano kit (Agilent Technology, USA)

treatment_protocol: Global gene expression in immortalized human fibroblast transduced with ERT2-TRF2dB gene was measured at 0, 12, 24, 36, 48 and 60 hours of 1 µM  4-hydroxytamoxifen (4-OHT).  Gene expression in immortalized human fibrobblast transduced with vector was measured at 0 and 48 hrs of 1 µM  4-hydroxytamoxifen (4-OHT) as controls. Three independent experiments were performed at each time using different donors for each experiment.

tag: cell line

value: BJ-5ta fibroblast immortalized with hTERT

tag: transduced with

tag: treatment


title: human primary dermal fibroblasts [PF]

country: USA

description: PF (normalized)

source_name: Cultured primary dermal fibroblasts

tag: cell type

value: Cultured primary dermal fibroblasts


title: NB4 cell line in co-culture rep2

description: Gene expression after 48 hours of co-culture

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

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

source_name: cell line

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

growth_protocol: The cells were grown in 10% RPMI and were maintained at a density between 0.5x10^6 cells/ml and 1x10^6cells/m

extract_protocol: RNA was extracted using the Qiagen Rneasy Mini kit with Dnase tre atment  following the manufacturer's recommendations.

treatment_protocol: The cells were co-cultured with HS-5 cells for 48 hours and the NB4 cells were taken back for RNA isolation

value: promyelocytic leukemic cell line

tag: morphology

value: single cells in suspension, round and polymorphic cells

value: 48 hours of co-culture


title: PB infected and SUMO1 over expressed 4.1

city: Hyderabad

first: Mulaka

last: Maruthi

state: Telangana

address: Gachibowli

department: Animal Biology

institute: University of Hyderabad

description: Gene expression of PB infected SUMO1 over expressing HepG2 cells

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

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

source_name: HepG2 cells

growth_protocol: HepG2 cells were grown in DMEM medium with 10% FBS and 50 U/ml of  Pencillin and streptomycin, cells were maintained at 37 C and 5% CO2

extract_protocol: RNA was extracted using the Ambion Pure Link RNA Isolation Kit following the manufacturer's recommendations.

treatment_protocol: 100,000 HepG2 cells/well grown in Labtek 8 well chambered slides were used per each experiment, and different conditions are applied as followed, 1. uninfected cells (control), 2. infected with 20,000 Plasmodium berghei sporozoites (PB+), 3. transfected with 0.5 microgram of SUMO1 encoding plasmid with Lipofectamine 2000 reagent (SUMO1+) and 4.infection with Plasmodium berghei sporozoites after SUMO1 encoding plasmid transfection (PB+,SUMO1+). All samples were processed for RNA isolation after 48 hrs post infection (PB+)/ SUMO1 over expression.

value: PB +, SUMO1 +


title: S08-0296


title: NB4 cell line rep2

description: Gene expression at basal level

value: basal level


title: NB4 cell line rep3

description: Gene expression at basal level


title: PB infected and SUMO1 over expressed 4

value: PB +, SUMO1+


title: SUMO1 over expressed 3.1

description: Gene expression of SUMO1 over expressed cells

value: transfected with 0.5 microgram of SUMO1


title: SUMO1 over expressed 3


title: PB infected 2

description: Gene expression of PB infected HepG2 cells

value: infected with 20,000 Plasmodium berghei sporozoites (PB+)


title: Panc-1_48 hr_PDHA1-siRNA

city: Fukuoka

first: Motofumi

last: Kumazoe

state: Fukuoka

address: 6-10-1 Hakozaki, Higashi-ku

department: Department of Bioscience and Biotechnology

country: Japan

institute: Faculty of Agriculture, Kyushu University, Fukuoka

description: Gene expression after 48 hr in PDHA1-siRNA-treated Panc-1 cells.

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: Panc-1 cells were maintained in 10%FCS RPMI1640 medium.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

treatment_protocol: Panc-1 Human PDCA cells were treated with scr-siRNA, FOXO3-siRNA and PDHA1-siRNA for 48 h .

tag: protocol


title: NB4 cell line rep1

description: Gene expression at basal level


title: Panc-1_48 hr_scr-siRNA

description: Gene expression after 48 hr in scr-siRNA-treated Panc-1 cells.

source_name: 48 hr in scr-siRNA-treated Panc-1 cells

value: control


title: PB infected 2.1


title: Panc-1_48 hr_FOXO3-siRNA

description: Gene expression after 48 hr in FOXO3-siRNA-treated Panc-1 cells.


title: Panc-1_48 hr_DMSO

description: Gene expression after 48 hr in DMSO-treated Panc-1 cells.

source_name: 48 hr in DMSO-treated Panc-1 cells

treatment_protocol: Panc-1 Human PDCA cells were treated with vehicle (DMSO) or 5 μM Bay41-2272 for 48 h .

tag: agent


title: HepG2 Control 1

description: Gene expression of uninfected HepG2 cells

value: Control


title: Panc-1_48 hr_Bay41-2272

description: Gene expression after 48 hr in Bay41-2272-treated Panc-1 cells.

value: cGMP inducer Bay41-2272


title: HepG2 control 1.1


title: NSCLC 15 - TABchip - normoxic

type: genomic

city: Heverlee

first: Bernard

last: thienpont

address: Herestraat 49

department: Vesalius Research Center

country: Belgium

institute: VIB

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 15

hyb_protocol: Infinium Human Methylation 450k BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended protocol.

data_processing: Intensity data files were read directly into R. Each sample was normalized using Subset-quantile within array normalization (SWAN) for Illumina Infinium HumanMethylation450 BeadChips. Batch effects between chips and experiments were corrected using the runComBat function from the ChAMP bioconductor package.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: non-small-cell lung tumor, normoxic, TAB-chip

label_protocol: Standard Illumina Protocol.

extract_protocol: DNA was extracted from fresh frozen tumor samples using the QIAGEN DNeasy Blood & Tissue Kit

tag: dna pretreatment

value: DNA was glycosylated and TET-oxidized as described by Yu and colleagues (Nat Protoc 2012).

tag: batch

tag: tumor name

value: NSCLC 15

tag: tabchip or bschip

value: TABchip

tag: hypoxia status

value: normoxic


title: NSCLC 17 - TABchip - normoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 17

value: NSCLC 17


title: NSCLC 23 - TABchip - normoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 23

value: NSCLC 23


title: NSCLC 16 - TABchip - normoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 16

value: NSCLC 16


title: NSCLC 24 - TABchip - normoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 24

value: NSCLC 24


title: NSCLC 19 - TABchip - normoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 19

value: NSCLC 19


title: NSCLC 22 - TABchip - normoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 22

value: NSCLC 22


title: NSCLC 20 - TABchip - normoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 20

value: NSCLC 20


title: NSCLC 12 - TABchip - hypoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 12

source_name: non-small-cell lung tumor, hypoxic, TAB-chip

value: NSCLC 12

value: hypoxic


title: NSCLC 13 - TABchip - normoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 13

value: NSCLC 13


title: NSCLC 21 - TABchip - normoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 21

value: NSCLC 21


title: NSCLC 14 - TABchip - normoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 14

value: NSCLC 14


title: NSCLC 11 - TABchip - hypoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 11

value: NSCLC 11


title: NSCLC 18 - TABchip - normoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 18

value: DNA was glycosylated and TET-oxidized as described by Yu and colleagues (Nat Protoc 2012).

value: NSCLC 18


title: NSCLC 8 - TABchip - hypoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 8

value: NSCLC 8

value: TABchip


title: NSCLC 5 - TABchip - hypoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 5

value: NSCLC 5


title: NSCLC 6 - TABchip - hypoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 6

value: NSCLC 6


title: P3 Math1-Cre;Atr-loxP/loxP;p53-loxP/loxP [1843_4]

city: Chapel Hill

first: Timothy

last: Gershon

state: NC

address: 6109 Neuroscience Research Building

department: Pediatric Hematology Oncology

institute: University of North Carolina at Chapel Hill

description: poly-A selected

hyb_protocol: Fragmented and labeled cDNA was then added to a hybridization cocktail (25 µg/µl fragmented cDNA, 50 pM control oligonucleotide B2, BioB, BioC, BioD and cre hybridization controls, 7 % DMSO, 100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween 20).  Affymetrix arrays (Affymetrix, Santa Clara, CA) were hybridized for 16 hours at 45°C in the GeneChip Hybridization Oven 645 (Affymetrix). The arrays were washed and stained with R-phycoerythrin streptavidin in the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: The arrays were scanned with the GeneChip Scanner 3000 7G Plus with autoloader. GeneChip Command Console Software (AGCC) was used for washing, staining and scanning control of the instrumentation.  Affymetrix Expression Console Software was used for basic data analysis and quality control.

data_processing: Downstream analysis was with Partek

label: biotin

organism: Mus musculus

source_name: P3 cerebellum

label_protocol: Total RNA was used to synthesize fragmented and labeled sense-strand cDNA and hybridize onto Affymetrx arrays. The Affymetrix GeneChip® WT PLUS Reagent Kit Manual was followed to prepare the samples. Briefly, the GeneChip® WT PLUS Reagent Kit (Affymetrix) was used to generate sense-strand cDNA from total RNA. Following synthesis of sense-strand cDNA, the cDNA was fragmented and labeled with the Affymetrix GeneChip Terminal Labeling Kit.

extract_protocol: Cerebella were harvested, meninges were removed from cerebella, and RNA was extracted immediately using the RNeasy Mini Kit (Qiagen #74104). Analysis was performed with 500 ng of total RNA

tag: strain

value: cerebellum

tag: age

value: Postnatal day 3

tag: genotype


title: NSCLC 10 - TABchip - hypoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 10

value: NSCLC 10


title: P3 Math1-Cre;p53-loxP/loxP [1843_7]

description: poly-A selected

tag: tissue


title: P3 Math1-Cre;p53-loxP/loxP [1845_4]

description: poly-A selected


title: NSCLC 9 - TABchip - hypoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 9

value: NSCLC 9


title: NSCLC 7 - TABchip - hypoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 7

value: NSCLC 7


title: P3 Math1-Cre;Atr-loxP/loxP;p53-loxP/loxP [1843_10]

description: poly-A selected


title: P3 Math1-Cre;p53-loxP/loxP [1845_11]

description: poly-A selected


title: P3 Math1-Cre;Atr-loxP/loxP;Bax-loxP/loxP;Bak--/- [1836_9]

description: poly-A selected


title: P3 Math1-Cre;Atr-loxP/loxP;Bax-loxP/loxP;Bak--/- [1836_3]

description: poly-A selected


title: P3 Math1-Cre;Atr-loxP/loxP;Bax-loxP/loxP;Bak--/- [1836_8]

description: poly-A selected


title: P3 Math1-Cre;Bax-loxP/loxP;Bak--/- [1842_11]

description: poly-A selected


title: HCT_DMSO_3d-2

city: Cambridge

first: Raymond

last: Pagliarini

state: MA

address: 250 Massachusetts Ave, Room 3C-292

institute: Novartis

description: HCT116 cells treated with 0.05% DMSO for 3 days

hyb_protocol: Hybridisation was performed according to manufacturer’s protocol, at Integragen, France

scan_protocol: Scanning was performed according to manufacturer’s protocol, at Integragen, France

data_processing:
Generation of methylation data using Bioconductor minfi package (from idat files)
Normalized beta values from Subset-quantile Within Array Normalisation (SWAN) implemented in the Bioconductor minfi package

label: Cy3 and Cy5

source_name: WT HCT116,0.05% DMSO,3 days

label_protocol: Labelling was performed according to manufacturer’s protocol, at  Integragen, France

growth_protocol: Parental, wild type HCT116 human cell line, 2 isogenic mutant IDH1 cell lines (IDH1-R132C/+ 2A9 clone & IDH1-R132H/+ 2H1 clone) were grown in DMEM with 10% FCS and 1% Non-Essential AminoAcides. IDH1 mutant tumor xenografts were grown.

extract_protocol: Genomic DNA was extracted according to manufacturer’s instruction using the Qiagen AllPrep kit (Qiagen #80204).

treatment_protocol: Treated with DMSO (0.05%), IDH889 (3uM in DMSO) for 3, 7, 14 or 28 days. Cells were kept in culture with regular splitting and compound was replaced twice weekly. Xenograft models were doeded with IDH889 orally at 200 mg/kg.

value: cell line

tag: mutant

value: WT HCT116

tag: duration

value: 3 days


title: HCT_DMSO_7d

description: HCT116 cells treated with 0.03% DMSO for 7 days

source_name: WT HCT116,0.03% DMSO,7 days

tag: cell line

value: 7 days


title: NSCLC 3 - TABchip - hypoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 3

value: NSCLC 3

value: hypoxic


title: HCT_DMSO_3d-1

description: HCT116 cells treated with 0.03% DMSO for 3 days

source_name: WT HCT116,0.03% DMSO,3 days

tag: treatment


title: HCT_DMSO_28d

description: HCT116 cells treated with 0.03% DMSO for 28 days

source_name: WT HCT116,0.03% DMSO,28 days

value: 28 days


title: NSCLC 1 - TABchip - hypoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 1

value: DNA was glycosylated and TET-oxidized as described by Yu and colleagues (Nat Protoc 2012).

value: NSCLC 1


title: HCT_889_7d

description: HCT116 cells treated with 3uM IDH889 for 7 days

source_name: WT HCT116,3uM IDH889,7 days

value: 3uM IDH889


title: HCT_DMSO_14d

description: HCT116 cells treated with 0.03% DMSO for 14 days

source_name: WT HCT116,0.03% DMSO,14 days

value: 14 days


title: NSCLC 24 - BSchip - normoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 48

source_name: non-small-cell lung tumor, normoxic, BS-chip

value: NSCLC 24

value: BSchip

value: normoxic


title: NSCLC 22 - BSchip - normoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 46

value: NSCLC 22


title: NSCLC 2 - TABchip - hypoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 2

value: NSCLC 2

value: TABchip


title: HCT_889_14d

description: HCT116 cells treated with 3uM IDH889 for 14 days

source_name: WT HCT116,3uM IDH889,14 days

value: cell line


title: P3 Math1-Cre;Bax-loxP/loxP;Bak--/- [100019_9]

description: poly-A selected

value: cerebellum

value: Postnatal day 3


title: NSCLC 4 - TABchip - hypoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 4

value: NSCLC 4


title: HCT_889_28d

description: HCT116 cells treated with 3uM IDH889 for 28 days

source_name: WT HCT116,3uM IDH889,28 days

value: WT HCT116


title: NSCLC 21 - BSchip - normoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 45

value: NSCLC 21


title: Spleen_Mock_Infected_12Mdays_rep3 [8049x8010]

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

hyb_protocol: Hydridized according to the manufacturer's protocol. http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf

scan_protocol: Scanned according to the manufacturer's protocol. http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf

data_processing: nSolver software, background and internal control standardization. Normalization was performed in nsolver with house keeping genes as internal controls

label: nanostring oligonucleotide probe

label_protocol: Labeled according to the manufacturer's protocol. http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf

extract_protocol: Total RNA was extracted using the RiboPure Kit

tag: timepoint

value: spleen

tag: infection

value: Mock


title: P3 Math1-Cre;Bax-loxP/loxP;Bak--/- [100019_7]

description: poly-A selected


title: HCT116_m3

description: HCT116 xenograft mouse 3

source_name: Xeno WT HCT116 3,Vehicule,48 days

value: xenograft

value: Xeno WT HCT116 3

value: Vehicule

value: 48 days


title: NSCLC 23 - BSchip - normoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 47

value: NSCLC 23

value: BSchip


title: HCT_889_3d

description: HCT116 cells treated with 3uM IDH889 for 3 days

source_name: WT HCT116,3uM IDH889,3 days

value: 3uM IDH889

value: 3 days


title: Spleen_Mock_Infected_12Mdays_rep2 [8049x8010]


title: NSCLC 20 - BSchip - normoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 44

value: NSCLC 20

value: normoxic


title: HCT116_m2

description: HCT116 xenograft mouse 2

source_name: Xeno WT HCT116 2,Vehicule,48 days

value: Xeno WT HCT116 2


title: R132H_m3

description: HCT116 IDH1-R132H R132H xenograft mouse 3

source_name: Xeno MUT IDH1 R132H 3,Vehicule,48 days

value: Xeno MUT IDH1 R132H 3


title: HCT116_DMSO_7d

description: HCT116 cells treated with 0.03% DMSO for 7 days

value: cell line

value: 7 days


title: Spleen_West Nile Virus_Infected_12days_rep3 [8049x8010]

source_name: Spleen_West Nile Virus_Infected_12days

value: West Nile Virus


title: Spleen_Mock_Infected_12Mdays_rep1 [8049x8010]

value: spleen


title: NSCLC 17 - BSchip - normoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 41

value: NSCLC 17


title: R132H_m2

description: HCT116 IDH1-R132H R132H xenograft mouse 2

source_name: Xeno MUT IDH1 R132H 2,Vehicule,48 days

value: xenograft

value: Xeno MUT IDH1 R132H 2


title: NSCLC 18 - BSchip - normoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 42

value: NSCLC 18


title: Spleen_West Nile Virus_Infected_12days_rep2 [8049x8010]


title: NSCLC 19 - BSchip - normoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 43

value: NSCLC 19


title: NSCLC 16 - BSchip - normoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 40

value: NSCLC 16


title: Spleen_West Nile Virus_Infected_12days_rep1 [8049x8010]


title: Spleen_West Nile Virus_Infected_7days_rep3 [8049x8010]

source_name: Spleen_West Nile Virus_Infected_7days


title: R132H_DMSO_7d-2

description: HCT116 IDH1-R132H R132H cells treated with 0.03% DMSO for 7 days

source_name: MUT IDH1 R132H ,0.03% DMSO,7 days

value: HCT116 IDH1-R132H

value: MUT IDH1 R132H


title: NSCLC 15 - BSchip - normoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 39

value: NSCLC 15

value: BSchip


title: R132H_DMSO_7d-1


title: P3 Math1-Cre;Atr-loxP/loxP;p53-loxP/loxP [1843_3]

description: poly-A selected

source_name: P3 cerebellum

value: cerebellum

value: Postnatal day 3


title: Spleen_West Nile Virus_Infected_7days_rep1 [8049x8010]


title: NSCLC 14 - BSchip - normoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 38

value: NSCLC 14

value: normoxic


title: R132H_DMSO_3d-2

description: HCT116 IDH1-R132H R132H cells treated with 0.05% DMSO for 3 days

source_name: MUT IDH1 R132H ,0.05% DMSO,3 days

value: cell line

value: 3 days


title: R132H_DMSO_3d-1

description: HCT116 IDH1-R132H R132H cells treated with 0.03% DMSO for 3 days

source_name: MUT IDH1 R132H ,0.03% DMSO,3 days


title: R132H_DMSO_28d

description: HCT116 IDH1-R132H R132H cells treated with 0.03% DMSO for 28 days

source_name: MUT IDH1 R132H ,0.03% DMSO,28 days

value: 28 days


title: Spleen_West Nile Virus_Infected_4days_rep3 [8049x8010]

source_name: Spleen_West Nile Virus_Infected_4days

value: spleen

value: West Nile Virus


title: NSCLC 9 - BSchip - hypoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 33

source_name: non-small-cell lung tumor, hypoxic, BS-chip

value: NSCLC 9

value: hypoxic


title: NSCLC 12 - BSchip - hypoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 36

value: NSCLC 12


title: R132H_889_3d

description: HCT116 IDH1-R132H R132H cells treated with 3uM IDH889 for 3 days

source_name: MUT IDH1 R132H ,3uM IDH889,3 days

value: 3uM IDH889


title: NSCLC 13 - BSchip - normoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 37

source_name: non-small-cell lung tumor, normoxic, BS-chip

value: NSCLC 13


title: Spleen_West Nile Virus_Infected_7days_rep2 [8049x8010]


title: R132H_889_28d

description: HCT116 IDH1-R132H R132H cells treated with 3uM IDH889 for 28 days

source_name: MUT IDH1 R132H ,3uM IDH889,28 days

value: HCT116 IDH1-R132H

value: MUT IDH1 R132H


title: Spleen_West Nile Virus_Infected_4days_rep1 [8049x8010]


title: NSCLC 10 - BSchip - hypoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 34

value: NSCLC 10

value: BSchip


title: Spleen_Mock_Infected_12Mdays_rep3 [8048x8026]

value: Mock


title: NSCLC 11 - BSchip - hypoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 35

value: NSCLC 11


title: R132H_DMSO_14d

description: HCT116 IDH1-R132H R132H cells treated with 0.03% DMSO for 14 days

source_name: MUT IDH1 R132H ,0.03% DMSO,14 days

value: 14 days


title: R132H_889_14d

description: HCT116 IDH1-R132H R132H cells treated with 3uM IDH889 for 14 days

source_name: MUT IDH1 R132H ,3uM IDH889,14 days

value: cell line


title: Spleen_Mock_Infected_12Mdays_rep1 [8048x8026]


title: Spleen_West Nile Virus_Infected_4days_rep2 [8049x8010]


title: NSCLC 6 - BSchip - hypoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 30

value: NSCLC 6


title: R132H_889_7d

description: HCT116 IDH1-R132H R132H cells treated with 3uM IDH889 for 7 days

source_name: MUT IDH1 R132H ,3uM IDH889,7 days

value: 7 days


title: Spleen_Mock_Infected_12Mdays_rep2 [8048x8026]

value: spleen


title: Spleen_West Nile Virus_Infected_12days_rep3 [8048x8026]

value: West Nile Virus


title: NSCLC 5 - BSchip - hypoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 29

value: NSCLC 5


title: Spleen_West Nile Virus_Infected_12days_rep2 [8048x8026]


title: R132H_25mpkBIDx2_m4

description: HCT116 IDH1-R132H R132H xenograft treated with 25mpk IDH889 BIDx2 mouse 4

source_name: Xeno MUT IDH1 R132H 4,25mpk IDH889 BIDx2 ,72 hrs

value: xenograft

value: Xeno MUT IDH1 R132H 4

value: 25mpk IDH889 BIDx2

value: 72 hrs


title: NSCLC 4 - BSchip - hypoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 28

value: NSCLC 4

value: hypoxic


title: NSCLC 8 - BSchip - hypoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 32

value: NSCLC 8


title: NSCLC 7 - BSchip - hypoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 31

value: NSCLC 7

value: BSchip


title: Spleen_West Nile Virus_Infected_12days_rep1 [8048x8026]

source_name: Spleen_West Nile Virus_Infected_12days


title: NSCLC 1 - BSchip - hypoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 25

value: NSCLC 1


title: Spleen_West Nile Virus_Infected_7days_rep2 [8048x8026]


title: Spleen_West Nile Virus_Infected_7days_rep3 [8048x8026]


title: NSCLC 2 - BSchip - hypoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 26

value: NSCLC 2


title: Spleen_West Nile Virus_Infected_7days_rep1 [8048x8026]


title: R132H_25mpkBIDx2_m2

description: HCT116 IDH1-R132H R132H xenograft treated with 25mpk IDH889 BIDx2 mouse 2

source_name: Xeno MUT IDH1 R132H 2,25mpk IDH889 BIDx2 ,72 hrs

value: Xeno MUT IDH1 R132H 2


title: Spleen_West Nile Virus_Infected_4days_rep3 [8048x8026]


title: COP

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description: Enriched methylated DNA (cy5) and genomic DNA (cy3) of each sample were competitively hybridizated to Human DNA Methylation microarrays platforms (Agilent)

hyb_protocol: The control genomic DNA and methylated dsDNA  labeled with Cy3 and Cy5 dye were competitively hybridized to Human DNA Methylation microarrays platforms.The hybridization was carried out at 67°C for 40 hours in a hybridization oven rotator (Agilent). The arrays were washed with Agilent ChiP-on-chip wash buffers as suggest by the supplier.

scan_protocol: Slides were scanned on an Agilent microarray scanner (model G2565CA), and Agilent Feature Extraction software version 10.7.3.1 was used for image analysis.

data_processing: Probe log ratio signals were Loess  and linear normalized .Inter-array normalization was performed with quantile normalization. Feature Extraction Software (Agilent) provides spot quality measures in order to evaluate the quality and the reliability of the hybridization data. In particular, flag glsFound  and “rlsFound”(set to 1 if the spot had an intensity value that was significantly different from the local background or to 0 in any other case) was used to filter out unreliable probes: flag equal to 0 was to be noted as not available (NA). In order to make more robust and unbiased statistical analyses, probes with a high proportion of NA values were removed from the dataset. Twenty-five percent of NA was used as the threshold in the filtering process, obtaining a total of 90,591 available probes.

source_name: COP_enriched methylated DNA

label_protocol: The control genomic DNA and enriched methylated dsDNA were labeled with Cy3 and Cy5 dye respectively using Agilent Genomic DNA labeling kit PLUS (Agilent)according to the manufacturer’s instructions

growth_protocol: fresh or frozen tumor tissue

extract_protocol: Genomic DNA was isolated from  RMS tumor biopsies using Trizol Reagent (Life Technologies) after RNA extraction, following the manufacturer’s protocol. The commercially available Qiamp DNA mini Kit (Qiagen) was used to DNA purification. Four ug of genomic DNA were fragmented using a sonicator, purified using Mini-Elute coloumns (Qiagen) and the amount of double-strand DNA (dsDNA) was measured using Qubit instrument. The success of fragmentation was evaluated using the Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). The MethylMiner Methylated DNA enrichment kit (Invitrogen, Life technologies) was used to the enrichment and fractioned of methylated dsDNA starting from 2ug of fragmented whole genomic DNA. Ten ng of methylated dsDNA for each sample was amplified using Whole genome Amplification (WGA, Sigma-Aldrich).

value: RMS tumor tissue

tag: tumor stage

value: stage III

source_name: COP_genomic DNA


title: CAS

source_name: CAS_enriched methylated DNA

source_name: CAS_genomic DNA


title: MES

source_name: MES_enriched methylated DNA

source_name: MES_genomic DNA


title: Epididymal fat wild type rep4

city: Trento

first: Alessandro

last: Provenzani

address: via delle regole 101

department: CIBIO

institute: University of Trento

description:
Gene expression after high fat diet in wild type mice
EPI-FAT   WT-4

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (average specific activity =12 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse Gene Expression 4x44K Microarray (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using the AgilentHD_GX_1Color Profile (Scan Area: 61x21.6 mm; Scan resolution: 5 mm, dye channel set to 100% Green PMT) of Agilent ScanControl software 8.1.3 (Agilent Technologies).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Limma package, background correction: normexp, Lowess normalized signal intensity

source_name: Epididymal_fat_wild type

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low Input Quick Amp Labeling Kit (p/n 5190-2331, Agilent Technologies)  according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mice were kept at the facility of the divison of Physiology University of Fribourg under standard  conditions of 12-h light and 12-h dark cycles at room temperature (23 °C)

extract_protocol: RNA was extracted from either  skin, liver, or epididymal adipose tissue by the guanidinium thiocyanate method

treatment_protocol: High Fat Diet from weaning 5 weeks of age until 44 weeks of age

tag: strain background

tag: genotype/variation

value: wild type

tag: gender

value: male

value: 45 weeks

tag: diet

value: high fat diet

value: Epididymal Fat


title: Spleen_West Nile Virus_Infected_4days_rep2 [8048x8026]

source_name: Spleen_West Nile Virus_Infected_4days

value: spleen

value: West Nile Virus


title: ALI

source_name: ALI_enriched methylated DNA

source_name: ALI_genomic DNA


title: MEN

source_name: MEN_enriched methylated DNA

source_name: MEN_genomic DNA


title: Spleen_West Nile Virus_Infected_4days_rep1 [8048x8026]


title: NSCLC 3 - BSchip - hypoxic

description:
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 27

source_name: non-small-cell lung tumor, hypoxic, BS-chip

tag: dna pretreatment

tag: batch

tag: tumor name

value: NSCLC 3

tag: tabchip or bschip


title: R132H_25mpkBIDx2_m5

description: HCT116 IDH1-R132H R132H xenograft treated with 25mpk IDH889 BIDx2 mouse 5

source_name: Xeno MUT IDH1 R132H 5,25mpk IDH889 BIDx2 ,72 hrs

value: xenograft

value: Xeno MUT IDH1 R132H 5

value: 25mpk IDH889 BIDx2

value: 72 hrs


title: SEL

source_name: SEL_enriched methylated DNA

value: stage IV

source_name: SEL_genomic DNA


title: MIR

source_name: MIR_enriched methylated DNA

value: stage II

source_name: MIR_genomic DNA


title: R132C_DMSO_7d-2

description: HCT116 IDH1-R132C R132C cells treated with 0.03% DMSO for 7 days

source_name: MUT IDH1 R132C ,0.03% DMSO,7 days

value: cell line

value: HCT116 IDH1-R132C

value: MUT IDH1 R132C

value: 7 days


title: PIE

source_name: PIE_enriched methylated DNA

value: RMS tumor tissue

source_name: PIE_genomic DNA


title: R132C_DMSO_7d-1


title: COL

source_name: COL_enriched methylated DNA

source_name: COL_genomic DNA


title: Spleen_Mock_Infected_12Mdays_rep2 [8021x16072]

value: Mock


title: Spleen_Mock_Infected_12Mdays_rep1 [8021x16072]


title: Spleen_Mock_Infected_12Mdays_rep3 [8021x16072]


title: R132C_DMSO_3d-2

description: HCT116 IDH1-R132C R132C cells treated with 0.05% DMSO for 3 days

source_name: MUT IDH1 R132C ,0.05% DMSO,3 days

value: 3 days


title: R132H_25mpkBIDx2_m1

description: HCT116 IDH1-R132H R132H xenograft treated with 25mpk IDH889 BIDx2 mouse 1

source_name: Xeno MUT IDH1 R132H 1,25mpk IDH889 BIDx2 ,72 hrs

value: Xeno MUT IDH1 R132H 1


title: Spleen_West Nile Virus_Infected_12days_rep3 [8021x16072]

source_name: Spleen_West Nile Virus_Infected_12days

value: spleen


title: R132C_DMSO_28d

description: HCT116 IDH1-R132C R132C cells treated with 0.03% DMSO for 28 days

source_name: MUT IDH1 R132C ,0.03% DMSO,28 days

value: 28 days


title: R132C_889_7d

description: HCT116 IDH1-R132C R132C cells treated with 3uM IDH889 for 7 days

source_name: MUT IDH1 R132C ,3uM IDH889,7 days

value: 3uM IDH889


title: Liver wild type rep3

description:
Gene expression after high fat diet in wild type mice
LIVER   WT-3

source_name: Liver_wild type

value: wild type

value: male

tag: age

value: 45 weeks

value: high fat diet

value: Liver


title: Spleen_West Nile Virus_Infected_12days_rep2 [8021x16072]

tag: tissue

value: West Nile Virus


title: R132C_DMSO_3d-1

description: HCT116 IDH1-R132C R132C cells treated with 0.03% DMSO for 3 days

source_name: MUT IDH1 R132C ,0.03% DMSO,3 days

value: cell line

tag: mutant


title: Spleen_West Nile Virus_Infected_7days_rep3 [8021x16072]

source_name: Spleen_West Nile Virus_Infected_7days


title: R132H_25mpkBIDx2_m3

description: HCT116 IDH1-R132H R132H xenograft treated with 25mpk IDH889 BIDx2 mouse 3

source_name: Xeno MUT IDH1 R132H 3,25mpk IDH889 BIDx2 ,72 hrs

value: xenograft

value: Xeno MUT IDH1 R132H 3

value: 25mpk IDH889 BIDx2

tag: duration

value: 72 hrs


title: Epididymal fat wild type rep3

description:
Gene expression after high fat diet in wild type mice
EPI-FAT   WT-3

source_name: Epididymal_fat_wild type

value: Epididymal Fat


title: Spleen_West Nile Virus_Infected_7days_rep2 [8021x16072]


title: BIO

source_name: BIO_enriched methylated DNA

value: RMS tumor tissue

value: stage IV

source_name: BIO_genomic DNA


title: Epididymal fat wild type rep1

description:
Gene expression after high fat diet in wild type mice
EPI-FAT   WT-1


title: Spleen_West Nile Virus_Infected_7days_rep1 [8021x16072]

value: spleen


title: BER

source_name: BER_enriched methylated DNA

source_name: BER_genomic DNA


title: Skin wild type rep2

description:
Gene expression after high fat diet in wild type mice
SKIN   WT-2

source_name: Skin_wild type

value: Skin


title: Liver wild type rep2

description:
Gene expression after high fat diet in wild type mice
LIVER   WT-2


title: R132C_DMSO_14d

description: HCT116 IDH1-R132C R132C cells treated with 0.03% DMSO for 14 days

source_name: MUT IDH1 R132C ,0.03% DMSO,14 days

tag: cell line

value: HCT116 IDH1-R132C

value: MUT IDH1 R132C

value: 14 days


title: Skin wild type rep3

description:
Gene expression after high fat diet in wild type mice
SKIN   WT-3

value: wild type

value: male

value: 45 weeks


title: Liver wild type rep1

description:
Gene expression after high fat diet in wild type mice
LIVER   WT-1

value: high fat diet

value: Liver


title: GAI

description: Enriched methylated DNA (cy5) and genomic DNA (cy3) of each sample were competitively hybridizated to Human DNA Methylation microarrays platforms (Agilent)

source_name: GAI_enriched methylated DNA

source_name: GAI_genomic DNA


title: Skin wild type rep1

description:
Gene expression after high fat diet in wild type mice
SKIN   WT-1


title: GUI

source_name: GUI_enriched methylated DNA

source_name: GUI_genomic DNA


title: Epididymal fat JNK1 Knock-out rep3

description:
Gene expression after high fat diet in JNK1 KO mice
EPI-FAT JNK1 KO-3

source_name: Epididymal_fat_JNK1 knock-out

value: JNK1 Knock-out


title: Spleen_West Nile Virus_Infected_4days_rep3 [8021x16072]

source_name: Spleen_West Nile Virus_Infected_4days

value: West Nile Virus


title: R132C_889_28d

description: HCT116 IDH1-R132C R132C cells treated with 3uM IDH889 for 28 days

source_name: MUT IDH1 R132C ,3uM IDH889,28 days

value: cell line

tag: treatment

value: 3uM IDH889

value: 28 days


title: R132C_889_3d

description: HCT116 IDH1-R132C R132C cells treated with 3uM IDH889 for 3 days

source_name: MUT IDH1 R132C ,3uM IDH889,3 days

value: 3 days


title: R132C_889_14d

description: HCT116 IDH1-R132C R132C cells treated with 3uM IDH889 for 14 days

source_name: MUT IDH1 R132C ,3uM IDH889,14 days


title: Spleen_Mock_Infected_12Mdays_rep3 [8024x8049]

tag: timepoint

value: Mock


title: Spleen_Mock_Infected_12Mdays_rep1 [8024x8049]

value: spleen

tag: infection


title: Spleen_West Nile Virus_Infected_4days_rep2 [8021x16072]


title: Spleen_West Nile Virus_Infected_12days_rep3 [8024x8049]

source_name: Spleen_West Nile Virus_Infected_12days


title: Spleen_West Nile Virus_Infected_7days_rep3 [8024x8049]

source_name: Spleen_West Nile Virus_Infected_7days


title: Spleen_West Nile Virus_Infected_12days_rep2 [8024x8049]


title: Spleen_West Nile Virus_Infected_12days_rep1 [8024x8049]


title: Spleen_Mock_Infected_12Mdays_rep2 [8024x8049]


title: Spleen_West Nile Virus_Infected_7days_rep2 [8024x8049]


title: Epididymal fat JNK1 Knock-out rep2

description:
Gene expression after high fat diet in JNK1 KO mice
EPI-FAT JNK1 KO-2

value: Epididymal Fat


title: Liver JNK1 Knock-out rep2

description:
Gene expression after high fat diet in JNK1 KO mice
LIVER JNK1 KO-2

source_name: Liver_JNK1 knock-out


title: Liver JNK1 Knock-out rep1

description:
Gene expression after high fat diet in JNK1 KO mice
LIVER JNK1 KO-1


title: Skin JNK1 Knock-out rep3

description:
Gene expression after high fat diet in JNK1 KO mice
SKIN JNK1 KO-3

source_name: Skin_JNK1 knock-out

value: Skin


title: Skin JNK1 Knock-out rep2

description:
Gene expression after high fat diet in JNK1 KO mice
SKIN JNK1 KO-2


title: Epididymal fat JNK1 Knock-out rep4

description:
Gene expression after high fat diet in JNK1 KO mice
EPI-FAT JNK1 KO-4


title: Skin JNK1 Knock-out rep4

description:
Gene expression after high fat diet in JNK1 KO mice
SKIN JNK1 KO-4


title: Liver JNK1 Knock-out rep3

description:
Gene expression after high fat diet in JNK1 KO mice
LIVER JNK1 KO-3


title: Spleen_West Nile Virus_Infected_7days_rep1 [8024x8049]


title: Skin JNK1 Knock-out rep1

description:
Gene expression after high fat diet in JNK1 KO mice
SKIN JNK1 KO-1


title: Epididymal fat JNK1 Knock-out rep1

description:
Gene expression after high fat diet in JNK1 KO mice
EPI-FAT JNK1 KO-1


title: Spleen_West Nile Virus_Infected_4days_rep3 [8024x8049]


title: Spleen_West Nile Virus_Infected_4days_rep2 [8024x8049]


title: Spleen_West Nile Virus_Infected_4days_rep1 [8024x8049]


title: Lhx2_10ng/ml TGFb_2h_rep2

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

description:
TGFB_2
Gene expression 2 hr after treatment.

hyb_protocol: Agilent’s recommended procedures (Version 5.7, March 2008) were followed for the hybridization and washing of Agilent 60-mer oligonucleotide microarrays.

scan_protocol: Arrays were scanned using the Agilent microarray scanner. Agilent's recommended procedures (Version 5.7, March 2008) were followed for the scanning and feature extraction of Agilent 60-mer oligonucleotide microarrays for microarray-based one-color gene expression analysis.

data_processing: Arrays were normalized using cyclic-loess, and differentially expressed genes were identified using LIMMA (16646809) FDR< 0.2. Expression profiles were clustered using Genesis (11836235).

source_name: Lhx2, TGFb, 2h

label_protocol: Agilent’s recommended procedures (Version 5.7, March 2008) were followed for the preparation and labeling of cDNA for microarray-based one-color gene expression analysis.

growth_protocol: Lhx2 cells were cultured in Iscove's modified Dulbecco’s medium containing L-glutamine and 25 mM HEPES (IMDM; Thermo scientific), supplemented with P/S, 10-4 2-Mercaptoethanol (Sigma-Aldrich), 5% FCS, 100 ng/ml mSCF and 10 ng/ml human interleukin 6 (hIL-6; (PeproTech).

extract_protocol: Total cellular RNA was isolated using Trizol reagent (Invitrogen) according to manufacturer’s protocol.

treatment_protocol: Prior to global gene expression analysis, Lhx2 cells were serum-starved (FCS was replaced by 0.5% BSA; StemCell Technologies) over night before treatment with 10 ng/ml TGF-β1 for 2 h.

value: TGFb


title: CD4+ T Cell_WT_T24_rep4

city: Toulouse

first: Anne

middle: S

last: Dejean

state: Haute-Garonne

address: Hopital Purpan

country: France

institute: INSERM

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE microarray (8X60K, Design 028005)  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 028005_D_F_20120201). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} After quality controls on raw data, we decided to exlude the samples KO_T24_24 and KO_T0_7 fom the study, getting 22 samples out of 24. We then selected the spots with a minimal weight of 1 for 18 out of 22 microarrays or with a minimal weight of 3 per group from at least one experimental group. At this step, 25497 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 23623 rows each corresponding to a unique ProbeName (provided as data Matrix) and 22 columns corresponding to the 22 samples selected out of 24 from original design.

source_name: CD4+ T Cell_WT_T24

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked with the Nanodrop ND2000 spectrophotometer (Thermo Scientific).

extract_protocol: RNA was prepared using the Quiagen Purification kit (ref # 74034) following the manufacturer's recommendations.

treatment_protocol: naive (CD62Lhigh, CD25low) CD4 T cells were either unstimulated (T0) or stimulated in vitro with 2 μg/mL of anti-CD3 mAbs for 12 (T12) or 24 hours (T24)

value: WT

tag: cell type

value: naive (CD62Lhigh, CD25low) CD4 T cells

tag: stimulated with

value: 2 μg/mL of anti-CD3 mAbs

tag: time point


title: Spleen_Mock_Infected_12Mdays_rep3 [15155x8054]


title: Spleen_Mock_Infected_12Mdays_rep2 [15155x8054]


title: Lhx2_10ng/ml TGFb_2h_rep3

description:
TGFB_3
Gene expression 2 hr after treatment.


title: Spleen_Mock_Infected_12Mdays_rep1 [15155x8054]


title: Spleen_West Nile Virus_Infected_12days_rep3 [15155x8054]


title: CD4+ T Cell_WT_T24_rep3

tag: strain background

tag: genotype/variation


title: Spleen_West Nile Virus_Infected_12days_rep1 [15155x8054]


title: Spleen_West Nile Virus_Infected_12days_rep2 [15155x8054]


title: CD4+ T Cell_WT_T24_rep2


title: Lhx2_0ng/ml TGFb_2h_rep3

description:
Untreated_3
Gene expression 2 hr after no treatment.

source_name: Lhx2, untreated, 2h


title: CD4+ T Cell_WT_T24_rep1


title: CD4+ T Cell_WT_T12_rep4

source_name: CD4+ T Cell_WT_T12


title: Epididymal fat wild type rep2

description:
Gene expression after high fat diet in wild type mice
EPI-FAT   WT-2

source_name: Epididymal_fat_wild type

value: wild type

tag: gender

value: male

value: 45 weeks

tag: diet


title: Lhx2_0ng/ml TGFb_2h_rep2

description:
Untreated_2
Gene expression 2 hr after no treatment.


title: CD4+ T Cell_WT_T12_rep3


title: Spleen_West Nile Virus_Infected_7days_rep3 [15155x8054]


title: CD4+ T Cell_WT_T12_rep1


title: CD4+ T Cell_WT_T0_rep3

source_name: CD4+ T Cell_WT_T0

value: none (unstimulated)


title: Epi_LG_rep1

first: MICHAEL

last: MINGUENEAU

address: 115 Broadway

department: Immunology

institute: Biogen

description: Gene expression data from ex vivo FACS-sorted T-cell subsets isolated from lacrimal gland and spleen cell suspensions

hyb_protocol: Two micrograms of biotin labeled sscDNA probe were hybridized to Affymetrix GeneChip HT HG-U133+ PM plate arrays with modified conditions as described in (Allaire et al., 2013, PMID: 23289891). Washing and staining of the hybridized arrays were completed as described in the GeneChip Expression analysis technical manual for HT plate arrays using the Genechip Array Station (Affymetrix) with modifications as described in (Allaire et al., 2013, PMID: 23289891).

scan_protocol: The processed GeneChip plate arrays were scanned using GeneTitan scanner (Affymetrix).

data_processing: The data were analyzed with Partek Genomics Suite (Partek) using Affymetrix default analysis settings: RMA background correction, quantile normalization and median polish probeset summarization (log2).

source_name: Lacrimal gland 16w NOD male

label_protocol: The amount of isolated RNA was normalized and automated sample amplification and biotin labeling were carried out using the NuGEN Ovation RNA Amplification system V2, Ovation WB reagent and Encore Biotin module according to manufacturer’s recommendations using an Arrayplex automated liquid handler (Beckman Coulter).

growth_protocol: cells were isolated ex vivo

extract_protocol: Total RNA was isolated using RNAqueous isolation kit (Ambion). RNA was QC'd using Bioanayzer and all samples had RIN scores >8 except: SAMPLE 145 (RIN=7.8), SAMPLE 108 (RIN=7.7), SAMPLE 111 (RIN=7.2).

treatment_protocol: Lacrimal gland cell suspensions were prepared by mechanical dissociation and enzymatic digestion before FACS cell sorting of epithelial and immune cell subsets. Each cell subset was sorted directly into lysis buffer on a FACSAria cytometer (BD Biosciences). Lysates were stored at -80°C until processing.

value: lacrimal gland

tag: subset

value: Epithelial


title: Lhx2_0ng/ml TGFb_2h_rep1

description:
Untreated_1
Gene expression 2 hr after no treatment.


title: CD4+ T Cell_WT_T0_rep4


title: Spleen_West Nile Virus_Infected_7days_rep2 [15155x8054]

value: West Nile Virus


title: Lhx2_10ng/ml TGFb_2h_rep1

description:
TGFB_1
Gene expression 2 hr after treatment.


title: Epi_LG_rep3


title: CD4T_Spleen_rep3

source_name: Spleen 16w NOD male


title: Epi_LG_rep2


title: CD4T_Spleen_rep2


title: CD4+ T Cell_WT_T0_rep2


title: Spleen_West Nile Virus_Infected_7days_rep1 [15155x8054]


title: CD4T_LG_rep4


title: CD4+ T Cell_WT_T0_rep1


title: CD4+ T Cell_WT_T12_rep2


title: Spleen_West Nile Virus_Infected_4days_rep2 [15155x8054]


title: Spleen_West Nile Virus_Infected_4days_rep3 [15155x8054]


title: CD4+ T Cell_Foxo3-/-_T24_rep3

source_name: CD4+ T Cell_Foxo3-/-_T24


title: Spleen_Mock_Infected_12Mdays_rep3 [8002x3032]


title: CD4T_Spleen_rep1


title: CD4+ T Cell_Foxo3-/-_T24_rep2


title: CD4T_LG_rep3


title: CD4+ T Cell_Foxo3-/-_T12_rep4

source_name: CD4+ T Cell_Foxo3-/-_T12


title: CD4+ T Cell_Foxo3-/-_T24_rep1


title: CD4T_LG_rep2


title: Spleen_Mock_Infected_12Mdays_rep2 [8002x3032]


title: B_Spleen_rep3

value: B


title: Spleen_Mock_Infected_12Mdays_rep1 [8002x3032]


title: Spleen_West Nile Virus_Infected_12days_rep3 [8002x3032]


title: Spleen_West Nile Virus_Infected_12days_rep2 [8002x3032]


title: Spleen_West Nile Virus_Infected_4days_rep1 [15155x8054]

source_name: Spleen_West Nile Virus_Infected_4days


title: B_Spleen_rep1


title: Spleen_West Nile Virus_Infected_12days_rep1 [8002x3032]


title: Spleen_West Nile Virus_Infected_7days_rep3 [8002x3032]


title: CD4+ T Cell_Foxo3-/-_T0_rep1

source_name: CD4+ T Cell_Foxo3-/-_T0


title: CD4T_LG_rep1


title: CD4+ T Cell_Foxo3-/-_T12_rep2


title: CD4+ T Cell_Foxo3-/-_T0_rep4


title: CD4+ T Cell_Foxo3-/-_T12_rep3


title: B_Spleen_rep2


title: CD4+ T Cell_Foxo3-/-_T12_rep1


title: B_LG_rep3


title: B_LG_rep4


title: B_LG_rep2


title: Spleen_West Nile Virus_Infected_7days_rep2 [8002x3032]


title: B_LG_rep1


title: Spleen_West Nile Virus_Infected_4days_rep3 [8002x3032]


title: Spleen_West Nile Virus_Infected_7days_rep1 [8002x3032]


title: Spleen_West Nile Virus_Infected_4days_rep2 [8002x3032]


title: Spleen_West Nile Virus_Infected_4days_rep1 [8021x16072]


title: Spleen_Mock_Infected_12Mdays_rep3 [8036x18018]


title: Spleen_Mock_Infected_12Mdays_rep2 [8036x18018]


title: Spleen_Mock_Infected_12Mdays_rep1 [8036x18018]


title: 20121206_PR8S_BG24

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

description: Influenza (PR8) S. aureus (Newman)

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using the Agilent G3-1-color scan setting for 8x60k arrays.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20101029). Files were imported to Analyst (GeneData, Basel, Switzerland)

source_name: wild-type C57BL/6 Broncho-alveolar lavage cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using Agilent’s Low Input Quick Amp One-Color Labeling Kit according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).

extract_protocol: Mice were sacrificed by CO2 inhalation. Broncho-alveolar lavage (BAL) was extracted with 2x 1ml HBSS. BAL was centrifuged for 5 min at 400xg. Cell pellet was resuspended in 1 ml Trizol. Samples snap frozen in liquid nitrogen.

treatment_protocol: On day 0, mice were either mock infected with PBS or influenza virus (PR8) via intranasal route (30ul). Virus aliquots stored at -80C; quick thawed to RT and immediate dilution. Viruses diluted to 100 PFU/30ul in ice-cold 1x PBS in polystyrene tubes. Virus dilution maintained at 4C until use. On day 7, mice were either mock infected with PBS or Staphylococcus aureus (Newman strain) via non-invasive intratracheal route (20ul). S. aureus stored at -80C; inoculated in LB and grew overnight at 37C 200rpm shaking. S. aureus was then subcultured and grew at 37C for 2h before diluted to 1x10^8 CFU/20ul. Mice were all female C57BL/6J from Jackson Lab.

value: Broncho-alveolar lavage cells

tag: primary infection (day 0)

value: Influenza virus (PR8)

tag: secondary infection (day 7)

value: S. aureus (Newman)

tag: strain

value: WT C57BL/6


title: Spleen_West Nile Virus_Infected_12days_rep2 [8036x18018]

source_name: Spleen_West Nile Virus_Infected_12days

tag: tissue

value: spleen


title: Spleen_West Nile Virus_Infected_12days_rep3 [8036x18018]


title: 20121206_PR8S_BG22

description: Influenza (PR8) S. aureus (Newman)


title: Spleen_West Nile Virus_Infected_4days_rep1 [8002x3032]


title: LG_naïve_rep3

extract_protocol: Total RNA was isolated using RNAqueous isolation kit (Ambion). RNA was QC'd using Bioanayzer and all samples had RIN scores >9.1 except SAMPLE 8 (RIN=7.8).

treatment_protocol: Lacrimal gland cell suspensions were prepared by mechanical dissociation and enzymatic digestion before FACS cell sorting of CD4+ T cell subsets. Each cell subset was sorted directly into lysis buffer on a FACSAria cytometer (BD Biosciences). Lysates were stored at -80°C until processing.

value: naïve

value: CD4+ T cell

tag: age

value: 16-week old

tag: Sex

value: NOD


title: Spl_CD8

value: total

value: CD8+ T cell


title: 20121206_PR8S_BG25

description: Influenza (PR8) S. aureus (Newman)


title: Spl_CD4

value: male


title: 20121206_PR8P_BG26

description: Influenza (PR8) Mock (PBS)

value: Mock (PBS)


title: CD4+ T Cell_Foxo3-/-_T0_rep2

value: naive (CD62Lhigh, CD25low) CD4 T cells

value: none (unstimulated)


title: 20121206_PR8P_BG30

description: Influenza (PR8) Mock (PBS)


title: 20120731_BA10L

description: Influenza (PR8) S. aureus (Newman)


title: LG_eTreg_rep2

value: lacrimal gland

value: eTreg


title: 20121206_PBSS_BG3

description: Mock (PBS) S. aureus (Newman)

value: Broncho-alveolar lavage cells


title: 20121206_PBSS_BG5

description: Mock (PBS) S. aureus (Newman)


title: LG_eTreg_rep3


title: LG_eTconv_rep2

value: eTconv


title: LG_eTconv_rep3


title: LG_naïve_rep2


title: LG_eTconv_rep1


title: 20120731_BA14L

description: Influenza (PR8) S. aureus (Newman)

value: Influenza virus (PR8)

value: S. aureus (Newman)


title: LG_eTreg_rep1


title: LG_naïve_rep1


title: Spleen_West Nile Virus_Infected_12days_rep1 [8036x18018]

value: spleen

value: West Nile Virus


title: 20121206_PR8P_BG29

description: Influenza (PR8) Mock (PBS)

value: WT C57BL/6


title: Spleen_West Nile Virus_Infected_7days_rep3 [8036x18018]

source_name: Spleen_West Nile Virus_Infected_7days


title: Spleen_West Nile Virus_Infected_7days_rep2 [8036x18018]


title: Spleen_West Nile Virus_Infected_4days_rep3 [8036x18018]


title: Spleen_West Nile Virus_Infected_7days_rep1 [8036x18018]


title: Spleen_West Nile Virus_Infected_4days_rep1 [8036x18018]


title: Spleen_West Nile Virus_Infected_4days_rep2 [8036x18018]


title: Spleen_Mock_Infected_12Mdays_rep2 [3252x8042]

description: 20151230_WNV2_Sample 23_11.RCC

value: Mock


title: Spleen_Mock_Infected_12Mdays_rep3 [3252x8042]

description: 20151230_WNV2_Sample 24_12.RCC


title: Spleen_West Nile Virus_Infected_12days_rep3 [3252x8042]

description: 20151230_WNV2_Sample 21_09.RCC


title: Spleen_West Nile Virus_Infected_12days_rep2 [3252x8042]

description: 20151230_WNV2_Sample 20_08.RCC


title: Spleen_Mock_Infected_12Mdays_rep1 [3252x8042]

description: 20151230_WNV2_Sample 22_10.RCC


title: Spleen_West Nile Virus_Infected_7days_rep3 [3252x8042]

description: 20151230_WNV2_Sample 18_06.RCC


title: 20120731_BA1L

description: Mock (PBS) S. aureus (Newman)


title: 20120731_BA3L

description: Mock (PBS) S. aureus (Newman)


title: 20121206_PBSP_BG6

description: Mock (PBS) Mock (PBS)


title: Hdac3 d/d 5

city: Columbia

first: Jae-Wook

last: Jeong

state: MO

address: 1030 Hitt Street

department: Obstetrics, Gynecology and Women's Health

institute: University of Missouri

description: Gene expression data from 6 weeks of age

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array.

scan_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 450. GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing:
The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. The normalized, and log transformed intensity values were then analyzed using GeneSpring GX 12.6 (Agilent technologies, CA).
Fold change filters included the requirement that the genes be present in at least 150% of controls for up-regulated genes and lower than 66% of controls for down-regulated genes. Hierarchical clustering data were clustered groups that behave similarly across experiments using GeneSpring GX 12.6 (Agilent technologies, CA). Clustering algorithm was Euclidean distance, average linkage.

source_name: uteri of Hdac3 d/d at 6 weeks of age

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Collect intact 6 week-old mice

extract_protocol: RNA was extracted from the uterine tissues using the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA).

value: Female

value: 6 weeks

value: Hdac3 d/d

value: uterus


title: Hdac3 f/f 3

source_name: uteri of Hdac3 f/f at 6 weeks of age

value: Hdac3 f/f


title: Hdac3 d/d 4


title: Liver_siControl_rep8

city: Frankfurt am Main

first: Daniel

last: Margerie

address: Industrial Park Hoechst, Building H831

department: R&D, Digital Data Sciences

country: Germany

institute: Sanofi-Aventis Deutschland GmbH

description: Gene expression data from mouse liver

hyb_protocol: 15 µg cRNA samples were fragmented at 94 degree Celsius for 35 min in 40 mM Tris/acetate pH 8.1, 100 mM KOAc and 30 mM MgOAc, added to hybridisation buffer and hybridised to Affymetrix GeneChip for 16-18 hours at 45 degree Celsius and 60 rpm in a rotating hybridization oven (Hybridization Oven 640, Affymetrix).

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data were analyzed with Array Studio (Omicsoft Corp., Cary, NC, USA) using default settings and RMA as normalization method.

label: Biotin

source_name: Mouse liver

label_protocol: Biotin-UPT and -CTP labelled cRNA was transcribed in vitro using Enzo BioArray High Yield RNA Transcript Labelling Kit (Enzo Diagnostics, NY, NY) and purified by RNeasy cleanup and ethanol precipitation.

extract_protocol: Total RNA was prepared using the Rneasy Mini Kit

treatment_protocol: 8-week-old male C57BL6/J mice were fed ad libitum a western diet consisting of a high-fat diet supplemented with 6% sucrose in the water to induce insulin resistance and hepatic lipid accumulation. All mice were maintained in individually ventilated cages (max. 5 per cage) in an environmentally controlled room with a 12 h light-dark cycle. Body weight was monitored weekly. For siRNA intervention mice were divided into three groups according to equal body weight and fat mass. For a total of 7 weeks each group was weekly injected with 1 mg modified siRNA per kg body weight in PBS of liver-selective Keap1-specific siRNA (group 1: siKeap1-1, group 2: siKeap1-2) or unspecific scrambled control siRNA (group 3: siControl) via the tail vein.

value: liver

tag: treatment

value: siControl


title: 20121206_PBSP_BG8

description: Mock (PBS) Mock (PBS)

value: Mock (PBS)


title: Liver_siControl_rep7

description: Gene expression data from mouse liver


title: Liver_siControl_rep6

description: Gene expression data from mouse liver


title: Spleen_West Nile Virus_Infected_12days_rep1 [3252x8042]

description: 20151230_WNV2_Sample 19_07.RCC

tag: timepoint


title: Liver_siControl_rep3

description: Gene expression data from mouse liver


title: Liver_siControl_rep4

description: Gene expression data from mouse liver


title: Liver_siControl_rep5

description: Gene expression data from mouse liver


title: Liver_siControl_rep2

description: Gene expression data from mouse liver


title: Liver_siControl_rep1

description: Gene expression data from mouse liver


title: Spleen_West Nile Virus_Infected_7days_rep1 [3252x8042]

description: 20151230_WNV2_Sample 16_04.RCC

tag: infection


title: Spleen_West Nile Virus_Infected_4days_rep3 [3252x8042]

description: 20151230_WNV2_Sample 15_03.RCC


title: Spleen_West Nile Virus_Infected_4days_rep1 [3252x8042]

description: 20151230_WNV2_Sample 13_01.RCC


title: Spleen_West Nile Virus_Infected_4days_rep2 [3252x8042]

description: 20151230_WNV2_Sample 14_02.RCC


title: Spleen_West Nile Virus_Infected_7days_rep2 [3252x8042]

description: 20151230_WNV2_Sample 17_05.RCC


title: Brain_Mock_Infected_12Mdays_rep3 [8049x8010]

tag: timepoint(days)

value: brain


title: Liver_siKeap1-2_rep8

description: Gene expression data from mouse liver


title: Brain_Mock_Infected_12Mdays_rep2 [8049x8010]


title: Liver_siKeap1-2_rep5

description: Gene expression data from mouse liver


title: Liver_siKeap1-2_rep6

description: Gene expression data from mouse liver


title: Liver_siKeap1-2_rep7

description: Gene expression data from mouse liver


title: Brain_Mock_Infected_12Mdays_rep1 [8049x8010]


title: Brain_West Nile Virus_Infected_12days_rep1 [8049x8010]

source_name: Brain_West Nile Virus_Infected_12days


title: Hypoxia_Ketamine_Rep2

city: Gainesville

first: Eileen

middle: I.

last: Chang

state: Florida

address: 1345 Center Drive/Room M552

department: Physiology and Functional Genomics

institute: University of Florida College of Medicine

description: Gene expression 24 hrs after 30 min hypoxia in ketamine treated fetuses

hyb_protocol: Hybridization was performed following Agilent protocol.  Briefly 600 ng of each labeled cRNA was fragmented and then mixed with hybridization buffer using the Agilent gene expression hybridization kit.  These were applied to a sheep 8 X 15 K array slide (019921, Agilent), containing 8 arrays with 15,744 oligomers with a length of 60 bases corresponding to 15,208 ovine genetic sequences published in the NCBI data base plus 500+ quality control probes provided by Agilent and hybridized at 65 °C  for 17 h at 10 rpm.

scan_protocol: The arrays were hybridized, washed, dried, stabilized, and scanned at 5 μm at both 10 and 100 PMT with Microarray Scanner System (G2505-90021, Agilent), and features were extracted with Agilent Feature Extraction 9.1 software at the Genomics Division of the University of Florida’s Interdisciplinary Center for Biotech Research.  Features flagged as Feature Non-uniform outliers were excluded from further analysis.

data_processing: The limma package was used to import the raw data into R (http://www.r-project.org), performed background corrections, and normalized data by quantile normalization method.  Probes that were at least 10% brighter than the negative controls on at least three arrays were retained for further analysis, and control probes and low expressed probes were filtered out.

organism: Ovis aries

source_name: Kidney cortex, hypoxia, ketamine

label_protocol: Agilent Quick Amp Labeling Kit (5190-0442, Santa Clara, CA) was used to label 500 ng of RNA with Cyanine 3 (Cy3) CTP according to manufacturer’s protocol, except that the microcentrifugation of the samples were performed at room temperature instead of 4 °C.  The labeled cRNA was analyzed with NanoDrop spectrophotometer, and the specific activities (10.4 to 12.7 pmol Cy3/μg RNA) and yields of the cRNAs were calculated (5.8 to 7.9 μg).  The labeled cRNA was stored at -80 °C until further use.

extract_protocol: The RNA was extracted from the snapped frozen kidney cortex using Trizol (Invitrogen, Carlsbad, CA), then purified by using RNeasy Plus Mini kit (Qiagen, Valencia, CA) with RNase-Free DNase Set (Qiagen, Valencia, CA).  The RNA concentration was measured using NanoDrop spectrophotometer (ND-1000, ThermoFisher, Wilmington, DE), and the quality was determined using 2100 Bioanalyzer (Agilent, Santa Clara, CA).  The RNA Integrity Number (RIN) values of the samples ranged from 7.7 to 9.1.

treatment_protocol: A total of 15 ovine fetuses were chronically catheterized: 8 were subjected to 30 min of maternal ventilatory hypoxia, and 7 were subjected to 30 min of normoxia.  Within each condition, half of the fetuses were treated with ketamine (3 mg/kg), and half with vehicle (saline).  Twenty-four hours following the onset of hypoxia or normoxia, the fetuses were euthanized and the kidney cortex were collected and snapped frozen.

value: Kidney cortex

tag: stimulus

value: Hypoxia

tag: agent

value: Ketamine


title: Hypoxia_Ketamine_Rep3


title: Hypoxia_Ketamine_Rep4


title: Hypoxia_Ketamine_Rep1


title: Brain_West Nile Virus_Infected_12days_rep3 [8049x8010]


title: Hypoxia_Vehicle_Rep3

description: Gene expression 24 hrs after 30 min hypoxia in vehicle treated fetuses

source_name: Kidney cortex, hypoxia, vehicle

value: Vehicle


title: Liver_siKeap1-2_rep3

description: Gene expression data from mouse liver


title: Brain_West Nile Virus_Infected_12days_rep2 [8049x8010]


title: Brain_West Nile Virus_Infected_7days_rep2 [8049x8010]

source_name: Brain_West Nile Virus_Infected_7days


title: Liver_siKeap1-1_rep8

description: Gene expression data from mouse liver


title: Liver_siKeap1-2_rep1

description: Gene expression data from mouse liver


title: Hypoxia_Vehicle_Rep4


title: Brain_West Nile Virus_Infected_7days_rep3 [8049x8010]


title: Hdac3 f/f 2


title: Brain_West Nile Virus_Infected_4days_rep3 [8049x8010]

source_name: Brain_West Nile Virus_Infected_4days


title: Brain_West Nile Virus_Infected_7days_rep1 [8049x8010]


title: Hypoxia_Vehicle_Rep1


title: Liver_siKeap1-1_rep5

description: Gene expression data from mouse liver


title: Normoxia_Ketamine_Rep4

description: Gene expression 24 hrs after 30 min normoxia in ketamine treated fetuses

source_name: Kidney cortex, normoxia, ketamine

value: Normoxia


title: Liver_siKeap1-1_rep7

description: Gene expression data from mouse liver


title: Hypoxia_Vehicle_Rep2


title: Liver_siKeap1-1_rep3

description: Gene expression data from mouse liver


title: Liver_siKeap1-1_rep6

description: Gene expression data from mouse liver


title: Liver_siKeap1-2_rep4

description: Gene expression data from mouse liver


title: Brain_West Nile Virus_Infected_4days_rep2 [8049x8010]

value: West Nile Virus


title: Brain_West Nile Virus_Infected_4days_rep1 [8049x8010]


title: Normoxia_Ketamine_Rep3


title: Normoxia_Ketamine_Rep2


title: Liver_siKeap1-2_rep2

description: Gene expression data from mouse liver


title: Brain_Mock_Infected_12Mdays_rep3 [8048x8026]


title: Normoxia_Ketamine_Rep1


title: Brain_West Nile Virus_Infected_12days_rep3 [8048x8026]


title: Brain_Mock_Infected_12Mdays_rep1 [8048x8026]


title: Normoxia_Vehicle_Rep3

description: Gene expression 24 hrs after 30 min normoxia in vehicle treated fetuses

source_name: Kidney cortex, normoxia, vehicle


title: Brain_Mock_Infected_12Mdays_rep2 [8048x8026]


title: Liver_siKeap1-1_rep2

description: Gene expression data from mouse liver


title: Brain_West Nile Virus_Infected_12days_rep2 [8048x8026]


title: Brain_West Nile Virus_Infected_12days_rep1 [8048x8026]


title: Normoxia_Vehicle_Rep1


title: Normoxia_Vehicle_Rep2


title: Sorted epidermal GL_02

city: Kumamoto

first: Aiko

last: Sada

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

department: International Research Center for Medical Sciences (IRCMS)

institute: Kumamoto University

hyb_protocol: The labeled cDNA was hybridized to Mouse Genome 430 2.0 genechips (Affymetrix) in the Cornell microarray core facility (Ithaca, NY), according to the protocol indicated in the Encore Biotin Module kit.

scan_protocol: The arrays were scanned on the Affymetrix GeneChip Scanner 7G.

data_processing: The scanned images were then imported and normalized with GeneSpring software 12.1 (Agilent Technologies). Exclude the probes with a signal value <100 or celled absent.

source_name: Skin cells from quadruple transgenic mice harboring K5-tTA, pTRE-H2B-GFP, K14-CreER and Rosa-tdTomato.

label_protocol: Five nanogram of total RNA was processed with the “Ovation Pico WTA System (NuGEN)” for cDNA amplification, followed by “Encore Biotin Module (NuGEN)” for labeling and fragmentation of cDNA.

growth_protocol: Mice are housed in the Biotechnology Building mouse facility of Cornell University approved by Cornell IACUC.

extract_protocol: Total RNA was extracted using Rnease micro kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Mice were fed doxy at 1g/KG of food (Bio-serv) for 2 weeks to repress H2BGFP expression. TM (75mg/kg body weight; Sigma) was intraperitoneally injected at single dose and sacrificed 1 week later at second telogen.

tag: cell type

value: Epidermal GL


title: Sorted epidermal SL non-LRCs_01

value: Epidermal SL non-LRCs


title: Brain_West Nile Virus_Infected_7days_rep3 [8048x8026]


title: Sorted epidermal SL non-LRCs_02


title: Brain_West Nile Virus_Infected_7days_rep1 [8048x8026]


title: Sorted epidermal GL_01


title: Sorted epidermal SL LRCs_01

value: Epidermal SL LRCs


title: Brain_West Nile Virus_Infected_4days_rep3 [8048x8026]


title: SV40-HCEC 6h 100nM Vitamin D (1,25D3) vs. control (0.1% ethanol)  Replicate 1

city: Stockholm

first: Cecilila

last: Williams

address: Tomtebodavägen 23A, Solna

department: Molecular & Cellular Proteomics

institute: KTH

description:
VitD treated-Rep1
Biological and technical replicate 1 of 2. Vitamin D (1,25D3) Sample labeled with Cy3, Ethanol sample labeled with Cy5

hyb_protocol: Human Genome OpArray- custom (Cat No: OPHS4V-25, Microarray, Inc.) were incubated in warm (42 degC) pre-hybridization buffer (1% BSA, 5x SSC, 0.1% SDS) for 30 minutes. Then, they were quickly washed with MilliQ H20 and isopropanol, dried, and placed in hybridization chambers. The Cy5 and Cy3 samples were pooled, and reduced to 13.6µL using a speed vac and then several reagents were added to a final volume of 65.05µL (5x SCC, 50% Formamide, 0.1% SDS, 0.1µg/µL tRNA, and 0.2µg/µL human Cot-1 DNA). The mixture was then heated for 3 minutes at 95 degC , cooled, and loaded under a coverslip onto the pre-hybridized arrays. The hybridization chambers were sealed and placed in a 42 degC water bath for 40 hours. After hybridization, they were washed 3 x 5 minutes in water with decreased concentrations of SSC and SDS each time (2x SSC and 0.1% SDS, then 0.1x SSC and 0.1% SDS, then just 0.1x SSC)

scan_protocol: Slides were scanned on a Gene Pix 4300A machine, and then quantified with GenePix Pro 6.0 software.

data_processing: Array reports were generated within GenePix Pro 6.0 to assess the quality of the arrays. R software was used to generate array comparisons, filter (background, signal-to-noise ratio) and normalize data, perform a dye-swap, generate log2(R/G) values for each slide, and derive B-test and t-test significance for each gene with changed expression. The specific R package used for microarray analysis in R was called the “Limma” package and was obtained from the Karolinska Institutet (Stockholm, Sweden)

source_name: SV40-HCEC Cells_VitD

label_protocol: Samples containing 20 µg of total RNA and 1µL (5µg/µL) of random hexamer primer were diluted to a final volume of 18.4µL using RNase-free H2O, and then incubated for 10 minutes at 70deg C. After cooling for 5 minutes on ice, 11.6µL of cDNA synthesis master mix was added (1x first-strand buffer, 0.01M DTT, 1x-aa-dUTP+dNTP mix, Superscript III). The mixture was first incubated for 10 minutes at 35deg C, and then for 2 hours at 46 degC. The remaining RNA was hydrolyzed by adding 3µL 0.2M EDTA (pH 8.0) and 4.5µL 1M NaOH, incubating for 15 minutes at 70 degC, cooling, and then adding 4.5µL 1M HCL. The cDNA was subsequently purified using Quiagen MinElute columns and buffers, and eluted in 20µL 100mM NaHCO3. Finally, the elute was transferred to dried (speed-vac'd) aliquots of either Cy3 or Cy5 mono-reactive ester, and incubated for 30 minutes in the dark at room temp. The dye-coupled samples were purified, again using Quiagen minElute columns and buffers, and eluted in a final amount of 20µL elution buffer.

growth_protocol: Cells were cultured in SHEM media with 10%FBS.

extract_protocol: TriZOL/ chloroform/ Quiagen Rneasy Kit according to manufacturer's guidelines.

treatment_protocol: SV40-HCEC treated for 6 hours either with Vitamin D (1,25D3) or control (0.1% ethanol).

value: female

tag: cell line

value: Human Corneal Epithelial Cells

tag: passage

tag: treated with

value: 100nM Vitamin D (1,25D3) for 6hrs

source_name: SV40-HCEC Cells_EtOH

value: 0.1% Ethanol for 6h


title: Brain_West Nile Virus_Infected_7days_rep2 [8048x8026]


title: SV40-HCEC 6h 100nM Vitamin D (1,25D3) vs. control (0.1% ethanol)  Replicate 2

description:
VitD treated-Rep2
Biological and technical replicate 2 of 2. Vitamin D (1,25D3) Sample labeled with Cy5, Ethanol sample labeled with Cy3

tag: gender


title: hTCEpi 6h 100nM Vitamin D (1,25D3) vs. control (0.1% ethanol)  Replicate 2

source_name: hTCEpi cells_EtOH

growth_protocol: hTCEpi cells were cultured in KGM-2 medium

treatment_protocol: hTCEpi cells were treated with either 100nM 1,25D3 or 0.1% Ethanol for 6h in 10mL cell culture media in a 10cm cell culture dish.

value: male

value: Human Corneal Epithelial Cells (hTCEpi)

source_name: hTCEpi cells_VitD


title: Sorted epidermal SL LRCs_02


title: Brain_West Nile Virus_Infected_4days_rep2 [8048x8026]


title: 3948

city: Indianapolis

first: Xiaoming

last: Yin

state: Indiana

address: 350 West 11th street

department: Department of Pathology and Laboratory Medicine

institute: Indiana University School of Medicine

description: The RNA was extracted from one sample

hyb_protocol: For hybridization, 15 to 20 µg of cRNA were fragmented by incubating in a buffer containing 200 mM Tris-acetate, pH 8.1, 500 mM KOAc, 150 mM MgOAc at 95°C for 35 minutes.  The fragmented cRNA were then hybridized with a pre-equilibrated Affymetrix mouse chip (U74Av2) at 45°C for 14-16 hours.  After the hybridization cocktails were removed, the chips were then washed in a fluidic station with low-stringency buffer (6x SSPE, 0.01% Tween 20, 0.005% antifoam) for 10 cycles (2 mixes/cycle) and stringent buffer (100 mM MES, 0.1 M NaCl and 0.01% Tween 20) for 4 cycles (15 mixes/cycle), and stained with SAPE (Strepto-avidin Phycoerythrin).  This was followed by incubation with biotinylated mouse anti-avidin antibody, and restained with SAPE.

scan_protocol: The chips were scanned in a HP ChipScanner (Affymetrix Inc, Santa Clara, CA) to detect hybridization signals.

data_processing: The CEL files generated from the microarray scanning were used as the raw data.  Data quality was examined using the RMAExpress program (v.1.0.5) (http://rmaexpress.bmbolstad.com/).  The density distribution along the Log2 scale was comparable among the samples, which indicated that the quality of the assay was acceptable for comparison.  Microarray data from individual mouse livers within each treatment group were then averaged and the averaged values were used for the subsequently comparisons and pathway analysis.  Significance of differential expression was assessed using un-paired t-test.  The threshold for the significant changes was a difference larger than 25% for upregulated genes and larger than 20% for downregulated genes (fold of change >1.25 or <0.8, p<0.05).  Pathway analysis was conducted using the Database for Annotation, Visualization and Integrated Discovery (DAVID) bioinformatics Resources 6.7 (https://david.ncifcrf.gov/), and Gene Set Enrichment Analysis (GSEA 2.1.)(http://software.broadinstitute.org/gsea/index.jsp), for the differentially expressed gene set and the total gene set, respectively.  The pathway database is from the KEGG annotation (http://www.genome.jp/kegg/pathway.html).

source_name: bid KO_Control_12

label_protocol: Biotinylated cRNA was prepared using standard protocol.

extract_protocol: Mouse livers were dissected and RNA was prepared.  In brief, 20 to 50 mg of liver tissues were disrupted in Buffer RLT (provided in Qiagen RNEasy kit), and homogenized.  One volume of ethanol (70%) was then added to the lysate, creating conditions that promote selective binding of RNA to the RNeasy membrane.  The sample was then applied to the RNeasy Mini spin column.  Contaminants were washed away using RW1 wash buffer (provided in the RNEasy kit).  RNA was eluted in RNase-free water. All binding, wash, and elution steps were performed by centrifugation in a micro-centrifuge.

treatment_protocol: Diethylnitrosamine (DEN, C4H10N2O,) was intraperitoneally administrated to wild type and bid-deficient mice at the age of day 15 as previously described (Bai et al, American Journal of Pathology, 166: 1523-1532, 2005).  Wild type mice were in C57Bl/6J background whereas bid-deficient mice had been backcrossed to C57Bl/6J background for at least 12 generations.  Male mice were used because they were susceptible to this model of carcinogenesis.  Untreated control mice in the same genetic background were age and sex-matched. All of the mice were bred in house.  Mice were euthanized by cervical dislocation following anesthesia at an early stage (4-6 months) and at a later stage (10-12 months) following DEN treatment.  Livers were examined and processed.  The treatment of mice were approved by the IACUC of the University of Pittsburgh.

value: Liver

tag: background strain

tag: genotype

value: bid KO-/-

tag: treament

value: Control

tag: treatment duration (months)


title: Liver_siKeap1-1_rep1

description: Gene expression data from mouse liver

tag: tissue

value: liver

tag: strain


title: Sorted epidermal BL non-LRCs_01

value: Epidermal BL non-LRCs


title: hTCEpi 6h 100nM Vitamin D (1,25D3) vs. control (0.1% ethanol)  Replicate 1


title: Sorted epidermal BL non-LRCs_02


title: GAB

description: Enriched methylated DNA (cy5) and genomic DNA (cy3) of each sample were competitively hybridizated to Human DNA Methylation microarrays platforms (Agilent)

source_name: GAB_enriched methylated DNA

value: RMS tumor tissue

tag: tumor stage

value: stage IV

source_name: GAB_genomic DNA


title: 3787

description: The RNA was extracted from one sample

source_name: bid KO_DEN_12

value: DEN


title: 3788

description: The RNA was extracted from one sample


title: Brain_West Nile Virus_Infected_4days_rep1 [8048x8026]

value: brain

value: West Nile Virus


title: Sorted epidermal BL non-LRCs_03


title: Brain_Mock_Infected_12Mdays_rep3 [8021x16072]

value: Mock


title: Sorted epidermal BL LRCs_03

value: Epidermial BL LRCs


title: 3947

description: The RNA was extracted from one sample


title: SCH

source_name: SCH_enriched methylated DNA

source_name: SCH_genomic DNA


title: 4144

description: The RNA was extracted from one sample

source_name: bid KO_DEN_10


title: Sorted epidermal BL LRCs_02


title: Brain_Mock_Infected_12Mdays_rep2 [8021x16072]


title: 4129

description: The RNA was extracted from one sample


title: 4016

description: The RNA was extracted from one sample

source_name: bid KO_Control_10


title: control

city: Yangzhou

first: Yongjiang

last: Mao

address: No.48 East Wenhui Road

country: China

institute: Yangzhou University

description: lncRNA expression in mammary gland of healthy cow

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028004 SurePrint G3 Human GE 8x60K array(Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

organism: Bos taurus

source_name: mammary gland-control

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's instructions

treatment_protocol: At 24 h post-inoculation, and before peak clinical signs, the mammary gland tissues infected,and un-infected quarters were sampled using surgical operation by experienced veterinarian.Surgeries were performed under aseptic field conditions.

value: mammary gland

value: female

tag: breed

value: Holstein


title: Lung_Caudal_HD_HDP42

city: Aberdeen Proving Ground

first: Heidi

last: Hoard-Fruchey

state: MD

address: 2900 Ricketts Point Rd

institute: USAMRICD

description: Gene expression data from the left caudal lung lobe; exposed to 100 μg/kg vapor HD

hyb_protocol: Labelled RNA was hybridized for 16 hrs at 48 degrees C on Affymetrix Porcine Genome Array GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using fluidics.

scan_protocol: GeneChips were scanned using Affymetrix 7G GeneChip Scanner using Affymetrix GeneChip Command Console Scan Control

organism: Sus scrofa

source_name: lung; left caudal; medium HD

label_protocol: 1ug total RNA was to generate cRNA following manufacturer's instructions (Enzo Life Sciences, Plymouth Meeting, PA).

growth_protocol: Animals were housed individually in straw lined pens and were fed standard pig diet and water ad libitum for 5 days prior to the experiment. From 12 hours prior to the experiment, access to food was withdrawn, but water was freely available.

extract_protocol: Following euthanasia (overdose of sodium pentobarbitone, 200 mg/mL i.v.), lung tissue samples from each lobe were stored in RNAlater at -80 deg C until processed. Tissue was homogenized in RLT buffer containing Beta-mercaptoethanol and total RNA was isolated using the RNeasy Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: Animals were pre-medicatd and inhalational anesthesia induced. The animals were intubated and exposed to HD vapor for 10 minutes to 60 ug/kg (low) or 100 ug/kg (medium) doses while in the supine position.

value: Lung

value: Female


title: S. aureus

description: lncRNA expression after 24hr in cow mammary gland infected with  S. aureus

source_name: mammary gland-infected by S. aureus


title: Brain_Mock_Infected_12Mdays_rep1 [8021x16072]

tag: infection


title: Brain_West Nile Virus_Infected_12days_rep3 [8021x16072]

source_name: Brain_West Nile Virus_Infected_12days

tag: timepoint(days)


title: 4010

description: The RNA was extracted from one sample

value: Liver

value: male


title: S. uberis

description: lncRNA expression after 24hr in cow mammary gland infected with S. uberis

source_name: mammary gland-infected by S. uberis


title: 3859

description: The RNA was extracted from two equally treated samples

source_name: bid KO_DEN_6

value: bid KO-/-


title: Lung_Median_HD_HDP42

description: Gene expression data from the left median lung lobe; exposed to 100 μg/kg vapor HD

source_name: lung; left median; medium HD


title: Brain_West Nile Virus_Infected_12days_rep2 [8021x16072]


title: SPECS_3949

city: Bethesda

first: Louis

middle: M.

last: Staudt

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: No additional information.

hyb_protocol: Affymetrix Hybridization Protocol Other: Fragmented single-stranded sense DNA were hybridized to the Affymetrix Genome-Wide Human SNP 6.0 array. Arrays were hybridized in the GeneChip Hybridization Oven 645 and stained in the GeneChip Fluidics Station 450.

scan_protocol: Scanning Protocol Other: Arrays were scanned on a GeneChip Scanner 3000-7G (Affymetrix).

data_processing:
Data Processing Protocol
Calculation Method: The Affy SNP datsets were normalized and signal called by Affy GTC (version 4.2.0.26) using CNV analysis with the default parameters.

label_protocol:
Affymetrix Labeling Protocol
Other: Fragmented PCR products were terminally labeled with biotin according to the manufacturer's protocol.

extract_protocol:
QIAGEN AllPrep DNA/RNA Mini Protocol
Other: Genomic DNA was isolated using QIAGEN AllPrep DNA/RNA Mini Kit.

value: tumor

value: ABC DLBCL cells

tag: disease state

value: activated B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)

tag: individual