title: 64d_P0_RPE-C_80K

description:
Bok081309 p0day64insert
raw data: Cy3 channel of RPE-C_64d_P0&P5.txt

value: 64 Days


title: Breast.Tumour.PreLet.patient214

status: Public on Jul 06 2015

type: RNA

city: Carrington Crescent

first: Andrew

middle: H

last: Sims

state: Edinburgh

address: Systems Medicine Building

department: Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: University of Edinburgh

hyb_protocol: Labelled cDNA was hybridised to Human HT-12v4 whole-genome expression beadarrays (Illumina) according to the standard protocol for NuGEN amplified samples.

scan_protocol: Scanning was performed on a Illumina scanner using the manufacturers protocol

data_processing: Illumina probe profiles were quantile normalised using the lumi package

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: PreLet

label_protocol: RNA was reverse transcribed and amplified using the WT-Ovation FFPE System Version 2 (NuGEN), purified using the Qiaquick PCR Purification Kit (Qiagen), biotinylated using the IL Encore Biotin Module (NuGEN), purified using minElute Reaction Cleanup Kit (Qiagen) and quantified once again using the Nanodrop 2000c (Thermo Scientific).

growth_protocol: Tumour biopsies were taken with a 14-guage needle before and approximately 2 weeks and 3 months following commencement of continuous letrozole treatment. Samples were snap-frozen in liquid nitrogen and frozen sections taken, stained with haematoxylin and eosin (H&E) and the cellularity and percentage presence of cancerous tissue within each specimen was assessed by a pathologist.

extract_protocol: Biopsies were homogenised and RNA was extracted using the RNeasy Mini Kit with RNAse-free DNAse treatment (Qiagen). RNA quantity and quality was verified on a Bioanalyser 2100 with RNA 6000 Nano Kit (Agilent) and Nanodrop 2000c (Thermo Scientific).

treatment_protocol: Patients were treated within a neoadjuvant protocol in which letrozole (Femara, 2.5mg; Novartis Pharma AG, Basel, Switzerland) was given daily

tag: patient id

tag: gender

value: Female

tag: clinical response

value: Non-responder

tag: time point

value: pre-treatment

tag: tissue

value: tumour biopsies


title: Breast.Tumour.3mLet.patient179

value: 3 months of letrozole treatment


title: Breast.Tumour.PreLet.patient203


title: 12hr2 (conditioning lesion)

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

country: USA

institute: Rutgers University

hyb_protocol: Hybridization was performed using an automated protocol on a Ventana Discovery System.

scan_protocol: Arrays were scanned on an Axon GenePix 4000B scanner using Axon GenePix 4.0 software.

data_processing: Images were aligned with array maps and data extracted.  Raw data was loaded into GeneSpring

organism: Rattus norvegicus

source_name: cultured rat DRG cells

label_protocol: RNA samples were labeled with the Genisphere 3DNA dendrimer system.  Control (untreated) cultures were labeled in one fluorescent color and the cAMP (treated) samples in another.

extract_protocol: DRS were collected in Trizol and homogenized with a tissue grinder.  Chloroform was added to extract the aqueous phase, which was adjusted to 35% ethanol and loaded onto a Qiagen RNeasy column.  The column was washed and eluted following the manufacturer's recommendations.  A260/A280 ratios were between 1.9 and 2.1 for all samples.

treatment_protocol: Postnatal day 20-24 Long-Evans rats were anesthetized using 2.5% isoflourane.  The sciatic nerve was transected using surgical micro-scissors.  The incision was closed.  Animals were allowed to survive for 4 to 294 hrs after which they were sacrificed by asphyxiation with CO2.  DRGs L4 and L5 were removed.

tag: treatment

value: lesioned

tag: time

value: 12 hrs

tag: cell type

value: cultured rat DRG cells

value: Intact


title: 12hr1 (conditioning lesion)


title: 32d_P5_RPE-B_80K

city: Santa Barbara

first: Monte

middle: J.

last: Radeke

state: CA

address: Neuroscience Research Institiute

department: Neuroscience Research Institute

institute: University of California, Santa Barbara

description:
Bok071709 p5day32insert
raw data: Cy3 channel of RPE-B_32d_P0&P5.txt

hyb_protocol: Probe fragmentation and hybridization was carried out using the Agilent Gene Expression Hybridization Kit (Part #: 5188-5242) according to the methods of the manufacturer (Quick Amp Labeling Protocol, Version 5.7). Two samples (one labeled with Cy3 and the other with Cy5 were hybidized to each array for 17 hr at 65°C. Arrays were washed for 1 min using Agilent Gene Expression Wash Buffer 1 (Part #: 5188-5325) + 0.005% Triton X-102 at room temperature and for 1 min at 37°C with Agilent Gene Expression Wash Buffer 2 (Part #: 5188-5326) + 0.005% Triton X-102. The washed arrays were then rinsed with acetonitrile for 10 sec and coated with Agilent Stabilization and Drying solution for 30 sec.

scan_protocol: Scanner: Bio-Rad VersArray™ ChipReader 3 micron System.  Median Raw Spot intensities (Threshold = 5 to 6535) were determined using  VersArray™ Analyzer 4.5. LOWESS Net Intensity Spot Intensity was calculated using Global Median Background Subtraction (global background from negative control cells, zero order polynomial approximation) and the uncorrected net intensity values were normalized using local regression cross-channel normalization of net intensity values (span = 10%, sub-sampling = 5, single pass). Raw data files contain the  LOWESS normalized net intensity values, the raw intensity values, and the background values.

data_processing: The LOWESS normalized data were further background corrected by subtraction of the minimum value of the Agilent negative controls (3xSLv1) to obtain the net intensity. Any values less than one standard deviation of the negative control probes were set to a value equal to the standard deviation of the negative controls for that sample. For the 200 unique probes with 10 replicates each, the average of the replicates were determined. The entire data set was then quantile normalized.

source_name: Fetal RPE-Donor B

label_protocol: All probe labeling was carried out using the Agilent Low Input Quick Amp Labeling Kit (Part #: 5190-2306, Version 5.7) according to the methods of the manufacturer using 250 ng of total RNA with the exception that spike-in controls were not used.

growth_protocol: RPE cells were isolated from fetal donor eyes (Advanced Biosciences Resources, Alameda, CA USA) according to the methods of Hu and Bok [Mol. Vis. 2001, 7:14-19; Methods Mol. Biol. 2010, 652:55-73]. Beyond the initial isolation, all cell culture was carried out using a base medium described by Maminiskis [Invest. Ophthalmol. Vis. Sci.2006, 47:3612-3624]. For 2-3 days post-plating the medium included 15% heat inactivated fetal calf serum. Thereafter, it was reduced to 5%. To generate a working cell bank, primary fetal RPE stocks were expanded approximately 10-fold and these working stocks were designated Passage 0. For routine serial passage, cells were harvested using trypsin digestion and plated at 4,000 cells/cm2. At approximately 80% confluence (every 3-5 days depending on passage number) the cells were enzymatically harvested and re-seeded at 4,000 cells/cm2. Cultures were carried out on laminin-coated porous supports (mouse laminin, Life Technologies, Grand Island, NY USA; Millicell-HA Culture Inserts, EMD Millipore Inc., Billerica, MA USA) or laminin-coated tissue culture plastic as indicated. All cultures were fed every 2-4 days by complete exchange of the medium.

extract_protocol: Total RNA was purified using miRNeasy mini-preps (Qiagen Inc., Valencia, CA USA)

tag: donor id

tag: plating density

tag: passage number

tag: culture time

value: 32 Days

tag: cultureware

value: Micropourous Membrane


title: 8hr1 (conditioning lesion)

value: 8 hrs


title: 8hr3 (conditioning lesion)


title: 32d_P5_RPE-A_80K

description:
Bok020207-2 p5day32insert
raw data: Cy5 channel of RPE-A_32d_P0&P5.txt

source_name: Fetal RPE-Donor A


title: 16d_P5_RPE-C_80K

description:
Bok081309 p5day16insert
raw data: Cy5 channel of RPE-C_16d_P0&P5.txt

source_name: Fetal RPE-Donor C

value: 16 Days


title: Breast.TumourwLet.patient179

value: 2 wks of letrozole treatment


title: Breast.Tumour.PreLet.patient179


title: 32d_P0_RPE-A_80K

description:
Bok020207-2 p0day32insert
raw data: Cy3 channel of RPE-A_32d_P0&P5.txt


title: 4hr3 (conditioning lesion)

value: 4 hrs


title: Breast.Tumour.3mLet.patient172

value: Responder


title: 8hr2 (conditioning lesion)


title: 4hr2 (conditioning lesion)


title: 16d_P0_RPE-C_80K

description:
Bok081309 p0day16insert
raw data: Cy3 channel of RPE-C_16d_P0&P5.txt


title: 4hr1 (conditioning lesion)


title: 32d_P0_RPE-B_80K

description:
Bok071709 p0day32insert
raw data: Cy5 channel of RPE-B_32d_P0&P5.txt


title: Breast.TumourwLet.patient329


title: Breast.Tumour.PreLet.patient172


title: Breast.TumourwLet.patient171


title: 16d_P5_RPE-A_80K

description:
Bok020207-2 p5day16insert
raw data: Cy3 channel of RPE-A_16d_P0&P5.txt


title: 16d_P5_RPE-B_80K

description:
071709p5day16insert
raw data: Cy5 channel of RPE-B_16d_P0&P5.txt


title: Breast.Tumour.3mLet.patient171


title: Breast.Tumour.PreLet.patient171


title: 16d_P0_RPE-B_80K

description:
071709p0day16insert
raw data: Cy3 channel of RPE-B_16d_P0&P5.txt


title: vec_rep3

city: Buffalo

first: AC

last: CHANG

address: Elm and Carlton

institute: RPCI

description: human breast cancer cells

hyb_protocol: Equal amounts of Cy3 labeled target were hybridized to Agilent whole human genome 4x44K arrays. Hybridizations were performed according to the manufacturers protocol (Agilent).

scan_protocol: Arrays were scanned by the Agilent Scanner G2505C

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software (Agilent).

source_name: vehicle treated cells, replicate3

label_protocol: RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol (Agilent)

growth_protocol: Human mammary epithelial cells MCF7 were purchased from ATCC and cultured in DMEM Medium with bovine serum.

extract_protocol: Total RNA was extracted by Rneasy mini kit followed by Dnase I treatment.

treatment_protocol: Cells were treated with leptin (Sample1-3) and control vehicle (Sample 4-6).

tag: cell line

value: epithelial tumor

value: mammary gland/breast

value: female


title: vec_rep2

description: human breast cancer cells

source_name: vehicle treated cells, replicate2


title: 16d_P0_RPE-A_80K

description:
Bok020207-2 p0day16insert
raw data: Cy5 channel of RPE-A_16d_P0&P5.txt


title: 3d_P5_RPE-C_4K

description:
081309p5day3flask
raw data: Cy5 channel of RPE-C_3d_P0&P5.txt

value: 4,000 cells/cm2

value: 3 Days


title: Breast.Tumour.3mLet.patient150

value: Female

value: Non-responder

value: 3 months of letrozole treatment

value: tumour biopsies


title: Breast.TumourwLet.patient172


title: Breast.TumourwLet.patient150


title: vec_rep1

description: human breast cancer cells

source_name: vehicle treated cells, replicate1


title: 3d_P0_RPE-C_4K

description:
081309p0day3flask
raw data: Cy3 channel of RPE-C_3d_P0&P5.txt


title: 3d_P0_RPE-B_4K

description:
071709p0day3flask
raw data: Cy5 channel of RPE-B_3d_P0&P5.txt


title: lep_rep2

description: human breast cancer cells

source_name: leptin treated cells, replicate2


title: lep_rep3

description: human breast cancer cells

source_name: leptin treated cells, replicate3


title: 3d_P5_RPE-A_4K

description:
020207-2p5day3flask
raw data: Cy3 channel of RPE-A_3d_P0&P5.txt


title: Breast.Tumour.PreLet.patient150

value: pre-treatment


title: 3d_P0_RPE-A_4K

description:
020207-2p0day3flask
raw data: Cy5 channel of RPE-A_3d_P0&P5.txt


title: lep_rep1

description: human breast cancer cells

source_name: leptin treated cells, replicate1


title: kidney_G10_injDEX-120h_rep4

city: Ft. Detrick

first: Christine

last: Baer

state: MD

address: 568 Doughten Drive

department: Environmental Health Program

institute: Excet, Inc. / USACEHR

hyb_protocol: Fragmented, labeled cDNA were hybridized to Affymetrix RatGene 1.1 ST array plates on an Affymetrix GeneTitan following manufacturer’s instructions using the GeneTitan Hybridization, Wash and Stain Kit for WT array plates (Affymetrix, #901622).

scan_protocol: Array plates were scanned immediately after hybridization, wash and staining by the Affymetrix GeneTitan using default settings.

data_processing: Microarray data was processed for background adjustment, normalization, and summarization using the interPLIER gene level method (background = PM-GCBG, normalization method = Sketch-Quantile) in Affymetrix Expression Console software (Version 1.1).

label: biotin

source_name: kidney

label_protocol: An initial input of 100 ng total RNA per sample was synthesized to cRNA using the Ambion Whole Transcript (WT) Expression Kit (Ambion, #4411974) according to manufacturer’s recommendations. Then 10 µg cRNA was used as a template to synthesize cDNA which were fragmented and labeled using the GeneChip WT Terminal Labeling Kit (Affymetrix, #901524).

growth_protocol: Male Wister rats (200-300g) were purchased from Harlan Laboratories and housed in accordance with the Guidelines for the Care and Use of Laboratory Animals. All experiments were conducted according to NIH and institutional guidelines with the approval of Madigan Army Medical Center Institutional Animal Care and Use Committee.

extract_protocol: Total RNA was isolated from the kidney tissue using Trizol (Invitrogen, Carlsbad, CA) followed by column purification with miRNeasy-96 kits (Qiagen, GmbH, Germany) to remove residual salt and organic solvents. Total RNA quality and quantity were evaluated using an Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA) and verified using the NanoDrop ND-1000 Spectrophotometer (NanoDrop, Wilmington, DE).

treatment_protocol: Briefly, rats were anesthetized by isofluorane inhalation induction followed by ketamine (40-80 mg/kg) and xylazine (5-10 mg/kg) intraperitoneally. Rats were premedicated with Valproic acid (150mg/kg), dexamethasone (3mg/kg) or saline (control) intraperitoneally thirty minutes prior to surgery. A sterile surgical site was prepared and midline incision was performed to access the abdominal cavity. Left kidney was located and its renal artery was clamped using an atraumatic microaneurysm clamp. The abdomen was reapproximated to prevent dehydration and maintain body temperature. Following 45 minutes of warm ischemia the abdomen was reopened and the renal clamp was removed to allow reperfusion. Reperfusion was confirmed by observing the color change in the kidney (pale to bright red). This was immediately followed by a right nephrectomy. The abdomen was then closed by suturing muscles with 6-O prolene and skin with 4-O nylon and clips.

tag: strain

value: Wister

tag: Sex

value: male

tag: weight

tag: group

value: Group 10

tag: injury

value: Yes

value: DEX

tag: time (h)

value: kidney


title: TGFβ_rep2

city: Bangalore

first: Neeraj

last: KUMAR

address: Indian Institute of Science Bangalore

department: MRDG

country: India

institute: Indian Institute of Science Bangalore

hyb_protocol: 825 ng of labelled cRNA each from treated and untreated were mixed with blocking agent and fragmentation buffer followd by incubation at 65 °C for 30 min. This is followed by addition of 55 ul of 2x GEx Hybridization Buffer HI-RPM to stop the fragmentation reaction. Later 100 µl of the above mix were added to each array.

scan_protocol: Agilent protocol

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: hGF cells

label_protocol: 200 ng of RNA each from untreated and treated samples were used. Labeling of the probes was done using the Low RNA Input Linear Amplification Kit (Agilent Technologies, USA). Briefly 200 ng of RNA were reverse transcribed using T7promoter attached Oligo-dT primers at 40 °C for 2 hrs followed by 65 °C for 15 min. This cDNA were transcribed using T7 polymerase with respective labelled nucleotides at 40 °C for 2hrs. This synthesized labelled cRNA were purified using RNeasy mini column.

growth_protocol: Primary human gingival fibroblast cells  (hGF) were maintained in DMEM (Sigma-Aldrich, USA) supplemented with 10% fetal bovine serum (Certified grade, Invitrogen corporation, USA), 100 units/mL penicillin and 100µg/mL streptomycin (Invitrogen Life Sciences, USA) at 37°C in a humidified chamber with 5% CO2.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: For treatments, hGF cells were serum starved for 24 hr and treated with 5 µg/ml areca nut water extract, 5ng/ml TGF-β (R&D systems, USA) and both areca nut (5 µg/ml) and TGF-β (5 ng/ml) for 72 hours.

value: primary human gingival fibroblast cells

tag: agent

value: none, untreated

value: TGF-β (5 ng/ml) treated


title: 5H+T_inhibitor_rep1

value: 5H+T treated


title: kidney_G09_injDEX-024h_rep3

value: Group 9

tag: tissue


title: 5H_rep2

value: 5H (5 µg/ml areca nut water extract) treated


title: 3d_P5_RPE-B_4K

description:
071709p5dya3flask
raw data: Cy3 channel of RPE-B_3d_P0&P5.txt

value: 4,000 cells/cm2

value: 3 Days

tag: treatment


title: kidney_G10_injDEX-120h_rep1


title: kidney_G10_injDEX-120h_rep2


title: kidney_G08_injDEX-003h_rep4

value: Group 8


title: kidney_G09_injDEX-024h_rep1


title: kidney_G09_injDEX-024h_rep5


title: 5H+T_inhibitor_rep2


title: kidney_G08_injDEX-003h_rep3


title: 5H_rep1


title: TGFβ_rep1


title: kidney_G09_injDEX-024h_rep2


title: kidney_G09_injDEX-024h_rep4


title: kidney_G10_injDEX-120h_rep3


title: kidney_G08_injDEX-003h_rep2


title: kidney_G08_injDEX-003h_rep1


title: CHLA-01R-MED

type: genomic

city: Scottsdale

first: Michael

middle: Thomas

last: Barrett

state: AZ

address: 13400 East Shea Boulevard

department: Molecular Pharmacology and Experimental Therapeutics

institute: Mayo Clinic Arizona

hyb_protocol: All labeling reactions were assessed using a Nanodrop assay (Nanodrop, Wilmington, DE) prior to mixing and hybridization to 400k CGH arrays (Agilent Technologies, Santa Clara, CA) for 40 hours in a rotating 65°C oven. All hybridizations were done with a pooled commercial 46,XX reference (Promega, Madison WI GSM540609).

scan_protocol: All microarray slides were scanned using an Agilent 2565C DNA scanner and the images were analyzed with Agilent Feature Extraction version 10.7 using default settings.

data_processing: The aCGH data was assessed with a series of QC metrics,dye  normalized and centralized, then analyzed using an aberration detection algorithm (ADM2) which is included in Agilent Genomic Workbench 6.5 software. The latter identifies all aberrant intervals in a given sample with consistently high or low log ratios based on the statistical score derived from the average normalized log ratios of all probes in the genomic interval multiplied by the square root of the number of these probes. This score represents the deviation of the average of the normalized log ratios from its expected value of zero and is proportional to the height h (absolute average )

molecule: genomic DNA

source_name: malignant pleural effusion

label_protocol: Extracted fresh frozen sourced genomic DNA was amplified using the phi29 based Illustra GenomiPhi V2 Amplification kit from GE Healthcare Bio-sciences Corp (Piscataway,NJ) according to our published protocols18.  A 100 ng aliquot of pooled 46,XX DNA (Promega, Madison, WI) was amplified with the matching amplification protocol to generate a suitable reference for each aCGH experiment using amplified DNA template.  In all cases the quality of the amplification product was assessed by gel electrophoresis.    Fresh frozen phi29 amplified and FFPE non-amplified DNAs were treated with DNAse 1 prior to Klenow based labeling. High molecular weight phi29 templates were digested for 30 minutes while the smaller fragmented FFPE samples were digested for only 1 minute. In each case 1ul of 10x DNase 1 reaction buffer and 2ul of DNase 1 dilution buffer were added to 7ul of DNA sample and incubated at room temperature then transferred to 70°C for 30 minutes to deactivate DNase 1.  In contrast the amplified FFPE sourced DNAs do not require DNase 1 treatment prior to Klenow-based labeling. Sample and reference templates were then labeled with Cy-5 dUTP and Cy-3 dUTP respectively using a BioPrime labeling kit (Invitrogen, Carlsbad, CA) according to our published protocols

extract_protocol: DNA from sorted nuclei was extracted using an amended protocol from QIAamp® DNA Micro Kit from Qiagen (Valencia, CA).  Briefly each sorted sample was resuspended in 180ul buffer ATL and 20ul proteinase K then incubated for 3 hours at 56°C for complete lysis.  Samples were bound and washed according to QIAamp® DNA Micro Kit instructions, eluted into 50ul of H20, then precipitated overnight with 5ul 3 M sodium acetate and 180 ul 100% EtOH.  Each sample was then centrifuged for 30 minutes at 20,000 x g, washed in 1 ml of 70% EtOH for 30 minutes at 20,000 x g. The samples were carefully decanted and the DNA pellet was dried by speed vacuum then resuspension in a small volume (e.g. 10-50ul) of H20 for final concentrations suitable for accurate quantification.

tag: gender

value: Pleural effusion therapy resistant

tag: genotype

value: heterozygous BRCA2 6174delT

source_name: Reference pooled 46XX

tag: reference type

value: Normal female genome


title: kidney_G06_injVPA-024h_rep5

value: Wister

value: male

value: Group 6

value: VPA


title: kidney_G06_injVPA-024h_rep4

value: Yes

value: kidney


title: CHLA-01-MED

source_name: original medulloblastoma tumor

tag: cell type

value: Primary medulloblastoma


title: kidney_G07_injVPA-120h_rep4

value: Group 7


title: kidney_G05_injVPA-003h_rep4

value: Group 5


title: kidney_G05_injVPA-003h_rep5


title: kidney_G06_injVPA-024h_rep1


title: kidney_G07_injVPA-120h_rep2


title: 64d_P0_RPE-B_80K

description:
Bok071709 p0day64insert
raw data: Cy5 channel of RPE-B_64d_P0&P5.txt

tag: donor id

tag: plating density

tag: passage number

value: 64 Days

value: Micropourous Membrane


title: erh020_+IV

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

hyb_protocol: Labeled targets were hybridized on the mogene2st arry and processed using the Affymetrix system.

scan_protocol: Scanning uses the Affymetrix scanner

data_processing: The data were analyzed with Partek Genomics Suite 6.6 by the RMA method.

organism: Mus musculus

label_protocol: RNA was amplified using the NuGEN Ovation Pico WTA V2 system and then labeled with the NuGEN Encore Biotin Module.

growth_protocol: BALB/c mice were infected with Influenza A virus 6:2 (PR8 backbone) HK wt, 6:2 HK HA +II and 6:2 HK HA +IV. PBS inoculated mice served as control

extract_protocol: On d2 after Infection, lungs were collected in Trizol. RNA isolation was done using Trizol method and PureLink RNA Mini kit (Ambion)

value: BALB/c

tag: infected with

value: Influenza A virus 6:2 HK HA +IV

value: lung


title: kidney_G04_injSaline-120h_rep2

tag: strain

value: Group 4

value: Saline


title: kidney_G07_injVPA-120h_rep3

tag: Sex


title: kidney_G04_injSaline-120h_rep3

tag: weight


title: erh017_+IV


title: erh016_+IV


title: kidney_G04_injSaline-120h_rep5

tag: group


title: kidney_G05_injVPA-003h_rep2

tag: injury


title: kidney_G05_injVPA-003h_rep3

tag: time (h)


title: erh015_+II

value: Influenza A virus 6:2 HK HA +II


title: erh018_+IV


title: kidney_G05_injVPA-003h_rep1

value: Wister


title: erh011_+II


title: erh014_+II


title: kidney_G03_injSaline-024h_rep4

value: male

value: Group 3


title: kidney_G06_injVPA-024h_rep3

value: Group 6

value: VPA


title: kidney_G04_injSaline-120h_rep4

value: Yes

value: kidney


title: erh012_+II


title: erh013_+II


title: erh008_wt

value: Influenza A virus 6:2 (PR8 backbone) HK wt


title: kidney_G03_injSaline-024h_rep1


title: kidney_G04_injSaline-120h_rep1


title: erh009_wt


title: kidney_G03_injSaline-024h_rep2


title: erh010_wt


title: kidney_G03_injSaline-024h_rep3


title: kidney_G02_injSaline-003h_rep5

value: Group 2


title: erh007_wt


title: erh019_+IV


title: kidney_G07_injVPA-120h_rep1

value: Group 7


title: erh003_PBS

value: PBS (control)


title: kidney_G06_injVPA-024h_rep2


title: erh005_PBS

value: BALB/c


title: kidney_G02_injSaline-003h_rep4


title: kidney_G02_injSaline-003h_rep2


title: kidney_G01_Control_rep5

value: Group 1

value: No

value: Control


title: kidney_G02_injSaline-003h_rep1

value: Saline


title: erh001_PBS

value: lung


title: erh002_PBS


title: kidney_G01_Control_rep4

value: Wister


title: kidney_G02_injSaline-003h_rep3

value: male


title: erh006_wt


title: erh004_PBS


title: kidney_G01_Control_rep3


title: kidney_G01_Control_rep2


title: kidney_G01_Control_rep1


title: abdominal subcutaneous white adipose tissue, after 10 days of cold acclimation, subject 8

status: Public on Jul 05 2015

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.30.0).

source_name: abdominal subcutaneous white adipose tissue, after 10 days of cold acclimation, obtained from subject 8

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Eight male overweight, type 2 diabetic patients (age 59.3±5.8 years, body weight 92.0±11.7 kg, BMI 29.8±3.2 kg/m2, body fat 26.2±4.0 %) were included in this study. All patients were screened for medical history and exclusion criteria included uncontrolled hypertension, active cardiovascular disease, liver or kidney dysfunction, smoking and use of insulin, beta-blockers or other medication known to interfere with brown adipose tissue (BAT) function. Type 2 diabetes was diagnosed >1.5 years before and was well-controlled (HbA1c 50.1 ± 6.6 mmol/mol). All patients used metformin, and four patients also used sulfonylurea agents (see table for detailed patient characteristics). Studies were performed between January and September 2014.

extract_protocol: Total RNA was prepared from the white adipose tissue samples using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0). Due to bad quality, the 2 samples from 1 subject were excluded from the study.

treatment_protocol: During the 10 day cold acclimation protocol, patients were exposed to an environmental temperature of 14-14.5 °C for 10 consecutive days: 2h on day one, 4h on day two, and 6h on days 3 through 10. Patients were instructed to maintain their normal medication use throughout the whole acclimation period, except for the days on which the clamps were performed. Patients consumed standardized meals on the evenings before each experimental day and were asked to refrain from heavy exercise at least 48h before these days. During cold acclimation, patients were dressed in shorts and T-shirt and remained sedentary while staying in the cold room. Food intake in the cold room was kept constant and patients were instructed not to change their normal dietary regime outside the cold room. Before and after  this 10 day cold acclimation intervention, an abdominal subcutaneous fat biopsy was taken after an overnight fast. Samples were snap-frozen in liquid nitrogen for RNA isolation and microarray analysis.

tag: sexe

tag: subjectid

tag: age (yrs)

tag: height (m)

tag: weight (kg)

tag: bmi (kg/m2)

tag: body fat % (before intervention)

tag: fasting  glucose (mmol/l)

tag: fasting insulin (pmol/l)

tag: diabetes duration (years)

tag: medication regimen

value: Metformin (850mg, 3x/day), Gliclazide (80mg, 2x/day)

tag: hba1c (mmol/mol)


title: abdominal subcutaneous white adipose tissue, after 10 days of cold acclimation, subject 7

source_name: abdominal subcutaneous white adipose tissue, after 10 days of cold acclimation, obtained from subject 7

value: Metformin (850mg, 2x/day), Vildagliptin (50mg, 2x/day)


title: abdominal subcutaneous white adipose tissue, before 10 days of cold acclimation, subject 4

source_name: abdominal subcutaneous white adipose tissue, before 10 days of cold acclimation, obtained from subject 4

value: Metformin (1000mg, 2x/day), Glimepiride (5mg, 1x/day)


title: abdominal subcutaneous white adipose tissue, before 10 days of cold acclimation, subject 8

source_name: abdominal subcutaneous white adipose tissue, before 10 days of cold acclimation, obtained from subject 8


title: abdominal subcutaneous white adipose tissue, after 10 days of cold acclimation, subject 4

source_name: abdominal subcutaneous white adipose tissue, after 10 days of cold acclimation, obtained from subject 4


title: abdominal subcutaneous white adipose tissue, before 10 days of cold acclimation, subject 7

source_name: abdominal subcutaneous white adipose tissue, before 10 days of cold acclimation, obtained from subject 7


title: abdominal subcutaneous white adipose tissue, after 10 days of cold acclimation, subject 3

source_name: abdominal subcutaneous white adipose tissue, after 10 days of cold acclimation, obtained from subject 3

value: Metformin (1000mg, 2x/day)


title: Control_PVAT replicate 2

city: Schlieren

first: Elvira

last: Haas

address: Wagistrasse 12, 3rd floor

department: Division of Internal Medicine

country: Switzerland

institute: University Hospital of Zurich

hyb_protocol: Affymetrix GeneChip Gene 1.0 ST Arrays

scan_protocol: Hewlett-Packard GeneArray Scanner G2500A

data_processing: Affymetrix Power Tools v1.10.2 using the RMA algorithm

source_name: thoracic perivascular adipose tissue

label_protocol: 5 μg of total RNA were reverse transcribed and cDNA amplified using Ambion WT Expression kit (Affymetrix, United Kingdom) and biotinylated cRNA was prepared using Encore Biotine Module (Nugen, Netherlands) according to manufacturer's recommendations.

growth_protocol: Mice were housed under constant 24 hour light/dark conditions with water and food ad libitum. Prior expriment, mice were starved over night and sacraficed the next morning at 9 am. Thoracic aorta with PVAT was dissected and pleased in ice-cold Krebs-Ringer bicarbonate solution (pH 7.4). After cleaning the thoracic aorta, PVAT was snap-frozen in RNAlater (Qiagen) and stored at -80°C until further usage.

extract_protocol: Total RNA was extracted from PVAT using a RNeasy Lipid Tissue Kit (Qiagen). Dnase digestion of total RNA samples was performed in solution using the RNase free DNase set (Qiagen) followed by an additional total RNA purification step using RNeasy Mini Kit (Qiagen). Procedure was done following manufacturer's recommendations.

treatment_protocol: None.

tag: genotype

value: Rictorfl/fl

tag: tissue

value: thoracic perivascular adipose tissue

tag: gender

tag: age

value: 17-22 weeks


title: Control_PVAT replicate 3


title: abdominal subcutaneous white adipose tissue, before 10 days of cold acclimation, subject 3

source_name: abdominal subcutaneous white adipose tissue, before 10 days of cold acclimation, obtained from subject 3


title: abdominal subcutaneous white adipose tissue, after 10 days of cold acclimation, subject 6

source_name: abdominal subcutaneous white adipose tissue, after 10 days of cold acclimation, obtained from subject 6

value: Metformin (850 mg, 3x/day), Glimepiride (6mg, 1x/day)


title: Control_PVAT replicate 4


title: Control_PVAT replicate 1


title: abdominal subcutaneous white adipose tissue, before 10 days of cold acclimation, subject 6

source_name: abdominal subcutaneous white adipose tissue, before 10 days of cold acclimation, obtained from subject 6


title: RictoraP2KO PVAT replicate 4


title: RictoraP2KO PVAT replicate 1


title: RictoraP2KO PVAT replicate 3


title: abdominal subcutaneous white adipose tissue, after 10 days of cold acclimation, subject 5

source_name: abdominal subcutaneous white adipose tissue,after 10 days of cold acclimation, obtained from subject 5

value: Metformin (500mg, 2x/day)


title: RictoraP2KO PVAT replicate 2


title: Array: 252523810023 / Green555= Coc-30; rep 3 -

status: Public on Jul 04 2015

city: Detroit

middle: J

last: Bannon

state: MI

address: 540 E Canfield

department: Pharmacology

institute: Wayne State University School of Medicine

hyb_protocol: Agilent manufacturer protocol: Dual colors labeled cDNAs were co-hybridized in a flip dye design to 60-mer Agilent human genome-wide oligonucleotide arrays (catalog #G4112A, Agilent) using a two-color dye-flip set up.

scan_protocol: Microarrays were scanned with an Agilent Technologies Microarray Scanner G2505A US1470236 and the fluorescence was accessed using the software Feature Extraction software (V10. 3. 1, Agilent Technologies, USA)

data_processing: Images were quantified using Agilent Feature Extraction (V10.3.1, Agilent technologies, USA) with the default protocol (GE2_107_Sep09).

label: Alexa 555

label_protocol: 500 ng of total RNA was used to label complementary RNA using Low RNA Input Linear Amp kit (Agilent).

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

tag: Cause of death

value: Cocaine abuse

tag: Sex

value: Male

tag: source

value: postmortem brain

value: Ventral midbrain

tag: raw file


title: Array: 252523810023 / Green555= Con-13; rep 2 +

value: Gunshot wound


title: abdominal subcutaneous white adipose tissue, after 10 days of cold acclimation, subject 2

source_name: abdominal subcutaneous white adipose tissue,after 10 days of cold acclimation, obtained from subject 2

tag: sexe

tag: subjectid

tag: age (yrs)

tag: height (m)


title: Array: 252523810022 / Green555= Coc-16; rep 3 -

value: Cocaine abuse, aortic dissection


title: Array: 252523810023 / Green555= Coc-30; rep 4 -


title: abdominal subcutaneous white adipose tissue, before 10 days of cold acclimation, subject 5

source_name: abdominal subcutaneous white adipose tissue, before 10 days of cold acclimation, obtained from subject 5

tag: weight (kg)

tag: bmi (kg/m2)

tag: body fat % (before intervention)

tag: fasting  glucose (mmol/l)


title: Array: 252523810023 / Green555= Con-13; rep 1 +


title: Array: 252523810022 / Green555= Con-52; rep 1 +

value: Hypertension, aortic dissection


title: Array: 252523810021 / Green555= Con-11; rep 2 +

value: Hypertensive arteriosclerotic cardiovascular disease


title: Array: 252523810022 / Green555= Con-52; rep 2 +


title: Array: 252523810022 / Green555= Coc-16; rep 4 -


title: abdominal subcutaneous white adipose tissue, before 10 days of cold acclimation, subject 2

source_name: abdominal subcutaneous white adipose tissue, before 10 days of cold acclimation, obtained from subject 2

value: male

tag: fasting insulin (pmol/l)

tag: diabetes duration (years)

tag: medication regimen

tag: hba1c (mmol/mol)


title: Array: 252523810021 / Green555= Coc-51; rep 3 -

tag: age

tag: tissue


title: Array: 252523810021 / Green555= Coc-51; rep 4 -

tag: Cause of death

tag: Sex


title: Array: 252523810020 / Green555= Coc-57; rep 4 -

tag: source

tag: raw file


title: Array: 252523810021 / Green555= Con-11; rep 1 +


title: Array: 252523810020 / Green555= Coc-57; rep 3 -


title: Array: 252523810020 / Green555= Con-15; rep 2 +

value: Hypertensive cardiomyopathy


title: Array: 252523810018 / Green555= Coc-14; rep 3 -


title: Array: 252523810018 / Green555= Coc-14; rep 4 -


title: Array: 252523810020 / Green555= Con-15; rep 1 +


title: Array: 252523810019 / Green555= Con-54; rep 2 +

value: Multiple gunshot wounds


title: Array: 252523810019 / Green555= Coc-55; rep 4 -

value: Acute cocaine intoxication


title: Array: 252523810019 / Green555= Coc-55; rep 3 -


title: Array: 252523810018 / Green555= Con-50; rep 1 +


title: Array: 252523810019 / Green555= Con-54; rep 1 +


title: Array: 252523810018 / Green555= Con-50; rep 2 +


title: Array: 252523810017 / Green555= Coc-28; rep 3 -

value: Cocaine abuse, intracerebral hemorrhage

value: Female


title: Array: 252523810014 / Green555= Coc-8; rep 3 -


title: Array: 252523810015 / Green555= Coc-12; rep 3 -

value: Cocaine abuse, aortic aneurysm


title: Array: 252523810015 / Green555= Con-9; rep 2 +


title: Array: 252523810015 / Green555= Coc-12; rep 4 -


title: Array: 252523810014 / Green555= Coc-8; rep 4 -


title: Array: 252523810013 / Green555= Coc-6; rep 3 -


title: Array: 252523810017 / Green555= Coc-28; rep 4 -


title: Array: 252523810015 / Green555= Con-9; rep 1 +


title: Array: 252523810013 / Green555= Con-5; rep 2 +


title: Array: 252523810017 / Green555= Con-27; rep 2 +


title: Array: 252523810017 / Green555= Con-27; rep 1 +


title: Array: 252523810014 / Green555= Con-7; rep 2 +

value: Acute myocardial infarction


title: Array: 252523810011 / Green555= Con-1; rep 2 +

value: Dilated cardiomyopathy


title: Array: 252523810022 / Red647= Coc-16; rep 1 +

label: Alexa 647


title: Array: 252523810014 / Green555= Con-7; rep 1 +


title: Array: 252523810011 / Green555= Coc-2; rep 4 -

value: Cocaine abuse


title: Array: 252523810022 / Red647= Con-52; rep 3 -

value: Male


title: Array: 252523810011 / Green555= Con-1; rep 1 +

value: postmortem brain


title: Array: 252523810013 / Green555= Coc-6; rep 4 -

value: Ventral midbrain


title: Array: 252523810013 / Green555= Con-5; rep 1 +

value: Gunshot wound


title: Array: 252523810023 / Red647= Con-13; rep 3 -


title: Array: 252523810023 / Red647= Coc-30; rep 2 +


title: Array: 252523810022 / Red647= Coc-16; rep 2 +

value: Cocaine abuse, aortic dissection


title: Array: 252523810023 / Red647= Coc-30; rep 1 +


title: Array: 252523810021 / Red647= Con-11; rep 3 -


title: Array: 252523810011 / Green555= Coc-2; rep 3 -


title: Array: 252523810023 / Red647= Con-13; rep 4 -


title: Array: 252523810021 / Red647= Con-11; rep 4 -


title: Array: 252523810022 / Red647= Con-52; rep 4 -

value: Hypertension, aortic dissection


title: Array: 252523810021 / Red647= Coc-51; rep 2 +


title: Array: 252523810019 / Red647= Con-54; rep 4 -


title: Array: 252523810020 / Red647= Con-15; rep 4 -


title: Array: 252523810020 / Red647= Coc-57; rep 1 +


title: Array: 252523810021 / Red647= Coc-51; rep 1 +


title: Array: 252523810018 / Red647= Con-50; rep 4 -

value: Hypertensive arteriosclerotic cardiovascular disease


title: Array: 252523810018 / Red647= Coc-14; rep 2 +

value: Cocaine Abuse


title: Array: 252523810019 / Red647= Coc-55; rep 2 +


title: Array: 252523810019 / Red647= Coc-55; rep 1 +


title: Array: 252523810017 / Red647= Coc-28; rep 1 +


title: Array: 252523810018 / Red647= Coc-14; rep 1 +


title: Array: 252523810017 / Red647= Coc-28; rep 2 +


title: E13.5 distal half of midgut-Id2 KO-3

city: Shimoaizuki, Matsuoka

first: Kentaro

last: Mori

state: Fukui

country: Japan

institute: University of Fukui

hyb_protocol: Digoxigenin-labeled cRNA samples were hybridized to Mouse Genome Survey Microarrays V2.0 (Applied Biosystems) at a temperature of 55℃. After several washing steps of increasing stringency, an anti-digoxigenin-antibody conjugated to alkaline phosphatase (Roche Diagnostics) was added.

scan_protocol: Chemiluminescence and fluorescence signals were detected on an AB1700 microarray reader. Reagents from the Chemiluminescence Detection Kit (Applied Biosystems) were used in this procedure.

data_processing: Detectable probes were determined by a signal to noise ratio (S/N) > 3 and quality flag < 5,000 determined by the AB1700 microarray software tool.

label: Digoxigenin

source_name: Embryo of littermate Id2 knock out mouse

label_protocol: One µg of total RNA was amplified with one round NanoAmpTM RT-IVT Labeling Kit (Applied Biosystems).

extract_protocol: Distal half of the midgut segments of Id2 WT and KO embryo were disected at E13.5. Total RNA of each samples were extarcted by RNeasyMicro Kit.

value: distal half of midgut

tag: genotype/variation

value: Id2 KO

tag: developmental stage

value: E13.5 embryo


title: E13.5 distal half of midgut-Id2 WT-3

source_name: Embryo of littermate Id2 wild type mouse

value: Id2 wild type


title: Array: 252523810017 / Red647= Con-27; rep 3 -

value: Female


title: E13.5 distal half of midgut-Id2 KO-1


title: Array: 252523810015 / Red647= Coc-12; rep 1 +

value: Cocaine abuse, aortic aneurysm


title: Array: 252523810014 / Red647= Con-7; rep 3 -

value: Acute myocardial infarction


title: Array: 252523810014 / Red647= Con-7; rep 4 -


title: Array: 252523810015 / Red647= Con-9; rep 3 -

value: Multiple gunshot wounds


title: Array: 252523810020 / Red647= Coc-57; rep 2 +

value: Cocaine abuse


title: Array: 252523810020 / Red647= Con-15; rep 3 -

value: Hypertensive cardiomyopathy

value: Male


title: Array: 252523810015 / Red647= Con-9; rep 4 -

value: postmortem brain

value: Ventral midbrain


title: Array: 252523810014 / Red647= Coc-8; rep 2 +

value: Acute cocaine intoxication


title: Array: 252523810017 / Red647= Con-27; rep 4 -


title: Array: 252523810018 / Red647= Con-50; rep 3 -


title: Array: 252523810019 / Red647= Con-54; rep 3 -


title: E13.5 distal half of midgut-Id2 KO-2


title: E13.5 distal half of midgut-Id2 WT-2


title: Array: 252523810015 / Red647= Coc-12; rep 2 +


title: E13.5 distal half of midgut-Id2 WT-1


title: Array: 252523810013 / Red647= Coc-6; rep 2 +


title: Array: 252523810013 / Red647= Con-5; rep 3 -

value: Gunshot wound


title: Array: 252523810011 / Red647= Con-1; rep 3 -

value: Dilated cardiomyopathy


title: Array: 252523810011 / Red647= Con-1; rep 4 -


title: Array: 252523810011 / Red647= Coc-2; rep 2 +


title: Array: 252523810013 / Red647= Con-5; rep 4 -


title: IFNg+IL-10- T cells donor B

status: Public on Jul 03 2015

city: Amsterdam

first: Anja

last: ten Brinke

address: Plesmanlaan 125

department: Immunopathology

institute: Sanquin Blood Supply Foundation

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data was log2 transformed and normalized between arrays using robust spline normalization method. Triplicate samples of IL-10+ T cells were compared to IFNg+/IL-10- T cells by LIMMA analysis.

source_name: naive CD4+ T cells

label_protocol: Biotinylated cRNA was prepared following standard Illumina labeling protocol.

extract_protocol: RNA was extracted with Trizol reagent, followed by DNase treatment.

value: PBMC

tag: activation

value: by allogeneic dendritic cells

tag: sort

value: IFNg+IL-10- T cells


title: Y15 treated TT cells rep2

city: buffalo

first: Dan

last: Wang

state: NY

address: Elm & Carlton Streets

hyb_protocol: The labeled probes were then mixed with hybridization reagents and hybridized overnight to the HumanHT12 v4 BeadChips.

scan_protocol: Following washing and staining, the BeadChips were imaged using the Illumina BeadArray Reader to measure fluorescence intensity at each probe.

data_processing: BeadChip data files are analyzed with Illumina’s GenomeStudio gene expression module (V1.6.0)

source_name: Y15 treated medullary thyroid cancer cells

label_protocol: Initially, we converted 250-500 ng total RNA to cDNA, followed by in vitro transcription to generate biotin-labeled cRNA (Illumina TotalPrep RNA Amplification Kit, Ambion Inc., Austin, TX).

extract_protocol: Total RNA was isolated from frozen tissue samples using TRIZOL reagent (Invitrogen).

tag: cell type

value: medullary thyroid cancer cell line

tag: cell line

value: TT

tag: treatment

value: FAK inhibitor Y15 small molecule at 10 microM


title: PF04554878 treated TT cells rep2

source_name: PF04554878 treated medullary thyroid cancer cells

value: FAK inhibitor PF04554878 at 10microM


title: Array: 252523810011 / Red647= Coc-2; rep 1 +

value: Female


title: WT2

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

hyb_protocol: Hybridisation samples were prepared for a 8-pack microarray using 600 ng cRNA each according to the hybridisation protocol from Agilent: One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling), loaded onto the 8-pack array slide and hybridised at 65 °C overnight

scan_protocol: After washing the microarray was scanned on an Agilent C Scanner using the Profile AgilentG3_GX_1Color for 8x60K microarrays (Dye channel: Green; Scan region: Scan Area (61 x 21.6 mm); Scan resolution (μm): 3; Tiff: 20 bit)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) (protocol GE1_107_Sep09, Grid: 028004_D_F_20110325 and platform Agilent SurePrint G3 Human GE 8x60K). The raw data output by Feature Extraction Software was analysed using the LIMMA R package with quantile normalisation and background subtraction.

source_name: FLT3 wild type AML patient sample

label_protocol: 25 ng RNA was labelled with Cyanine 3-CTP according to the sample preparation protocol from Agilent: One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling). Amplified labelled RNA samples were purified by using Qiagen's RNeasy mini spin columns and cRNA quantified by using a Nanodrop

growth_protocol: Patient and donor samples were obtained either from blood or bone marrow. Lymphoprep extraction of leukocytes was performed following 30 min no brake centrifugation. Enrichment for CD34 and CD117 were checked via FACS analysis. For CD14 samples, enricment for CD14 was controlled by FACS analysis. Where available, purification was performed using MACS columns following anti-CD34 bead conjugation to samples (anti-CD14 for CD14 samles).

extract_protocol: RNA was extracted from cells using TRIzol® (Invitrogen) according to manufacturers instruction. First strand cDNA synthesis was carried out using M-MLV reverse transcriptase (Invitrogen) according to manufacturers instructions using 1-2 μg of RNA. Real Time PCR was carried out using ABI SYBR® green master mix with 2 μl of diluted cDNA and 0.25 μM primer per 10 μl reaction on an ABI 7500 machine.

value: FLT3 wild type AML patient sample


title: IL10+ T cells donor A

value: IL-10 positive T cells


title: TT cells untreated rep2

source_name: untreated medullary thyroid cancer cell line

value: untreated


title: WT1


title: WT10


title: Y15 treated TT cells rep1


title: TT cells untreated rep1


title: IFNg+IL-10- T cells donor A


title: WT5


title: WT3


title: IFNg+IL-10- T cells donor C


title: WT7


title: IL10+ T cells donor B


title: PF04554878 treated TT cells rep1


title: IL10+ T cells donor C


title: WT6


title: WT8


title: ITD9

source_name: FLT3-ITD AML patient sample

value: FLT3-ITD AML patient sample


title: ITD7


title: JAK2

source_name: FLT3 wild type JAK2 V716F AML patient sample


title: ITD5


title: 720 T-ALL AI-9-54 rep4

city: Philadelphia

first: Nancy

middle: Asmussen

last: Speck

state: Pennsylvania

address: 421 Curie Blvd, 554 BRB II/III

department: Cell and Developmental Biology

institute: University of Pennsylvania Perelman School of Medicine

hyb_protocol: 25 ug of fragmented and labeled DNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 2.0 ST Array according to GeneChip WT Terminal Labeling and Hybridization User Manual (Affymetrix). GeneChips were washed and stained in the Affymetrix Fludics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 7G Scanner.

data_processing: Cel files RMA normalized using Partek Genomics Suite v6.6

source_name: Mouse T-ALL Cell line_treated_with_RDI_AI-9-54

label_protocol: 5.5 ug of single-stranded cDNA were fragmented and biotin-labeled according to GeneChip WT Terminal Labeling and Hybridization User Manual (Affymetrix).

growth_protocol: 720 T-ALL cells were grown in RPMI 1640 with 10% FBS 1% glutamine, penicillin/streptomycin in 37C under 5% CO2

extract_protocol: Live 720 T-ALL cells from treatment were washed and recovered. RNA for microarray was isolated with the RNeasy Kit (QIAGEN). Total RNA quantity and integrity were verified using Bioanalyzer (Agilent Technologies), and amplified using Ambion WT Expression Kit (Applied Biosystems).

treatment_protocol: Runt domain inhibitors were aded to 720 T-ALL cell cultures such that the final concentrations were 100 uM for AI-7-54, 100 uM for AI-8-45, and 50 uM for AI-9-54. The cells were treated for 8 hours.

value: Murine T-ALL cell line derived from Tcf12+/- mouse expressing a Tal1 transgene under the control of the Lck promoter


title: ITD6


title: ITD8


title: 720 T-ALL AI-9-54 rep2


title: 720 T-ALL AI-9-54 rep1


title: 720 T-ALL AI-8-45 rep3

source_name: Mouse T-ALL Cell line_treated_with_RDI_AI-8-45


title: 720 T-ALL AI-8-45 rep1


title: 720 T-ALL AI-8-45 rep2


title: 720 T-ALL AI-9-54 rep3


title: 720 T-ALL AI-8-45 rep4


title: ITD2_2


title: Ewing_PBSC_1

source_name: CD34+ PBSC from donor

value: CD34+ PBSC from donor


title: ITD1_2


title: 720 T-ALL AI-7-54 rep4

source_name: Mouse T-ALL Cell line_treated_with_RDI_AI-7-54


title: 720 T-ALL AI-7-54 rep3


title: ITD4


title: Ewing_PBSC_2


title: ITD1_1


title: ITD3


title: Melan_Ink4a_Arf1_Sox10lacZ_rep2

city: Bethesda

first: Laura

middle: L

last: Baxter

address: 35A Convent Drive

department: NHGRI

institute: NIH

hyb_protocol: Total RNA was reverse transcribed to obtain labeled cDNA. Labeled cDNA was hybridized to the chips. Chips were washed and stained using standard protocols for the Affymetrix Fluidics Station.

scan_protocol: Arrays were scanned using the Affymetrix Gene Chip Scanner 3000 and gene expression intensities were calculated using the Affymetrix GeneChip Command Console software (AGCC).

data_processing:
Raw probe intensities from the microarray hybridization were normalized and analyzed by implementing the robust multi-chip average (RMA) algorithm followed by log2 transformation using Partek Genomic Suite v6.6 software (Partek, Inc; St. Louis, MO).
Differentially expressed genes were identified by ANOVA using a false discovery rate adjusted p-value cutoff of 0.05 (Benjamini-Hochberg method).

source_name: melan-Ink4a-Arf-1; Sox10LacZ/+ cell line

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol.

growth_protocol: According to guidelines from Bennett et al. 1987 (PMID 3102392), cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum (Gibco), 200 nM 12-O-tetradecanoylphorbol 13-acetate (Sigma-Aldrich, St Louis, MO, USA) and 200 pM cholera toxin (Sigma- Aldrich, St Louis, MO, USA) at 37°C in humidified air with 10% CO2.

extract_protocol: For RNA isolation, cells were lysed in Trizol reagent and RNA was isolated using RNAeasy Mini Kit (Qiagen) per manufacturer's instructions.

tag: strain background

value: backcrossed for multiple generations to C57BL/6J mice

value: Sox10LacZ/+; Ink4a-Arf null mice

value: immortalized melanocyte cell line

tag: cell line genotype/variation


title: 720 T-ALL AI-7-54 rep1


title: Melan_Ink4a_Arf1_Sox10lacZ_rep1

value: melan-Ink4a-Arf-1; Sox10LacZ/+ cell line


title: Melan_Ink4a_Arf1_Sox10lacZ_rep3


title: ITD2_1


title: Array: 252523810014 / Red647= Coc-8; rep 1 +

value: Acute cocaine intoxication

value: Male

value: postmortem brain

value: Ventral midbrain


title: Skeletal muscle biopsy_T2D_60min_rep7

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

hyb_protocol: According to the Affymetrix expression protocol

data_processing: Expression console (v.1.3.0.187, Affymetrix) was used to obtain normalized RMA gene-level data (standard settings including median polish and sketch-quantile normalisation)

source_name: Skeletal muscle biopsy, subject with type 2 diabetes, after 60min excercise

label_protocol: Ovation Pico WTA System V2 in combination with the Encore Biotin Module (Nugen)

extract_protocol: miRNeasy Micro Kit (Qiagen) including DNase treatment

tag: height (cm)

tag: weight (kg)

tag: bmi


title: Skeletal muscle biopsy_T2D_recovery_rep6

scan_protocol: According to the Affymetrix expression protocol

source_name: Skeletal muscle biopsy, subject with type 2 diabetes, 3h after excercise

tag: age


title: Skeletal muscle biopsy_T2D_recovery_rep5


title: Skeletal muscle biopsy_T2D_recovery_rep7


title: Melan_Ink4a_Arf1_rep2

source_name: melan-Ink4a-Arf-1 (melan-a) cell line

value: Cdkn2a tm1RDp/tm1RDp mice

value: melan-Ink4a-Arf-1 (melan-a) cell line


title: Melan_Ink4a_Arf1_rep1


title: Skeletal muscle biopsy_T2D_recovery_rep2


title: Skeletal muscle biopsy_T2D_recovery_rep1


title: Skeletal muscle biopsy_T2D_recovery_rep4


title: Skeletal muscle biopsy_T2D_recovery_rep3


title: normal_CD14_BM

source_name: CD14+ PBSC from donor

value: CD14+ PBSC from donor


title: Skeletal muscle biopsy_T2D_60min_rep5


title: Melan_Ink4a_Arf1_rep3


title: Kidney_SHRSP_6w-biological rep3

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

hyb_protocol: Before hybridization, 1650 ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: The array was scanned using Agilent G2505C DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction, LOWESS normalization, and dye-normalization .

source_name: kidneys derived from 6 week-old SHRSP rat strain

label_protocol: 200 ng of total RNA was labeled using Low Input Quick-Amp Labeling Kit (Agilent Technologies, Pato Alto, CA, USA). In brief, cDNA was reverse transcribed from 200 ng of total RNA with an oligo-dT-T7 promoter primer and AffinityScript MT -RT. Fluorescent antisense cRNA was synthesized with cyanine 3-CTP (Cy3-CTP), and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with miRNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: Total RNAs were extracted from kidneys stored in RNA later (Ambion), derived from WKY, SHR and SHRSP rats using miRNeasy extraction kit (Qiagen) following manufacturer's instructions.

treatment_protocol: no teatment

tag: tissue

value: kidney

value: 6 weeks

value: SHRSP


title: Skeletal muscle biopsy_T2D_60min_rep4


title: Skeletal muscle biopsy_T2D_60min_rep6


title: Skeletal muscle biopsy_T2D_60min_rep3


title: Kidney_SHRSP_6w-biological rep2


title: Skeletal muscle biopsy_T2D_60min_rep1


title: Kidney_SHR_6w-biological rep3

source_name: kidneys derived from 6 week-old SHR rat strain

value: SHR


title: Skeletal muscle biopsy_T2D_0min_rep7

source_name: Skeletal muscle biopsy, subject with type 2 diabetes, before excercise


title: Skeletal muscle biopsy_T2D_60min_rep2


title: Skeletal muscle biopsy_T2D_0min_rep5


title: Array: 252523810013 / Red647= Coc-6; rep 1 +

tag: Cause of death

tag: Sex


title: Kidney_SHR_6w-biological rep2


title: Kidney_SHRSP_6w-biological rep1


title: Skeletal muscle biopsy_T2D_0min_rep6


title: Kidney_WKY_6w-biological rep3

source_name: kidneys derived from 6 week-old WKY rat strain

value: WKY


title: Kidney_SHR_6w-biological rep1


title: Kidney_WKY_6w-biological rep2


title: Kidney_SHRSP_3w-biological rep3

source_name: kidneys derived from 3 week-old SHRSP rat strain

value: 3 weeks


title: Kidney_WKY_6w-biological rep1


title: Kidney_SHRSP_3w-biological rep2


title: Skeletal muscle biopsy_T2D_0min_rep2


title: Kidney_SHRSP_3w-biological rep1


title: Kidney_SHR_3w-biological rep2

source_name: kidneys derived from 3 week-old SHR rat strain


title: Skeletal muscle biopsy_NGT_recovery_rep7

source_name: Skeletal muscle biopsy, subject with normal glucose tolerance, 3h after excercise


title: Skeletal muscle biopsy_T2D_0min_rep4


title: Skeletal muscle biopsy_NGT_recovery_rep5


title: Skeletal muscle biopsy_NGT_recovery_rep6


title: Kidney_SHR_3w-biological rep1


title: Skeletal muscle biopsy_T2D_0min_rep3


title: Skeletal muscle biopsy_NGT_60min_rep7

source_name: Skeletal muscle biopsy, subject with normal glucose tolerance, after 60min excercise


title: Skeletal muscle biopsy_NGT_recovery_rep3


title: Kidney_WKY_3w-biological rep1

source_name: kidneys derived from 3 week-old WKY rat strain


title: Skeletal muscle biopsy_NGT_recovery_rep4


title: Skeletal muscle biopsy_T2D_0min_rep1


title: Kidney_SHR_3w-biological rep3


title: Kidney_WKY_3w-biological rep2


title: Skeletal muscle biopsy_NGT_recovery_rep1


title: Skeletal muscle biopsy_NGT_60min_rep6


title: Skeletal muscle biopsy_NGT_recovery_rep2


title: pBABE Tbx15  rep2

city: Boston

first: Kevin

middle: Yu-sun

last: Lee

state: MA

address: 1 Joslin Place

institute: Joslin Diabetes Center

description: Control cells for Tbx15 Knockdown in C2C12 Myoblasts

hyb_protocol: After fragmenting, 15ug cRNA was used to make the hybridization cocktail which was hybridized to GeneChip Mouse M430 2.0 array for 16 hours at 45°C. Arrays were washed and stained using Affymetrix Fluidics Station 450 with user-prepared reagents.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 G7

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1500.

source_name: Tbx15 Overexpression

label_protocol: Simultaneous cRNA synthesis and biotin labeling via 3' IVT Express protocol (Affymetrix).

growth_protocol: RNA was extracted from three independent transfections of the four stable C2C12 myoblast cell lines: shTbx15, shGFP, pBABE-Empty-puro, pBABE-Tbx15-puro. Stably transfected cells were selected for Puromycin resistance. Cells were grown in D-MEM High Glucose Supplemented with 10% FBS, Glutamax, and Pen/Strep, and collected at 90% confluency.

extract_protocol: RNeasy extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

treatment_protocol: Cells were rinsed with PBS prior to RNA extraction.

value: pBABE Tbx15

value: myoblasts


title: Skeletal muscle biopsy_NGT_60min_rep5


title: Skeletal muscle biopsy_NGT_60min_rep4


title: pBABE-empty rep3

description: Tbx15 Knockdown in C2C12 Myoblasts

value: pBABE-empty


title: pBABE Tbx15  rep1


title: Kidney_WKY_3w-biological rep3


title: pBABE Tbx15 rep3


title: pBABE-empty  rep2

description: Tbx15 Knockdown in C2C12 Myoblasts


title: pBABE-empty  rep1

description: Tbx15 Knockdown in C2C12 Myoblasts


title: Skeletal muscle biopsy_NGT_60min_rep3


title: Skeletal muscle biopsy_NGT_0min_rep6

source_name: Skeletal muscle biopsy, subject with normal glucose tolerance, before excercise


title: Skeletal muscle biopsy_NGT_60min_rep1


title: shSCR control  rep2

source_name: Tbx15 Knockdown

value: shSCR control


title: shSCR control rep3


title: Skeletal muscle biopsy_NGT_0min_rep5


title: shTbx15 rep1

description: Tbx15 Knockdown in C2C12 Myoblasts


title: Skeletal muscle biopsy_NGT_0min_rep4


title: shSCR control  rep1


title: Skeletal muscle biopsy_NGT_60min_rep2


title: Skeletal muscle biopsy_NGT_0min_rep1


title: shTbx15 rep3

description: Tbx15 Knockdown in C2C12 Myoblasts


title: shTbx15 rep2

description: Tbx15 Knockdown in C2C12 Myoblasts


title: Skeletal muscle biopsy_NGT_0min_rep7


title: Day 3 L/L Intestine

city: Singapore

last: Silver

address: 8 College Road

country: Singapore

institute: Duke-NUS Graduate Medical School

description: Gene expression data from small intestine

hyb_protocol: Following fragmentation, samples were hybridized on the Affymetrix GeneChip® Mouse Genome 430 2.0 Array for 16hrs at 45 degrees Celsius. GeneChips were washed and stained using the GeneChip® Fluidics Station 450 (Affymetrix).

scan_protocol: Scanning was done using the GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: The data were analyzed with Partek Genomics Suit 6.6 using Affymetrix default analysis settings and quantile normalization with median polish as probeset summarization. RMA background correction was used.

source_name: L/L small intestine at day 3 post- tamoxifen

label_protocol: Biotinylated cRNA were prepared according the Affymetrix protocol from 250ng of total RNA (GeneChip® 3’ IVT Plus Reagent Kit User Manual, 2013, Affymetrix).

growth_protocol: 100ug/g of tamoxifen was intraperitoneally injected at days 1,2,3. Mice were sacrificed at days 2,3,5 for harvesting of the small intestine.

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

treatment_protocol: Whole small intestine was flushed with cold PBS to remove intestinal contents and flash frozen in liquid nitrogen before storage at -80dc. The samples were then homogenized using ceramic beads in 1mL of Trizol.

value: small intestine


title: Skeletal muscle biopsy_NGT_0min_rep2


title: Day 5 KO Intestine

source_name: KO small intestine at day 5 post- tamoxifen


title: Day 2 L/L Intestine

source_name: L/L small intestine at day 2 post- tamoxifen


title: Day 3 KO Intestine

source_name: KO small intestine at day 3 post- tamoxifen


title: Day 5 L/L Intestine

source_name: L/L small intestine at day 5 post- tamoxifen


title: Day 2 KO Intestine

source_name: KO small intestine at day 2 post- tamoxifen


title: Skeletal muscle biopsy_NGT_0min_rep3


title: ITD2

hyb_protocol: HumanMethylation 450K BeadChip

scan_protocol: HumanMethylation 450K BeadChip

data_processing: For the analysis of methylation sample data, image scanning, processing, feature extraction and normalization were performed in Illumina GenomeStudio. All intensities are combined in the TPS1928_SampleMethylationProfile_FinalReport_20Jun11_HL_NHL.txt file. Higher-level analysis was performed in R using IMA (https://www.rforge.net/IMA/index.html) followed by a custom R pipeline where probe  methylation levels were aggregated per promoter. Promoter methylation fold changes were computed as log2 ratios

label: Biotin, DNP

source_name: FLT3-ITD AML patient sample

label_protocol: HumanMethylation 450K BeadChip

extract_protocol: Phenol-choroform

value: FLT3-ITD AML


title: WT4

source_name: FLT3 wild type AML patient sample

value: FLT3 wild type AML


title: Bone Marrow proB and preB cells of WT mouse, biological replicate 2

city: Salamanca

first: Isidro

last: Sánchez García

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

country: Spain

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

description: Gene expression data from WT bone marrow proB and preB cells

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The RMA function provided by the package oligo from R/Bioconductor was applied to the raw expression data.

source_name: WT 2

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Ambion)

growth_protocol: Animals were housed in conventional facility and they have been exposed to common pathogens.

treatment_protocol: Not applicable

value: bone marrow proB and preB

tag: genotype/variations

value: WT


title: WT3


title: Scid: Atm, no infection, rep 2

city: Saint Louis

first: Barry

last: Sleckman

state: MO

address: 4940 Parkview Place

department: Pathology and Immunology

institute: Washington University in St Louis

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Gene expression levels were determined using Partek's plug-in for GenomeStudio Gene Expression Module.

source_name: bone marrow-derived macrophage

label_protocol: Purified RNA was labeled according to manufacturer's protocol.

growth_protocol: Bone marrow-derived macrophages were generated from whole bone marrow isolated from 4-8 wk.-old mice.  Whole bone marrow was cultured for 6 days in complete DMEM containing 20% supernatant from L929 fibroblasts as a source of M-CSF

extract_protocol: RNA was purified using Qiagen RNeasy Kits according to the manufacturer’s protocol.

treatment_protocol: Bone marrow-derived macrophages were infected with Listeria monocytogenes at an MOI of 5 for 24 hrs

tag: genotype

tag: time

value: 0 hr

value: no infection

value: bone marrow-derived macrophage


title: Scid: Atm, Listeria, rep 2

description: replicate 2

value: 24 hr

value: infected with Listeria monocytogenes at an MOI of 5 for 24 hrs


title: Bone Marrow proB and preB cells of ETV6/RUNX1 mouse, biological replicate 2

description: Gene expression data from ETV6/RUNX1 bone marrow proB and preB cells

source_name: ETV6RUNX1 2


title: Bone Marrow proB and preB cells of ETV6/RUNX mouse1, biological replicate 3

source_name: ETV6RUNX1 3


title: ITD1


title: Bone Marrow proB and preB cells of Pax5+/- mouse, biological replicate 2

description: Gene expression data from Pax5+/- bone marrow proB and preB cells


title: Scid: Atm, Listeria, rep 1

description: replicate 1


title: LysMcre, Listeria, rep 1

description: replicate 1

value: LysMcre/+


title: LysMcre, no infection, rep 2

description: replicate 2


title: Bone Marrow proB and preB cells of W mouseT, biological replicate 3

source_name: WT 3


title: LysMcre, Listeria, rep 2

description: replicate 2


title: Bone Marrow proB and preB cells of ETV6/RUNX1 mouse, biological replicate 4

source_name: ETV6RUNX1 4


title: Bone Marrow proB and preB cells of WT mouse, biological replicate 1

source_name: WT 1


title: Bone Marrow proB and preB cells of Pax5+/- mouse, biological replicate 3


title: ITD4


title: 72_V411_90%confl_3.3

status: Public on Jul 02 2015

city: Lund

first: Markus

last: Ringner

address: Sölvegatan 35

country: Sweden

institute: Lund University

description:
D492M at 90 % confluency replicate 3.3
scan setting file: mirna

hyb_protocol: Fluorescently labelled cDNA PCR products were hybridized to Illumina Human v2 MicroRNA Expression BeadChips according to the protocols provided by the manufacturer.

scan_protocol: Standard BeadArray Reader scanning protocol

data_processing: The data was processed using BeadStudio 3.1.3.0

source_name: Cell line

label_protocol: standard Illumina protocol

extract_protocol: The total RNA was extracted from cell lines at 50% and 90% confluency in monolayer culture according to the standard protocol of the RNeasy mini kit (QIAGEN).

tag: confluency

tag: replicate


title: WT2

tag: cell type


title: WT5


title: 71_V411_90%confl_3.2

description:
D492M at 90 % confluency replicate 3.2
scan setting file: mirna

tag: cell line


title: Bone Marrow proB and preB cells of Pax5+/- mouse, biological replicate 1


title: 69_V411_90%confl_2.3

description:
D492M at 90 % confluency replicate 2.3
scan setting file: mirna


title: 70_V411_90%confl_3.1

description:
D492M at 90 % confluency replicate 3.1
scan setting file: mirna


title: Bone Marrow proB and preB cells of ETV6/RUNX1 mouse, biological replicate 1

source_name: ETV6RUNX1 1


title: Scid: Atm, no infection, rep 1

description: replicate 1

tag: treatment


title: LysMcre, no infection, rep 1

description: replicate 1


title: 66_V411_90%confl_1.3

description:
D492M at 90 % confluency replicate 1.3
scan setting file: mirna


title: 64_V411_90%confl_1.1

description:
D492M at 90 % confluency replicate 1.1
scan setting file: mirna


title: 65_V411_90%confl_1.2

description:
D492M at 90 % confluency replicate 1.2
scan setting file: mirna


title: 67_V411_90%confl_2.1

description:
D492M at 90 % confluency replicate 2.1
scan setting file: mirna


title: 61_V411_50%confl_3.1

description:
D492M at 50 % confluency replicate 3.1
scan setting file: mirna


title: 62_V411_50%confl_3.2

description:
D492M at 50 % confluency replicate 3.2
scan setting file: mirna


title: 60_V411_50%confl_2.3

description:
D492M at 50 % confluency replicate 2.3
scan setting file: mirna


title: 68_V411_90%confl_2.2

description:
D492M at 90 % confluency replicate 2.2
scan setting file: mirna


title: 52_D492_90%confl_3.1

description:
D492 at 90 % confluency replicate 3.1
scan setting file: mirna


title: 63_V411_50%confl_3.3

description:
D492M at 50 % confluency replicate 3.3
scan setting file: mirna


title: 57_V411_50%confl_1.3

description:
D492M at 50 % confluency replicate 1.3
scan setting file: mirna


title: 56_V411_50%confl_1.2

description:
D492M at 50 % confluency replicate 1.2
scan setting file: mirna


title: 53_D492_90%confl_3.2

description:
D492 at 90 % confluency replicate 3.2
scan setting file: mirna


title: 51_D492_90%confl_2.3

description:
D492 at 90 % confluency replicate 2.3
scan setting file: mirna


title: 58_V411_50%confl_2.1

description:
D492M at 50 % confluency replicate 2.1
scan setting file: mirna


title: 59_V411_50%confl_2.2

description:
D492M at 50 % confluency replicate 2.2
scan setting file: mirna


title: CD34

source_name: CD34+ PBSC from donor

value: CD34+ PBSC


title: 54_D492_90%confl_3.3

description:
D492 at 90 % confluency replicate 3.3
scan setting file: mirna


title: 55_V411_50%confl_1.1

description:
D492M at 50 % confluency replicate 1.1
scan setting file: mirna


title: 49_D492_90%confl_2.1

description:
D492 at 90 % confluency replicate 2.1
scan setting file: mirna


title: 50_D492_90%confl_2.2

description:
D492 at 90 % confluency replicate 2.2
scan setting file: mirna


title: 48_D492_90%confl_1.3

description:
D492 at 90 % confluency replicate 1.3
scan setting file: mirna


title: 47_D492_90%confl_1.2

description:
D492 at 90 % confluency replicate 1.2
scan setting file: mirna


title: DMSO-treated NRK-52E cells at 72h_biological rep2

city: Manchester

first: Kate

last: Bloch

address: Alderley Park, Alderley Edge

institute: Manchester University

description:
Gene expression data from cells treated with aristolochic acids
DMSO-72h-R-2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray scanner.

data_processing: Signal condensation and normalization was performed using GC-RMA (Robust Multiarray Analysis algorithm) using GeneSpring GX11.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: NRK-52E cells (DeLarco and Todaro, 1978) (ATCC, CRL-1571) were cultured in Dulbecco’s Modified Eagle Medium (DMEM) with 10% fetal calf serum, penicillin 100 I.U./ml, and streptomycin solution 100 µg/ml in a humidified 5% CO2 incubator at 370C.

treatment_protocol: NRK-52E cells were cultured to confluence on 6-well plates. Cells were then exposed to aristolochic acid dissolved in DMSO (0.1%) at the IC10 concentration at 72h (1.65μM) or DMSO only as control. After 6h, 24h and 72h the medium was removed and RNA was extracted from the cells. Three studies were conducted at each time point.

tag: strain

value: Osborne-Mendel

value: NRK-52E renal proximal tubular cell line

tag: agent

value: DMSO


title: Aristolochic acid-treated NRK-52E cells at 72h_biological rep1

description:
Gene expression data from cells treated with aristolochic acids
AA-72h-R-1

source_name: NRK-52E cells (DeLarco and Todaro, 1978) (ATCC, CRL-1571)

value: AA


title: DMSO-treated NRK-52E cells at 72h_biological rep3

description:
Gene expression data from cells treated with aristolochic acids
DMSO-72h-R-3


title: Aristolochic acid-treated NRK-52E cells at 72h_biological rep3

description:
Gene expression data from cells treated with aristolochic acids
AA-72h-R-3


title: Aristolochic acid-treated NRK-52E cells at 72h_biological rep2

description:
Gene expression data from cells treated with aristolochic acids
AA-72h-R-2


title: CD14

source_name: CD14+ PBSC from donor

value: CD14+ PBSC


title: 45_D492_50%confl_3.3

description:
D492 at 50 % confluency replicate 3.3
scan setting file: mirna


title: 39_D492_50%confl_1.3

description:
D492 at 50 % confluency replicate 1.3
scan setting file: mirna


title: 44_D492_50%confl_3.2

description:
D492 at 50 % confluency replicate 3.2
scan setting file: mirna


title: 41_D492_50%confl_2.2

description:
D492 at 50 % confluency replicate 2.2
scan setting file: mirna


title: 43_D492_50%confl_3.1

description:
D492 at 50 % confluency replicate 3.1
scan setting file: mirna


title: DMSO-treated NRK-52E cells at 72h_biological rep1

description:
Gene expression data from cells treated with aristolochic acids
DMSO-72h-R-1


title: 42_D492_50%confl_2.3

description:
D492 at 50 % confluency replicate 2.3
scan setting file: mirna


title: 38_D492_50%confl_1.2

description:
D492 at 50 % confluency replicate 1.2
scan setting file: mirna


title: DMSO-treated NRK-52E cells at 24h_biological rep3

description:
Gene expression data from cells treated with aristolochic acids
DMSO-24h-R-3


title: 40_D492_50%confl_2.1

description:
D492 at 50 % confluency replicate 2.1
scan setting file: mirna


title: 37_D492_50%confl_1.1

description:
D492 at 50 % confluency replicate 1.1
scan setting file: mirna


title: DMSO-treated NRK-52E cells at 24h_biological rep2

description:
Gene expression data from cells treated with aristolochic acids
DMSO-24h-R-2


title: Aristolochic acid-treated NRK-52E cells at 24h_biological rep3

description:
Gene expression data from cells treated with aristolochic acids
AA-24h-R-3


title: DMSO-treated NRK-52E cells at 6h_biological rep2

description:
Gene expression data from cells treated with aristolochic acids
DMSO-6h-R-2


title: Aristolochic acid-treated NRK-52E cells at 24h_biological rep1

description:
Gene expression data from cells treated with aristolochic acids
AA-24h-R-1


title: DMSO-treated NRK-52E cells at 24h_biological rep1

description:
Gene expression data from cells treated with aristolochic acids
DMSO-24h-R-1


title: 46_D492_90%confl_1.1

description:
D492 at 90 % confluency replicate 1.1
scan setting file: mirna


title: DMSO-treated NRK-52E cells at 6h_biological rep3

description:
Gene expression data from cells treated with aristolochic acids
DMSO-6h-R-3


title: Aristolochic acid-treated NRK-52E cells at 6h_biological rep2

description:
Gene expression data from cells treated with aristolochic acids
AA-6h-R-2


title: Aristolochic acid-treated NRK-52E cells at 24h_biological rep2

description:
Gene expression data from cells treated with aristolochic acids
AA-24h-R-2


title: Aristolochic acid-treated NRK-52E cells at 6h_biological rep1

description:
Gene expression data from cells treated with aristolochic acids
AA-6h-R-1


title: Aristolochic acid-treated NRK-52E cells at 6h_biological rep3

description:
Gene expression data from cells treated with aristolochic acids
AA-6h-R-3


title: HFD memory phenotype CD4 T cells-1

city: Chiba-city

first: Yusuke

last: ENDO

state: Chiba

address: 1-8-1 Inohana, Chuo-ku

department: Immunology

institute: Chiba University

description: Gene expression data from memory phenotype CD4 T cells in HFD mice

hyb_protocol: RNA was hybridized to GeneChip Mouse Genome 430 2.0 Arrays from Affymetrix according to the manufacture's protocol.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Expression values were determined using GeneChip Operating Software (GCOS) v1.2 software.

source_name: primary CD4 T cells from spleen

label_protocol: Total RNA was extracted usin the IVT Labeling kit from Affymetrix.

growth_protocol: BALB/c mice were fed either a normal diet or a high fat (60kcal% fat) diet (Research Diets) for 10 weeks.

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

treatment_protocol: Splenic memory phenotype CD4 T cells from ND or HFD mice were prepared using a cell sorter (Aria III; BD) yielding a purity of >99%, and were resuspendet in the Trizol solution (GibcoBRL).

value: BALB/c

tag: protocol

value: high fat diet

value: spleen

value: memory phenotype CD4 T cells


title: 11d SET 1

city: Dublin

first: Pat

last: Ryan

address: College Green

country: Ireland

institute: TCD

description: Biological Replicate 1: several plants (approx 20-25) pooled per replicate and genotype

hyb_protocol: Fragmentation buffer and Hybridization Buffer HI-RPM (Agilent Gene Expression Hybridization Kit) were added and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridized for 16 hrs at 65°C. After hybridization, slides were washed sequentially according to the manufacturer's instruction.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (v 9.5.3.1).

data_processing: Agilent Feature Extraction Software (v 10.5.1) was used for background subtraction and LOWESS normalization

organism: Arabidopsis thaliana

source_name: 11d SET 1

label_protocol: 500ng of total RNA were primed with 0.6µl of T7 DNA primer at 65°C for 10 min, then reverse transcribed at 40°C  for 2 hrs in the presence of 300 U MMLV Reverse Transcriptase and 10mM dNTP mix, with Cy3-label and Cy5- label.

growth_protocol: Plants were grown on a soil:vermiculite:perlite (3:1:1) mixture at 20 degrees (16 degrees for plants used for temperature-sensitive perturbation experiments) under constant illumination with cool white fluorescent light

extract_protocol: Total RNA was isolated from tissue samples using the Plant Total RNA kit (Sigma-Aldrich), according to the manufacturer's instructions

treatment_protocol: For all experiments,  ~4 week-old plants were used. For experiments using the FIS (35S:AP1-GR ap1-1 cal-1 plants), flower development was induced using a solution containing 10 μM dexamethasone (Sigma-Aldrich), 0.01% (v/v) ethanol and 0.015% (v/v) Silwet L-77 (De Sangosse) – as described in  Wellmer F, et al. (2006) Genome-Wide Analysis of Gene Expression during Early Arabidopsis Flower Development. PLoS Genetics 2(7):e117.

tag: developmental stage

value: 11 days after Dexamethasone induction

value: FIS (ap1 cal AP1-GR)

value: meristematic tissue

source_name: Pooled RNA

value: Pooled RNA from all time points used in sample 1


title: 9d SET 2

description: Biological Replicate 2: several plants (approx 20-25) pooled per replicate and genotype

source_name: 9d SET 2

value: 9 days after Dexamethasone induction


title: 13d SET 2

source_name: 13d SET 2

value: 13 days after Dexamethasone induction


title: 13d SET 1

source_name: 13d SET 1


title: ND memory phenotype CD4 T cells

description: Gene expression data from memory phenotype CD4 T cells in ND mice

value: normal diet


title: HFD memory phenotype CD4 T cells-2


title: 13d SET 3

description: Biological Replicate 3: several plants (approx 20-25) pooled per replicate and genotype

source_name: 13d SET 3


title: 7d SET 3

source_name: 7d SET 3

value: 7 days after Dexamethasone induction


title: 4.5d SET 3

source_name: 4.5d SET 3

value: 4.5 days after Dexamethasone induction


title: 5d SET 2

source_name: 5d SET 2

value: 5 days after Dexamethasone induction


title: 11d SET 3

source_name: 11d SET 3


title: 5d SET 3

source_name: 5d SET 3


title: DMSO-treated NRK-52E cells at 6h_biological rep1

description:
Gene expression data from cells treated with aristolochic acids
DMSO-6h-R-1

value: Osborne-Mendel

value: NRK-52E renal proximal tubular cell line

value: DMSO


title: 4.5d SET 1

source_name: 4.5d SET 1


title: 7d SET 1

source_name: 7d SET 1


title: 9d SET 1

source_name: 9d SET 1


title: 7d SET 2

source_name: 7d SET 2


title: 4.5d SET 2

source_name: 4.5d SET 2


title: 4d SET 3

source_name: 4d SET 3

value: 4 days after Dexamethasone induction


title: 3.5d SET 1

source_name: 3.5d SET 1

value: 3.5 days after Dexamethasone induction


title: 3d SET 3

source_name: 3d SET 3

value: 3 days after Dexamethasone induction

source_name: Pooled RNA


title: 11d SET 2

source_name: 11d SET 2


title: 4d SET 1

source_name: 4d SET 1


title: 3.5d SET 2

source_name: 3.5d SET 2


title: 9d SET 3

source_name: 9d SET 3


title: 5d SET 1

source_name: 5d SET 1


title: 3d SET 2

source_name: 3d SET 2


title: 4d SET 2

source_name: 4d SET 2


title: 3.5d SET 3

source_name: 3.5d SET 3


title: 2.5d SET 3

source_name: 2.5d SET 3

value: 2.5 days after Dexamethasone induction


title: 3d SET 1

source_name: 3d SET 1


title: 2d SET 2

source_name: 2d SET 2

value: 2 days after Dexamethasone induction


title: 2d SET 3

source_name: 2d SET 3

value: FIS (ap1 cal AP1-GR)


title: 2.5d SET 1

source_name: 2.5d SET 1

value: meristematic tissue


title: 1.5d SET 2

source_name: 1.5d SET 2

value: 1.5 days after Dexamethasone induction

value: Pooled RNA from all time points used in sample 1


title: 1d SET 3

source_name: 1d SET 3

value: 1 day after Dexamethasone induction


title: MNC_4h_LPS+Pep19-2.5_rep3

city: Borstel

first: Sebastian

last: Marwitz

address: Parkallee 3a

department: Histology

institute: Research Center Borstel - Leibniz Lung Center

hyb_protocol: 1650 ng of Cy3-labelled cRNA was fragmented according to Low Input Quick Amp Labelling Kit Protocol (Agilent) with 2xHI-RPM Hybridization Buffer for 30 min at 60°C. Hybridization on Agilent Human Whole Genome 4x44k V2 arrays was performed at 65°C for 17h under constant rotation in a hybidization oven. Washing was performed using the GE Wash buffer 1 (Agilent) at RT and Ge Wash Buffer 2 (Agilent) at 37°C for each 1 min. Washed slides were air-dried and immediately scanned.

scan_protocol: Slides were immediately scannend on an Agilent SureScan Scanner with Dye Channel =Green, 5 µm Resolution and scanning area=61 x 21.6 mm.

data_processing: Agilent Feature Extraction Software V 11.5 was used with default options (GE 1-color protocol) to extract raw data. Txt files were imported into GeneSpring software Version 13 under omission of compromised flags. Fags were accepted if at least 100 percent of samples in any 1 out of 7 conditions were detected.

source_name: Monocytes, 4h,LPS+Pep19-2.5, replicate 3

label_protocol: Cy3-labelling of total RNA was conducted with the Low Input Quick Amp Labelling Kit (Agilent) according to manufacturer´s instructions. Dye incorporation rate and specific yield was calculated using an NanoDrop spectrophotometer.

extract_protocol: Total RNA was extracted directly after stimulation with the Qiagen Rneasy Mini Kit according to manufacturer´s instructions. RNA was stored at -80°C until further use.

treatment_protocol: cells were isolated from heparinized blood of 3 healthy donors by the Hypaque-Ficoll density gradient method.The cell number was equilibrated at 5 x 105 cells/ml RPMI 1640 containing 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin. For stimulation, 200 µl/well MNC were transferred into 96-well culture plates. The stimuli were serially diluted in RPMI 1640 and added to the cultures at 20 µl per well. Concentrations of 0.1 ng/ml LPS R60 from Salmonella enterica Minnesota rough mutants, 10 ng/ml Pep19-2.5 (Bachem, Lot. 1053821) and 1 µg/ml ibuprofen (Fluka 11892, Lot. BCBI499V) were applied in 0.9 % NaCl. The cultures were incubated for 4 h at 37°C under 5% CO2.

value: Monocytes


title: MNC_4h_LPS+Ibuprofen+Pep19-2.5_rep3

source_name: Monocytes, 4h,LPS+Ibuprofen+Pep19-2.5, replicate 3

value: LPS + Ibuprofen + Pep19-2.5


title: 2d SET 1

source_name: 2d SET 1

source_name: Pooled RNA


title: 0d SET 1

source_name: 0d SET 1

value: undifferentiated meristematic tissue


title: Basal_cells_CD10minus_rep5

description:
Bmin_M10
Gene expression data from basal cells CD10- rep5.

hyb_protocol: According to the Affymetrix expression protocol.

data_processing: Expression Console (v.1.3.0.187, Affymetrix) was used to obtain normalized RMA gene-level data (standard settings including sketch-quantile normalisation).

source_name: Basal cells CD10minus (Lin-/CD49f_high/EpCAM-/CD10-) isolated from donor M10

label_protocol: Ovation Pico WTA System V2 in combination with the Encore Biotin Module (Nugen).

extract_protocol: RNeasy Mini Kit (Qiagen) in combination with the RNase-Free DNase Set.

treatment_protocol: Primary human mammary epithelial cells (HMECs) were isolated from healthy donors and FACS-sorted as described in the paper to obtain the three populations as described in the sample information.

value: primary human mammary epithelial cells (HMECs)

tag: cell population

value: CD10- basal cells (Lin-/CD49f_high/EpCAM-/CD10-)

tag: gender

value: female

tag: disease status

value: healthy

tag: donor


title: Basal_cells_CD10plus_rep4

description:
Bplus_M09
Gene expression data from basal cells CD10+ rep4.

scan_protocol: According to the Affymetrix expression protocol.

source_name: Basal cells CD10plus (Lin-/CD49f_high/EpCAM-/CD10+) isolated from donor M09

value: CD10+ basal cells (Lin-/CD49f_high/EpCAM-/CD10+)


title: Basal_cells_CD10plus_rep5

description:
Bplus_M10
Gene expression data from basal cells CD10+ rep5.

source_name: Basal cells CD10plus (Lin-/CD49f_high/EpCAM-/CD10+) isolated from donor M10


title: Basal_cells_CD10minus_rep2

description:
Bmin_M06
Gene expression data from basal cells CD10- rep2.

source_name: Basal cells CD10minus (Lin-/CD49f_high/EpCAM-/CD10-) isolated from donor M06


title: 1d SET 2

source_name: 1d SET 2

tag: tissue


title: 2.5d SET 2

source_name: 2.5d SET 2


title: 1.5d SET 3

source_name: 1.5d SET 3


title: Basal_cells_CD10plus_rep6

description:
Bplus_M12
Gene expression data from basal cells CD10+ rep6.

source_name: Basal cells CD10plus (Lin-/CD49f_high/EpCAM-/CD10+) isolated from donor M12


title: Basal_cells_CD10minus_rep6

description:
Bmin_M12
Gene expression data from basal cells CD10- rep6.

source_name: Basal cells CD10minus (Lin-/CD49f_high/EpCAM-/CD10-) isolated from donor M12


title: 0d SET 2

source_name: 0d SET 2


title: 1d SET 1

source_name: 1d SET 1


title: Basal_cells_CD10minus_rep4

description:
Bmin_M09
Gene expression data from basal cells CD10- rep4.

source_name: Basal cells CD10minus (Lin-/CD49f_high/EpCAM-/CD10-) isolated from donor M09


title: 1.5d SET 1

source_name: 1.5d SET 1

value: 1.5 day after Dexamethasone induction


title: Basal_cells_CD10minus_rep3

description:
Bmin_M08
Gene expression data from basal cells CD10- rep3.

source_name: Basal cells CD10minus (Lin-/CD49f_high/EpCAM-/CD10-) isolated from donor M08


title: 0d SET 3

source_name: 0d SET 3


title: Basal_cells_CD10minus_rep1

description:
Bmin_M03
Gene expression data from basal cells CD10- rep1.

source_name: Basal cells CD10minus (Lin-/CD49f_high/EpCAM-/CD10-) isolated from donor M03


title: Basal_cells_CD10plus_rep3

description:
Bplus_M08
Gene expression data from basal cells CD10+ rep3.

source_name: Basal cells CD10plus (Lin-/CD49f_high/EpCAM-/CD10+) isolated from donor M08


title: Basal_cells_CD10plus_rep2

description:
Bplus_M06
Gene expression data from basal cells CD10+ rep2.

source_name: Basal cells CD10plus (Lin-/CD49f_high/EpCAM-/CD10+) isolated from donor M06


title: MNC_4h_LPS+Ibuprofen_rep3

source_name: Monocytes, 4h,LPS+Ibuprofen, replicate 3

value: LPS + Ibuprofen


title: MNC_4h_LPS_rep3

source_name: Monocytes, 4h,LPS, replicate 3

value: LPS


title: Untreated control, technical replicate of CTRL_2

description:
Gene expression data from untreated control, technical replicate of CTRL_2
CTRL_2_TR

hyb_protocol: According to the Affymetrix expression protocol (HWS kit)

data_processing: RMA probeset summary and quantile normalization (Expression console v.1.2, Affymetrix)

source_name: Dentate gyrus, untreated control, technical replicate of CTRL_2

label_protocol: WT Expression Kit (Ambion) and WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Animals per housed under standard laboratory conditions

extract_protocol: RNeasy Mini Kit (Qiagen) including DNase treatment

treatment_protocol: As described in the paper. Briefly, male Wistar rats (200–250g, 2 month-old; Charles-River Laboratories) were maintained under standard laboratory conditions (12h light: 12h dark cycles, 22oC, relative humidity of 55%, ad libitum access to food and water). A validated unpredictable Chronic Mild Stress protocol (uCMS) was applied for 6 weeks, as previously described (Bessa et al, 2009b). During the last 2 weeks of the uCMS, animals were injected intraperitoneally daily with one of the four antidepressants (ADs): fluoxetine (10mg.kg-1 in ultra-pure water; Kemprotec); imipramine (10mg.kg-1 in 0.9% saline solution; Sigma-Aldrich); tianeptine (10mg.kg-1 in 0.9% saline solution; Kemprotec) and agomelatine (40mg.kg-1 in 0.5% hydroxyethylcellulose; Kemprotec). The doses were chosen based on previous studies (Banasr et al, 2006; Bessa et al, 2009b; McEwen et al, 2010; Morley-Fletcher et al, 2011; Rocher et al, 2004). Bodyweight gain was monitored weekly throughout the protocol (Supplementary Figure S1a). All procedures were carried out in accordance with EU Directive 2010/63/EU and NIH guidelines on animal care and experimentation.

value: Wistar

tag: age

value: 2 months

value: Male

value: wild type

tag: stress

value: control

value: untreated

value: Dentate gyrus


title: MNC_4h_Ibuprofen_rep3

source_name: Monocytes, 4h, Ibuprofen, replicate 3

value: Monocytes

value: Ibuprofen


title: Basal_cells_CD10plus_rep1

description:
Bplus_M03
Gene expression data from basal cells CD10+ rep1.

source_name: Basal cells CD10plus (Lin-/CD49f_high/EpCAM-/CD10+) isolated from donor M03

value: primary human mammary epithelial cells (HMECs)


title: Luminal_progenitor_rep5

description:
LP_M10
Gene expression data from luminal progenitors rep5.

source_name: Luminal progenitor cells (Lin-/CD49f+/EpCAM+) isolated from donor M10

value: luminal progenitor cells (Lin-/CD49f+/EpCAM+)


title: MNC_4h_Pep19-2.5_rep3

source_name: Monocytes, 4h,Pep19-2.5, replicate 3


title: Untreated control, technical replicate of CTRL_1

description:
Gene expression data from untreated control, technical replicate of CTRL_1
CTRL_1_TR

source_name: Dentate gyrus, untreated control, technical replicate of CTRL_1

tag: genotype


title: Untreated control, biological replicate 3

description:
Gene expression data from untreated control, biological replicate 3
CTRL_3

source_name: Dentate gyrus, untreated control, biological replicate 3


title: Luminal_progenitor_rep6

description:
LP_M12
Gene expression data from luminal progenitors rep6.

source_name: Luminal progenitor cells (Lin-/CD49f+/EpCAM+) isolated from donor M12

value: female


title: Luminal_progenitor_rep4

description:
LP_M09
Gene expression data from luminal progenitors rep4.

source_name: Luminal progenitor cells (Lin-/CD49f+/EpCAM+) isolated from donor M09

value: healthy


title: MNC_4h_LPS+Ibuprofen+Pep19-2.5_rep2

source_name: Monocytes, 4h,LPS+Ibuprofen+Pep19-2.5, replicate 2

value: LPS + Ibuprofen + Pep19-2.5


title: Luminal_progenitor_rep3

description:
LP_M08
Gene expression data from luminal progenitors rep3.

source_name: Luminal progenitor cells (Lin-/CD49f+/EpCAM+) isolated from donor M08


title: Untreated control, biological replicate 2

description:
Gene expression data from untreated control, biological replicate 2
CTRL_2

source_name: Dentate gyrus, untreated control, biological replicate 2


title: Luminal_progenitor_rep2

description:
LP_M06
Gene expression data from luminal progenitors rep2.

source_name: Luminal progenitor cells (Lin-/CD49f+/EpCAM+) isolated from donor M06


title: Untreated control, technical replicate of CTRL_3

description:
Gene expression data from untreated control, technical replicate of CTRL_3
CTRL_3_TR

source_name: Dentate gyrus, untreated control, technical replicate of CTRL_3


title: Unpredictable chronic mild stress, tianeptine treatment, biological replicate 2

description:
Gene expression data from unpredictable chronic mild stress, tianeptine treatment, biological replicate 2
uCMS_TIAN_2

source_name: Dentate gyrus, unpredictable chronic mild stress, tianeptine treatment

value: unpredictable chronic mild stress

value: tianeptine


title: MNC_4h_Pep19-2.5_rep2

source_name: Monocytes, 4h,Pep19-2.5, replicate 2


title: Luminal_progenitor_rep1

description:
LP_M03
Gene expression data from luminal progenitors rep1.

source_name: Luminal progenitor cells (Lin-/CD49f+/EpCAM+) isolated from donor M03


title: Unpredictable chronic mild stress, tianeptine treatment, biological replicate 1

description:
Gene expression data from unpredictable chronic mild stress, tianeptine treatment, biological replicate 1
uCMS_TIAN_1


title: CD24neg_T_on_rep3

description: Gene expression data from CD24neg_T_on_rep3

data_processing: Expression console (v.1.3.0.187, Affymetrix) was used to obtain normalized RMA gene-level data (standard settings including sketch-quantile normalisation)

source_name: CD24negative population, HMLE-Twist1-ER, treated with 4-hydroxytamoxifen for 15 days

growth_protocol: HMLE-Snail1-Er and HMLE-Twist1-ER cells were propagated in mammary epithelial cell growth medium (PromoCell) containing Pen/Strep (Invitrogen) according to standard protocols.

extract_protocol: RNeasy Mini Kit (Qiagen)

treatment_protocol: Treatment with 4-hydroxytamoxifen, mammosphere assay and FACS-sorting was performed as described in the paper

value: HMLE

value: mammary epithelial cell line


title: MNC_4h_Ibuprofen_rep2

source_name: Monocytes, 4h, Ibuprofen, replicate 2


title: CD24neg_T_on_rep2

description: Gene expression data from CD24neg_T_on_rep2


title: MNC_4h_LPS+Ibuprofen_rep2

source_name: Monocytes, 4h,LPS+Ibuprofen, replicate 2

value: LPS + Ibuprofen


title: Unpredictable chronic mild stress, tianeptine treatment, biological replicate 3

description:
Gene expression data from unpredictable chronic mild stress, tianeptine treatment, biological replicate 3
uCMS_TIAN_3

value: Wistar

value: 2 months

value: Male


title: Untreated control, biological replicate 1

description:
Gene expression data from untreated control, biological replicate 1
CTRL_1

source_name: Dentate gyrus, untreated control, biological replicate 1

value: wild type

value: control

value: untreated


title: MNC_4h_Medium_rep3

source_name: Monocytes, 4h, Medium, replicate 3

value: Monocytes

value: Medium


title: CD24neg_T_on_rep1

description: Gene expression data from CD24neg_T_on_rep1


title: MNC_4h_LPS+Pep19-2.5_rep2

source_name: Monocytes, 4h,LPS+Pep19-2.5, replicate 2


title: Unpredictable chronic mild stress, imipramine treatment, biological replicate 3

description:
Gene expression data from unpredictable chronic mild stress, imipramine treatment, biological replicate 3
uCMS_IMIP_3

source_name: Dentate gyrus, unpredictable chronic mild stress, imipramine treatment

value: imipramine

value: Dentate gyrus


title: MNC_4h_LPS_rep12

source_name: Monocytes, 4h,LPS, replicate 2

value: LPS


title: MNC_4h_LPS+Ibuprofen+Pep19-2.5_rep1

source_name: Monocytes, 4h,LPS+Ibuprofen+Pep19-2.5, replicate 1

value: LPS + Ibuprofen + Pep19-2.5


title: CD24neg_T_off_rep1

description: Gene expression data from CD24neg_T_off_rep1

source_name: CD24negative population, HMLE-Twist1-ER, control

value: female


title: MNC_4h_LPS_rep1

source_name: Monocytes, 4h,LPS, replicate 1


title: CD24neg_T_off_rep2

description: Gene expression data from CD24neg_T_off_rep2


title: Unpredictable chronic mild stress, fluoxetine treatment, biological replicate 2

description:
Gene expression data from unpredictable chronic mild stress, fluoxetine treatment, biological replicate 2
uCMS_FLX_2

source_name: Dentate gyrus, unpredictable chronic mild stress, fluoxetine treatment

value: unpredictable chronic mild stress

value: fluoxetine


title: Unpredictable chronic mild stress, imipramine treatment, biological replicate 2

description:
Gene expression data from unpredictable chronic mild stress, imipramine treatment, biological replicate 2
uCMS_IMIP_2


title: Unpredictable chronic mild stress, agomelatine treatment, biological replicate 2

description:
Gene expression data from unpredictable chronic mild stress, agomelatine treatment, biological replicate 2
uCMS_AGOM_2

source_name: Dentate gyrus, unpredictable chronic mild stress, agomelatine treatment

value: agomelatine


title: MNC_4h_Medium_rep2

source_name: Monocytes, 4h, Medium, replicate 2


title: CD24hi_T_onoff_3D_rep1

description: Gene expression data from CD24hi_T_onoff_3D_rep1

source_name: CD24high population, HMLE-Twist1-ER, treated with 4-hydroxytamoxifen for 15 days, then cultered 9 days in mammosphere assay without 4-hydroxytamoxifen

value: HMLE

value: mammary epithelial cell line


title: MNC_4h_LPS+Pep19-2.5_rep1

source_name: Monocytes, 4h,LPS+Pep19-2.5, replicate 1


title: CD24hi_T_onoff_3D_rep3

description: Gene expression data from CD24hi_T_onoff_3D_rep3