title: Spleen of non-infected Balb/c mice (Ba-nr23: BIOMARKERS)

description:
Ba-nr23
LOGISTIC MODEL DEVELOPMENT


title: Spleen of non-infected Balb/c mice (Ba-nr22: BIOMARKERS)

status: Public on May 22 2018

type: RNA

city: La Laguna

first: Emma

last: Carmelo

state: SANTA CRUZ DE TENERIFE

address: C/ Astrofisico Francisco Sanchez s/n, Campus de Anchieta

department: University Institute of Tropical Diseases and Public Health

country: Spain

institute: University of La Laguna

description:
Ba-nr22
LOGISTIC MODEL DEVELOPMENT

data_processing: Cq values from the 61 samples analyzed were exported for normalization using geNorm (qBasePLUS software (Biogazelle, Gent, Belgium)). Two genes showed the most stable expression (Stat6 and Itgb2)  and were used for normalization.

label: FAM

molecule: total RNA

organism: Mus musculus

source_name: SPLEEN

label_protocol:
The reverse transcription was performed with 2 ug of RNA with random hexamers using the High Capacity cDNA Reverse Transcription Kit (Life Technologies, Carlsbad, CA) according to manufacturer’s instructions.
Real-time PCR and fluorescence detection were performed using QuantStudio 12K Flex Real-Time PCR System (Life  Technologies, Carlsbad, CA) following manufacturer’s instructions, using Custom TaqMan OpenArray Real-Time PCR Plates

growth_protocol: 61 BALB/c (purchased to Charles River Laboratories, France) mice (14-15 weeks old) were used  in this study. Mice were randomly separated in two groups: (i) 30 control mice and (ii) 31 mice  that were infected with 10^6 stationary-phase L. infantum promastigotes via tail vein. Mice were euthanized by cervical dislocation and spleens were removed and immediately stored in RNAlater at -70ºC (Sigma-Aldrich, St. Louis, USA). F

extract_protocol: Total RNA isolation from spleens (9-11 mg) was performed by cell disruption using FastPrep®  System (ProScientific, Cedex, France) and Lysing Matrix D (MP Biomedicals, Solon, USA) in TRI-Reagent (Sigma-Aldrich, St. Louis, USA). RNeasy Mini Kit (Qiagen) was subsequently used for mRNA enrichment following manufacturer’s instructions

treatment_protocol: 31 out of the 61 mice were infected with 10^6 stationary-phase L. infantum promastigotes via tail vein.

tag: strain

value: Balb/c


title: PD2_post_DBS_ON_stim

city: London

first: Lilach

last: Soreq

address: Queen Square

department: Molecular  Neuroscience

country: United Kingdom

institute: UCL

hyb_protocol: The RNA was hybridized to Affymetrix® GeneChip miRNA Arrays with probes interrogating 847 human miRNAs (miRNAs were derived from the Sanger miRBase miRNA database v11 (April 15, 2008, http://microrna.sanger.ac.uk)).

scan_protocol: The GeneChip® Scanner 3000G protocol.

data_processing: The Affymetrix® miRNA QC Tool (Version 1.0.33.0) served for probe-set summarization. Detection was based on a Wilcoxon Rank-Sum test of the miRNA probe set signals compared to the distribution of signals from GC content-matched anti-genomic probes. If the resulting p-value of the probes is p<=0.06, it is considered “detected above background”. This GC-specific background contribution was estimated by the median signal from the distribution of GC-matched anti-genomic probes. Probe level normalization was conducted through the quantile normalization method and probe sets summarization through the RMA method.

label: Biotin

organism: Homo sapiens

source_name: Blood leukocytes, PD, post-DBS on electrical stimulation

label_protocol: The RNA targets were labeled using the Affymetrix® FlashTag™ Biotin RNA Labeling Kit.

growth_protocol: Leukocytes were filtered from total blood sample (collected with EDTA vacutainer tubes) with Ambion Inc. LeukoLOCK™ filters within up to 10 minutes from blood extraction.

extract_protocol: RNA was harvested using the alternative protocol for extraction of RNA from cells captured on LeukoLOCK™ Filters Using TRI Reagent®. The amount of ethanol was adjusted to include the small RNA fraction.

treatment_protocol: The captured leukocytes were treated with RNAlater immediately after filtration of the blood and were maintained frozen (-80 Celsius degrees) until RNA extraction.

tag: cell type

value: blood leukocytes

tag: disease status

value: Parkinson's disease (PD)

tag: treatment

value: post-deep brain stimulation (DBS) on electrical stimulation

tag: gender

value: male

tag: individual identifier


title: PD3_post_DBS_OFF_stim_restain

description: Blood leukocyte sample was taken following one hour of stimulation cessation post-DBS (i.e., one hour after the on-stimulation sample was taken).

source_name: Blood leukocytes, PD, post-DBS off electrical stimulation

value: post-deep brain stimulation (DBS) off electrical stimulation 1 hr


title: PD3_post_DBS_ON_stim


title: PD2_post_DBS_OFF_stim


title: PD3_post_DBS_OFF_stim


title: PD1_post_DBS_OFF_stim


title: HFD2, biological rep 2

city: Columbia

first: Prakash

last: Nagarkatti

state: SC

address: 6439 Garners Ferry Road

country: USA

institute: University of South Carolina School of Medicine

hyb_protocol: Labeled samples were hybridized to miRNA 4.0 chips overnight (16h, 48°C, 60 RPM) then washed and stained on an Affymetrix GCS 3000 system Fluidics station using the FS450_0002 protocol.

scan_protocol: Chips were scanned on a Affymetrix GCS 3000 system scanner.

data_processing: Affymetrix Expression Console Version 1.4.1.46 was used for quality control, data summarization, and normalization. The processing algorithm used was RMA-DABG. Affymetrix Transcriptome Analysis Console Version 3.1.0.5 was used to perform differential expression analyses. MicroRNAs were considered differentially expressed between the two groups if linear fold change was greater than ±2 and the ANOVA p-value was less than 0.05

source_name: Epididymal fat macrophages

label_protocol: 500ng total RNA was used as starting material for labeling according to the Affymetrix FlashTag Biotin HSR RNA Labeling Kit manufacturer protocol.

growth_protocol: Mice were fed a normal chow diet (Envigo Teklad 8904) or 60% high fat diet (Research Diets D12492) for 16 weeks starting at 6 weeks of age.

extract_protocol: Total RNA was isolated with Qiagen miRNeasy micro kit.

treatment_protocol: Epididymal fat stromal vascular fractions (SVF) were isolated by collagenase digestion. F4/80+ cells (ATMs) were purified by labeling SVF cells with anti-F4/80-PE (clone: BM8) followed by immunomagnetic selection with StemCell EasySep PE Positive Selection Kit. Each biological replicate is pools of ATMs isolated from either 20 NCD-fed mice or 10 HFD-fed mice.

value: Male

tag: age

value: 22 weeks

tag: weeks of diet

value: 16 weeks


title: NCD3, biological rep 3


title: Spleen of non-infected Balb/c mice (Ba-nr21: BIOMARKERS)

description:
Ba-nr21
LOGISTIC MODEL DEVELOPMENT


title: HFD1, biological rep 1


title: HFD3, biological rep 3


title: PD3_pre_DBS

source_name: Blood leukocytes, PD, pre-DBS

value: pre-deep brain stimulation (DBS)


title: PD1_post_DBS_ON_stim


title: Spleen of non-infected Balb/c mice (Ba-nr20: BIOMARKERS)

description:
Ba-nr20
LOGISTIC MODEL DEVELOPMENT


title: Spleen of non-infected Balb/c mice (Ba-nr19: BIOMARKERS)

description:
Ba-nr19
LOGISTIC MODEL DEVELOPMENT


title: PD2_pre_DBS


title: NCD2, biological rep 2


title: NCD1, biological rep 1


title: Her2/Neu+ mammary gland, sample 114

city: Rome

first: Luciano

last: Castiello

address: Viale Regina Elena 291

country: Italy

institute: Istituto Pasteur Italia - Fondazione Cenci Bolognetti

description:
Her2/Neu+ mammary gland, sample 114  cohibridized with Universal Reference RNA
Block # in raw data file 1

hyb_protocol: 825ng of Cy3-labeled and Cy5-labeled, were fragmented, mixed and co-hybridized to Mouse Gene Expression 4x44K v2 Microarray Slides (G4646A)

scan_protocol: Scanning and image file processing were performed with GenePix® 4200A instrument (Axon Instruments) and ScanArray Express software

data_processing: data files were analyzed via BRB ArrayTool, signals were background adjusted, Spots were filtered when size was <10, flag <> 0, or both Cy5 and Cy3 intensity were below 20. If only one of the two signals was below 20, it was raised to 20. Each array was normalized using lowess smoother, intensity ratios above 64 were truncated. Genes missing in more than 50% of the whole dataset were excluded

source_name: Her2/Neu+ mammary gland, sample 114

label_protocol: Sample RNA and Universal Reference mouse RNA (Stratagene) underwent cRNA preparation and cyanin (Cy)5 or Cy3 labeling by Low Input Quick Amp Labeling Kit Standard Dual Color (Agilent Technologies, Palo Alto, CA), according to manufacturers’ instruction

growth_protocol: Inguinal mammary glands were isolated from 19 weeks old mice

extract_protocol: Tissues were submerged with RNA later (Qiagen) and stored at -20C. For RNA extraction, the mammary glands were washed twice in PBS, immersed in Trizol (QIAzol Lysis reagent), and disrupted by homogenization. Total RNA was extracted by Chloroform/isopropanol precipitation.

tag: mouse background

tag: mouse phenotype

tag: tissue

value: mammary gland

tag: sample type

value: reference


title: Her2/Neu+ mammary gland, sample 119

description:
Her2/Neu+ mammary gland, sample 119  cohibridized with Universal Reference RNA
Block # in raw data file 2

source_name: Her2/Neu+ mammary gland, sample 119

source_name: Universal Reference mouse RNA (Stratagene)


description:
Her2/Neu+/IFNAR1-/- mammary gland, sample 108  cohibridized with Universal Reference RNA
Block # in raw data file 4


description:
Her2/Neu+/IFNAR1-/- mammary gland, sample 105  cohibridized with Universal Reference RNA
Block # in raw data file 1


title: PD1_pre_DBS


description:
Her2/Neu+/IFNAR1-/- mammary gland, sample107  cohibridized with Universal Reference RNA
Block # in raw data file 3


description:
Her2/Neu+/IFNAR1-/- mammary gland, sample 106  cohibridized with Universal Reference RNA
Block # in raw data file 2


title: 3T3-L1-LIGHT-Diff rep3

type: SRA

city: Xuzhou

first: Yanbo

last: Kou

address: Tongshan Road No. 209

country: China

institute: Xuzhou Medical University

library_source: transcriptomic

data_processing:
The BGI internal software SOAPnuke was used to filter reads
Firstly, we filter the low quality reads, reads with adaptors and reads with unknown bases to get the clean reads.
Then we map those clean reads onto reference genome, followed with novel gene prediction, SNP& INDEL calling and gene splicing detection.
Finally, we identify DEGs (differentially expressed genes) between samples and do clustering analysis and functional annotations.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: adipose

growth_protocol: Murine 3T3-L1 preadipocytes were plated in 6-well or 12-well plate and cultured in complete medium (DMEM/high glucose with 10% fetal bovine serum， 1% penicillin-streptomycin).

extract_protocol:
Total RNA was extracted from cells homogenized in TRIzol, and total RNA sample QC was analyzed using Agilent 2100 Bioanalyzer before sequwncing
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To induce differentiation, induction medium including complete medium plus beige differentiation cocktail (2 µg/ml dexamethasone, 0.5 mM IBMX, 1µM rosiglitazone, 1 nM tri-iodothyronine, 125 mM indomethacin, 5 µg/ml insulin). After 48 hr. the medium was switched to maintenance medium with 1uM rosiglitazone, 1 nM tri-iodothyronine, 5 µg/ml insulin for beige fat differentiation.

value: 3T3-L1 adipose precusors

tag: Stage

value: after differentiation into beige adipocytes

value: adipose

tag: genotype/variation

value: LIGHT (tnfsf14) overexpression

tag: cell line


title: 3T3-L1-LIGHT-Diff rep1


title: 3T3-L1-NC-Diff rep3

value: control


title: 3T3-L1-LIGHT-Diff rep2


description:
Her2/Neu+/IFNAR1-/- mammary gland, sample 102  cohibridized with Universal Reference RNA
Block # in raw data file 4


title: IFNAR1-/- mammary gland, sample 41

description:
IFNAR1-/- mammary gland, sample 41  cohibridized with Universal Reference RNA
Block # in raw data file 3

source_name: IFNAR1-/- mammary gland, sample 41


title: 3T3-L1-NC-Diff rep2


title: HC3

source_name: Blood leukocytes, healthy control

value: healthy


title: HC2

value: blood leukocytes


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL17: BIOMARKERS)

description:
Ba-rL17
LOGISTIC MODEL DEVELOPMENT
LINEAR REGRESSION MODEL DEVELOPMENT

value: Balb/c


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL18: BIOMARKERS)

description:
Ba-rL18
LOGISTIC MODEL DEVELOPMENT
LINEAR REGRESSION MODEL DEVELOPMENT


title: 3T3-L1-NC-Diff rep1


title: HC1


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL16: BIOMARKERS)

description:
Ba-rL16
LOGISTIC MODEL DEVELOPMENT
LINEAR REGRESSION MODEL DEVELOPMENT


title: Overexpress replicate 2 vs Control replicate 2

city: Santa Fe

first: Elina

last: WELCHEN

state: Santa Fe

address: Colectora Ruta Nac. Nº168 km. 0

country: Argentina

institute: Instituto de Agrobiotecnologia del Litoral

description: Biological replicate 2-2

hyb_protocol: Agilent protocol

scan_protocol: Scanned on an Agilent G2505B-C scanner using Agilent Feature Extraction Software (10.7.31)

data_processing:
Median intensity signals were processed in the R statistical programming environment using the limma package. Probes were filtered to exclude those with log2-background intensities above 7.2. Intensities were then background corrected employing the ‘normexp’ method with an offset of 16. Next, arrays were normalized using the locally weighted scatter plot smoothing (LOESS) procedure.
Normalized log2 ratio representing oeOXR2/WT

organism: Arabidopsis thaliana

source_name: WT 2

label_protocol: 200 ng total RNA per sample were used to generate cRNA with labelling protocol version GE2 v6.5 for CY3 and CY5

growth_protocol: Arabidopsis seeds from control and oeOXR2 plants were grown on soil under long day (16-h/8-h dark) at 23°C and 100 µM.m-1.s-1 of light intensity

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

treatment_protocol: Plants grown on soil until develop rosette with six-leaf pairs

tag: genotype

value: WT

tag: ecotype

value: rosette containing six-leaf pairs

tag: day

source_name: oeOXR2 2


title: Overexpress replicate 1 vs Control replicate 1

description: Biological replicate 1-2

source_name: oeOXR2 1

source_name: WT 1


title: 3T3-L1-LIGHT-Undiff rep3

tag: cell type

value: undifferentiated


title: WT mammary gland, sample 54

description:
WT mammary gland, sample 54  cohibridized with Universal Reference RNA
Block # in raw data file 2

source_name: WT mammary gland, sample 54


title: WT mammary gland, sample 57

description:
WT mammary gland, sample 57  cohibridized with Universal Reference RNA
Block # in raw data file 3

source_name: WT mammary gland, sample 57


title: IFNAR1-/- mammary gland, sample 47

description:
IFNAR1-/- mammary gland, sample 47  cohibridized with Universal Reference RNA
Block # in raw data file 4

source_name: IFNAR1-/- mammary gland, sample 47


title: IFNAR1-/- mammary gland, sample 46

description:
IFNAR1-/- mammary gland, sample 46  cohibridized with Universal Reference RNA
Block # in raw data file 3

source_name: IFNAR1-/- mammary gland, sample 46


title: Spleen of non-infected Balb/c mice (Ba-nr18: BIOMARKERS)

description:
Ba-nr18
LOGISTIC MODEL DEVELOPMENT

source_name: SPLEEN

tag: strain


title: 3T3-L1-LIGHT-Undiff rep2


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL14: BIOMARKERS)

description:
Ba-rL14
LOGISTIC MODEL DEVELOPMENT
LINEAR REGRESSION MODEL DEVELOPMENT


title: 3T3-L1-LIGHT-Undiff rep1


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL13: BIOMARKERS)

description:
Ba-rL13
LOGISTIC MODEL DEVELOPMENT
LINEAR REGRESSION MODEL DEVELOPMENT


title: 3T3-L1-NC-Undiff rep2


title: Spleen of non-infected Balb/c mice (Ba-nr17: BIOMARKERS)

description:
Ba-nr17
LOGISTIC MODEL DEVELOPMENT


title: WT mammary gland, sample 53

description:
WT mammary gland, sample 53  cohibridized with Universal Reference RNA
Block # in raw data file 1

source_name: WT mammary gland, sample 53


title: 3T3-L1-NC-Undiff rep1


title: Her2/Neu+ mammary gland, sample 115

description:
Her2/Neu+ mammary gland, sample 115  cohibridized with Universal Reference RNA
Block # in raw data file 3

source_name: Her2/Neu+ mammary gland, sample 115


title: IFNAR1-/- mammary gland, sample 44

description:
IFNAR1-/- mammary gland, sample 44  cohibridized with Universal Reference RNA
Block # in raw data file 2

source_name: IFNAR1-/- mammary gland, sample 44


title: IFNAR1-/- mammary gland, sample 39

description:
IFNAR1-/- mammary gland, sample 39  cohibridized with Universal Reference RNA
Block # in raw data file 1

source_name: IFNAR1-/- mammary gland, sample 39


title: Her2/Neu+ mammary gland, sample 113

description:
Her2/Neu+ mammary gland, sample 113  cohibridized with Universal Reference RNA
Block # in raw data file 4

source_name: Her2/Neu+ mammary gland, sample 113

source_name: Universal Reference mouse RNA (Stratagene)


title: Spleen of non-infected Balb/c mice (Ba-nr15: BIOMARKERS)

description:
Ba-nr15
LOGISTIC MODEL DEVELOPMENT


title: WT_4C-1

city: Baton Rouge

first: Ji Suk

last: Chang

state: LA

address: 6400 Perkins Rd.

department: Gene Regulation and Metabolism

institute: Pennington Biomedical Research Center

description: housed at 28°C and exposed to 4°C for 6h

data_processing:
demultiplex, trimming, and mapping using Applied Biosystems SOLiD_SAGE Analysis software V1.10 allowing 0 mismatches
differential expression analysis performed with DESeq V 1.12.1 and EdgeR V 3.2.4, R V 3.0.1 and Rstudio V0.97.551, P value cutoff of 0.05 and a relative fold change cutoff of +/- 1.5
Principal Component Analysis and additional statistical tests performed with JMP Genomics V 6.0
Unsupervised hierarchical clustering and heat maps generated using the Morpheus (https://software.broadinstitute.org/morpheus)
Pathway enrichment analysis performed with Gene Set Enrichment Analysis (GSEA) (http://software.broadinstitute.org/gsea/index.jsp)
Genome_build: GRC38/mm10
Supplementary_files_format_and_content: tab-delimited text, DESeq normalized counts

source_name: Brown adipose tissue

extract_protocol:
Brown adipose tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent and Rneasy mini kit.
The SOLiD SAGE technology (Serial Analysis of Gene Expression) was utilized to determine mRNA expression levels by generating the SOLiD SAGE libraries of unique 27-bp sequence tags for all mRNAs and sequencing unique sequence tags isolated from the 3’ ends of mRNAs using the Life Technologies 5500XL SOLiD system. Briefly, total RNA was bound to Dynabeads Oligo(dT) EcoP magnetic beads and transcribed into cDNA on the beads using SuperScript III Reverse Transcriptase and E.coli DNA polymerase. Double-stranded cDNA was digested with NlaIII restriction enzyme and ligated to Barcode adaptor A containing an EcoP15L restriction enzyme recognition site and a truncated internal adaptor sequence. An EcoP15I digestion was carried out to cleave the tag off from the magnetic beads. The tag consists of the adaptor sequence and 27 bp of unique sequence from the 3¢ end of a single mRNA. The 5¢ end of each tag was ligated to adaptor B that contains the P1 primer binding site for SOLiD emulsion PCR. Each library was amplified in a PCR reaction with a different barcoded SOLiD 3¢ Primer from the SOLiD RNA Barcoding kit and a SOLiD 5¢ Primer. SOLiD SAGE library sequencing was performed with next-generation sequencing using the Life Technologies 5500XL SOLiD system.

treatment_protocol: BL6 mice were housed at 28C or exposed to 4C for 6h prior to brown adipose tissue isolation.

value: Brown adipose tissue

tag: condition

value: housed at 28C and exposed to 4C for 6h


title: Spleen of non-infected Balb/c mice (Ba-nr14: BIOMARKERS)

description:
Ba-nr14
LOGISTIC MODEL DEVELOPMENT


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL15: BIOMARKERS)

description:
Ba-rL15
LOGISTIC MODEL DEVELOPMENT
LINEAR REGRESSION MODEL DEVELOPMENT


title: Her2/Neu+ mammary gland, sample 118

description:
Her2/Neu+ mammary gland, sample 118  cohibridized with Universal Reference RNA
Block # in raw data file 2

source_name: Her2/Neu+ mammary gland, sample 118


title: WT_4C-4


title: 3T3-L1-NC-Undiff rep3

source_name: adipose


title: WT_4C-7


title: Spleen of non-infected Balb/c mice (Ba-nr12: BIOMARKERS)

description:
Ba-nr12
LOGISTIC MODEL DEVELOPMENT


title: Her2/Neu+ mammary gland, sample 120

description:
Her2/Neu+ mammary gland, sample 120  cohibridized with Universal Reference RNA
Block # in raw data file 1

source_name: Her2/Neu+ mammary gland, sample 120


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL12: BIOMARKERS)

description:
Ba-rL12
LOGISTIC MODEL DEVELOPMENT
LINEAR REGRESSION MODEL DEVELOPMENT


description:
Her2/Neu+/IFNAR1-/- mammary gland, sample 109  cohibridized with Universal Reference RNA
Block # in raw data file 2


description:
Her2/Neu+/IFNAR1-/- mammary gland, sample 103  cohibridized with Universal Reference RNA
Block # in raw data file 4


description:
Her2/Neu+/IFNAR1-/- mammary gland, sample 104  cohibridized with Universal Reference RNA
Block # in raw data file 3


description:
Her2/Neu+/IFNAR1-/- mammary gland, sample 110  cohibridized with Universal Reference RNA
Block # in raw data file 1


title: Spleen of non-infected Balb/c mice (Ba-nr16: BIOMARKERS)

description:
Ba-nr16
LOGISTIC MODEL DEVELOPMENT


title: WT_4C-8


title: WT_4C-10


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL11: BIOMARKERS)

description:
Ba-rL11
LOGISTIC MODEL DEVELOPMENT
LINEAR REGRESSION MODEL DEVELOPMENT


title: Spleen of non-infected Balb/c mice (Ba-nr13: BIOMARKERS)

description:
Ba-nr13
LOGISTIC MODEL DEVELOPMENT


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL10: BIOMARKERS)

description:
Ba-rL10
LOGISTIC MODEL DEVELOPMENT
LINEAR REGRESSION MODEL DEVELOPMENT


title: WT_4C-2


title: WT_28C-4

description: housed at 28°C

value: housed at 28C


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL9: BIOMARKERS)

description:
Ba-rL9
LOGISTIC MODEL DEVELOPMENT
LINEAR REGRESSION MODEL DEVELOPMENT


title: WT_28C-6

description: housed at 28°C


title: WT mammary gland, sample 55

description:
WT mammary gland, sample 55  cohibridized with Universal Reference RNA
Block # in raw data file 4

source_name: WT mammary gland, sample 55


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL8: BIOMARKERS)

description:
Ba-rL8
LOGISTIC MODEL DEVELOPMENT
LINEAR REGRESSION MODEL DEVELOPMENT


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL7: BIOMARKERS)

description:
Ba-rL7
LOGISTIC MODEL DEVELOPMENT
LINEAR REGRESSION MODEL DEVELOPMENT


title: WT_28C-5

description: housed at 28°C


title: Spleen of non-infected Balb/c mice (Ba-nr11: BIOMARKERS)

description:
Ba-nr11
LOGISTIC MODEL DEVELOPMENT


title: WT mammary gland, sample 59

description:
WT mammary gland, sample 59  cohibridized with Universal Reference RNA
Block # in raw data file 2

source_name: WT mammary gland, sample 59


title: WT_28C-8

description: housed at 28°C


title: Spleen of non-infected Balb/c mice (Ba-nr9: BIOMARKERS)

description:
Ba-nr9
LOGISTIC MODEL DEVELOPMENT


title: Spleen of non-infected Balb/c mice (Ba-nr10: BIOMARKERS)

description:
Ba-nr10
LOGISTIC MODEL DEVELOPMENT


title: WT2_Input

library_source: genomic

data_processing:
csfasta and qual raw data files were converted to fastqsanger using Galaxy FastQC; Quality Stats run for each sample
reads aligned with Bowtie for SOLiD  V1.1.2 in Galaxy
CHiP-seq peak calls were done with MACS V1.0.1; Peaks meeting FDR < or = 5%  (0.05) were included in the analysis, MFOLD=4
Join V1.0.0 on Intervals-Galaxy
Fetch V4.0.1 closest non-overlapping feature
Slice V0.0.1 bam selects bam fragments within MACS peak intervals from Bowtie alignment
Pileup V1.1.1 to create the pileup dataset
Pileup to Interval-Conversion of single base per row pileup table to an interval dataset
Subtract V1.0.0 intervals-  The remaining intervals are present only in the dataset from which the subtraction was done.
Genome_build: GRC38/mm10
Supplementary_files_format_and_content: bedgraph-chromosome, start, end, dataValue

molecule: genomic DNA

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared using the SOLiD ChIP-Seq Sample Prep Kit according to the manufacturer’s instruction.

treatment_protocol: BL6 mice were exposed to 4C for 6h prior to brown adipose tissue isolation.

value: Cold exposure 4C for 6h

tag: chip antibody


title: WT mammary gland, sample 56

description:
WT mammary gland, sample 56  cohibridized with Universal Reference RNA
Block # in raw data file 3

source_name: WT mammary gland, sample 56

value: mammary gland


title: WT mammary gland, sample 60

description:
WT mammary gland, sample 60  cohibridized with Universal Reference RNA
Block # in raw data file 1

source_name: WT mammary gland, sample 60

value: reference


title: Spleen of non-infected Balb/c mice (Ba-nr8: BIOMARKERS)

description:
Ba-nr8
LOGISTIC MODEL DEVELOPMENT


title: VCaP_ODQ_L001

city: Boston

first: Dong

last: Han

state: MA

address: 100 Morrissey Blvd

department: Biology-CPCT

institute: Umass Boston

description:
technical replicate for ODQ treatment
VCAPODQ_CTTGTA_L001
processed data file: RNASEQ_VCaP_VEH_ODQ.csv

data_processing:
Cufflinks pipeline was adapted and carried out on Galaxy platform, fastq files were imported into galaxy and reads were mapped using HISAT2 (v2.0.5) against Human hg19 reference genome.
Cufflinks (v2.2.1) analysis was performed on the HISAT2 output bam files to have assembled transcripts.
Using Cuffmerge (v.2.2.1) to merge all assembled transcripts from Cufflinks to have final transcriptome assembly.
Using Cuffquant (v2.2.1) to compare mapped reads from each sample including technical replicates to the final transcriptome assembly.
Using Cuffnorm (v2.2.1) to compare the Cuffquant output cxb files including biological replicates to the final transcriptome assembly to have the normalized gene expression and gene FPKM tables.
Genome_build: Human hg19
Supplementary_files_format_and_content: csv file for gene FPKM table output

growth_protocol: VCaP cells are cultured routinely in 10% FBS containing DMEM and passed every 5-6 days. LNCaP cells are cultured in 10% FBS containing RPMI 1640 and passed every 3-4 days.

extract_protocol:
RNA was extracted with Rneasy Mini Kit (QIAGEN) following manufacturer’s protocol
TruSeq® Strnd Total RNA LT (Illumina) was used for library construction

treatment_protocol: VCaP cells were transfected with siRNA against GUCY1A1, GUCY1B1, non-target control (NTC) using lipofectatimine 2000.

value: VCaP

value: Prostate Cancer Cells

tag: passage

tag: treated with

value: ODQ


title: IFNAR1-/- mammary gland, sample 42

description:
IFNAR1-/- mammary gland, sample 42  cohibridized with Universal Reference RNA
Block # in raw data file 3

source_name: IFNAR1-/- mammary gland, sample 42


title: IFNAR1-/- mammary gland, sample 45

description:
IFNAR1-/- mammary gland, sample 45  cohibridized with Universal Reference RNA
Block # in raw data file 2

source_name: IFNAR1-/- mammary gland, sample 45


title: Spleen of non-infected Balb/c mice (Ba-nr7: BIOMARKERS)

description:
Ba-nr7
LOGISTIC MODEL DEVELOPMENT

source_name: SPLEEN


title: VCaP_ODQ_L002

description:
technical replicate for ODQ treatment
VCAPODQ_CTTGTA_L002
processed data file: RNASEQ_VCaP_VEH_ODQ.csv


title: VCaP_Veh_L002

description:
technical replicate for VEH treatment
VCAPVEH_CAGATC_L002
processed data file: RNASEQ_VCaP_VEH_ODQ.csv

value: vehicle


title: IFNAR1-/- mammary gland, sample 50

description:
IFNAR1-/- mammary gland, sample 50  cohibridized with Universal Reference RNA
Block # in raw data file 1

source_name: IFNAR1-/- mammary gland, sample 50


title: WT2_ChIP

value: PGC-1α (Millipore, ST1204)


title: WT1_Input


title: VCaP_Veh_L001

description:
technical replicate for VEH treatment
VCAPVEH_CAGATC_L001
processed data file: RNASEQ_VCaP_VEH_ODQ.csv


title: Spleen of non-infected Balb/c mice (Ba-nr6: BIOMARKERS)

description:
Ba-nr6
LOGISTIC MODEL DEVELOPMENT


title: WT1_ChIP


title: WT_28C-7

description: housed at 28°C


title: VCaP_siGUCY1B1-2_L002

description:
technical replicate for biological replicate for siGUCY1B1
SIGUCY1B1-2_CTTGTA_L002
processed data file: RNASEQ_VCaP_siNTC_siGUCY1A1_siGUCY1B1.csv

tag: transfected with

value: siRNA against GUCY1B1 (siGUCY1B1)


title: VCaP_siGUCY1B1-2_L001

description:
technical replicate for biological replicate for siGUCY1B1
SIGUCY1B1-2_CTTGTA_L001
processed data file: RNASEQ_VCaP_siNTC_siGUCY1A1_siGUCY1B1.csv


title: WT_28C-9

description: housed at 28°C


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL5: BIOMARKERS)

description:
Ba-rL5
LOGISTIC MODEL DEVELOPMENT
LINEAR REGRESSION MODEL DEVELOPMENT


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL6: BIOMARKERS)

description:
Ba-rL6
LOGISTIC MODEL DEVELOPMENT
LINEAR REGRESSION MODEL DEVELOPMENT


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL4: BIOMARKERS)

description:
Ba-rL4
LOGISTIC MODEL DEVELOPMENT
LINEAR REGRESSION MODEL DEVELOPMENT


title: VCaP_siGUCY1B1-1_L002

description:
technical replicate for siGUCY1B1
SIGUCY1B1-1_CAGATC_L002
processed data file: RNASEQ_VCaP_siNTC_siGUCY1A1_siGUCY1B1.csv


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL3: BIOMARKERS)

description:
Ba-rL3
LOGISTIC MODEL DEVELOPMENT
LINEAR REGRESSION MODEL DEVELOPMENT


title: limd4

first: Tyson

middle: V.

last: Sharp

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

institute: Queen Mary University of London

description:
SAMPLE 12
replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Illumina Bead Array Reader

data_processing: The raw average intensities were processed by quantile normalization with limma package in R.

source_name: HBEC cell line (Lonza)

label_protocol: Ambion TotalPrep™-96

growth_protocol: HBEC cells were maintained in BEGM™ Bronchial Epithelial Cell Growth Medium (Lonza) supplemented with BEGM™ BulletKit (Lonza)

extract_protocol: ReliaPrep™ RNA Miniprep System (Promega)

treatment_protocol: Cells were transfected with siRNA (indicated conditions) using INTERFERin® (Polyplus) for 72 hours

tag: sirna treatment type

value: LIMD1 targetting siRNA 80nM

tag: group

value: Treatment


title: limd3

description:
SAMPLE 11
replicate 3


title: VCaP_siGUCY1A1-2_L002

description:
technical replicate for biological replicate for siGUCY1A1
SIGUCY1A1-2_GCCAAT_L002
processed data file: RNASEQ_VCaP_siNTC_siGUCY1A1_siGUCY1B1.csv

value: siRNA against GUCY1A1 (siGUCY1A1)


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL2: BIOMARKERS)

description:
Ba-rL2
LOGISTIC MODEL DEVELOPMENT
LINEAR REGRESSION MODEL DEVELOPMENT

value: Balb/c


title: VCaP_siGUCY1B1-1_L001

description:
technical replicate for siGUCY1B1
SIGUCY1B1-1_CAGATC_L001
processed data file: RNASEQ_VCaP_siNTC_siGUCY1A1_siGUCY1B1.csv


title: limd2

description:
SAMPLE 10
replicate 2


title: VCaP_siGUCY1A1-2_L001

description:
technical replicate for biological replicate for siGUCY1A1
SIGUCY1A1-2_GCCAAT_L001
processed data file: RNASEQ_VCaP_siNTC_siGUCY1A1_siGUCY1B1.csv


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL1: BIOMARKERS)

description:
Ba-rL1
LOGISTIC MODEL DEVELOPMENT
LINEAR REGRESSION MODEL DEVELOPMENT


title: Spleen of non-infected Balb/c mice (Ba-nr5: BIOMARKERS)

description:
Ba-nr5
LOGISTIC MODEL DEVELOPMENT


title: VCaP_siGUCY1A1-1_L001

description:
technical replicate for siGUCY1A1
SIGUCY1A1-1_ACAGTG_L001
processed data file: RNASEQ_VCaP_siNTC_siGUCY1A1_siGUCY1B1.csv


title: VCaP_siGUCY1A1-1_L002

description:
technical replicate for siGUCY1A1
SIGUCY1A1-1_ACAGTG_L002
processed data file: RNASEQ_VCaP_siNTC_siGUCY1A1_siGUCY1B1.csv


title: Spleen of non-infected Balb/c mice (Ba-nr4: BIOMARKERS)

description:
Ba-nr4
LOGISTIC MODEL DEVELOPMENT


title: VCaP_siNTC-2_L002

description:
technical replicate for biological replicate for siNTC
SINTC-2_TGACCA_L002
processed data file: RNASEQ_VCaP_siNTC_siGUCY1A1_siGUCY1B1.csv

value: siRNA against non-target-control (siNTC)


title: Spleen of non-infected Balb/c mice (Ba-nr3: BIOMARKERS)

description:
Ba-nr3
LOGISTIC MODEL DEVELOPMENT


title: scr4

description:
SAMPLE 8
replicate 4

value: scrambelled siRNA 80nM

value: Control 2


title: Spleen of non-infected Balb/c mice (Ba-nr2: BIOMARKERS)

description:
Ba-nr2
LOGISTIC MODEL DEVELOPMENT


title: limd1

description:
SAMPLE 9
replicate 1


title: M-CSF Mϕ, IL-4, biological rep 3

city: Vienna

first: Anna

last: Ohradanova-Repic

address: Lazarettgasse 19

country: Austria

institute: Medical University of Vienna

description: Gene expression data from human adult monocyte-derived macrophages that were differentiated in vitro with 50ng/ml M-CSF for 7d, followed by activation with 20ng/ml IL-4 for 2d (48h)

hyb_protocol: Affymetrix GeneChip® Human PrimeView arrays were washed, stained and scanned according to the protocol described in GeneChip® 3` IVT Express Labeling Assay User Manual (Fluidics Protocol FS450_0002)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: Data were normalized using RMA

label: biotin

source_name: M-CSF Mϕ, activated with 20 ng/ml IL-4 for 2d, biological rep 3

label_protocol: 250ng of total RNA were amplified and labeled using the Affymetrix 3` IVT Express Kit (Catalog Number 901229, Affymetrix, Santa Clara, CA)

growth_protocol: CD14+ monocytes isolated by magnetic-activated cell sorting using CD14 microbeads were cultured with the indicated collony stimulated factor in the RPMI1640 medium supplemented with 2 mM L-glutamine, 100 µg/ml streptomycin, 100 U/ml penicillin and 10% heat-inactivated FCS for 7d.

extract_protocol: Total RNA was extracted using PureLink RNA Mini Kit (Ambion) according to the recommendations of the manufacturer. Quality control was perfomed using Agilent Bioanalyzer.

treatment_protocol: Differentiated macrophages were resuspended in macrophage serum free medium (Invitrogen), supplemented with 2 mM L-glutamine and 2% FCS and activated with the indicated activation stimulus (100 ng/ml LPS + 25ng/ml IFNγ; 20 ng/ml IL-4; 20 ng/ml IL-10) or left untreated for 2d (48h).

value: M-CSF-differentiated macrophage

tag: treatment

value: activated with 20 ng/ml IL-4 for 2d


title: scr3

description:
SAMPLE 7
replicate 3


title: VCaP_siNTC-1_L002

description:
technical replicate for siNTC
SINTC-1_CGATGT_L002
processed data file: RNASEQ_VCaP_siNTC_siGUCY1A1_siGUCY1B1.csv


title: co3

description:
SAMPLE 3
replicate 3

value: Untreated

value: Control 1


title: Spleen of non-infected Balb/c mice (Ba-nr1: BIOMARKERS)

description:
Ba-nr1
LOGISTIC MODEL DEVELOPMENT


title: M-CSF Mϕ, LPS+IFNγ, biological rep 3

description: Gene expression data from human adult monocyte-derived macrophages that were differentiated in vitro with 50ng/ml M-CSF for 7d, followed by activation with 100 ng/ml LPS + 25ng/ml IFNγ for 2d (48h)

source_name: M-CSF Mϕ, activated with 100ng/ml LPS +25 ng/ml IFNγ for 2d, biological rep 3

value: activated with 100 ng/ml LPS + 25ng/ml IFNγ for 2d


title: GM-CSF Mϕ, IL-4, biological rep 3

description: Gene expression data from human adult monocyte-derived macrophages that were differentiated in vitro with 25ng/ml GM-CSF for 7d, followed by activation with 20ng/ml IL-4 for 2d (48h)

source_name: GM-CSF Mϕ, activated with 20 ng/ml IL-4 for 2d, biological rep 3

value: GM-CSF-differentiated macrophage


title: VCaP_siNTC-2_L001

description:
technical replicate for biological replicate for siNTC
SINTC-2_TGACCA_L001
processed data file: RNASEQ_VCaP_siNTC_siGUCY1A1_siGUCY1B1.csv

value: VCaP

value: Prostate Cancer Cells


title: scr1

description:
SAMPLE 5
replicate 1


title: M-CSF Mϕ, IL-10, biological rep 3

description: Gene expression data from human adult monocyte-derived macrophages that were differentiated in vitro with 50ng/ml M-CSF for 7d, followed by activation with 20ng/ml IL-10 for 2d (48h)

source_name: M-CSF Mϕ, activated with 20 ng/ml IL-10 for 2d, biological rep 3

value: activated with 20 ng/ml IL-10 for 2d


title: co4

description:
SAMPLE 4
replicate 4


title: GM-CSF Mϕ, control, biological rep 3

description: Gene expression data from human adult monocyte-derived macrophages that were differentiated in vitro with 25ng/ml GM-CSF for 7d, followed by mock activation (medium only) for 2d (48h)

source_name: GM-CSF Mϕ, mock-activated (control) for 2d, biological rep 3

value: mock-activated (medium only; control) for 2d


title: scr2

description:
SAMPLE 6
replicate 2


title: GM-CSF Mϕ, LPS+IFNγ, biological rep 3

description: Gene expression data from human adult monocyte-derived macrophages that were differentiated in vitro with 25ng/ml GM-CSF for 7d, followed by activation with 100 ng/ml LPS + 25ng/ml IFNγ for 2d (48h)

source_name: GM-CSF Mϕ, activated with 100ng/ml LPS +25 ng/ml IFNγ for 2d, biological rep 3


title: co1

description:
SAMPLE 1
replicate 1


title: co2

description:
SAMPLE 2
replicate 2


title: M-CSF Mϕ, control, biological rep 3

description: Gene expression data from human adult monocyte-derived macrophages that were differentiated in vitro with 50ng/ml M-CSF for 7d, followed by mock activation (medium only) for 2d (48h)

source_name: M-CSF Mϕ, mock-activated (control) for 2d, biological rep 3


title: VCaP_siNTC-1_L001

description:
technical replicate for siNTC
SINTC-1_CGATGT_L001
processed data file: RNASEQ_VCaP_siNTC_siGUCY1A1_siGUCY1B1.csv


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL24: MODEL)

description:
TEST 8 WEEKS
Ba-rL24

data_processing: Cq values from the 47 samples analyzed were exported for normalization using geNorm (qBasePLUS software (Biogazelle, Gent, Belgium)). Two genes showed the most stable expression (Stat6 and Itgb2)  and were used for normalization.

growth_protocol: 47 BALB/c (purchased to Charles River Laboratories, France) mice (14-15 weeks old) were used  in this study. Mice were randomly separated in two groups: (i) 23 control mice and (ii) 24 mice  that were infected with 10^6 stationary-phase L. infantum promastigotes via tail vein. Mice were euthanized by cervical dislocation and spleens were removed and immediately stored in RNAlater at -70ºC (Sigma-Aldrich, St. Louis, USA).

treatment_protocol: 24 out of the 47 mice were infected with 10^6 stationary-phase L. infantum promastigotes via tail vein.


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL22: MODEL)

description:
TEST 8 WEEKS
Ba-rL22


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL21: MODEL)

description:
TEST 8 WEEKS
Ba-rL21


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL23: MODEL)

description:
TEST 8 WEEKS
Ba-rL23


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL20: MODEL)

description:
TEST 8 WEEKS
Ba-rL20


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL19: MODEL)

description:
TEST 8 WEEKS
Ba-rL19


title: Spleen of non-infected Balb/c mice (Ba-nr23: MODEL)

description:
CONTROL 8 WEEKS
Ba-nr23


title: Spleen of non-infected Balb/c mice (Ba-nr21: MODEL)

description:
CONTROL 8 WEEKS
Ba-nr21


title: Spleen of non-infected Balb/c mice (Ba-nr22: MODEL)

description:
CONTROL 8 WEEKS
Ba-nr22


title: M-CSF Mϕ, LPS+IFNγ, biological rep 2

source_name: M-CSF Mϕ, activated with 100ng/ml LPS +25 ng/ml IFNγ for 2d, biological rep 2


title: M-CSF Mϕ, control, biological rep 2

source_name: M-CSF Mϕ, mock-activated (control) for 2d, biological rep 2


title: BCP1_OdDHL

city: New Orleans

first: Zhiqiang

last: Qin

address: 1700 Tulane Ave

institute: LSUHSC-NO

hyb_protocol: Hybridization using standard hybridization protocols from Illumina

scan_protocol: Standard Illumina protocols for HumanHT-12 chip v4.0 from Illumina using the Illumina BeadArray Reader

data_processing: The data were normalised using the cubic spline algorithm (GenomeStudio) and background removed with the GenomeStudio's Detection P-value algorithm

source_name: Primary effusion lymphoma cell line

label_protocol: cRNA was labeled with the TargetAmp Nano Labeling kit for Illumina Expression BeadChip (Epicentre Catalog Number TAN07924)

growth_protocol: BCP-1 were maintained in ATCC RPMI-1640 media supplemented with 20% fetal bovine serum.

extract_protocol: RNA was extracted using  RNeasy Mini kit (Qiagen) including the DNAseI treatment

treatment_protocol: BCP-1 were incubated with 25μM of OdDHL from P. aeruginosa for 48 h

value: OdDHL


title: GM-CSF Mϕ, LPS+IFNγ, biological rep 2

source_name: GM-CSF Mϕ, activated with 100ng/ml LPS +25 ng/ml IFNγ for 2d, biological rep 2


title: F121-6_mef_PC-HiC_R2

city: Tallahassee

first: David

middle: M

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Biology

institute: Florida State University

description:
F1216_ESC_iCounts_129
F1216_ESC_iCount_Cas
F1216_ESC_iDistance_129
F1216_ESC_iDistance_Cas

data_processing:
Library strategy: HiC-Seq
Reads were mapped to corresponding genome (129/sv and CAST/Ei) using bowtie2.
Reads were assigned to each allele using HARP (haplotype-assisted read parsing, https://github.com/dvera/harp)
Read-pair interactions were counted in 50kb windows
Average read-pair interaction distance was calculated in 50kb windows
Genome_build: mm10
Supplementary_files_format_and_content: processed data are number of interactions and interaction distances in 50kb windows.

source_name: hybrid mouse ESCs

growth_protocol: Hybrid mouse ES cells  F121-6,were grown on mitomycin-C-inactivated MEFs in ES media: DMEM supplemented with fetal calf serum (Seralab, seralab EU-000-F), 200mM L-glutamine (Gibco, life technologies 25030-024), 50mM 2-mercaptoethanol (Gibco, life technologies 31380-010), penicillin/streptomycin (Gibco, life technologies 15140-122), 5ml non-essential amino acids (Gibco, life technologies 11140-035) and 10^3 U/mL LIF.

extract_protocol:
Promoter Capture Hi-C was performed as previously described (Schoenfelder et al. 2015a). Briefly, in-nucleus ligation method for Hi-C library preparation (Nagano et al. 2015) was performed with 3–4 x 10^7 cells fixed in 2% formaldehyde. Chromatin was digested with Hind-III (NEB) and Klenow (NEB) was used to label restriction sites with biotin-14-dATP (Life Technologies). In-nucleus ligation was performed with 25 units of T4 DNA ligase (Invitrogen) at 16°C overnight, and crosslinks were reversed with Proteinase K at 65 ̊C overnight. Samples were treated with RNase A, and ligation products were purified by phenol/chloroform extraction and sonicated (Covaris E220). Hi-C library DNA was end-repaired with Klenow, T4 DNA polymerase, and T4 polynucleotide kinase (NEB). Hi-C DNA was amplified with 7 or 8 PCR cycles and amplified libraries were purified using AMPure XP beads (Beckman Coulter). For the capture step, 500 ng of Hi-C library DNA were denatured by heating to 95 ̊C for 5 min, and incubated at 65 ̊C for 24 hrs with a custom-designed biotinylated RNA bait system targeting the ends of Hind-III restriction fragments at 22,225 mouse gene promoters (Schoenfelder et al. 2015a) (Agilent Technologies). The Sure Select Target enrichment protocol (Agilent Technologies) was followed for biotin pull-down and washes, using MyOne Streptavidin T1 Dynabeads (Life Technologies). Captured Hi-C DNA was amplified and  libraries purified using AMPure XP beads (Beckman Coulter).
Promoter Capture Hi-C libraries were sequenced (100 bp paired-end) on the HiSeq 1000 platform (Illumina).

tag: cross

value: hybrid 129 / cas

tag: gender

value: Female

tag: replicate


title: GM-CSF Mϕ, control, biological rep 2

source_name: GM-CSF Mϕ, mock-activated (control) for 2d, biological rep 2


title: BCBL1_vehicle_for OdDHL

growth_protocol: BCBL-1 were maintained in RPMI-1640 media supplemented with 10% fetal bovine serum, 10mM HEPES (pH 7.5), 100 U/ml penicillin, 100 mg/ml streptomycin, 2mM L-glutamine, 0.05mM β-mercaptoethanol and 0.02% (wt/vol) sodium bicarbonate.

treatment_protocol: BCBL-1 were incubated with 25μM of OdDHL from P. aeruginosa for 48 h

tag: cell line

value: vehicle


title: GM-CSF Mϕ, IL-4, biological rep 2

source_name: GM-CSF Mϕ, activated with 20 ng/ml IL-4 for 2d, biological rep 2


title: M-CSF Mϕ, IL-4, biological rep 2

source_name: M-CSF Mϕ, activated with 20 ng/ml IL-4 for 2d, biological rep 2


title: BCBL1_OdDHL


title: BCP1_vehicle_for_OdDHL


title: BCP1_vehicle

treatment_protocol: BCP-1 were incubated with 25μM of PQS from P. aeruginosa for 48 h


title: M-CSF Mϕ, LPS+IFNγ, biological rep 1

source_name: M-CSF Mϕ, activated with 100ng/ml LPS +25 ng/ml IFNγ for 2d, biological rep 1


title: M-CSF Mϕ, IL-10, biological rep 1

source_name: M-CSF Mϕ, activated with 20 ng/ml IL-10 for 2d, biological rep 1


title: M-CSF Mϕ, IL-4, biological rep 1

source_name: M-CSF Mϕ, activated with 20 ng/ml IL-4 for 2d, biological rep 1


title: BCP1_PQS


title: M-CSF Mϕ, control, biological rep 1

source_name: M-CSF Mϕ, mock-activated (control) for 2d, biological rep 1


title: BCBL1_PQS

description: SAMPLE 2

treatment_protocol: BCBL-1 were incubated with 25μM of PQS from P. aeruginosa for 48 h

value: PQS


title: M-CSF Mϕ, IL-10, biological rep 2

source_name: M-CSF Mϕ, activated with 20 ng/ml IL-10 for 2d, biological rep 2


title: F121-6_mef_PC-RNA-Seq_R2

description:
counts_129_r2
counts_cas_r2

data_processing:
Reads were mapped to corresponding genome (129/sv and CAST/Ei) using bowtie2.
Reads were assigned to each allele using HARP (haplotype-assisted read parsing, https://github.com/dvera/harp)
RPKM of all Mouse GENCODE genes were calculated
Genome_build: mm10
Supplementary_files_format_and_content: processed data are RPKMs of all Mouse GENCODE genes.

extract_protocol:
To measure all transcriptional events we performed total nuclear RNA-seq. Previously reported strand-specific nuclear RNA-seq libraries (Schoenfelder et al. 2015b) were re-sequenced and reads were merged with the published data for downstream analysis.
Total nuclear RNA-seq libraries were sequenced (100 bp paired-end) on the HiSeq 1000 platform (Illumina).


title: F121-6_mef_PC-HiC_R1


title: F121-6_mef_PC-RNA-Seq_R1

description:
counts_129_r1
counts_cas_r1


title: Spleen of non-infected Balb/c mice (Ba-nr20: MODEL)

description:
CONTROL 8 WEEKS
Ba-nr20

source_name: SPLEEN

value: Balb/c


title: F121-6_mef_ATACseq_R2

data_processing:
Reads are mapped to corresponding genome (129/sv and CAST/Ei) using bowtie2.
ATAC-seq peaks were identified using MACS2
Coverage data are calculated from mapped reads using samtools and bedtools
Coverage peaks was calculated in 50kb windows
Genome_build: mm10
Supplementary_files_format_and_content: processed data are number of peaks in 50kb windows in mm10 genome.

extract_protocol:
Genome-wide ATAC-seq (Assay for Transposase-Accessible Chromatin using Sequencing) libraries were generated as previously described (Buenrostro et al. 2013). Briefly, nuclei from 200,000 cells were treated with transposase (Illumina) and DNA purified on a MinElute column (Qiagen), libraries were amplified using Nextera DNA Sample Preparation Kit and  purified twice with PCR clean-up kit columns (Qiagen).
Libraries were sequenced (100 bp paired-end) on the HiSeq 2500 platform (Illumina).


title: F121-6_mef_ATACseq_R1


title: Spleen of non-infected Balb/c mice (Ba-nr19: MODEL)

description:
CONTROL 8 WEEKS
Ba-nr19


title: Spleen of non-infected Balb/c mice (Ba-nr18: MODEL)

description:
CONTROL 8 WEEKS
Ba-nr18


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL16: MODEL)

description:
TEST 4 WEEKS
Ba-rL16


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL15: MODEL)

description:
TEST 4 WEEKS
Ba-rL15


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL18: MODEL)

description:
TEST 4 WEEKS
Ba-rL18


title: BCBL1_vehicle

description: SAMPLE 1


title: GM-CSF Mϕ, LPS+IFNγ, biological rep 1

source_name: GM-CSF Mϕ, activated with 100ng/ml LPS +25 ng/ml IFNγ for 2d, biological rep 1


title: GM-CSF Mϕ, IL-4, biological rep 1

source_name: GM-CSF Mϕ, activated with 20 ng/ml IL-4 for 2d, biological rep 1


title: GM-CSF Mϕ, control, biological rep 1

source_name: GM-CSF Mϕ, mock-activated (control) for 2d, biological rep 1


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL14: MODEL)

description:
TEST 4 WEEKS
Ba-rL14


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL13: MODEL)

description:
TEST 4 WEEKS
Ba-rL13


title: Spleen of non-infected Balb/c mice (Ba-nr17: MODEL)

description:
CONTROL 4 WEEKS
Ba-nr17


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL17: MODEL)

description:
TEST 4 WEEKS
Ba-rL17


title: Spleen of non-infected Balb/c mice (Ba-nr16: MODEL)

description:
CONTROL 4 WEEKS
Ba-nr16


title: Spleen of non-infected Balb/c mice (Ba-nr14: MODEL)

description:
CONTROL 4 WEEKS
Ba-nr14


title: Spleen of non-infected Balb/c mice (Ba-nr13: MODEL)

description:
CONTROL 4 WEEKS
Ba-nr13


title: Spleen of non-infected Balb/c mice (Ba-nr12: MODEL)

description:
CONTROL 4 WEEKS
Ba-nr12


title: BE2C_JQ1THZ1_4h_2

city: Cambridge

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

hyb_protocol: Samples were prepared for hybridization using 10 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays (Human PrimeView, Affymetrix 901837) were hybridized in a GeneChip Hybridization Oven at 45C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console. A Primeview CDF that included probe information for the ERCC controls (GPL16043), provided by Affymetrix, was used to generate .CEL files.

data_processing: A CDF provided by Affymetrix, which contained the ERCC probes (PrimeView_withERCC_binary.cdf) was used instead of the standard PrimeView cdf. The data were analyzed with Bioconductor using the MAS5 normalization method. Then, these data were renormalized per batch (B1/B2) to the external spike-ins. See Loven, Orlando et al., Cell, 2012 for additional details.

source_name: Cells were treated with 3uM JQ1 and 125nM THZ1 for 4 hours

label_protocol: For microarray analysis, 100 ng of total RNA containing ERCC RNA Spike-In Mix (see above) was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (3' IVT Express Kit, Affymetrix 901228).  Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.

growth_protocol: BE2C cells were grown in RPMI medium supplemented with 1% glutamine and 10% FBS.  Cells were cultured at 37 degrees C in a humidified chamber in the presence of 5% CO2, unless otherwise noted.

extract_protocol: Total RNA from biological replicates (equivalent to 5 million cells per replicate) was subsequently isolated using TRIzol (Thermo Fisher, cat# 15596026) following the manufacturer’s instructions and re-suspended in 50 μL nuclease-free water (Ambion, AM9938). Total RNA was spiked-in with ERCC RNA Spike-In Mix (Ambion, 4456740) and analyzed on Agilent 2100 Bioanalyzer for integrity.

treatment_protocol: BE2C cells were plated at 500,000 cells/ mL and incubated in media containing 3uM JQ1 and 125nM THZ1,  or with DMSO, for 1, 4, or 12 hrs.  At the end of the experiment cells were collected by centrifugation and cell numbers were determined by manually counting cells using C-Chip disposable hemocytometers (Digital Bio, DHC-N01).  5,000,000 cells were isolated from each treatment condition.

value: BE2C Neuroblastoma

value: 3uM JQ1 and 125nM THZ1

tag: time

value: 4 hours


title: BE2C_JQ1THZ1_4h_3


title: HFD3, biological rep 3

hyb_protocol: Labeled samples were hybridized to MTA 1.0 chips overnight (16h, 45°C, 60 RPM) then washed and stained on an Affymetrix GCS 3000 system Fluidics station using the FS450_0001 protocol.

data_processing: Affymetrix Expression Console Version 1.4.1.46 was used for quality control, data summarization, and normalization. The processing algorithm used was SST-RMA. Affymetrix Transcriptome Analysis Console Version 3.1.0.5 was used to perform differential expression analyses. Transcripts were considered differentially expressed between the two groups if linear fold change was greater than ±2 and the ANOVA p-value was less than 0.05

source_name: Epididymal fat macrophages

label_protocol: 100ng total RNA was used as starting material for labeling according to the Affymetrix GeneChip WT PLUS Reagent Kit manufacturer protocol.

value: Male

tag: age

value: 22 weeks

tag: weeks of diet

value: 16 weeks


title: Spleen of non-infected Balb/c mice (Ba-nr15: MODEL)

description:
CONTROL 4 WEEKS
Ba-nr15


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL12: MODEL)

description:
TEST 2 WEEKS
Ba-rL12


title: BE2C_JQ1THZ1_1h_2

source_name: Cells were treated with 3uM JQ1 and 125nM THZ1 for 1 hour

value: 1 hour


title: BE2C_JQ1THZ1_12h_1

source_name: Cells were treated with 3uM JQ1 and 125nM THZ1 for 12 hours

value: 12 hours


title: BE2C_JQ1THZ1_12h_3


title: HFD2, biological rep 2


title: BE2C_JQ1THZ1_4h_1


title: BE2C_JQ1THZ1_1h_1


title: BE2C_JQ1THZ1_12h_2


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL11: MODEL)

description:
TEST 2 WEEKS
Ba-rL11


title: HFD1, biological rep 1


title: BE2C_JQ1THZ1_0h_3

source_name: Cells were treated with DMSO

value: control


title: BE2C_JQ1THZ1_0h_2


title: NCD3, biological rep 3


title: mouse nasal cavity_DEP 8 weeks treatment  - replicate 1

city: Goyang-si

first: Young Rok

last: Seo

address: Dongguk-ro 32

department: Life science

country: South Korea

institute: Dongguk University

description: Biological replicate 1 of 3.

hyb_protocol: Labeled cRNA was hybridized on the Mouse Gene Expression Microarray chip 4x44K V2 (ID G2519F-026655; Agilent technologies) with Gene expression Hybridization kit (Agilent Technologies, USA) according to the manufacturer’s protocol.

scan_protocol: Hybridized chip was scanned using the Agilent DNA Microarray Scanner

data_processing: Probe signals were quantified using Feature Extraction Software (Agilent Technologies, USA). Normalized data were analyzed using GeneSpringSoftware (Agilent Technologies, USA).

source_name: Mouse nasal cavity (DEP treated)

label_protocol: Extracted RNA were then labeled using Low Input Quick Amp Labeling Kit (Agilent Technologies, USA) following the manufacturer’s procedure.

growth_protocol: The 32 female BALB/c mice, 6 weeks of age were used.

extract_protocol: total RNA was extracted from mouse nasal cavity in each experimental group using RNeasy Mini kits (Qiagen, USA) in accordance with manufacturer’s instructions.

treatment_protocol: DEPs were suspended in saline solution for 30 minutes before administration. The DEP 4 week and DEP 8 week groups were exposed to 100 μg/m3 DEPs for 1 hour a day for 5 days a week from 4 to 8 weeks in a closed-system chamber attached to an ultrasonic nebulizer (NE-UO7; Omron Corporation, Tokyo, Japan) with an output of 1 mL/min and 1- to 5-μm particle size.

value: BALB/c

value: 100 ug/m3 DEP

value: 6 weeks

source_name: Mouse nasal cavity (Control)


title: Fetal Sheep 08-075-2HT p3

city: Aurora

first: Reuben

middle: Blair

last: Dodson

state: CO

address: 13123 East 16th Ave

department: Surgery

institute: University of Colorado Denver

description: Near-term Fetal Pulmonary Artery Endothelial Cell IUGR Model

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: R/Bioconductor used to identify significant genes with lima and identify enriched pathways with GSEA.

organism: Ovis aries

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: Cells of Passage 2-6 were cultured in DMEM with 10% FBS suplemented with 1% antimicrobial and antibacterial

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

tag: cell type

value: Fetal Pulmonary Artery Endothelial Cell

value: IUGR Hyperthermic


title: BE2C_JQ1THZ1_1h_3


title: mouse nasal cavity_DEP 8 weeks treatment  - replicate 2

description: Biological replicate 2 of 3.

value: Female

tag: strain


title: Fetal Sheep 09-006-1HT p3

source_name: Near-term Fetal Pulmonary Artery Endothelial Cell IUGR Model


title: mouse nasal cavity_DEP 4 weeks treatment  - replicate 4

description: Biological replicate 4 of 4.


title: NCD2, biological rep 2


title: NCD1, biological rep 1


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL10: MODEL)

description:
TEST 2 WEEKS
Ba-rL10

extract_protocol: Total RNA isolation from spleens (9-11 mg) was performed by cell disruption using FastPrep®  System (ProScientific, Cedex, France) and Lysing Matrix D (MP Biomedicals, Solon, USA) in TRI-Reagent (Sigma-Aldrich, St. Louis, USA). RNeasy Mini Kit (Qiagen) was subsequently used for mRNA enrichment following manufacturer’s instructions


title: BE2C_JQ1THZ1_0h_1


title: Fetal Sheep 09-024-1HT p4


title: mouse nasal cavity_DEP 4 weeks treatment  - replicate 3

description: Biological replicate 3 of 4.


title: Profilin-allergic patient 19

city: Madrid

first: Leticia

last: Mera

state: Madrid

address: Carretera Boadilla km 5300

institute: CEU San Pablo University

description: Gene expression data from grass pollen allergic patients with severe allergic reactions to profilin

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 20 hr at 48ºC on GeneChip™ Human Gene 2.1 ST Array Strip. GeneChips were washed and stained in the GeneAtlas™ System for Academic Customers, 230V (Applied Biosystems™)

scan_protocol: GeneChips were scanned using the GeneAtlas™ System for Academic Customers, 230V (Applied Biosystems™).

data_processing: The data was RMA-normalized (.chp files) using Expression Console (Affymetrix). Gene expression analysis of .chp files was performed with Transcriptome Analysis Console 3.0 (TAC) (Affymetrix)

source_name: Ficoll isolated PBMCs from allergic patients to profilin

label_protocol: Biotinylated cRNA was prepared according to the GeneChip ™ WT PLUS Reagent Kit manual from 100 ng total RNA (Affymetrix, Thermo Fisher Scientific).

extract_protocol: PBMCs from allergic patients were isolated using Ficoll gradient protocol. Total RNA was extracted using Rneasy Mini Kit (QIAGEN). RNA was stored at -80ºC until microarray hybridization

tag: tissue

value: blood

value: PBMC

tag: allergic classification

value: Severe


title: mouse nasal cavity_DEP 8 weeks treatment  - replicate 3

description: Biological replicate 3 of 3.


title: Fetal Sheep 13-047-6HT p3


title: Adult RNA-seq 1

city: Cleveland

first: Donny

last: Licatalosi

state: OH

address: 2109 Adelbert Rd

institute: Case Western Reserve University

data_processing:
Read mapping and gene expression quantification was performed using Olego and Quantas
Genome_build: mm9
Supplementary_files_format_and_content: Sample 1 BED (rep1bed v2 bdgraph) and expression values (Frank_DL1.expr.txt) and Sample 2 BED (rep2bed v2 bdgraph) and expression values (Frank_DL2.expr.txt)

source_name: Testes

extract_protocol: Libraries were prepared using the TruSeq RNA Library Prep kit (Illumina)

tag: Sex

value: 8 weeks


title: mouse nasal cavity_DEP 4 weeks treatment  - replicate 2

description: Biological replicate 2of 4.


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL7: MODEL)

first: Emma

last: Carmelo

address: C/ Astrofisico Francisco Sanchez s/n, Campus de Anchieta

institute: University of La Laguna

description:
TEST 2 WEEKS
Ba-rL7

value: Balb/c


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL8: MODEL)

description:
TEST 2 WEEKS
Ba-rL8


title: Adult PolyA Seq 2

data_processing:
Reads consisting of two or more consecutive N’s or all poly(A) were filtered out, then remaining reads were processed to remove adapter and poly(A) sequences. Remaining reads were mapped to mouse genome mm9 with GSNAP allowing 2 mismatches. Reads with identical genomic footprint and 4N’s were then collapsed into single reads as likely PCR duplicates. Mapped reads that were likely internal priming events rather than true poly(A) tails were discarded if they had 6 or more consecutive A’s or 7 or more A’s in the 10 nt window downstream of the read 3’ end (cleavage and polyadenylation site). We accepted only 3’ ends with 1 of 14 hexamers within 50 nt upstream of the 3’ end (as described in (Martin et al., 2012))
Genome_build: mm9
Supplementary_files_format_and_content: Excel sheet with the genomic coordinates of 28032 adult 3'UTRs from two biological replicates

molecule: polyA RNA

extract_protocol: PolyA+ RNA was selected by oligodT-hybridization (Dynal) and fragmented by alkaline hydrolysis.  RNA fragments 50-100 nt long were gel purified from 10% PAGE/Urea gels, and used as template for reverse transcriptions with SuperScript III (Invitrogen).  First strand cDNA was gel purified, then circularized with CircLigase (EpiCentre).  Circularized DNA was used as the template for PCR.  After cycle number optimization to obtain the minimal amount of PCR product detectable by Sybr Gold (Invitrogen), the PCR product was gel purified and used as template for a second PCR with primers containing Illumina adaptor sequences.

value: Male

value: 8 week


title: Spleen of non-infected Balb/c mice (Ba-nr11: MODEL)

description:
CONTROL 2 WEEKS
Ba-nr11


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL9: MODEL)

description:
TEST 2 WEEKS
Ba-rL9


title: Spleen of non-infected Balb/c mice (Ba-nr10: MODEL)

description:
CONTROL 2 WEEKS
Ba-nr10


title: Dazl HITS CLIP 3

data_processing:
Reads were mapped using Bowtie and Tophat (Trapnell et al., 2012) and filtered as previously described (Hannigan et al., 2017)
Genome_build: mm9
Supplementary_files_format_and_content: BED file contains processed reads from individual samples (color coded:)

extract_protocol:
Testes were detunicated in cold HBSS and seminiferous tubules UV-irradiated on ice.
All steps were performed as previously described (Licatalosi et al., 2008; Licatalosi et al., 2012., Hannigan et al., 2017)


title: Fetal Sheep 12-040-3 p6

description: Near-term Fetal Pulmonary Artery Endothelial Cell

value: Control Normothermic


title: Spleen of non-infected Balb/c mice (Ba-nr9: MODEL)

description:
CONTROL 2 WEEKS
Ba-nr9


title: 539-14

city: Copenhagen

first: Xiaoyu

last: Pan

address: Dyrlægevej 68

country: Denmark

institute: University of Copenhagen

data_processing:
Raw reads were trimmed to produce clean reads, including removal of the adapter sequence and low-quality reads containning more than 50% bases with Q-value < 10, and more than 10% N bases, as detected by the FASTX tool kit (v0.0.13).
Clean reads were aligned to the porcine genome (Sscrofa10.2) using Tophat v2.1.1.
The bam files aligned by Tophat were assembled to the porcine annotated gene/transcript information by Cufflinks v2.2.1.
The assemblies of all the samples created by Cufflinks were merged together using Cuffmerge.
The bam files were mapped to the merged transcripts, and the expression level of each transcript was estimated using Fragments Per Kilobases per Million reads (FPKM) values by Cuffdiff.
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: Tab delimited files list the results of gene-level differential expression testing between two groups.

organism: Sus scrofa

source_name: Hippocampus

extract_protocol:
Intact frozen left hippocampi were homogenized by cryogenic tissue pulveriser in liquid nitrogen and total RNA was isolated with RNeasy Lipid Tissue Mini Kit (Qiagen, Copenhagen, Denmark).
Sequencing libraries were constructed using NEBNext UltraTM RNA library Prep Kit for Illumina (New England BioLabs, Ipswich, MA, USA), following the manufacturer’s recommendations. After amplification, products were purified with a AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: siNEC


title: 226-15


title: Fetal Sheep 12-045-6 p6

source_name: Near-term Fetal Pulmonary Artery Endothelial Cell


title: Spleen of non-infected Balb/c mice (Ba-nr8: MODEL)

city: La Laguna

description:
CONTROL 2 WEEKS
Ba-nr8


title: Dazl HITS CLIP 2


title: 246-15


title: Spleen of non-infected Balb/c mice (Ba-nr7: MODEL)

description:
CONTROL 2 WEEKS
Ba-nr7


title: Profilin-allergic patient 17


title: Profilin-allergic patient 14


title: Profilin-allergic patient 16


title: mouse nasal cavity_DEP 4 weeks treatment  - replicate 1

description: Biological replicate 1 of 4.


title: Profilin-allergic patient 13


title: 547-14


title: Adult PolyA Seq 1


title: Profilin-allergic patient 12


title: Profilin-allergic patient 15


title: 224-15


title: Fetal Sheep 14-019-3 p6


title: Fetal Sheep 09-086-1 p5


title: Profilin-allergic patient 11

description: Gene expression data from grass pollen allergic patients with moderate allergic reactions to profilin

value: Moderate


title: Spleen of non-infected Balb/c mice (Ba-nr6: MODEL)

description:
CONTROL 2 WEEKS
Ba-nr6


title: Profilin-allergic patient 9


title: Profilin-allergic patient 8


title: 550-14

value: noNEC


title: 253-15


title: 223-15


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL6: MODEL)

description:
TEST 1 WEEK
Ba-rL6


title: Dazl HITS CLIP 1


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL5: MODEL)

description:
TEST 1 WEEK
Ba-rL5


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL4: MODEL)

description:
TEST 1 WEEK
Ba-rL4


title: 230-15


title: 228-15


title: 540-14


title: Profilin-allergic patient 10


title: Profilin-allergic patient 5

description: Gene expression data from grass pollen allergic patients with mild reactions to profilin

value: Mild


title: Profilin-allergic patient 7


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL2: MODEL)

description:
TEST 1 WEEK
Ba-rL2


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL3: MODEL)

description:
TEST 1 WEEK
Ba-rL3


title: 231-15

value: coNEC


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL1: MODEL)

description:
TEST 1 WEEK
Ba-rL1


title: Profilin-allergic patient 6


title: Profilin-allergic patient 4


title: Spleen of non-infected Balb/c mice (Ba-nr5: MODEL)

description:
CONTROL 1 WEEK
Ba-nr5


title: Spleen of non-infected Balb/c mice (Ba-nr4: MODEL)

description:
CONTROL 1 WEEK
Ba-nr4


title: 552-14


title: 255-15


title: Spleen of non-infected Balb/c mice (Ba-nr3: MODEL)

description:
CONTROL 1 WEEK
Ba-nr3


title: 545-14


title: Spleen of non-infected Balb/c mice (Ba-nr2: MODEL)

description:
CONTROL 1 WEEK
Ba-nr2


title: 225-15


title: Profilin-allergic patient 3


title: Spleen of non-infected Balb/c mice (Ba-nr1: MODEL)

description:
CONTROL 1 WEEK
Ba-nr1


title: Profilin-allergic patient 2


title: Non-allergic subject 5

description: Gene expression data from non-allergic subjects

source_name: Ficoll isolated PBMCs from non-allergic subjects

value: Non-allergic


title: Non-allergic subject 6


title: Profilin-allergic patient 1


title: Non-allergic subject 2


title: Non-allergic subject 1


title: N8 Hui 04142016

status: Public on May 21 2018

city: New York

first: Ariel

last: Israel

state: NY

address: 1425 Madison Avenue

department: Department of Dermatology

institute: Icahn School of Medicine at Mount Sinai

description: Gene expression data from normal skin

hyb_protocol: Encore Biotin Module (Nugen) and Ambion

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

data_processing: GC-RMA (using gcrma package from R/Bioconductor)

label_protocol: Encore Biotin Module (Nugen) and Ambion

extract_protocol: Cells lysed in RLT with Beta-2-mercaptoethanol, RNA was extracted using RNeasy-Micro kit (QIAGEN, Valencia, CA).

tag: lesion

value: N

value: skin

value: M

tag: agegroup

value: Adult

tag: ethnicity

value: White


title: L8 Hui 04142016

description: Gene expression data from lesional skin

value: LS

value: Caucasian


title: L43 Susan 05092013

description: Gene expression data from non-lesional skin

value: NL


title: L26 Susan 05092013

description: Gene expression data from lesional skin


title: L14 Hui 04192016

description: Gene expression data from lesional skin

value: AA


title: N15 Hui 04192016

description: Gene expression data from normal skin

value: Black


title: N5 Hui 01162014

description: Gene expression data from normal skin

value: F


title: L19 Hui 04152016

value: Asian


title: L44 Susan 05092013

description: Gene expression data from lesional skin


title: N11 Hui 02062014

description: Gene expression data from normal skin


title: N17 Hui 02042014

description: Gene expression data from normal skin


title: N8 Hui 01162014

description: Gene expression data from normal skin


title: N17 Hui 04152016

description: Gene expression data from normal skin

value: Hispanic


title: L20 Hui 04152016

description: Gene expression data from lesional skin


title: L13 Hui 04192016


title: 99L Hui 04152016

description: Gene expression data from lesional skin

value: Children

value: Hispanic/Latino


title: N21 Hui 02062014

description: Gene expression data from normal skin


title: L25 Susan 05092013


title: L8 Susan 05022013

description: Gene expression data from lesional skin


title: N18 Hui 02042014

description: Gene expression data from normal skin


title: L7 Susan 05022013


title: N12 Hui 02042014

description: Gene expression data from normal skin


title: 96N Hui 04152016

value: Black/African American


title: L7 Hui 04142016


title: N13 Hui 02042014

description: Gene expression data from normal skin


title: 97N Hui 04152016


title: 99N Hui 04152016


title: 97L Hui 04152016

description: Gene expression data from lesional skin


title: Adult RNA-seq 2

value: Male

value: 8 weeks


title: 81N Hui 04192016

value: skin


title: 8L Hui 04142016

description: Gene expression data from lesional skin


title: 7N Hui 04142016

value: Black/White/Mexican/Puerto Rican


title: 8N Hui 04142016


title: 81L Hui 04192016

description: Gene expression data from lesional skin


title: 8 Susan 03282013

description: Gene expression data from lesional skin

value: Adult


title: 96L Hui 04152016

description: Gene expression data from lesional skin


title: 78C Hui 04142016

description: Gene expression data from normal skin

value: N

value: M

value: White/Caucasian


title: 80C Hui 04142016

description: Gene expression data from normal skin


title: 79C Hui 04142016

description: Gene expression data from normal skin


title: 72 Susan 04112013

description: Gene expression data from lesional skin

value: LS

value: Caucasian


title: 6L Hui 04142016 2

description: Gene expression data from lesional skin


title: 7 Susan 03282013

value: NL


title: 60 Susan 04112013

description: Gene expression data from lesional skin


title: 71 Susan 04112013


title: 5L Hui 04142016

description: Gene expression data from lesional skin

value: Black


title: 7L Hui 04142016

description: Gene expression data from lesional skin

value: F


title: 59 Susan 04112013


title: 54C Hui 04142016

description: Gene expression data from normal skin


title: 64C Hui 04192016

description: Gene expression data from normal skin


title: 6N Hui 04142016


title: 62C Hui 04192016

description: Gene expression data from normal skin


title: 65 Susan 04112013


title: 66 Susan 04112013

description: Gene expression data from lesional skin


title: 5N Hui 04142016


title: 63 Susan 04112013


title: 64 Susan 04112013

description: Gene expression data from lesional skin


title: 61C Hui 04192016

description: Gene expression data from normal skin


title: 53 Susan 04112013


title: 48 Susan 04092013

description: Gene expression data from lesional skin


title: 40 Susan 04092013

description: Gene expression data from lesional skin


title: 4L Hui 04142016

description: Gene expression data from lesional skin


title: 47 Susan 04092013


title: 30 Susan 04092013

description: Gene expression data from lesional skin


title: 3L Hui 04142016

description: Gene expression data from lesional skin


title: 4N Hui 04142016


title: 41 Susan 04092013


title: 36 Susan 04092013

description: Gene expression data from lesional skin


title: 39 Susan 04092013


title: 25L Hui 04192016

description: Gene expression data from lesional skin


title: 25N Hui 04192016


title: 29 Susan 04092013


title: 31N Hui 04192016

value: white


title: 31L Hui 04192016

description: Gene expression data from lesional skin

value: Children


title: 42 Susan 04092013

description: Gene expression data from lesional skin


title: 28N Hui 04192016

value: white/Asian/Pacific Islander


title: 3N Hui 04142016


title: 24N Hui 04192016


title: 28L Hui 04192016

description: Gene expression data from lesional skin


title: 35C Hui 04142016

description: Gene expression data from normal skin


title: 21L Hui 04192016

description: Gene expression data from lesional skin


title: 23 Susan 03282013


title: 1N Hui 04142016

value: Asian/Pacific Islander


title: 24L Hui 04192016

description: Gene expression data from lesional skin


title: 35 Susan 04092013


title: 24 Susan 03282013

description: Gene expression data from lesional skin


title: 21N Hui 04192016


title: 175C Hui 04152016

description: Gene expression data from normal skin


title: 18N Hui 04192016


title: 18L Hui 04192016

description: Gene expression data from lesional skin


title: 126N Hui 04152016 2


title: 12 Susan 03282013

description: Gene expression data from lesional skin


title: 122C Hui 04152016

description: Gene expression data from normal skin


title: 17 Susan 03282013


title: 167C Hui 04152016

description: Gene expression data from normal skin


title: 197C Hui 04152016 2

description: Gene expression data from normal skin

value: Black/African American


title: 18 Susan 03282013

description: Gene expression data from lesional skin


title: 157C Hui 04152016

description: Gene expression data from normal skin


title: 152C Hui 04152016

description: Gene expression data from normal skin


title: 120C Hui 04192016

description: Gene expression data from normal skin


title: 114C Hui 04192016

description: Gene expression data from normal skin


title: 101N Hui 04152016


title: 126L Hui 04152016

description: Gene expression data from lesional skin


title: 113C Hui 04142016

description: Gene expression data from normal skin


title: 121C Hui 04192016

description: Gene expression data from normal skin


title: 101L Hui 04152016

description: Gene expression data from lesional skin


title: HMVEC-L_TNF-α-induced premature senescent_rep3

city: KUALA LUMPUR

first: Pooi-Fong

last: Wong

address: Faculty of Medicine

department: Pharmacology

country: Malaysia

institute: University of malaya

description: Gene expression of TNF-α-induced premature senescent HMVEC-L

hyb_protocol: 1.65 μg of Cy3-labelled cRNA (specific activity > 6.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute with moderate stirring at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with moderate stirring at 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner C using scan one color setting  for 4x44k array slide (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and output is 20 bit TIFF).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using protocol: GE1_105_Dec08 and Grid: 014850_D_20070820.

source_name: HMVEC-L_PD < 5; treated with 20ng/ml TNF-α_replicate 3

label_protocol: Total RNAs (50ng) were labeled with Cyanine 3-CTP using Low Input Quick Amp Labeling Kit (Agilent Technologies Inc., USA) according to manufacturer’s protocol, followed by RNAeasy mini column purification (Qiagen, Germany). Dye incorporation and cRNA yield were checked with the Nanophotometer (Implen GmbH, Germany).

growth_protocol: HMVEC-L was purchased from Lonza (Walkersville, MD, USA) and maintained in Microvascular Endothelial Cell Growth Medium-2 (EGM-2MV) (Lonza), at 37oC in a humidified atmosphere of 95% air/5% CO2. Young and RS cells used in experiments are cells with PD < 5 and PD > 20 respectively.

extract_protocol: Total RNAs were isolated from cells using miRNeasy mini kit (Qiagen) according to manufacturer’s protocol. RNA was quantified using Nanophotometer (Implen GmbH, Germany). RNA integrity was accessed using Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA, USA).

treatment_protocol: TNF-α (Sigma-Aldrich, USA) was used to induce premature senescence in HMVEC-L. The cells were subjected to fifteen successive sub-lethal treatments of 20 ng/ml TNF-α in EGM-2MV containing 5% FBS, with one treatment per day for fifteen consecutive days. Control cultures were maintained in parallel without TNF-α.

value: TNFalpha

value: pulmonary microvascular


title: 11 Susan 03282013

value: skin


title: 1 Susan 03282013

value: Adult


title: SPT16-TET spt6D202-H3_dox_1

type: genomic

city: Rochester

first: Chhabi

last: Govind

state: mi

address: 333 Science and Engineering Building

department: Biological Sciences

institute: Oakland University

description: Biological Replicate-1

hyb_protocol: The samples were labeled using BioPrime Array CGH Genomic Labeling Module kit and hybridized according to the Manufacturer's recommended protocol.

scan_protocol: Agilent Technologies Scanner G2505B US45102973

data_processing: Data processed on R. Median normalization carried out.

organism: Saccharomyces cerevisiae

source_name: SPT16-TET spt6D202-H3_dox

label_protocol: The manufacturer's recommended protocol was followed.

growth_protocol: Chromatin immunoprecipitation experiments were performed as described previously (Govind et al., 2012). Briefly, 100 ml of cells (A600 = 0.6) were cross-linked with 1% formaldehyde for 15 minutes at ambient temperature and quenched with glycine. Chromatin was isolated and fragmented by sonication (Branson450) to an average size of 300-400 base pairs. The soluble fraction of chromatin was used for ChIP using the appropriate antibodies.

extract_protocol: The ChIP and Input DNA was extracted by Phenol:Chloform method after reverse-crosslinking at 65 degree C, and after proteinase K treatment. DNA was fragmented with DNase prior to labeling

treatment_protocol: The cells were grown in SC and induced for Gcn4, by treating cells grown in SC with with 0.65 µM of sulfometuron methyl (SM; Chemservice, cat# N-13254) for 20 minutes and processed for ChIP analysis. The kin28as cells were treated with 1NA-PP1 before processing for cross-linking and chromatin preparation. For depleting Spt6 or Spt16, SPT16-TET and SPT6-TET cells were cultured in the presence of 10µg/ml of doxycycline.

tag: strain background

tag: genotype/variation

tag: epitope tag or untagged genotype

value: SPT16-TET promoter /spt6∆202

tag: treated with

value: Sulfometuron methyl + doxycycline

tag: antibody used

tag: molecule subtype

value: ChIP DNA

source_name: SPT16-TET spt6D202-H3_dox_input

tag: name

value: Input genomic DNA


title: HMVEC-L_replicative senescent_rep2

description: Gene expression of replicative senescent HMVEC-L

source_name: HMVEC-L_PD > 20_replicate2

value: replicative senescent HMVEC-L


title: HMVEC-L_TNF-α-induced premature senescent_rep2

source_name: HMVEC-L_PD < 5; treated with 20ng/ml TNF-α_replicate 2

value: TNF-α-induced premature senescent HMVEC-L

tag: treatment


title: HMVEC-L_TNF-α-induced premature senescent_rep1

source_name: HMVEC-L_PD < 5; treated with 20ng/ml TNF-α_replicate 1


title: HMVEC-L_replicative senescent_rep3

source_name: HMVEC-L_PD > 20_replicate3


title: HMVEC-L_replicative senescent_rep1

source_name: HMVEC-L_PD > 20_replicate1


title: SPT16-TET spt6D202-H3_dox_2

description: Biological Replicate-2


title: HMVEC-L_young_rep1

description: Gene expression of young HMVEC-L

source_name: HMVEC-L_PD < 5_replicate 1

value: young HMVEC-L


title: SPT16-TET spt6D202-H3_ND_2

description: Biological Replicate-2

source_name: SPT16-TET spt6D202-H3_ND

value: Sulfometuron methyl

source_name: SPT16-TET spt6D202-H3_ND_input


title: SPT16-TET spt6D202-Rpb3_dox_1

description: Biological Replicate-1

source_name: SPT16-TET spt6D202-Rpb3_dox

value: Rpb3 (Neoclone:W0012)

source_name: SPT16-TET spt6D202-Rpb3_dox_input


title: SPT16-TET spt6D202-Rpb3_dox_2

description: Biological Replicate-2


title: HMVEC-L_young_rep2

description: Gene expression of young HMVEC-L

source_name: HMVEC-L_PD < 5_replicate 2


title: SPT16-TET spt6D202-Rpb3_ND_1

description: Biological Replicate-1

source_name: SPT16-TET spt6D202-Rpb3_ND

source_name: SPT16-TET spt6D202-Rpb3_ND_input


title: SPT16-TET-H3_dox_1

description: Biological Replicate-1

value: SPT16-TET promoter


title: SPT6-TET-Rpb3_dox_1

description: Biological Replicate-1

value: SPT6-TET promoter


title: SPT16-TET-Rpb3_dox_1

description: Biological Replicate-1


title: SPT6-TET-H3_dox_2

description: Biological Replicate-2


title: SPT16-TET-Rpb3_dox_2

description: Biological Replicate-2


title: SPT6-TET-Rpb3_dox_2

description: Biological Replicate-2


title: SPT6-TET-H3_dox_1

description: Biological Replicate-1


title: SPT16-TET-H3_ND_1

description: Biological Replicate-1


title: SPT16-TET spt6D202-Rpb3_ND_2

description: Biological Replicate-2


title: SPT16-TET-H3_dox_2

description: Biological Replicate-2


title: SPT16-TET spt6D202-H3_ND_1

description: Biological Replicate-1


title: SPT16-TET-H3_ND_2

description: Biological Replicate-2


title: 54 Susan 04112013

description: Gene expression data from lesional skin

value: LS

tag: age

value: F

value: Caucasian


title: kin28as_Rpb3_1

description: Biological Replicate-1

value: SPT16-Myc tagged

value: Sulfometuron methyl + 1NA-PP1


title: SPT16-TET-Rpb3_ND_2

description: Biological Replicate-2


title: kin28as_Rpb3_2

description: Biological Replicate-2


title: WT_Rpb3_2

description: Biological Replicate-2

value: WT


title: WT_Spt16-Myc_2

description: Biological Replicate-2


title: SPT16-TET-Rpb3_ND_1

description: Biological Replicate-1


title: kin28as_Spt16_2

description: Biological Replicate-2


title: WT_Rpb3_1

description: Biological Replicate-1


title: A-G TMP-009-1 LMP S06-21343

city: Toronto

first: Benjamin

last: Haibe-Kains

state: Ontario

address: 610 University Avenue

department: Princess Margaret Research

country: Canada

institute: Princess Margaret Cancer Centre

scan_protocol: Standard Illumina scanning protocol

data_processing: Data files were quantified with GenomeStudio Version 2011.1 (Illumina). Data was checked for overall quality using R (v3.0.2) with the lumi Bioconductor package. The data was imported into GeneSpring v12.6.1 (Agilent), log2 transformed and normalized using a quantile normalization.

source_name: testicular germ cell tumor (TGCT)

label_protocol: 200 ng of RNA was labelled and amplified using Illumina Whole Genome -DASL Assay kit for partially degraded and FFPE derived RNA samples.

extract_protocol: Total RNA from FFPE blocks were extracted using High Pure FFPE Micro Kit (Roche) 200 nanograms of total RNA for 59 samples were converted to cDNA using biotinylated oligo dT and random nonamer primers. Biotinylated cDNA was then annealed to oligonucleotides designed to query continuous 50nt sequences (DASL assay DAP pool) during a 16 hour temperature gradient incubation (70 -30 °C) and then bounded to streptavidin conjugated paramagnetic particles The gap between the query oligos were enzymatically extended and ligated to generate a PCR template. A pair of universal PCR primers coupled with Cy3 were used for amplification after which single stranded amplified labeled PCR product were precipitated and hybridized to 5 Human HT-12 Whole Genome expression beadchips. The Beadchips were hybridized at 58°C with rotation speed 5 for 18 hours.  After hybridization the beadchips were washed and coated as per Illumina protocol then scanned on the iScan. The data files were quantified in GenomeStudio version 2011.1. All samples passed Illumina’s sample dependent and independent controls QC metrics.

tag: relapsed (r) vs. non-relapsed (nr)

value: NR

tag: non-seminoma (ns) and seminoma (s)

value: NS


title: WT_Spt16-Myc_1

description: Biological Replicate-1

value: ChIP DNA


title: MJW TMP-013-1 St. Joseph's SP-10-05368


title: I-S TMP-007-1 LMP S10-4995


title: kin28as_Spt16_1

description: Biological Replicate-1

value: Input genomic DNA


title: R-V TMP-028-2 LMP S07-26204

value: R

value: S


title: M-G TMP-057-4 LMP S09-17085


title: B-M TMP-012-1 Lakeridge 08:S9264


title: A-T TMP-005-1 LMP S06-1629


title: B-L TMP-030-2 LMP S03-7931


title: E-K TMP-049-4 LMP S09-34996


title: S-P TMP-053-4 TEGH 08-SP-07781


title: J-A TMP-052-4 Trillium 03-S334


title: R-S TMP-040-3 St. Josephs SP-08-02449-6


title: NOP TMP-039-3 St. Mikes 08-SL-19439, 1E


title: AWD TMP-059-4 LMP S09-28327 Sample is NRS


title: DRZ TMP-029-2 LMP S10-10838


title: DW TMP-022-2 Royal Victoria Barrie S-10340-06


title: J-K TMP-045-3 LMP S06-24525


title: B-G TMP-044-3 LMP S04-28808


title: 1L Hui 04142016

description: Gene expression data from lesional skin

tag: tissue

value: skin

value: Children

value: Asian/Pacific Islander


title: R-N TMP-034-3 LMP S09-29921


title: P-H TMP-011-1 LMP S08-4908


title: BWM TMP-056-4 Peterborough 07-S009844


title: M-S TMP-037-3 St.Mikes 08-SL-14894,1G


title: AWD TMP-059-4 LMP S09-28327 Sample is NRS 1


title: K-T TMP-027-2 LMP S10-43232


title: B-A TMP-010-1 LMP S09-41460


title: M-S TMP-035-3 Joseph Brant S08-679-B3


title: G-R TMP-026-2 LMP S10-41697


title: B-P TMP-041-3 Toronto East General 07-SP-3284 ,9-07


title: J-S TMP-042-3 William Osler Health Centre S03-2516 A2


title: M-M TMP-015-1 Pembroke General PTH*10-55372


title: AMM TMP-058-4 LMP S03-12592


title: S-N TMP-025-2 LMP S07-6779


title: D-J TMP-024-2 LMP S04-17360


title: LJM TMP-050-4 LMP S10-27493


title: J-T TMP-006-1 LMP S10-33565


title: AD TMP-021-2 William Osler Health Centre S10-17008-A04


title: J-Z TMP-043-3 William Osler Health Centre S09-1701 A6


title: D-B TMP-036-3 Mount Sinai SP-07-7342


title: A-M TMP-038-3 Mount Sinai SP-09-6509


title: MDS TMP-023-2 NYGH S06-16954


title: J-R TMP-008-1 LMP S05-2637


title: J-P TMP-051-4 Halton Heathcare 09-SP3233 A5


title: G-P TMP-004-1 LMP S09-8895


title: Z-X TMP-055-4 St. Joseph's SP00-1968


title: KJW TMP-020-2 Peterborough 08-S008495 A


title: DSL TMP-054-4 TEGH TS11-813


title: DJR TMP-014-1 William Osler S10-10400


title: 59452_T1_(POOL 2+3)


title: 28474_T1_A


title: 26349_T1,2_A


title: GIST-T1

city: Worcester

first: Matthew

last: Hemming

address: 364 Plantation Street

institute: UMass Medical School

description: RNA-seq in a human GIST cell line.

data_processing:
RNA-seq data were aligned using HISAT with expression quantification using Cufflinks to generate gene expression values in FPKM units.
Genome_build: hg19
Supplementary_files_format_and_content: Processed RNA-seq data files with FPKM values are in text format

source_name: KIT-dependent GIST cell line

growth_protocol: Dulbecco’s modified Eagle’s medium containing 10% FBS, 2 mM L- glutamine, 100 mg/ml penicillin, and 100 mg/ml streptomycin

extract_protocol:
Total RNA was isolated using an RNeasy Plus Kit (Qiagen).
Libraries for Illumina NextSeq 500 sequencing were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) and equimolar multiplexed libraries were sequenced with single-end 75 bp reads.

value: KIT-dependent GIST cell line GIST-T1


title: GIST48B

description: RNA-seq in a human GIST cell line.

source_name: KIT-independent GIST cell line

value: KIT-independent GIST cell line GIST48B


title: GIST430

description: RNA-seq in a human GIST cell line.

value: KIT-dependent GIST cell line GIST430


title: PG27

description: RNA-seq in a human GIST PDX.

source_name: GIST patient derived xenograft

value: GIST patient derived xenograft PG27


title: GIST48

description: RNA-seq in a human GIST cell line.

value: KIT-dependent GIST cell line GIST48


title: GIST-1_KIT exon 11

description: RNA-seq in a human GIST tumor.

source_name: GIST Tumor

value: Gastrointestinal stromal tumor (GIST)


title: 36984_T1_A


title: 40551_T1_A


title: D-W TMP-019-2 LMP S08-33370


title: 36047_T1_A


title: 23568_T1_A


title: 20122_T1,2_A


title: 01-2873_T1_A


title: 22562_T1,2_A


title: GIST-6_KIT exon 11/16

description: RNA-seq in a human GIST tumor.


title: 32357_T1_A


title: 59926_T1,2_A


title: GIST-14_KIT exon 9

description: RNA-seq in a human GIST tumor.


title: GIST226

description: RNA-seq in a human GIST cell line.

value: KIT-independent GIST cell line GIST226


description: miRNA expression of TNF-α-induced premature senescent HMVEC-L

hyb_protocol: 18 µl nuclease free water was added to resuspend the dried Cy3-labelled RNAs. 4.5 µl of the 10x GE Blocking Agent and 22.5 µl of 2x Hi-RPM Hybridization Buffer were added to each sample and incubated 100°C for 5 minutes. 45 µl mixture was then hybridized to Agilent Human MicroRNAs Miroarrays (G4770C) for 20 hours at at 55°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minutes with moderate stirring at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with moderate stirring at 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner C using one color scan setting for the 8x15K array slides (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and output is 20 bit TIFF).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using protocol: miRNA_107_Sep09 and Grid: 021827_D_F_20110707.

source_name: HUVEC_PD < 5; treated with 20ng/ml TNF-α_replicate 1

label_protocol: Total RNAs (100ng) were labeled with Cyanine 3-pCp using miRNA Complete Labeling and Hyb Kit (Agilent Technologies Inc., USA) according to manufacturer’s protocol. After labeling, Cy3-labelled RNAs were dried completely using vacuum concentrator (Genevac, USA) at 45oC to 55oC for 2 to 3 hours.

tag: cell type

value: TNFalpha

value: pulmonary microvascular


source_name: HUVEC_PD < 5; treated with 20ng/ml TNF-α_replicate 2

value: TNF-α-induced premature senescent HMVEC-L


title: HMVEC-L_replicative senescent_rep2

description: miRNA expression of replicative senescent HMVEC-L

source_name: HUVEC_PD > 20_replicate2

value: replicative senescent HMVEC-L


title: HMVEC-L_young_rep2

description: miRNA expression of young HMVEC-L

source_name: HUVEC_PD < 5_replicate 2

value: young HMVEC-L


title: HMVEC-L_replicative senescent_rep1

source_name: HUVEC_PD > 20_replicate1


title: HMVEC-L_replicative senescent_rep3

source_name: HUVEC_PD > 20_replicate3


source_name: HUVEC_PD < 5; treated with 20ng/ml TNF-α_replicate 3


title: GIST-7_PDGFRA exon 18

description: RNA-seq in a human GIST tumor.


title: GIST-3_KIT exon 11

description: RNA-seq in a human GIST tumor.


title: GIST-15_KIT exon 11

description: RNA-seq in a human GIST tumor.


title: GIST-5_KIT exon 9

description: RNA-seq in a human GIST tumor.


title: RD_1

city: Montreal

first: Carl

last: Ernst

state: Quebec

address: 6875 Boulevard LaSalle

institute: Douglas Mental Health University Institute

data_processing:
Trimming was conducted using  the FastX toolkit version 0.0.13.2 and Trimmomatic version 0.35 using parameters “PE -phred33 ILLUMINACLIP:TruSeq3-PE.fa:3:30:9  LEADING:5  TRAILING:5  SLIDINGWINDOW:4:15 MINLEN:20”. Prinseq-lite v.0.20.3 was used to remove any poly-A tail longer than 5 bases
Tophat 2.1.0 (with parameters -p 8 --b2-sensitive --no-novel-indels) was used to align the reads to hg19 with an Ensembl77 reference for splice-junction alignment.
HTSeq-count version 0.6.1 was used to counts the number of reads mapping to each gene. Ensembl77 was used as a reference annotation
DESeq2 v1.6.3 was used to normalize the feature counts of each gene.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including DESeq2 normalized reads counts

source_name: iPSC-dervied cortical neurons

growth_protocol: iPSCs were differentiated into cortical neurons. RNA was extracted thity days after initation of differentiation of neurons from NPCs

extract_protocol:
Samples were extracted using a QIAGEN RNeasy mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CRISPR was used to induce mutations in the GRIN2B gene of non-control lines

tag: grin2b mutation

value: Frameshift in one allele

tag: cell line of origin

tag: number of passages when lysed


title: LOF_2

value: In frame deletion in glutamate binding domain


title: LOF_4


title: Control_4

value: No mutation


title: LOF_3


title: LOF_1


title: RD_2


title: HMVEC-L_young_rep1

description: miRNA expression of young HMVEC-L

source_name: HUVEC_PD < 5_replicate 1


title: GIST-9_PDGFRA exon 18

description: RNA-seq in a human GIST tumor.


title: Control_3


title: Control_2


title: Control_1


title: GIST-18_KIT exon 11

description: RNA-seq in a human GIST tumor.


title: GIST-17_KIT exon 13

description: RNA-seq in a human GIST tumor.


title: GIST-8_PDGFRA exon 18

description: RNA-seq in a human GIST tumor.


title: GIST-16_KIT exon 11/13

description: RNA-seq in a human GIST tumor.


title: GIST-13_KIT exon 9

description: RNA-seq in a human GIST tumor.


title: SW948_ITRA_3

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

data_processing:
Aligned with Tophat
Htseq-count
DESEQ
Genome_build: hg19

growth_protocol: Cells were grown in adherent culture in the presence of foetal bovine serum and antibiotics.

extract_protocol:
RNAeasy Micro (Qiagen)
Truseq (Illumina)

treatment_protocol: Cells were treated with either itraconazole (5uM) or control (DMSO)

tag: cell line

value: ITRACONAZOLE

value: colorectal cancer cell line


title: SW948_ITRA_1


title: HT55_ITRA_3


title: SW948_CONT_3

value: DMSO


title: HT55_ITRA_4


title: SW948_CONT_2


title: SW948_ITRA_4


title: SW948_CONT_4


title: SW948_CONT_1


title: HT55_CONT_3


title: HT55_ITRA_2


title: HT55_ITRA_1


title: HT55_CONT_4


title: HT55_CONT_2


title: GIST-12_SDHC deletion_H3K27Ac

data_processing:
All Chip-Seq data were aligned to the human reference genome assembly hg19, GRCh37 (ncbi.nlm.nih.gov/assembly/2758/) using Bowtie2 (version 2.2.1), and gene annotations by gencode annotation release 19 (gencodegenes.org/releases/19.html)
Normalized read density was calculated using Bamliquidator (version 1.0) read density calculator. Aligned reads were extended by 200 bp and the density of reads per base pair was calculated. In each region, the density of reads was normalized to the total number of million mapped reads, generating read density in units of reads per million mapped reads per bp (rpm/bp).
Peak finding was performed using Model-based Analysis for ChIP-Seq (MACS, version 1.4.2). As control, matched input chromatin was used to generate background signal for peak determination.
Genome_build: hg19
Supplementary_files_format_and_content: Processed ChIP-Seq data files are in wiggle format

source_name: GIST tumor

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries for single-end 75 bp sequencing on an Illumina NextSeq 500 were prepared with a ThruPLEX DNA-seq Kit (Rubicon) for ChIP-seq or Nextera DNA Preparation Kit (Illumina) for ATAC-seq.

tag: chip antibody

value: H3K27ac, Abcam ab4729


title: GIST-T1_HAND1

value: Gastrointestinal stromal tumor (GIST) cell line

value: HAND1, Origene, OTI1G10


title: GIST-T1_ETV1

value: ETV1, Abcam, ab81086


title: GIST-11_SDHC deletion_H3K27Ac

value: Gastrointestinal stromal tumor (GIST)


title: GIST-12_SDHC deletion_input


title: GIST-T1_ETV1_input


title: GIST-11_SDHC deletion_input


title: GIST-10_PDGFRA e1_input


title: HT55_CONT_1


title: SW948_ITRA_2


title: GIST-T1_HAND1_input


title: EXP_SW948_4_LRC_47

growth_protocol: Cell lines were grown in non-adherent spheroid culture in the presence of bFGF and EGF.

tag: control treatment

tag: dormant (lrc) or cycling (bulk)

value: LRC


title: EXP_SW948_4_BULK_48

value: BULK


title: GIST-10_PDGFRA e1_H3K27Ac


title: GIST-9_PDGFRA e18_input


title: EXP_SW948_3_BULK_46


title: EXP_SW948_2_BULK_44


title: GIST-6_KIT e11/16_H3K27Ac


title: GIST-8_PDGFRA e18_H3K27Ac


title: EXP_SW948_3_LRC_45


title: GIST-6_KIT e11/16_input


title: GIST-8_PDGFRA e18_input


title: GIST-9_PDGFRA e18_H3K27Ac


title: GIST-7_PDGFRA e18_input


title: EXP_SW48_4_LRC_23


title: EXP_SW948_1_BULK_42


title: GIST-3_KIT e11_H3K27Ac


title: EXP_SW48_3_BULK_22


title: EXP_SW48_2_LRC_19


title: EXP_SW48_1_LRC_17


title: GIST-4_KIT e9_H3K27Ac


title: GIST-3_KIT e11_input


title: EXP_SW948_1_LRC_41


title: GIST-5_KIT e9_H3K27Ac


title: GIST-4_KIT e9_input


title: EXP_RKO_4_LRC_15

source_name: RKO

value: RKO


title: EXP_SW948_2_LRC_43


title: EXP_SW48_1_BULK_18


title: GIST-7_PDGFRA e18_H3K27Ac


title: GIST-2_KIT e11_H3K27Ac


title: GIST-5_KIT e9_input


title: EXP_SW48_3_LRC_21


title: EXP_SW48_4_BULK_24


title: GIST-1_KIT e11_H3K27Ac


title: EXP_SW48_2_BULK_20


title: EXP_RKO_3_LRC_13