title: Whole blood from rheumatoid arthritis(K6149_2)

description: Whole blood transcriptome from rheumatoid arthritis(K6149_2)

tag: haq


title: Whole blood from rheumatoid arthritis(K6221_2)

status: Public on Jul 16 2018

type: RNA

city: Fujisawa

first: Shinya

last: Tasaki

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-chome

country: Japan

institute: Takeda Pharmaceutical Company Limited

description: Whole blood transcriptome from rheumatoid arthritis(K6221_2)

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 18 hr at 45C on Human Genome U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetryx GeneChip Scanner 3000.

data_processing: The data were analyzed with the frozen robust multiarray analysis (fRMA) using Bioconductor with default settings and absence/presence calls were estimated by Microarray Suite version 5.0 (MAS 5.0).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood from rheumatoid arthritis

label_protocol: Biotinylated cDNA were prepared using NuGEN Encore Biotin Module from 5ug of amplified cDNA.

extract_protocol: Total  RNA was isolated with  the  PAXgeneTM  Blood  RNA Kit  (Qiagen,  Valencia,   CA,  USA) after  freezing and  storage. The  Ambion  GLOBINclearTM  (Ambion,  Austin  TX, USA) was applied to  total  RNA samples to remove globin transcripts.

treatment_protocol: Blood  samples were collected from healthy  and  RA  human  donors in  PAXGene tubes.

tag: individual id

tag: disease state

value: RA

tag: tissue

value: whole blood

tag: batch

tag: rin

tag: age

tag: gender

value: F

tag: cdai

tag: kowabari

tag: crp

tag: esr

tag: acr

tag: sdai

tag: rf

tag: ccp

tag: ana


title: Whole blood from rheumatoid arthritis(K6147_2)

description: Whole blood transcriptome from rheumatoid arthritis(K6147_2)

tag: haq


title: Whole blood from rheumatoid arthritis(K5776_2)

description: Whole blood transcriptome from rheumatoid arthritis(K5776_2)

tag: individual id


title: Whole blood from rheumatoid arthritis(K5715_2)

description: Whole blood transcriptome from rheumatoid arthritis(K5715_2)

tag: disease state


title: Whole blood from rheumatoid arthritis(K5713_2)

description: Whole blood transcriptome from rheumatoid arthritis(K5713_2)

tag: tissue


title: Whole blood from rheumatoid arthritis(K5703_2)

description: Whole blood transcriptome from rheumatoid arthritis(K5703_2)

tag: batch


title: Whole blood from rheumatoid arthritis(K6146_2)

description: Whole blood transcriptome from rheumatoid arthritis(K6146_2)

tag: rin


title: Whole blood from rheumatoid arthritis(K5692_2)

description: Whole blood transcriptome from rheumatoid arthritis(K5692_2)

tag: age


title: Whole blood from rheumatoid arthritis(K5327_2)

description: Whole blood transcriptome from rheumatoid arthritis(K5327_2)

tag: gender


title: Whole blood from rheumatoid arthritis(K5954_2)

description: Whole blood transcriptome from rheumatoid arthritis(K5954_2)

tag: cdai


title: Whole blood from rheumatoid arthritis(K5594_2)

description: Whole blood transcriptome from rheumatoid arthritis(K5594_2)

tag: kowabari


title: Whole blood from rheumatoid arthritis(K5354_2)

description: Whole blood transcriptome from rheumatoid arthritis(K5354_2)

tag: crp


title: Whole blood from rheumatoid arthritis(K5278_2)

description: Whole blood transcriptome from rheumatoid arthritis(K5278_2)

tag: esr


title: Whole blood from rheumatoid arthritis(K5779_2)

description: Whole blood transcriptome from rheumatoid arthritis(K5779_2)

tag: acr


title: Whole blood from rheumatoid arthritis(K5495_2)

description: Whole blood transcriptome from rheumatoid arthritis(K5495_2)

tag: sdai


title: Whole blood from rheumatoid arthritis(K5214_2)

description: Whole blood transcriptome from rheumatoid arthritis(K5214_2)

value: M

tag: rf


title: Whole blood from rheumatoid arthritis(K5188_2)

description: Whole blood transcriptome from rheumatoid arthritis(K5188_2)

tag: ccp


title: Whole blood from rheumatoid arthritis(K5326_2)

description: Whole blood transcriptome from rheumatoid arthritis(K5326_2)

tag: ana


title: Whole blood from rheumatoid arthritis(K5260_2)

description: Whole blood transcriptome from rheumatoid arthritis(K5260_2)

tag: haq


title: Whole blood from rheumatoid arthritis(K4679_2)

description: Whole blood transcriptome from rheumatoid arthritis(K4679_2)

tag: individual id


title: Whole blood from rheumatoid arthritis(K5112_2)

description: Whole blood transcriptome from rheumatoid arthritis(K5112_2)

tag: disease state


title: Whole blood from rheumatoid arthritis(K5352_2)

description: Whole blood transcriptome from rheumatoid arthritis(K5352_2)

tag: tissue


title: Whole blood from rheumatoid arthritis(K5005_2)

description: Whole blood transcriptome from rheumatoid arthritis(K5005_2)

tag: batch


title: Whole blood from rheumatoid arthritis(K4491_2)

description: Whole blood transcriptome from rheumatoid arthritis(K4491_2)

tag: rin


title: Whole blood from rheumatoid arthritis(K4499_2)

description: Whole blood transcriptome from rheumatoid arthritis(K4499_2)

tag: age


title: Whole blood from rheumatoid arthritis(K5110_2)

description: Whole blood transcriptome from rheumatoid arthritis(K5110_2)

tag: gender


title: Whole blood from rheumatoid arthritis(K4214_2)

description: Whole blood transcriptome from rheumatoid arthritis(K4214_2)

tag: cdai


title: Whole blood from rheumatoid arthritis(K4878_2)

description: Whole blood transcriptome from rheumatoid arthritis(K4878_2)

tag: kowabari


title: Whole blood from rheumatoid arthritis(K4493_2)

description: Whole blood transcriptome from rheumatoid arthritis(K4493_2)

tag: crp


title: Whole blood from rheumatoid arthritis(K4450_2)

description: Whole blood transcriptome from rheumatoid arthritis(K4450_2)

tag: esr


title: Whole blood from rheumatoid arthritis(K4309_2)

description: Whole blood transcriptome from rheumatoid arthritis(K4309_2)

tag: acr


title: Whole blood from rheumatoid arthritis(K4311_2)

description: Whole blood transcriptome from rheumatoid arthritis(K4311_2)

tag: sdai


title: Whole blood from rheumatoid arthritis(K5001_2)

description: Whole blood transcriptome from rheumatoid arthritis(K5001_2)

tag: rf


title: Whole blood from rheumatoid arthritis(K5002_2)

description: Whole blood transcriptome from rheumatoid arthritis(K5002_2)

tag: ccp


title: Whole blood from rheumatoid arthritis(K4223_2)

description: Whole blood transcriptome from rheumatoid arthritis(K4223_2)

tag: ana


title: Whole blood from rheumatoid arthritis(K4136_2)

description: Whole blood transcriptome from rheumatoid arthritis(K4136_2)

tag: haq


title: Whole blood from rheumatoid arthritis(K4492_2)

description: Whole blood transcriptome from rheumatoid arthritis(K4492_2)

tag: individual id


title: Whole blood from rheumatoid arthritis(K4445_2)

description: Whole blood transcriptome from rheumatoid arthritis(K4445_2)

tag: disease state


title: Whole blood from rheumatoid arthritis(K4115_2)

description: Whole blood transcriptome from rheumatoid arthritis(K4115_2)

tag: tissue


title: Whole blood from rheumatoid arthritis(K4112_2)

description: Whole blood transcriptome from rheumatoid arthritis(K4112_2)

tag: batch


title: Whole blood from rheumatoid arthritis(K5003_2)

description: Whole blood transcriptome from rheumatoid arthritis(K5003_2)

tag: rin


title: Whole blood from rheumatoid arthritis(K4168_2)

description: Whole blood transcriptome from rheumatoid arthritis(K4168_2)

tag: age


title: Whole blood from rheumatoid arthritis(K3944_2)

description: Whole blood transcriptome from rheumatoid arthritis(K3944_2)

tag: gender


title: Whole blood from rheumatoid arthritis(K3992_2)

description: Whole blood transcriptome from rheumatoid arthritis(K3992_2)

tag: cdai


title: Whole blood from rheumatoid arthritis(K3898_2)

description: Whole blood transcriptome from rheumatoid arthritis(K3898_2)

tag: kowabari


title: Whole blood from rheumatoid arthritis(K3397_2)

description: Whole blood transcriptome from rheumatoid arthritis(K3397_2)

tag: crp


title: Whole blood from rheumatoid arthritis(K3773_2)

description: Whole blood transcriptome from rheumatoid arthritis(K3773_2)

tag: esr


title: Whole blood from rheumatoid arthritis(K3418_2)

description: Whole blood transcriptome from rheumatoid arthritis(K3418_2)

tag: acr


title: Whole blood from rheumatoid arthritis(K3647_2)

description: Whole blood transcriptome from rheumatoid arthritis(K3647_2)

tag: sdai


title: Whole blood from rheumatoid arthritis(K3792_2)

description: Whole blood transcriptome from rheumatoid arthritis(K3792_2)

tag: rf


title: Whole blood from rheumatoid arthritis(K3399_2)

description: Whole blood transcriptome from rheumatoid arthritis(K3399_2)

tag: ccp


title: Whole blood from rheumatoid arthritis(K3174_2)

description: Whole blood transcriptome from rheumatoid arthritis(K3174_2)

tag: ana


title: Whole blood from rheumatoid arthritis(K3791_2)

description: Whole blood transcriptome from rheumatoid arthritis(K3791_2)

tag: haq


title: Whole blood from rheumatoid arthritis(K2999_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2999_2)

tag: individual id


title: Whole blood from rheumatoid arthritis(K3259_2)

description: Whole blood transcriptome from rheumatoid arthritis(K3259_2)

tag: disease state


title: Whole blood from rheumatoid arthritis(K3262_2)

description: Whole blood transcriptome from rheumatoid arthritis(K3262_2)

tag: tissue


title: Whole blood from rheumatoid arthritis(K2816_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2816_2)

tag: batch


title: Whole blood from rheumatoid arthritis(K3264_2)

description: Whole blood transcriptome from rheumatoid arthritis(K3264_2)

tag: rin


title: Whole blood from rheumatoid arthritis(K2995_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2995_2)

tag: age


title: Whole blood from rheumatoid arthritis(K3203_2)

description: Whole blood transcriptome from rheumatoid arthritis(K3203_2)

tag: gender


title: Whole blood from rheumatoid arthritis(K3790_2)

description: Whole blood transcriptome from rheumatoid arthritis(K3790_2)

tag: cdai


title: Whole blood from rheumatoid arthritis(K2695_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2695_2)

tag: kowabari


title: Whole blood from rheumatoid arthritis(K2974_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2974_2)

tag: crp


title: Whole blood from rheumatoid arthritis(K3658_2)

description: Whole blood transcriptome from rheumatoid arthritis(K3658_2)

tag: esr


title: Whole blood from rheumatoid arthritis(K2934_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2934_2)

tag: acr


title: Whole blood from rheumatoid arthritis(K2830_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2830_2)

tag: sdai


title: Whole blood from rheumatoid arthritis(K2996_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2996_2)

tag: rf


title: Whole blood from rheumatoid arthritis(K2933_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2933_2)

tag: ccp


title: Whole blood from rheumatoid arthritis(K2998_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2998_2)

tag: ana


title: Whole blood from rheumatoid arthritis(K3235_2)

description: Whole blood transcriptome from rheumatoid arthritis(K3235_2)

tag: haq


title: Whole blood from rheumatoid arthritis(K2537_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2537_2)

tag: individual id


title: Whole blood from rheumatoid arthritis(K2675_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2675_2)

tag: disease state


title: Whole blood from rheumatoid arthritis(K2101_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2101_2)

tag: tissue


title: Whole blood from rheumatoid arthritis(K2676_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2676_2)

tag: batch


title: Whole blood from rheumatoid arthritis(K2177_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2177_2)

tag: rin


title: Whole blood from rheumatoid arthritis(K2515_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2515_2)

tag: age


title: Whole blood from rheumatoid arthritis(K2641_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2641_2)

tag: gender


title: Whole blood from rheumatoid arthritis(K2223_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2223_2)

tag: cdai


title: Whole blood from rheumatoid arthritis(K2709_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2709_2)

tag: kowabari


title: Whole blood from rheumatoid arthritis(K2644_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2644_2)

tag: crp


title: Whole blood from rheumatoid arthritis(K1835_2)

description: Whole blood transcriptome from rheumatoid arthritis(K1835_2)

tag: esr


title: Whole blood from rheumatoid arthritis(K2225_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2225_2)

tag: acr


title: Whole blood from rheumatoid arthritis(K2359_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2359_2)

tag: sdai


title: Whole blood from rheumatoid arthritis(K2253_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2253_2)

tag: rf


title: Whole blood from rheumatoid arthritis(K2638_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2638_2)

tag: ccp


title: Whole blood from rheumatoid arthritis(K1837_2)

description: Whole blood transcriptome from rheumatoid arthritis(K1837_2)

tag: ana


title: Whole blood from rheumatoid arthritis(K2250_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2250_2)

tag: haq


title: Whole blood from rheumatoid arthritis(K2631_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2631_2)

tag: individual id


title: Whole blood from rheumatoid arthritis(K2534_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2534_2)

tag: disease state


title: Whole blood from rheumatoid arthritis(K2224_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2224_2)

tag: tissue


title: Whole blood from rheumatoid arthritis(K2178_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2178_2)

tag: batch


title: Whole blood from rheumatoid arthritis(K1751_2)

description: Whole blood transcriptome from rheumatoid arthritis(K1751_2)

tag: rin


title: Whole blood from rheumatoid arthritis(K1395_2)

description: Whole blood transcriptome from rheumatoid arthritis(K1395_2)

tag: age


title: Whole blood from rheumatoid arthritis(K1340_2)

description: Whole blood transcriptome from rheumatoid arthritis(K1340_2)

tag: gender


title: Whole blood from rheumatoid arthritis(K1338_2)

description: Whole blood transcriptome from rheumatoid arthritis(K1338_2)

tag: cdai


title: Whole blood from rheumatoid arthritis(K1780_2)

description: Whole blood transcriptome from rheumatoid arthritis(K1780_2)

tag: kowabari


title: Whole blood from rheumatoid arthritis(K2103_2)

description: Whole blood transcriptome from rheumatoid arthritis(K2103_2)

tag: crp


title: 5 days post gentamycin- atoh1 treated rep 2

type: SRA

city: London

first: Michael

last: Lovett

address: National Heart & Lung Institute, Guy Scadding Building

country: United Kingdom

institute: Imperial College London

library_source: transcriptomic

data_processing:
Illumina Casava software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using tophat v.2.1.1
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using  Cufflinks v2.1 using ensembl87 annotations
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for all samples

source_name: utricle

extract_protocol:
Zymo Research Quick-RNA™ MicroPrep protocol
Illumina Truseq Stranded mRNA Library Prep protocol according to manufacturer's guidelines

tag: treatment

value: 5 days post gentamycin- atoh1

value: utricle


title: Whole blood from rheumatoid arthritis(K1630_2)

description: Whole blood transcriptome from rheumatoid arthritis(K1630_2)

tag: esr

tag: acr


title: 5 days post gentamycin- atoh1 treated rep 1


title: 8 days post gentamycin-control

value: 8 days post gentamycin-control


title: Whole blood from rheumatoid arthritis(K1394_2)

description: Whole blood transcriptome from rheumatoid arthritis(K1394_2)

tag: sdai

tag: rf


title: untreated_2

value: untreated


title: Whole blood from rheumatoid arthritis(K1139_2)

description: Whole blood transcriptome from rheumatoid arthritis(K1139_2)

tag: ccp

tag: ana


title: untreated_1


title: untreated_3


title: 14 days post gentamycin-control

value: 14 days post gentamycin-control


title: 2 days post gentamycin-control

value: 2 days post gentamycin-control


title: Whole blood from rheumatoid arthritis(K1129_2)

description: Whole blood transcriptome from rheumatoid arthritis(K1129_2)

tag: individual id

tag: haq


title: Whole blood from rheumatoid arthritis(K1164_2)

description: Whole blood transcriptome from rheumatoid arthritis(K1164_2)

tag: disease state

tag: tissue


title: HaCaT_entinostat_WGBS_rep_4

city: Cambridge

first: Avazeh

middle: T

last: Ghanbarian

address: Robinson Way

department: Cancer Research UK, Cambridge Inst

institute: University of Cambridge

library_source: genomic

data_processing:
The data was processed as described in the associated manuscript. Details about the analysis have previously been described at https://github.com/sblab-bioinformatics/dna-secondary-struct-chrom-lands/blob/master/Methods.md.
Genome_build: hg19
Supplementary_files_format_and_content: For narrowPeak format see MACS2 documentation at https://github.com/taoliu/MACS/.

molecule: genomic DNA

source_name: HaCaT cell line

growth_protocol: K562 cells were cultured in RPMI-1640 medium supplemented with 10%FBS and 100 U/ml penicillin-streptomycin (life technologies).

extract_protocol:
Chromatin was isolated from K562 cells that were cross-linked using 1% formaldehyde for 10 min at RT and prepared using a ChIP-qPCR Kit (Chromatrap, cat. no. 500117). Chromatin was sonicated using a Bioruptor Plus (Diagenode) to give a fragment distribution of 100-500 bp. WGBS was performed using Pico Methyl-seq kit from Zymo Research.
G4 ChIPed DNA was subjected to Nextera library preparation (Illumina, cat. no. FC-121-1030). For further details see methods section in the associated manuscript.

treatment_protocol: HaCaT cells were treated with 10 uM entinostat for 48 hours.

tag: cell line

value: HaCaT

value: entinostat


title: 18 days post gentamycin-control

value: 18 days post gentamycin-control


title: Whole blood from rheumatoid arthritis(K4109_2)

description: Whole blood transcriptome from rheumatoid arthritis(K4109_2)

tag: batch

tag: rin

tag: age


title: HaCaT_entinostat_WGBS_rep_3


title: HaCaT_entinostat_WGBS_rep_2


title: Whole blood from healthy control(HC034_2)

description: Whole blood transcriptome from healthy control(HC034_2)

source_name: Whole blood from healthy control

value: healthy control

tag: gender

tag: cdai

tag: kowabari


title: HaCaT_WGBS_rep_4

tag: treatment

value: control


title: HaCaT_WGBS_rep_2


title: HaCaT_WGBS_rep_3


title: HaCaT_WGBS_rep_1


title: Whole blood from rheumatoid arthritis(K1138_2)

description: Whole blood transcriptome from rheumatoid arthritis(K1138_2)

tag: crp

tag: esr

tag: acr


title: Whole blood from rheumatoid arthritis(K1102_2)

description: Whole blood transcriptome from rheumatoid arthritis(K1102_2)

tag: sdai

tag: rf

tag: ccp


title: HaCaT_entinostat_WGBS_rep_1


title: Whole blood from healthy control(HC036_2)

description: Whole blood transcriptome from healthy control(HC036_2)

tag: individual id

tag: haq

tag: ana


title: Whole blood from healthy control(HC005_2)

description: Whole blood transcriptome from healthy control(HC005_2)

tag: disease state

tag: tissue


title: Whole blood from healthy control(HC025_2)

description: Whole blood transcriptome from healthy control(HC025_2)

tag: batch

tag: rin


title: Whole blood from healthy control(HC008_2)

description: Whole blood transcriptome from healthy control(HC008_2)

tag: age

tag: gender


title: EBC_1_RCRIZ_rep1

city: Candiolo

first: Davide

last: Cora'

state: TO

department: Dept. of Oncology

country: Italy

institute: Piemonte Orientale University and IRCCS Candiolo Cancer Institute

description:
EBCRES-1
Lung squamous cell carcinoma cell line rendered resistant in vitro to 150nM Crizotinib

data_processing:
Base calling was performed by using the BCL to FASTQ file converter program (bcl2fastq).
The Bowtie program was used to align reads to the reference human hg19 genome
Gene annotations provided by Ensembl GRCh37, version 84 (GENECODE 19) were set as reference for the RSEM computational pipeline  (Li et al., BMC Bioinformatics 2011) used for quantification of gene expression levels.
Genome_build: GRCh37 / hg19
Supplementary_files_format_and_content: TAB-delimited text providing RSEM_expected_counts for all the samples.

extract_protocol:
RNA was extracted from subconfluent GTL16 and EBC-1 (wt and R-CRIZ) cells using miRNeasy Mini Kit (Qiagen #217004) according to manufacturer's instructions.
For the RNA-Seq library construction, the Illumina "TruSeq mRNA stranded kit" (code RS-122-2101) was used, with 1000ng of input RNA. Initial RNA quality was assessed by means of Agilent Bioanalyzer (RNA 6000 Nano kit, Agilent code 5067-1511) and the corresponding concentration with Qubit (RNA BR Assay kit code Q10210). Library quality was then assessed by Bioanalyzer using DNA HS kit by Agilent (code 5067-4626) and libraries quantified by Qubit with DNA kit HS code Q32851. All libraries were subsequently normalized to 10nM with TrisHC and then pooled. Finally, 1.8pM of the pooled RNA was loaded into an Illumina NextSeq 500.

tag: cell line

value: skin metastasis of lung carcinoma

value: Resistant in vitro to 150nM Crizotinib, replicate_1


title: GTL16_RCRIZ_rep1

description:
GTL16RES-1
Gastric cancer cell line isolated by clonal selection of MKN45 cell line rendered resistant in vitro to 200nM Crizotinib
GTL16 cells are an historical clone of MKN45. PMID: 3211149, 19074879

value: liver metastasis of gastric adenocarcinoma

value: Resistant in vitro to 200nM Crizotinib, replicate_1


title: GTL16_WT_rep2

description:
GTL16WT-2
Gastric cancer cell line isolated by clonal selection of MKN45 cell line
GTL16 cells are an historical clone of MKN45. PMID: 3211149, 19074879

value: WT, replicate_2


title: GTL16_RCRIZ_rep2

description:
GTL16RES-2
Gastric cancer cell line isolated by clonal selection of MKN45 cell line rendered resistant in vitro to 200nM Crizotinib
GTL16 cells are an historical clone of MKN45. PMID: 3211149, 19074879

value: Resistant in vitro to 200nM Crizotinib, replicate_2


title: GTL16_WT_rep1

description:
GTL16WT-1
Gastric cancer cell line isolated by clonal selection of MKN45 cell line
GTL16 cells are an historical clone of MKN45. PMID: 3211149, 19074879

value: WT, replicate_1


title: EBC_1_WT_rep1

description:
EBCWT-1
Lung squamous cell carcinoma cell line

source_name: Lung squamous cell carcinoma cell line


title: EBC_1_WT_rep2

description:
EBCWT-2
Lung squamous cell carcinoma cell line


title: EBC_1_RCRIZ_rep2

description:
EBCRES-2
Lung squamous cell carcinoma cell line rendered resistant in vitro to 150nM Crizotinib

value: Resistant in vitro to 150nM Crizotinib, replicate_2


title: Whole blood from healthy control(BA_2)

description: Whole blood transcriptome from healthy control(BA_2)

value: whole blood

value: M

tag: cdai

tag: kowabari


title: Whole blood from healthy control(AU_2)

description: Whole blood transcriptome from healthy control(AU_2)

tag: crp

tag: esr


title: Whole blood from healthy control(AY_2)

description: Whole blood transcriptome from healthy control(AY_2)

tag: acr

tag: sdai


title: Whole blood from rheumatoid arthritis(K7718_1)

description: Whole blood transcriptome from rheumatoid arthritis(K7718_1)

value: RA

value: F

tag: rf

tag: ccp


title: Whole blood from healthy control(HC026_2)

description: Whole blood transcriptome from healthy control(HC026_2)

tag: individual id

tag: haq


title: Whole blood from rheumatoid arthritis(K7898_1)

description: Whole blood transcriptome from rheumatoid arthritis(K7898_1)

tag: disease state

tag: ana


title: Whole blood from rheumatoid arthritis(K9617_1)

description: Whole blood transcriptome from rheumatoid arthritis(K9617_1)

tag: tissue

tag: batch


title: Whole blood from healthy control(HC003_2)

description: Whole blood transcriptome from healthy control(HC003_2)

tag: rin

tag: age


title: Whole blood from rheumatoid arthritis(K9963_1)

description: Whole blood transcriptome from rheumatoid arthritis(K9963_1)

tag: gender


title: Whole blood from rheumatoid arthritis(K7155_1)

description: Whole blood transcriptome from rheumatoid arthritis(K7155_1)

tag: cdai


title: Whole blood from healthy control(BB_2)

description: Whole blood transcriptome from healthy control(BB_2)

tag: kowabari


title: Whole blood from rheumatoid arthritis(K8815_1)

description: Whole blood transcriptome from rheumatoid arthritis(K8815_1)

tag: crp


title: Whole blood from healthy control(HC023_2)

description: Whole blood transcriptome from healthy control(HC023_2)

tag: esr


title: Whole blood from rheumatoid arthritis(K9538_1)

description: Whole blood transcriptome from rheumatoid arthritis(K9538_1)

tag: acr


title: Whole blood from rheumatoid arthritis(K9765_1)

description: Whole blood transcriptome from rheumatoid arthritis(K9765_1)

tag: sdai


title: Whole blood from rheumatoid arthritis(K7142_1)

description: Whole blood transcriptome from rheumatoid arthritis(K7142_1)

tag: rf


title: Whole blood from healthy control(AW_2)

description: Whole blood transcriptome from healthy control(AW_2)

tag: ccp


title: Whole blood from rheumatoid arthritis(K6691_1)

description: Whole blood transcriptome from rheumatoid arthritis(K6691_1)

tag: individual id


title: Whole blood from rheumatoid arthritis(K9452_1)

description: Whole blood transcriptome from rheumatoid arthritis(K9452_1)

tag: haq


title: BAR1_HU

city: Amsterdam

first: Tessy

last: Korthout

state: Noord-Holland

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: The Netherlands Cancer Institute

data_processing:
Reads were aligned to the Saccharomyces cerevisiae reference genome version R64 with bowtie.
Aligned BAM files were converted to bedgraph files by using DeepTools
bedgraph files were used to plot DNA coverage
Genome_build: R64-1-1 S288C reference genome assembly (SacCer3)
Supplementary_files_format_and_content: bedgraph files to plot DNA coverage

organism: Saccharomyces cerevisiae

source_name: Epi-decoder library

growth_protocol: Grown in YEPD to OD660 0.4

extract_protocol:
Cells were lysed by bead beating and purified with an Isolate II genomic DNA kit (Bioline) and sheared with an E220 ultrasonicator (Covaris).
Libraries were prepared using the KAPA HTP Library Preparation Kit (Illumina), using Illumina-provided adapters at 200nM. After eleven PCR cycles, cleanup and pooling was as described above. After 11 PCR cycles, a size selection cleanup was performed using 0.5X Agencourt AMPure XP PCR Purification beads to get rid of large fragments due to crosslinking DNA. The supernatant of the 0.5X cleanup was used to catch the smaller fragments; this supernatant was cleaned up 2 times with 1X beads to remove primers present in the libraries.

treatment_protocol: 180 mM hydroxyurea

tag: strain

value: WT (BAR1-TAP)

tag: treatment

value: hydroxyurea


title: RPO21_UN

value: WT (RPO21-TAP)

value: untreated


title: 60.St. Olav176.nIND.HUS

city: Trondheim

first: Christina

middle: Gabrielsen

last: Aas

address: Erling Skjalgssons gt 1

department: Dept. of Medical Microbiology

country: Norway

institute: St. Olavs University Hospital

data_processing:
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor).
Lowly expressed genes (<1 read per million) were removed.
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor)
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files

organism: Escherichia coli

source_name: E. coli strain St. Olav176

growth_protocol: Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3.

extract_protocol:
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre).
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina).

treatment_protocol: The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C.

value: St. Olav176

tag: group (hus/non-hus)

value: HUS

tag: induced/non-induced

value: Non-induced

tag: genome accession


title: Whole blood from rheumatoid arthritis(K6755_1)

description: Whole blood transcriptome from rheumatoid arthritis(K6755_1)

tag: disease state

tag: tissue

tag: batch

tag: rin

tag: age

tag: ana


title: RPO21_HU


title: 58.St. Olav173.nIND.nHUS

source_name: E. coli strain St. Olav173

value: St. Olav173

value: Non-HUS


title: 59.St. Olav173.IND.nHUS

value: Induced


title: BAR1_UN


title: 56.St. Olav176.IND.HUS


title: 57.St. Olav39.nIND.nHUS

source_name: E. coli strain St. Olav39

value: St. Olav39


title: 54.St. Olav164 .nIND.HUS

source_name: E. coli strain St. Olav164

value: St. Olav164


title: 55.St. Olav164 .IND.HUS


title: 52.St. Olav63.nIND.nHUS

source_name: E. coli strain St. Olav63

value: St. Olav63


title: 53.St. Olav63.IND.nHUS


title: 51.St. Olav39.IND.nHUS


title: 48.FHI83.IND.HUS

source_name: E. coli strain FHI83


title: 49.St. Olav17.nIND.nHUS

source_name: E. coli strain St. Olav17

value: St. Olav17


title: 46.FHI66.IND.nHUS

source_name: E. coli strain FHI66


title: Whole blood from rheumatoid arthritis(K6255_1)

description: Whole blood transcriptome from rheumatoid arthritis(K6255_1)

value: whole blood

tag: gender

tag: cdai

tag: kowabari

tag: crp

tag: esr

tag: acr


title: 50.St. Olav17.IND.nHUS

tag: strain


title: Whole blood from rheumatoid arthritis(K6146_1)

description: Whole blood transcriptome from rheumatoid arthritis(K6146_1)

tag: individual id

value: RA

tag: haq

tag: sdai

tag: rf

tag: ccp


title: 47.FHI83.nIND.HUS

tag: group (hus/non-hus)

tag: induced/non-induced

tag: genome accession


title: Whole blood from rheumatoid arthritis(K5276_1)

description: Whole blood transcriptome from rheumatoid arthritis(K5276_1)

tag: disease state

tag: tissue

tag: batch

tag: rin

tag: age

value: F


title: Whole blood from rheumatoid arthritis(K4498_1)

description: Whole blood transcriptome from rheumatoid arthritis(K4498_1)

tag: gender

tag: cdai

tag: kowabari

tag: crp

tag: ana


title: 6-48 control_18240

city: Taipei

first: Ting-Shuan

last: Wu

address: 5F ,No 1, Sec 1, Jen-Ai Rd

country: Taiwan

institute: ntu

hyb_protocol: 1.65 mg of Cy3-labled cRNA is then pooled and hybridized to Agilent Zebrafish V3 array 4´44K Microarray (Agilent Technologies, USA) at 65℃ for 17h.

scan_protocol: After washing and drying by nitrogen fun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535nm for Cy3.

data_processing: The scanned images were analyzed with Feature Extraction 10.5.1.1 Software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.

organism: Danio rerio

source_name: embryos

label_protocol: 0.2 mg of total RNA was amplified by a low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Vy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

growth_protocol: zebrafish embryos were selected at 6 hph with normal development.

extract_protocol: Total RNA was extracted by Trizol® Reagent (Invitrogen, USA) according to the instruction manual. RNA purified was quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology, USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 labchip kit (Agilent Technologies, USA).

treatment_protocol: 6 hpf embryos  were treated with ochratoxin A (0.5 µM) till 48 hpf.

tag: developemental stage

value: 6 hpf embryos

tag: exposed to

value: none (control)


title: Whole blood from rheumatoid arthritis(K4172_1)

description: Whole blood transcriptome from rheumatoid arthritis(K4172_1)

tag: individual id

tag: haq

tag: esr

tag: acr

tag: sdai

tag: rf


title: Whole blood from rheumatoid arthritis(K4271_1)

description: Whole blood transcriptome from rheumatoid arthritis(K4271_1)

tag: disease state

tag: tissue

tag: ccp


title: 6-48 0.5mM OTA_18238

value: 0.5 µM ochratoxin A from 6 hpf to 48 hpf


title: Whole blood from rheumatoid arthritis(K3572_1)

description: Whole blood transcriptome from rheumatoid arthritis(K3572_1)

tag: batch

tag: rin

tag: age


title: Whole blood from rheumatoid arthritis(K4578_1)

description: Whole blood transcriptome from rheumatoid arthritis(K4578_1)

tag: gender

tag: cdai

tag: kowabari


title: Whole blood from rheumatoid arthritis(K3259_1)

description: Whole blood transcriptome from rheumatoid arthritis(K3259_1)

value: M

tag: crp

tag: ana


title: 36.St. Olav172.IND.nHUS

source_name: E. coli strain St. Olav172

tag: strain

value: St. Olav172

tag: group (hus/non-hus)

tag: induced/non-induced

tag: genome accession


title: 45.FHI66.nIND.nHUS


title: 40.St. Olav178.IND.nHUS

source_name: E. coli strain St. Olav178

value: St. Olav178


title: Whole blood from rheumatoid arthritis(K2100_1)

description: Whole blood transcriptome from rheumatoid arthritis(K2100_1)

source_name: Whole blood from rheumatoid arthritis

tag: individual id

tag: haq

tag: esr

tag: acr

tag: sdai


title: 43.FHI63.nIND.HUS

source_name: E. coli strain FHI63

value: HUS

value: Non-induced


title: 38.St. Olav174.IND.nHUS

source_name: E. coli strain St. Olav174

value: St. Olav174

value: Non-HUS


title: 41.St. Olav179.nIND.nHUS

source_name: E. coli strain St. Olav179

value: St. Olav179


title: 42.St. Olav179.IND.nHUS

value: Induced


title: 37.St. Olav174.nIND.nHUS


title: 44.FHI63.IND.HUS


title: 39.St. Olav178.nIND.nHUS


title: 34.St. Olav157.IND.nHUS

source_name: E. coli strain St. Olav157

value: St. Olav157


title: 32.St. Olav104.IND.nHUS

source_name: E. coli strain St. Olav104

value: St. Olav104


title: 33.St. Olav157.nIND.nHUS


title: 31.St. Olav104.nIND.nHUS


title: 28.FHI95.IND.nHUS

source_name: E. coli strain FHI95


title: 29.St. Olav40.nIND.nHUS

source_name: E. coli strain St. Olav40

value: St. Olav40


title: 30.St. Olav40.IND.nHUS


title: 35.St. Olav172.nIND.nHUS


title: Whole blood from rheumatoid arthritis(K1436_1)

description: Whole blood transcriptome from rheumatoid arthritis(K1436_1)

tag: disease state

value: RA

tag: tissue

value: whole blood

tag: batch

tag: rf

tag: ccp


title: Whole blood from rheumatoid arthritis(K1138_1)

description: Whole blood transcriptome from rheumatoid arthritis(K1138_1)

tag: rin

tag: age

tag: gender

value: F

tag: cdai

tag: kowabari


title: Whole blood from rheumatoid arthritis(K1151_1)

description: Whole blood transcriptome from rheumatoid arthritis(K1151_1)

tag: crp

tag: ana


title: Whole blood from healthy control(HC035_1)

description: Whole blood transcriptome from healthy control(HC035_1)

source_name: Whole blood from healthy control

tag: individual id

value: healthy control


title: Whole blood from rheumatoid arthritis(K1892_1)

description: Whole blood transcriptome from rheumatoid arthritis(K1892_1)

tag: haq


title: Whole blood from healthy control(HC034_1)

description: Whole blood transcriptome from healthy control(HC034_1)

tag: esr


title: Whole blood from rheumatoid arthritis(K2223_1)

description: Whole blood transcriptome from rheumatoid arthritis(K2223_1)

tag: acr


title: 26.FHI79.IND.HUS

source_name: E. coli strain FHI79

tag: strain

tag: group (hus/non-hus)

tag: induced/non-induced

tag: genome accession


title: 25.FHI79.nIND.HUS


title: 23.FHI48.nIND.HUS

source_name: E. coli strain FHI48


title: 24.FHI48.IND.HUS


title: 20.FHI36.IND.nHUS

source_name: E. coli strain FHI36


title: 27.FHI95.nIND.nHUS


title: 21.FHI43.nIND.nHUS

source_name: E. coli strain FHI43


title: Whole blood from healthy control(HC036_1)

description: Whole blood transcriptome from healthy control(HC036_1)

tag: disease state

tag: tissue

tag: batch

tag: sdai

tag: rf


title: Whole blood from rheumatoid arthritis(K1779_1)

description: Whole blood transcriptome from rheumatoid arthritis(K1779_1)

tag: rin

tag: age

tag: gender

tag: cdai

tag: ccp


title: 18.FHI27.IND.HUS

source_name: E. coli strain FHI27


title: 19.FHI36.nIND.nHUS


title: Whole blood from rheumatoid arthritis(K1102_1)

description: Whole blood transcriptome from rheumatoid arthritis(K1102_1)

tag: individual id

tag: kowabari

tag: haq

tag: crp

tag: ana


title: Whole blood from healthy control(HC031_1)

description: Whole blood transcriptome from healthy control(HC031_1)

tag: esr

tag: acr


title: Whole blood from healthy control(HC028_1)

description: Whole blood transcriptome from healthy control(HC028_1)

tag: disease state


title: Whole blood from healthy control(HC030_1)

description: Whole blood transcriptome from healthy control(HC030_1)

tag: tissue


title: 22.FHI43.IND.nHUS

tag: strain

tag: group (hus/non-hus)

tag: induced/non-induced

tag: genome accession


title: 17.FHI27.nIND.HUS


title: 16.FHI25.IND.HUS

source_name: E. coli strain FHI25


title: 15.FHI25.nIND.HUS


title: Whole blood from healthy control(HC027_1)

description: Whole blood transcriptome from healthy control(HC027_1)

tag: batch

tag: rin

tag: age

tag: sdai

tag: rf


title: 14.FHI24.IND.HUS

source_name: E. coli strain FHI24


title: 13.FHI24.nIND.HUS


title: 12.FHI12.IND.HUS

source_name: E. coli strain FHI12


title: 10.FHI9.IND.HUS

source_name: E. coli strain FHI9


title: 11.FHI12.nIND.HUS


title: 8.FHI8.IND.HUS

source_name: E. coli strain FHI8


title: 9.FHI9.nIND.HUS


title: Whole blood from healthy control(HC025_1)

description: Whole blood transcriptome from healthy control(HC025_1)

tag: individual id

tag: gender

tag: cdai

tag: kowabari

tag: ccp


title: Whole blood from healthy control(HC026_1)

description: Whole blood transcriptome from healthy control(HC026_1)

tag: haq

tag: crp

tag: esr

tag: acr

tag: ana


title: 5.FHI7.nIND.HUS

source_name: E. coli strain FHI7

tag: strain

tag: group (hus/non-hus)

tag: induced/non-induced


title: 7.FHI8.nIND.HUS

tag: genome accession


title: 6.FHI7.IND.HUS


title: Whole blood from rheumatoid arthritis(K7818_1)

description: Whole blood transcriptome from rheumatoid arthritis(K7818_1)

source_name: Whole blood from rheumatoid arthritis

tag: disease state

tag: tissue

tag: batch

tag: rin

tag: age


title: Amhr2Cre/+, R26R YFP/+ male biological rep2

city: Houston

first: Rachel

middle: Diane

last: Mullen

state: TX

address: 1515 Holcombe Blvd

department: Genetics

country: USA

institute: MD Anderson Cancer Center

data_processing:
read aligment with Tophat
sorting with samtool
read count with HT-seq count
DE Analysis with DESeq
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: text file with raw read count

organism: Mus musculus

source_name: Müllerian Duct mesenchymal cells

extract_protocol:
YFP+ Müllerian duct mesenchymal cells were directly sorted into TRI reagent RT-LS (Molecular Research Center Inc., Cincinnati, OH, USA) using a BD FACS Aria I cell sorter (BD Biosciences, USA) and homogenized. Total RNA was isolated following the manufacturer’s recommended protocol with the following modifications; PelletPaint (EMD Millipore, Billerica, MA, USA) was added to samples to visualize RNA pellets and an additional ethanol precipitation was performed to remove any remaining phenol.
cDNA libraries were generated using the TruSeq v2 kit (Illumina, San  Diego, CA,USA) following the manufacturer’s recommended protocol from three biological replicates each of male and female. Each replicate consisted of ≥ 100 ng of total RNA isolated from pooled YFP+ Müllerian duct mesenchyme cells from 2-7 embryos. Individual library quality was assessed by high sensitivity DNA Bioanalyzer chip (Aligent, Santa Clara, CA) and the concentration of each library was determined using the Qubit picogreen assay (Life Technologies, Grand Island, NY). Equal quantities of each indexed library were pooled and sequenced on the Illumina HiSeq 2000 platform to generate paired end 76 base pair reads.

value: Mullerian Duct mesenchymal cells

tag: genotype

value: Amhr2Cre/+, R26R YFP/+

value: C57BL/6J x 129/SvEv mixed

tag: embryonic age

value: embryonic day 14.5

tag: Sex

value: male


title: Whole blood from healthy control(HC023_1)

description: Whole blood transcriptome from healthy control(HC023_1)

tag: individual id

tag: gender

tag: cdai

tag: kowabari

tag: haq

tag: sdai

tag: rf

tag: ccp


title: AAV-Rbm24 3

city: Heidelberg

first: Maarten

last: van den Hoogenhof

state: (select)

address: In Neuenheimer Feld 669

country: Germany

institute: Institute of Experimental Cardiology

hyb_protocol: not provided

scan_protocol: not provided

data_processing: RMA expression value derived from Expression Console software;

source_name: 1 week old male C57/Bl6 mice

label_protocol: not provided

extract_protocol: RNA was isolated from left ventricles from the heart, and used for analysis using Affymatrix Mouse Transcriptome Array 1.0

treatment_protocol: 1 week old male C57/bl6 mice were intraperitonally injected with 4 x 10^12 vg of either AAV9-GFP or AAV9-Rbm24 and sacrificed 2 weeks later.

tag: strain

value: left ventricle

value: 1 week


title: Amhr2Cre/+, R26R YFP/+ female biological rep3

value: female


title: Amhr2Cre/+, R26R YFP/+ male biological rep3


title: AAV-Rbm24 1


title: Whole blood from healthy control(HC019_1)

description: Whole blood transcriptome from healthy control(HC019_1)

tag: disease state

tag: crp

tag: esr

tag: acr

tag: ana


title: Whole blood from healthy control(HC022_1)

description: Whole blood transcriptome from healthy control(HC022_1)

tag: tissue

tag: batch

tag: rin

tag: age


title: Whole blood from healthy control(HC024_1)

description: Whole blood transcriptome from healthy control(HC024_1)

tag: individual id

tag: gender


title: AAV-GFP 3


title: Whole blood from healthy control(HC015_1)

description: Whole blood transcriptome from healthy control(HC015_1)

tag: cdai

tag: kowabari


title: AAV-Rbm24 2


title: AAV-GFP 2


title: Amhr2Cre/+, R26R YFP/+ male biological rep1

tag: genotype

tag: embryonic age

tag: Sex


title: Whole blood from healthy control(HC016_1)

description: Whole blood transcriptome from healthy control(HC016_1)

tag: haq

tag: sdai

tag: rf

tag: ccp


title: Whole blood from healthy control(HC021_1)

description: Whole blood transcriptome from healthy control(HC021_1)

tag: disease state

tag: crp

tag: esr

tag: acr


title: Whole blood from healthy control(HC018_1)

description: Whole blood transcriptome from healthy control(HC018_1)

tag: tissue

tag: batch

tag: rin

tag: ana


title: Amhr2Cre/+, R26R YFP/+ female biological rep1

tag: strain


title: Amhr2Cre/+, R26R YFP/+ female biological rep2


title: Whole blood from healthy control(HC017_1)

description: Whole blood transcriptome from healthy control(HC017_1)

tag: individual id

tag: age

tag: gender

tag: cdai

tag: kowabari


title: 2.FHI4.IND.HUS

source_name: E. coli strain FHI4

tag: group (hus/non-hus)

value: HUS

tag: induced/non-induced

tag: genome accession


title: 4.FHI6.IND.HUS

source_name: E. coli strain FHI6

value: Induced


title: 1.FHI4.nIND.HUS

value: Non-induced


title: 3.FHI6.nIND.HUS


title: Whole blood from healthy control(HC020_1)

description: Whole blood transcriptome from healthy control(HC020_1)

source_name: Whole blood from healthy control

tag: disease state

tag: haq

tag: sdai

tag: rf

tag: ccp


title: AAV-GFP 1

tag: tissue


title: Whole blood from healthy control(HC013_1)

description: Whole blood transcriptome from healthy control(HC013_1)

tag: batch

tag: rin

tag: crp

tag: esr

tag: acr


title: Gal-HO+Gal_Rad52ChIP-seq_1

city: Berkeley

first: lorenzo

last: costantino

state: CA

address: 16 Barker Hall # 3202

department: MCB

institute: university of california, berkeley

description: ChIP DNA

data_processing:
The sequencing files were aligned to the SacCer3 yeast genome using Bowtie2 tool using standard parameters.
Peak regions were called using MACS2 tool using the standard parameters.
Genome_build: SacCer3
Supplementary_files_format_and_content: *.bed: Bed files include the peak regions using MACS2.

source_name: yeast

growth_protocol: Cells were grown in YEPD till OD600=0.5.

extract_protocol:
Cells were fixed with paraformaldehyde (final 1%) for 1h. Glycine was added to stop the reaction at 0.125M for 10’. After cell lysis, chromatin was sheared 20 times for 45 s each using a Covaris S2.
The library was prepared using the Accel-NGS 1S Plus DNA Library Kit (Swift Bioscience) following the manufacturer protocol.

treatment_protocol: Cells were treated with 0.5uM Auxin where indicated for 4h, or with 2% galactose where indicated.

tag: strain/background

value: JKM

tag: genotype/variation

value: Gal-HO

tag: treatment

value: Galactose

tag: chip antibody

value: RAD52 (D. Bishop Lab)


title: h1D-h2D_Top1-AID+Aux_Rad52ChIP-seq_2

description: ChIP DNA

value: Auxin


title: Whole blood from healthy control(HC012_1)

description: Whole blood transcriptome from healthy control(HC012_1)

tag: individual id

value: healthy control

value: whole blood

tag: age

tag: gender

value: F

tag: cdai

tag: kowabari

tag: ana


title: h1D-h2D_Rad52ChIP-seq_2

description: ChIP DNA


title: Whole blood from healthy control(HC011_1)

description: Whole blood transcriptome from healthy control(HC011_1)

tag: disease state

tag: haq

tag: sdai

tag: rf

tag: ccp


title: Sen1-AID+Aux_Rad52ChIP-seq_2

description: ChIP DNA


title: WT_Rad52ChIP-seq_2

description: ChIP DNA

value: Wild type


title: Gal-HO+Gal_Rad52ChIP-seq_2

description: ChIP DNA


title: h1D-h2D_Top1-AID+Aux_Rad52ChIP-seq_1

description: ChIP DNA


title: Top1-AID+Aux_Rad52ChIP-seq_1

description: ChIP DNA


title: h1D-h2D_Sen1-AID+Aux_Rad52ChIP-seq_2

description: ChIP DNA


title: LIVE-2

city: wuhan

first: Wei

last: Miao

state: hubei

address: donghu south road #7

country: China

institute: Institute of hydrobiology, CAS

data_processing:
Clean reads were trimed by trim_galore_v0.4.0, and then mapped to transcriptome obtained from GSE111498 by Trinity (trinityrnaseq_r20140717). FPKM values were calculated as recommended by Trinity (doi: 10.1038/nprot.2013.084.)
Supplementary_files_format_and_content: FPKM

organism: Colpoda aspera

source_name: living cells

growth_protocol: Cells were cultured in sterile medium mixed with 1% Luria-Bertani and phosphate-buffered saline (PBS, pH 7.4) at 30℃, reaching a density of about 5×104 cells/ml at 3 days cultureafter inoculation.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols. First strand specific libraries were constructed using the Illumina TruSeq Stranded mRNA Sample Prep Kit (RS-122-2101). The Poly-A tailed mRNA as purified using the Sera‐Mag Magnetic Oligo(dT) Beads. The mRNA fragmentation, first strand cDNA synthesis, second strand cDNA synthesis, A tailing, adaptor ligation and PCR amplification were performed according to the stranded mRNA sample preparation guide of the kit.  Sequencing was performed using an Illumina HiSeq 4000 sequencer (DNA Sequencing Core of University of Michigan).

treatment_protocol: For encystment induction, vegetative cells were collected by centrifugation at 6,500g for 1min and rinsed twice in PBS;most cells then formed cysts within 24h

tag: genotype

value: WT

tag: time point

value: living


title: Whole blood from healthy control(HC010_1)

description: Whole blood transcriptome from healthy control(HC010_1)

tag: tissue

tag: batch

tag: rin

tag: crp

tag: esr

tag: acr


title: SVFN10 (Hi)

first: Muy-Teck

last: Teh

state: England

address: Blizard Building, 4, Newark Street,

department: Centre for Clinical & Diagnostic Oral Sciences

institute: Queen Mary University of London

description:
Sample name: +SVFN10 (Hi)
Cancer Exosomes, high conc
OK113 cells treated with SVFN10 exosomes (4x concentration).

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Illumina iScan

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in GenomeStudio V2011.1.

label: Biotin

source_name: OK113 cells, SVFN10 exosomes (4x concentration), 48h

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

growth_protocol: OK113 primary normal human oral keratinocytes were grown in serum-free medium in 6-well plate at 50% confluent prior to experiment.

extract_protocol: Total RNA were extracted from each well using Qiagen RNeasy Micro Kit.

treatment_protocol: OK113 cells were exposed to 2E+10 particles of exosome per well (in a total volume of 1.5mL SFM/well).

tag: cell type

tag: treatment

value: SVFN10 exosomes (4x concentration)

tag: incubation time


title: SVFN10

description:
Sample name: +SVFN10
Cancer Exosomes
OK113 cells treated with SVFN10 exosomes.

source_name: OK113 cells, SVFN10 exosomes, 48h

value: OK113 primary normal human oral keratinocytes

value: SVFN10 exosomes


title: SVFN10 (Hi, 24h)

description:
Sample name: +SVFN10 (Hi 24h)
Cancer Exosomes, high conc, 24h
OK113 cells treated with SVFN10 exosomes (4x concentration, 24h).

source_name: OK113 cells, SVFN10 exosomes (4x concentration), 24h


title: h1D-h2D_Sen1-AID+Aux_Rad52ChIP-seq_1

description: ChIP DNA

tag: strain/background

tag: genotype/variation

tag: chip antibody


title: Whole blood from healthy control(HC009_1)

description: Whole blood transcriptome from healthy control(HC009_1)

tag: individual id

tag: disease state

tag: age

tag: gender

tag: cdai

tag: kowabari

tag: haq

tag: sdai

tag: ana


title: SVpgC2A

description:
Sample name: +SVpgC2A
Cancer Exosomes
OK113 cells treated with SVpgC2A exosomes.

source_name: OK113 cells, SVpgC2A exosomes, 48h

value: SVpgC2A exosomes


title: Whole blood from healthy control(HC008_1)

description: Whole blood transcriptome from healthy control(HC008_1)

tag: tissue

tag: batch

tag: rin

tag: crp

tag: esr

tag: rf

tag: ccp


title: Whole blood from healthy control(HC006_1)

description: Whole blood transcriptome from healthy control(HC006_1)

tag: acr


title: Gal-HO_NoGal_Rad52ChIP-seq_1

description: ChIP DNA

tag: strain/background

tag: genotype/variation

tag: treatment

value: Dextrose

tag: chip antibody


title: SqCC/Y1

description:
Sample name: +SqCCY1
Cancer Exosomes
OK113 cells treated with SqCC/Y1 exosomes.

source_name: OK113 cells, SqCC/Y1 exosomes, 48h

tag: cell type

value: SqCC/Y1 exosomes

tag: incubation time


title: Whole blood from healthy control(HC007_1)

description: Whole blood transcriptome from healthy control(HC007_1)

tag: individual id

tag: disease state

tag: age

tag: gender

tag: cdai

tag: kowabari

tag: haq


title: Whole blood from healthy control(HC003_1)

description: Whole blood transcriptome from healthy control(HC003_1)

tag: tissue

tag: batch

tag: rin

tag: crp

tag: esr

tag: sdai

tag: ana


title: Whole blood from healthy control(HC004_1)

description: Whole blood transcriptome from healthy control(HC004_1)

tag: acr

tag: rf

tag: ccp


title: NK4

description:
Sample name: +NK4
Normal Exosomes
OK113 cells treated with NK4 exosomes

source_name: OK113 cells, NK4 exosomes, 48h

tag: cell type

tag: treatment

value: NK4 exosomes

tag: incubation time


title: OK113

description:
Sample name: +OK113
Normal Exosomes
OK113 cells treated with OK113 exosomes.

source_name: OK113 cells, OK113 exosomes, 48h

value: OK113 exosomes


title: CALH2

description:
Sample name: +CALH2
Cancer Exosomes
OK113 cells treated with CALH2 exosomes.

source_name: OK113 cells, CALH2 exosomes, 48h

value: CALH2 exosomes


title: Whole blood from healthy control(HC005_1)

description: Whole blood transcriptome from healthy control(HC005_1)

tag: individual id

tag: disease state

tag: age

tag: gender


title: SVpgC2A (Hi)

description:
Sample name: +SVpgC2A (Hi)
Cancer Exosomes, high conc
OK113 cells treated with SVpgC2A exosomes (4x concentration).

source_name: OK113 cells, SVpgC2A exosomes (4x concentration), 48h

value: SVpgC2A exosomes (4x concentration)


title: h1D-h2D_Rad52ChIP-seq_1

description: ChIP DNA

tag: strain/background

tag: genotype/variation

value: Auxin

tag: chip antibody

value: RAD52 (D. Bishop Lab)


title: NOK368

description:
Sample name: +NOK368
Normal Exosomes
OK113 cells treated with NOK368 exosomes.

source_name: OK113 cells, NOK368 exosomes, 48h

value: NOK368 exosomes


title: Sen1-AID+Aux_Rad52ChIP-seq_1

description: ChIP DNA


title: WT_Rad52ChIP-seq_1

description: ChIP DNA


title: CYST-2

source_name: encysting cells

tag: genotype

tag: time point

value: encysting


title: CA1

description:
Sample name: +CA1
Cancer Exosomes
OK113 cells treated with CA1 exosomes.

source_name: OK113 cells, CA1 exosomes, 48h

value: CA1 exosomes


title: Control (SFM)

description:
Sample name: untreated
Control Untreated
OK113 cells treated with vehicle serum-free medium (SFM).

source_name: OK113 cells, vehicle serum-free medium, 48h

value: vehicle serum-free medium (SFM)


title: CYST

description: FPKM.txt

data_processing:
Clean reads were merged and de novo assembled by Trinity (trinityrnaseq_r20140717). Downstream analyses as recommended by Trinity (doi: 10.1038/nprot.2013.084.).
Genome_build: FPKM values were calculated by EdgeR(3.20.9).
Supplementary_files_format_and_content: text file with FPKM values. A FASTA file with the transcript sequences is available on the series record.

growth_protocol: Cells were cultured in sterile medium mixed with 1% Luria-Bertani and phosphate-buffered saline (PBS, pH 7.4) at 30℃, reaching a density of about 5×10^4 cells/ml at 3 days cultureafter inoculation.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols. First strand specific libraries were constructed using the Illumina TruSeq Stranded mRNA Sample Prep Kit (RS-122-2101). The Poly-A tailed mRNA as purified using the Sera‐Mag Magnetic Oligo(dT) Beads. The mRNA fragmentation, first strand cDNA synthesis, second strand cDNA synthesis, A tailing, adaptor ligation and PCR amplification were performed according to the stranded mRNA sample preparation guide of the kit.  Sequencing (Single-end (52X1) for C3 and C6, Paired-end (101x2) FOR C10) was performed using an Illumina HiSeq 2000 sequencer (DNA Sequencing Core of University of Michigan).

treatment_protocol: For encystment induction, vegetative cells were collected by centrifugation at 6,500g for 1min and rinsed twice in PBS; most cells then formed cysts within 24h

value: WT

tag: Stage


title: LIVE

description: FPKM.txt

value: living


title: CRCE_2d_females_rep2

status: Public on Jul 15 2018

city: Maastricht

first: Héloïse

last: Proquin

address: Universiteitssingel 50

institute: Maastricht University

hyb_protocol: Hybridization was performed according to the manufacturer’s protocol on SurePrint G3 mouse Gene exp 60kv2 microarrays slides

scan_protocol: After hybridization, the microarray slides were scanned using an Agilent DNA Microarray Scanner with Surescan High-resolution Technology (Agilent Technologies, The Netherlands) with scanner settings to Dye Channel: G, Profile: AgilentG3_GX_1Color, Scan region: Agilent HD (61 x 21.3 mm), Scan resolution 3 µm, Tiff file dynamic range: 20 bit, Red PMT gain: 100%, Green PMT gain: 100%.

data_processing: First the quality of the microarrays was checked by the quality control pipeline provided by Agilent (Feature extraction software (FES) version 10.7.3.1). All samples met the quality criteria of the FES. In order to have a thorough quality check and normalize the data, an in-house QC pipeline was developed and is publically available (github.com/BiGCAT-UM/arrayQC_Module). All samples met the in-house quality check. Raw data with expression values and genes were selected for data analysis based on flags and missing values. Height groups were defined: E171 2 days, 7 days, 14 days, 21 days for the exposed samples and control 2 days, 7 days, 14 days, 21 days for the controls. Within each group, at least four out of six or five out of seven samples had to have a pass for the spot. Also, within each group, unique identifiers passed when there were less than three missing values out of six or seven values. The unique identifiers with an average expression less than four in all of the groups were omitted. The missing values were pre-processed using the GenePattern ImputeMissingValues.KNN module v13, with standard settings. Unique identifiers were removed and identical Agilent probe identifiers were merged with Babelomics 5, using the median method for pre-processing data. Next, the data was re-annotated from Agilent probe identifiers to EntrezGene identifiers (EntrezGene IDs). The expression data for all genes with an identical EntrezGeneIDs were subsequently merged with Babelomics 5, using the median method for pre-processing data. Using an R-script, a Linear Mixed Model Analysis for Microarrays (LIMMA) (version 1.0) was performed to extract differentially expressed genes (DEG). The data of each control time point (control) was subtracted from the time-matched exposed mice to E171. The standard cut-off values of a fold-change (FC) of 1.5 and a p-value of 0.05 were used in LIMMA. The DEG for each time point were subsequently used in Consensus Pathway Database (CPDB) for an over-expression gene set analysis. All the available databases from CPDB were used (release 31, 1 sept. 2015) with a p<0.01.

source_name: exposed to AOM/DSS and 5mg/kg bw/day of E171 (CRCE), 2 days, females

label_protocol: Total RNA was synthesized into cRNA and labelled according to the One-Color Microarray-Based Gene Expression Analysis protocol version 6.6

extract_protocol: Isolation of RNA was performed using the miRNeasy Mini Kit (Qiagen, The Netherlands) including a DNase treatment, according to the manufacturer’s protocols for “Animal Cells and Animal Tissues”

treatment_protocol: Gavage of vehicle (water)

tag: strain

value: BALB/c

value: female

tag: tissue

value: colon


title: CRCE_7d_males_rep2

source_name: exposed to AOM/DSS and 5mg/kg bw/day of E171 (CRCE), 7 days, males

value: male


title: CRCE_14d_females_rep2

source_name: exposed to AOM/DSS and 5mg/kg bw/day of E171 (CRCE), 14 days, females


title: CRCE_21d_females_rep2

source_name: exposed to AOM/DSS and 5mg/kg bw/day of E171 (CRCE), 21 days, females


title: CRC_2d_males_rep2

source_name: exposed to AOM and DSS (CRC), 2 days, males

value: exposed to AOM and DSS (CRC), 2 days


title: CRC_7d_males_rep2

source_name: exposed to AOM and DSS (CRC), 7 days, males

value: exposed to AOM and DSS (CRC), 7 days


title: CRCE_7d_males_rep1

value: exposed to AOM/DSS and 5mg/kg bw/day of E171 (CRCE), 7 days


title: CRC_14d_males_rep1

source_name: exposed to AOM and DSS (CRC), 14 days, males

value: exposed to AOM and DSS (CRC), 14 days


title: CRCE_14d_males_rep2

source_name: exposed to AOM/DSS and 5mg/kg bw/day of E171 (CRCE), 14 days, males


title: CRC_21d_females_rep1

source_name: exposed to AOM and DSS (CRC), 21 days, females

value: exposed to AOM and DSS (CRC), 21 days


title: CRCE_21d_males_rep2

source_name: exposed to AOM/DSS and 5mg/kg bw/day of E171 (CRCE), 21 days, males


title: CRCE_7d_females_rep1

source_name: exposed to AOM/DSS and 5mg/kg bw/day of E171 (CRCE), 7 days, females


title: CRCE_7d_females_rep2


title: CRC_14d_females_rep1

source_name: exposed to AOM and DSS (CRC), 14 days, females


title: CRC_21d_males_rep1

source_name: exposed to AOM and DSS (CRC), 21 days, males


title: CRC_7d_females_rep2

source_name: exposed to AOM and DSS (CRC), 7 days, females


title: CRCE_2d_females_rep1

value: exposed to AOM/DSS and 5mg/kg bw/day of E171 (CRCE), 2 days


title: CRC_2d_females_rep2

source_name: exposed to AOM and DSS (CRC), 2 days, females


title: CRCE_14d_males_rep1

value: exposed to AOM/DSS and 5mg/kg bw/day of E171 (CRCE), 14 days


title: CRCE_2d_males_rep1

source_name: exposed to AOM/DSS and 5mg/kg bw/day of E171 (CRCE), 2 days, males


title: CRC_14d_females_rep2


title: CRC_7d_females_rep1


title: CRC_21d_females_rep2


title: CRCE_2d_males_rep2


title: CRCE_14d_females_rep1


title: CRC_2d_females_rep1


title: Mock_051916

city: Santa Cruz

first: Upasna

last: Sharma

state: California

address: 1156 High St

department: MCD Biology

institute: UCSC

description:
Sharma_2018_TableS5.xlsx
Sharma_2018_TableS4.xlsx

data_processing:
For each small RNA library, rRNA-mapping reads (which were highly abundant in testis and epididymis samples, but rare in epididymosome and sperm samples) were removed. Remaining reads were mapped to murine tRNAs, to the unique sequences present in the 467 defined pachytene piRNA clusters, to Repeatmasker (tRNA entries from Repeatmasker were deleted to avoid duplicating tRNA-mapping reads), to miRbase, and to Refseq, yielding 27385 data points for each library
Genome_build: mm10
Supplementary_files_format_and_content: counts

source_name: Testicular sperm

growth_protocol: Mice were fed control diet and various tissue samples were collected from mice at age 8-12 weeks old.

extract_protocol:
Total RNA was extracted from the tissues and subjected to gel electrophoresis to isolate small RNA (<40nts).
Small RNA cloning was carried out as in Gu et al, Cell 151, 1488-1500 (2013)

tag: location in epididymis

value: testis

value: Mock fusion


title: Mock_1_042016


title: Fusion_1_042016

source_name: Testicular sperm + caput epididymosomes

value: Testicular sperm + caput epididymosomes

value: fusion


title: Fusion_051916


title: CRC_2d_males_rep1


title: CRC_14d_males_rep2


title: CRCE_21d_females_rep1

value: exposed to AOM/DSS and 5mg/kg bw/day of E171 (CRCE), 21 days


title: Test_sp_somatic_042016


title: Fraction5_042016

source_name: Primary spermatocytes


title: Test_sp2X_031016


title: Fraction4_042016

source_name: Round spermatids (early)


title: Fraction3_042016

source_name: Round spermatids (late)


title: CA_sperm_27_9W_042016

source_name: sperm

value: Cauda epididymis


title: CA_sperm_26_9W_042016


title: CP_sperm_042016

value: Caput epididymis


title: CA_sperm_27_12W_042016


title: CA_EpiM1_051916

source_name: epididymosomes

value: Cauda epididymosomes


title: Test_sp_NaCl_042016


title: CA_sperm_262_12W_042016


title: CA_EpiM3_051916


title: CA_EpiM2_051916


title: Test_sp_fusion_untreated_051916


title: CA_sperm_031016


title: CP3_pnk

description:
Sharma_2018_TableS3.xlsx
Sharma_2018_TableS4.xlsx

value: caput epididymis

value: PNK


title: CA_sperm_262_9W_042016


title: CA_sperm_26_12W_042016


title: CA2

value: cauda epididymis

value: no treatment


title: CP2_pnk


title: CA3_pnk


title: CP3


title: CP2


title: CP1


title: CP1_pnk


title: CA1_pnk


title: CA2_pnk


title: CA3


title: testis_2_base_rpph

source_name: testis

value: base, RPPH


title: CA1


title: CRCE_21d_males_rep1

value: BALB/c

value: male

value: colon


title: testis_2_base_pnk3minus

value: base, PNK 3 minus


title: testis_2_base_alkb

value: testis

value: base, Alkb


title: testis_2_base

value: base , no enzyme treatment


title: testis_2_acid_pnk3minus

value: PNK 3 minus


title: testis_2_acid


title: testis_1_base_pnk3minus


title: testis_2_base_pnk

value: base, PNK


title: testis_1_base_rpph


title: testis_1_base_pnk


title: testis_1_base


title: testis_2_acid_rpph

value: RPPH


title: testis_1_acid_pnk


title: testis_1_acid_alkb

value: Alkb


title: testis_1_base_alkb


title: testis_2_acid_alkb


title: testis_2_acid_pnk


title: testis_1_acid


title: testis_1_acid_rpph


title: epi_2_base_pnk3minus

source_name: cauda epididymis


title: testis_1_acid_pnk3minus


title: epi_2_base_pnk


title: epi_2_base_alkb


title: epi_2_acid_alkb


title: epi_2_acid_pnk3minus


title: epi_2_acid_rpph


title: epi_2_base


title: epi_2_acid


title: epi_1_base_rpph


title: epi_2_base_rpph


title: epi_1_base_pnk3minus


title: epi_1_base_alkb


title: epi_1_base


title: epi_1_acid_rpph


title: epi_1_base_pnk


title: epi_1_acid_pnk3minus


title: epi_1_acid


title: epi_2_acid_pnk


title: epi_1_acid_pnk


title: tail_1

source_name: sperm tail

tag: sperm washes

value: Hypotonic


title: epi_1_acid_alkb


title: so_tail


title: hy_tail_b


title: head_1

source_name: sperm head


title: so_sprm2_a

source_name: whole sperm


title: so_head_a


title: head_2


title: sperm_1


title: sperm_2


title: so_sprm1_b


title: hy_sprm1_a


title: hy_sprm1_b


title: T-head_c


title: T_head_b


title: T-tail_a


title: hy_tail_a


title: T-sprm_c


title: T_sprm_b


title: set1_noslb_20_FVBTA

source_name: Sperm

value: Cauda epididymis

value: No SLB


title: T-tail_b


title: set5_noslb_41_FVBCDIET


title: set5_low_42_FVBCDIET

description:
Sharma_2018_TableS1.xlsx
Sharma_2018_TableS4.xlsx


title: set1_mid_22_FVBTA


title: set4_mid_39_FVBCDIET


title: set1_low_21_FVBTA


title: set4_mid_40_FVBCDIET

value: 0.1% SDS, 0.5% Triton-X


title: set1_high_23_FVBTA


title: set4_noslb_37_FVBCDIET


title: set3_low_22_FVBCDIET


title: set2_mid_19_FVBCDIET


title: set2_high_20_FVBCDIET


title: set3_noslb_21_FVBCDIET


title: set5_high_44_FVBCDIET


title: set2_noslb_17_FVBCDIET


title: set2_low_18_FVBCDIET


title: set3_high_24_FVBCDIET


title: C30: BDE-47 exposed

city: Amherst

first: Alexander

last: Suvorov

state: MA

address: 149A Goessman, 686 N.Pleasant Str

department: Environmental Health Sciences

institute: University of Massachusetts

data_processing:
To analyze the data from our mRNA sequencing experiment, read filtering, trimming and de-multiplexing were performed via the BaseSpace cloud computing service supported by Illumina (https://basespace.illumina.com/home/index).
The preprocessed reads were mapped to the reference mouse genome (MM10) using TopHat 2 aligner
Aligned reads were then used for assembly of novel transcripts with Cufflinks 2.1.1 and differential expression of novel and reference transcripts with Cuffdiff 2.1.1
Genome_build: mm10
Supplementary_files_format_and_content: xlsx file containing log2(FPKM) for control and exposed samples, Log2(Ratio) and q-values

source_name: Gonadal adipose tissue exposed to BDE-47

extract_protocol:
Gonadal fat from the right side of each animal was collected, weighed and snap frozen in liquid nitrogen and stored at -80°C. Total RNA was isolated using TRIzol reagent (Invitrogen).
The NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490, New England BioLabs Inc., Ipswich, MA) was then used to isolate intact poly(A)+ RNA from 3 µg of total RNA. Libraries were constructed using NEBNext mRNA Library Prep Reagent Set for Illumina with multiplexing indexes from NEBNext Multiplex Oligos for Illumina (E6100 and E7335 respectively, New England BioLabs Inc., Ipswich, MA).
High-throughput sequencing was performed on a NextSeq500 sequencing system (Illumina, San-Diego, CA) in the Genomic Resource Laboratory of the University of Massachusetts, Amherst. cDNA libraries were single-end sequenced in 75 cycles using NextSeq 500 High Output Kit (FC-404-1005, Illumina, San-Diego, CA) in a multiplex run.

treatment_protocol: The dams were assigned to one of two treatment groups (n=5 per group) based on weight match, and were exposed to tocopherol-stripped corn oil (MP Biomedicals, Solon, OH) or 0.2 mg/ml solution of BDE-47 (AccuStandard, Inc., New Haven, CT; 100% purity) in tocopherol-stripped corn oil daily from pregnancy day 8 through postpartum day 21; the females were fed 1 µl/gram BW from the tip of a pipette, resulting in exposure of 0.2 mg/kg BW/day.

value: gonadal adipose

tag: Sex

value: postnatal day 21


title: X31: Control

source_name: Gonadal adipose tissue exposed to vehicle (corn oil)


title: X1: Control


title: X10: Control


title: T-head_a


title: C19: BDE-47 exposed


title: C13: BDE-47 exposed


title: set5_mid_43_FVBCDIET


title: set3_mid_23_FVBCDIET


title: set4_low_38_FVBCDIET


title: Whole cell extract (Input)  from Gatad2a-/- system, Day4

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
We used Illumina bcl2fastq version 2.17.1.14 software to generate fastq files.
reads were aligned to mouse mm10 reference genome using bowtie2 software, with default parameters.
for transcription factors, peaks were identified with MACS version 1.4.2-157.  Whole-cell extract was used as control to define a background model. Duplicate reads aligned to the exact same location are excluded by MACS default configuration.
Chromatin modification coverage in the promoters  was calculated using in-house script. Shortly, promoters were defined as 1Kb region around the TSS, based on mm10 assembly. Each promoter was divided to 50bp size bins, and the coverage in each bin is estimated.
In the proccessed matrix file, for each promoter is the coverage in 20 bins, 50bp each.
Genome_build: mm10

source_name: Gatad2a-/- cell line, Day4 post DOX induction

growth_protocol: Maintenance and reprogramming (Day 3 and beyond)  of murine naïve pluripotent cells were conducted in bovine serum-free N2B27-based media or KSR media:   N2B27- based media: 500ml KO-DMEM (Invitrogen), 5ml N2 supplement (Invitrogen; 17502048), 5ml B27 supplement (Invitrogen; 17504044), 15% knockout serum replacement (Invitrogen – 10828), 1mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1mM β-mercaptoethanol (Sigma), penicillin-streptomycin (Invitrogen), 5mg/ml BSA (Sigma).   KSR media: 500 ml DMEM (Invitrogen) , 1mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1mM β-mercaptoethanol (Sigma), penicillin- streptomycin (Invitrogen).   Naïve conditions for murine PSCs included 10μg recombinant human LIF (Millipore; LIF1005). Where indicated 2i was added 48 hours after OSKM induction: small-molecule inhibitors CHIR99021 (CH, 3μM- Axon Medchem) and PD0325901 (PD 0.2 or 1μM - Axon Medchem).

extract_protocol:
Approximately 25*10^6 cells were cross-linked in formaldehyde (1% final concentration, 10 min at room temperature (RT)), and then quenched with glycine (5 min at RT). Fixed cells were lysed in 50mM HEPES KOH pH 7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP-40 alternative, 0.25% Triton supplemented with protease inhibitor at 4°C (Roche, 04693159001), centrifuged at 950 x g for 10 min and re-suspended in 0.2% SDS, 10mM EDTA, 140mM NaCl and 10mM Tris-HCL. Cells were then fragmented with a Branson Sonifier (model S-450D) at -4°C to a size range between 200 and 800 bp, and precipitated by centrifugation. 10 ug of antibody were pre-bound by incubating with Protein-G Dynabeads (Invitrogen100-07D) in blocking buffer (PBS supplemented with 0.5% TWEEN and 0.5% BSA) for 2 hours at room temperature. Washed beads were added to the chromatin lysate, and then incubated overnight. Samples were washed 5 times with RIPA buffer, twice with RIPA buffer supplemented with 500 mM NaCl, twice with LiCl buffer (10 mM TE, 250mM LiCl, 0.5% NP-40, 0.5% DOC), once with TE (10Mm Tris-HCl pH 8.0, 1mM EDTA), and then eluted in 0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris Hcl pH 8.0 at 65°C. Eluate was incubated in 65°C for 4 hours, and then treated sequentially with RNaseA (Roche, 11119915001) for 30 min and Proteinase K (NEB, P8102S) for two hours. DNA was purified with The Agencourt AMPure XP system (Beckman Coulter Genomics, A63881).
120ul SPRI AMPure XP beads (Agencourt) were added to the reverse-crosslinked samples, pipette-mixed 15 times and incubated for 2 minutes. Supernatant were separated from the beads using a magnet for 4 minutes. Beads were washed on the magnet with 70% ethanol and then air dried for 4 minutes. The DNA was eluted in 40 ul EB buffer (10 mM Tris-HCl pH 8.0) by pipette mixing 25 times. For the remainder of the library construction process (DNA end-repair, A-base addition, adaptor ligation and enrichment) a general SPRI cleanup involves addition of buffer containing 20% PEG and 2.5 M NaCl to the DNA reaction products (without moving them from their original well position). After thorough mixing and a 2-minute incubation at room temperature, plates are transferred to a magnet plate, incubated for 4 minutes and supernatant removed. Beads are then washed on the magnet with 150ul 70% ethanol and then air dried for 4 minutes. The DNA is eluted with 40ul of EB buffer by pipette mixing 25 times. Reagent kits are prepared in advance for all enzymatic steps (New England Biolabs). The DNA end-repair was performed by adding 27 µl of a master mix (17 µl master mix (5 ul T4 buffer, 5ul BSA-1mg/ml, 5ul ATP-10mM -2ul dNTPs 10 mM), 5 ul T4 PNK enzyme, 5 µl T4 polymerase (3 units) to each well. Samples were incubated in a thermal cycler at 12C for 15 min, 25C for 15 min, and finally cooled to 4C. The SPRI bead clean up method was used to purify the product (147 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 40 µl EB). The A-base addition was performed by adding 20 µl master mix (17 µl A-base add mix, 3 µl Klenow (3’->5’ exonuclease) to each well and incubated at 37C for 30 min. in a thermal cycler. SPRI bead clean up method was used to purify the product (132 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 19 µl EB). Adaptor ligation was performed by adding 34 µl of a master mix (29 µl 2x DNA ligase buffer, 5 µl DNA ligase) to each well. Finally 5 µl PE Indexed oligo adaptors (0.75 uM ) was added to each well and samples were incubated 25C for 15 min in a thermal cycler. SPRI bead clean up with size selection was used to purify the ligated products (15.5 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 40 µl EB). Finally, enrichment PCR was performed by adding 10 µl of a master mix (2 µl Forward/Reverse Index Primer, 0.5 µl dNTP mix, 5 µl 10x Pfu Ultra Buffer, 1 µl Pfu Ultra-II Fusion, 1.5 µl Nuclease free water) to each well. Plate was transferred to a thermal cycler and ran a Pfu amplification program at 95C for 2 min, 16 cycles of: 95C for 30 sec, 55C for 30 sec, 72C for 60 sec, and finally 72C for 10 min. The final SPRI clean up coupled to size selection was performed (35 µl SPRI beads was added to each sample and eluted in 40 µl).

treatment_protocol: Reprogramming dynamics samples were generated by adding Dox to Secondary MEF. ES and iPSC samples were harvested after 3-4 days of growth in N2B27 2i\LIF medium. Reprogramming samples of days 3-8, ES and iPSC samples were plated on irradiated human foreskin fibroblasts (HFF).

tag: cell line

value: Gatad2a-/- cell line

tag: target protein

value: Input


title: K27Ac Chip-seq in Gatad2a-/- system, Day8

source_name: Gatad2a-/- cell line, Day8 post DOX induction

tag: antibody

value: Abcam ab4729


title: K27Ac Chip-seq in Gatad2a-/- system, Day6

source_name: Gatad2a-/- cell line, Day6 post DOX induction


title: K27Ac Chip-seq in Gatad2a-/- system, Day2

source_name: Gatad2a-/- cell line, Day2 post DOX induction


title: K27Ac Chip-seq in Gatad2a-/- system, MEF

source_name: Gatad2a-/- cell line, MEF post DOX induction


title: Sox2 ChIP-seq, in Mbd3f/- system, Day6

source_name: Mbd3f/- cell line, Day6 post DOX induction

value: Mbd3f/- cell line

value: Millipore AB5603


title: K27Ac Chip-seq in Gatad2a-/- system, Day4


title: Sox2 ChIP-seq, in Mbd3f/- system, ES

source_name: v6.5 WT Embryonic stem cells


title: H3K9me2 ChIP-seq, in Mbd3f/- system, Day3

source_name: Mbd3f/- cell line, Day3 post DOX induction

value: MBL MABI0317


title: H3K9me2 ChIP-seq, in Mbd3f/- system, Day4

source_name: Mbd3f/- cell line, Day4 post DOX induction


title: H3K9me2 ChIP-seq, in Mbd3f/- system, Day6


title: H3K9me2 ChIP-seq, in Mbd3f/- system, Day2

source_name: Mbd3f/- cell line, Day2 post DOX induction


title: H3K9me2 ChIP-seq, in Mbd3f/- system, Day1

source_name: Mbd3f/- cell line, Day1 post DOX induction


title: Klf4 ChIP-seq, in Mbd3f/- system, MEF

source_name: Mbd3f/- cell line, Mouse embryonic fibroblasts


title: C8: BDE-47 exposed

value: male


title: Klf4 ChIP-seq, in Mbd3f/- system, Day6


title: H3K9me2 ChIP-seq, in Mbd3f/- system, Day8

source_name: Mbd3f/- cell line, Day8 post DOX induction


title: H3K9me2 ChIP-seq, in Mbd3f/- system, IPS

source_name: Mbd3f/- cell line, Established induced pluripotent stem cells


title: H3K9me2 ChIP-seq, in Mbd3f/- system, MEF


title: c-Myc ChIP-seq, in Mbd3f/- system, MEF

value: c-Myc

value: Santa Cruz sc764


title: H3K27ac ChIP-seq, in Mbd3f/- system, Day2


title: Oct4 ChIP-seq, in Mbd3f/- system, Day1

value: Santa Cruz SC8628


title: H3K9me2 ChIP-seq, in Mbd3f/- system, Day7

source_name: Mbd3f/- cell line, Day7 post DOX induction


title: H3K9me2 ChIP-seq, in Mbd3f/- system, Day5

source_name: Mbd3f/- cell line, Day5 post DOX induction


title: Small RNA-seq from Mbd3f/- system day8

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
Bowtie software version 2 was used to align reads to mouse mm10 reference genome (UCSC, December 2011).
FPKM values were calculated over all genes in mm10 assembly GTF (UCSC, December 2011), using cufflinks version 2.2.1.
Genes annotated as rRNA, miRNA, snoRNA were selected for further analysis.
Genome_build: mm10

extract_protocol: 1ug of total RNA from each sample was processed using the Truseq small RNA sample preparation kit (RS-200-0012 Illumina) followed by 12 cycles of PCR amplification. Libraries were evaluated by Qubit and TapeStation. For purification of the small RNA fragments, they were size selected using Blupippne machine (Sage Science) with 3% gel cassette followed by clean-up with minielute PCR purification kit (Qiagen). The libraries were constructed with different barcodes to allow multiplexing of 11 samples.

tag: genotype/cell type

tag: stage of reprogramming

value: Day8 post DOX induction


title: Small RNA-seq from Mbd3f/- system day4

value: Day4 post DOX induction


title: Small RNA-seq from Mbd3f/- system day7

value: Day7 post DOX induction


title: Small RNA-seq from Mbd3f/- system IPS

value: Established induced pluripotent stem cells


title: Small RNA-seq from Mbd3f/- system day6

value: Day6 post DOX induction


title: Small RNA-seq from Mbd3f/- system ES

source_name: Mbd3f/- cell line, Embryonic stem cells

value: Embryonic stem cells


title: Small RNA-seq from Mbd3f/- system day5

value: Day5 post DOX induction


title: Small RNA-seq from Mbd3f/- system day1

value: Day1 post DOX induction


title: RNA_KO_repeat3

city: new york

first: Xufeng

last: Chen

state: NY

address: 550 First Avenue, Smilow 1307

institute: NYU Langone Medical Center

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were cleaned for trimming adaptor sequence, low-quality sequence (Q<20) from the 3' end, and filtering the reads with the length less than 25, as well as those from ribosome RNA.
Cleaned reads were then mapped to mm10 whole genome using TopHat（version:2.0.9）with the default parameters for paired-end data.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
HTSeq was used to count the Fragments for each gene. Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using TMM.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Counts and FPKM values for each Sample.

source_name: hematopoietic stem cells

extract_protocol:
Bone marrow HSCs from WT or Med23-dificient adult mice were isolated by cell sorting (LSKsCD150+CD34-CD48-).
Total RNA were extracted from Rneasy Micro Kit(Qiagen), and were amplified by SMART-Seq v4 Ultra Low Input RNA for Illumina Kit. This amplified double-stranded cDNA is then fragmented by acoustic shearing to the appropriate size and used in a standard Illumina library preparation (involving end-repair and kination, A-tailing and adapter ligation, followed by additional amplification by PCR).

value: Bone marrow


title: Small RNA-seq from Mbd3f/- system day3

value: Day3 post DOX induction


title: Small RNA-seq from Mbd3f/- system day2

value: Mbd3f/- cell line

value: Day2 post DOX induction


title: Small RNA-seq from Mbd3f/- system MEF

value: Mouse embryonic fibroblasts


title: H3K4me1 ChIP-seq, in Mbd3f/- system, Day5

value: Abcam ab8895


title: CRC_7d_males_rep1

source_name: exposed to AOM and DSS (CRC), 7 days, males

value: BALB/c

tag: treatment

value: exposed to AOM and DSS (CRC), 7 days

tag: gender

value: male

value: colon


title: RNA_KO_repeat1


title: RNA_WT_repeat2


title: RNA_WT_repeat1


title: RNA_KO_repeat2


title: ATAC_KO_repeat2

description:
KO_ATAC_MACS2_summits.bed
KO_ATAC_MACS2_peaks.narrowPeak

data_processing:
Illumina Casava1.7 software used for basecalling
Raw data from the sequencer were treated using trim_galore. Illumina adapter sequence and low quality (phred score <20) at the 3’ end were trimmed. The paired reads were removed if any of the two reads doesn’t meet the minimum length (20bp).
Reads were aligned to mm10 using BOWTIE2 using the parameter –X 2000, which ensures fragments up to 2 kb were allowed to align. For all data files duplicates and mitochondiral reads were removed using Picard.
Bam files of the replicates from the Med23-dificient case (labeled as KO_ATAC in the processed data) and the wild type control (labeled asWT_ATAC in the processed data)are merged respectively with the consideration of low quantity of coverage. The merged bam files are then used as input for peaks calling.
We used MACS2 to call ATAC-seq peaks, using the --nomodel option.
Genome_build: mm10
Supplementary_files_format_and_content: peak files output from MACS2, including bed and narrowpeak files

extract_protocol:
Bone marrow HSCs from WT or Med23-dificient adult mice were isolated by cell sorting (LSKsCD150+CD34-CD48-).
5,000 sorted cells in FACS Buffer were pelleted by centrifugation at 500 RCF for 5 minutes at 4C in a pre-cooled fixed-angle centrifuge. 50 ul transposase mixture (25 ul of 2x TD buffer, 2.5 ul of TDE1, 0.5 ul of 1% digitonin, 22 ul of nuclease-free water) (Cat# FC-121-1030, Illumina; Cat# G9441, Promega) was added to the cells and the pellet was disrupted by pipetting. Transposition reactions were incubated at 37°C for 30 minutes. Transposed DNA was purified using a QIAgen MinElute Reaction Cleanup kit (Cat# 28204) and purified DNA was eluted in 10 ul elution buffer (10 mM Tris-HCl, pH 8). Transposed fragments were amplified and purified as described previously with primers. Libraries were quantified using qPCR prior to sequencing.


title: ATAC_KO_repeat1


title: Sox2 ChIP-seq, in Mbd3f/- system, IPS

value: Millipore AB5603


title: ATAC_WT_repeat2

description:
WT_ATAC_MACS2_summits.bed
WT_ATAC_MACS2_peaks.narrowPeak


title: Sox2 ChIP-seq, in Mbd3f/- system, Day8


title: Sox2 ChIP-seq, in Mbd3f/- system, Day7


title: ATAC_WT_repeat1


title: Sox2 ChIP-seq, in Mbd3f/- system, Day3


title: Sox2 ChIP-seq, in Mbd3f/- system, Day2


title: Sox2 ChIP-seq, in Mbd3f/- system, Day5


title: Sox2 ChIP-seq, in Mbd3f/- system, Day4


title: Sox2 ChIP-seq, in Mbd3f/- system, Day1


title: PolII ChIP-seq, in Mbd3f/- system, Day8

value: PolII

value: Santa Cruz sc899(N20)


title: PolII ChIP-seq, in Mbd3f/- system, ES


title: RNA_WT_repeat3


title: PolII ChIP-seq, in Mbd3f/- system, Day7


title: PolII ChIP-seq, in Mbd3f/- system, MEF


title: PolII ChIP-seq, in Mbd3f/- system, Day5


title: PolII ChIP-seq, in Mbd3f/- system, IPS


title: PolII ChIP-seq, in Mbd3f/- system, Day1


title: Klf4 ChIP-seq, in Mbd3f/- system, IPS


title: PolII ChIP-seq, in Mbd3f/- system, Day3


title: Klf4 ChIP-seq, in Mbd3f/- system, ES


title: PolII ChIP-seq, in Mbd3f/- system, Day2


title: PolII ChIP-seq, in Mbd3f/- system, Day6


title: Klf4 ChIP-seq, in Mbd3f/- system, Day5


title: Klf4 ChIP-seq, in Mbd3f/- system, Day3


title: Klf4 ChIP-seq, in Mbd3f/- system, Day2


title: Klf4 ChIP-seq, in Mbd3f/- system, Day4


title: Klf4 ChIP-seq, in Mbd3f/- system, Day1


title: H3K9me3 ChIP-seq, in Mbd3f/- system, Day8

value: Abcam ab8898


title: H3K9me3 ChIP-seq, in Mbd3f/- system, ES


title: Klf4 ChIP-seq, in Mbd3f/- system, Day7


title: H3K9me3 ChIP-seq, in Mbd3f/- system, IPS


title: H3K9me3 ChIP-seq, in Mbd3f/- system, Day4


title: PolII ChIP-seq, in Mbd3f/- system, Day4


title: Klf4 ChIP-seq, in Mbd3f/- system, Day8


title: H3K9me3 ChIP-seq, in Mbd3f/- system, Day3


title: H3K9me3 ChIP-seq, in Mbd3f/- system, Day6


title: H3K9me3 ChIP-seq, in Mbd3f/- system, Day5


title: H3K9me3 ChIP-seq, in Mbd3f/- system, Day7


title: H3K9me3 ChIP-seq, in Mbd3f/- system, Day2


title: H3K9me3 ChIP-seq, in Mbd3f/- system, Day1


title: H3K4me3 ChIP-seq, in Mbd3f/- system, IPS

description: Raw data from GSM2739977 and GSM2912473 were combined to produce a single processed data file available at the foot of this sample.

value: Abcam 8580


title: H3K4me3 ChIP-seq, in Mbd3f/- system, Day8


title: H3K4me3 ChIP-seq, in Mbd3f/- system, Day5


title: H3K4me3 ChIP-seq, in Mbd3f/- system, Day7


title: H3K4me3 ChIP-seq, in Mbd3f/- system, Day6


title: H3K4me3 ChIP-seq, in Mbd3f/- system, ES


title: H3K9me3 ChIP-seq, in Mbd3f/- system, MEF


title: H3K4me3 ChIP-seq, in Mbd3f/- system, Day4


title: H3K4me3 ChIP-seq, in Mbd3f/- system, Day3


title: H3K4me1 ChIP-seq, in Mbd3f/- system, ES


title: H3K4me1 ChIP-seq, in Mbd3f/- system, Day8


title: H3K4me1 ChIP-seq, in Mbd3f/- system, IPS


title: H3K4me1 ChIP-seq, in Mbd3f/- system, MEF

source_name: Mbd3f/- cell line,  Mouse embryonic fibroblasts


title: H3K4me3 ChIP-seq, in Mbd3f/- system, Day1


title: H3K4me1 ChIP-seq, in Mbd3f/- system, Day4


title: H3K4me1 ChIP-seq, in Mbd3f/- system, Day7


title: H3K4me1 ChIP-seq, in Mbd3f/- system, Day6


title: H3K4me1 ChIP-seq, in Mbd3f/- system, Day2


title: H3K4me1 ChIP-seq, in Mbd3f/- system, Day1


title: H3K36me3 ChIP-seq, in Mbd3f/- system, IPS

value: Abcam ab9050


title: H3K36me3 ChIP-seq, in Mbd3f/- system, MEF


title: H3K4me1 ChIP-seq, in Mbd3f/- system, Day3


title: H3K36me3 ChIP-seq, in Mbd3f/- system, Day7


title: H3K36me3 ChIP-seq, in Mbd3f/- system, ES


title: H3K4me3 ChIP-seq, in Mbd3f/- system, Day2


title: H3K36me3 ChIP-seq, in Mbd3f/- system, Day8


title: H3K36me3 ChIP-seq, in Mbd3f/- system, Day5


title: H3K27me3 ChIP-seq, in Mbd3f/- system, MEF 2

value: Millipore 07-449


title: H3K36me3 ChIP-seq, in Mbd3f/- system, Day1


title: H3K27me3 ChIP-seq, in Mbd3f/- system, MEF 1


title: H3K27me3 ChIP-seq, in Mbd3f/- system, ES


title: H3K36me3 ChIP-seq, in Mbd3f/- system, Day2


title: H3K27me3 ChIP-seq, in Mbd3f/- system, IPS


title: H3K36me3 ChIP-seq, in Mbd3f/- system, Day3


title: H3K27me3 ChIP-seq, in Mbd3f/- system, Day7


title: H3K27me3 ChIP-seq, in Mbd3f/- system, Day6


title: H3K27me3 ChIP-seq, in Mbd3f/- system, Day8


title: H3K27me3 ChIP-seq, in Mbd3f/- system, Day5


title: H3K27me3 ChIP-seq, in Mbd3f/- system, Day4


title: H3K27me3 ChIP-seq, in Mbd3f/- system, Day2


title: H3K27me3 ChIP-seq, in Mbd3f/- system, Day1


title: H3K27ac ChIP-seq, in Mbd3f/- system, Day6

value: Abcam ab4729


title: H3K27ac ChIP-seq, in Mbd3f/- system, Day7


title: H3K36me3 ChIP-seq, in Mbd3f/- system, Day6


title: H3K27ac ChIP-seq, in Mbd3f/- system, Day5


title: H3K36me3 ChIP-seq, in Mbd3f/- system, Day4


title: H3K27ac ChIP-seq, in Mbd3f/- system, Day4


title: H3K27ac ChIP-seq, in Mbd3f/- system, Day1


title: H3K27ac ChIP-seq, in Mbd3f/- system, Day3


title: c-Myc ChIP-seq, in Mbd3f/- system, ES

value: c-Myc

value: Santa Cruz sc764


title: c-Myc ChIP-seq, in Mbd3f/- system, Day7

value: Mbd3f/- cell line


title: H3K27ac ChIP-seq, in Mbd3f/- system, ES


title: c-Myc ChIP-seq, in Mbd3f/- system, Day5


title: c-Myc ChIP-seq, in Mbd3f/- system, Day6


title: c-Myc ChIP-seq, in Mbd3f/- system, IPS


title: H3K27ac ChIP-seq, in Mbd3f/- system, IPS


title: H3K27ac ChIP-seq, in Mbd3f/- system, Day8


title: H3K27me3 ChIP-seq, in Mbd3f/- system, Day3


title: c-Myc ChIP-seq, in Mbd3f/- system, Day4


title: c-Myc ChIP-seq, in Mbd3f/- system, Day1


title: BJ_sgFoxF1_Ras

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

institute: Tel Aviv University

data_processing:
Reads were aligned to the human genome (hg19) using TopHat2
Number of reads mapping to each gene was counted using HTseq and normalzed to RPKM and then further normalized using quantile normalziation. Last, floor level of 1.0 was set.
Genome_build: hg19
Supplementary_files_format_and_content: RPKMs.qnorm

molecule: polyA RNA

source_name: Immortalized primary fibroblasts

growth_protocol: Immortalized human BJ primary fibroblast cells (by hTERT expression) were cultured in DMEM supplemented with 10% heat-inactivated fetal calf serum (FCS) in 5% CO2 at 37 °C.

extract_protocol:
Total RNA was isolated using Trizol Reagent (Invitrogen), following the  manufacturer's instructions. Poly(A) was isolated using the Oligotex mRNA mini kit (Qiagen)
Libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) following the  manufacturer's instructions.

treatment_protocol: cells treated with 4-OHT for 14 days

value: BJ cells

tag: condition

value: RASG12V-induced BJ transduced with sgRNA targeting FOXF1, the target gene of Enh.AP1.OIS1


title: BJ_sg71_Ras

value: RASG12V-induced BJ transduced with sgRNA targeting enhancer Enh.AP1.OIS1 by sgRNA.71


title: Oct4 ChIP-seq, in Mbd3f/- system, ES

value: Santa Cruz SC8628


title: c-Myc ChIP-seq, in Mbd3f/- system, Day3


title: c-Myc ChIP-seq, in Mbd3f/- system, Day2


title: BJ_sgNT_Ras

value: RASG12V-induced BJ cells transduced with a control non targeting sgRNA


title: Oct4 ChIP-seq, in Mbd3f/- system, Day7


title: Oct4 ChIP-seq, in Mbd3f/- system, Day8


title: Oct4 ChIP-seq, in Mbd3f/- system, Day6


title: BJ_sg69_Ras

value: RASG12V-induced BJ transduced with sgRNA targeting enhancer Enh.AP1.OIS1 by sgRNA.69


title: Psoriasis 10

city: Worcester

first: John

middle: E

last: Harris

address: 364 Plantation St

department: Dermatology

institute: University of Massachusetts Medical School

description:
9464921080_C
c.8

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized with R/Bioconductor and Lumi package using a variance-stabilizing transformation and Robust Spline Normalization

source_name: skin, psoriasis

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

extract_protocol: RNA was extracted using Roche high pure RNA paraffin kit according to the manufacturer’s instructions

tag: disease state

value: Psoriasis

tag: fas ligand level

value: skin


title: Psoriasis 11

description:
9464921080_D
c.8


title: Psoriasis 12

description:
9464921080_E
c.8


title: Oct4 ChIP-seq, in Mbd3f/- system, Day5


title: Psoriasis 5

description:
9464921079_H
c.8


title: Psoriasis 7

description:
9464921079_K
c.8


title: SkinControl 14

description:
9440308052_L
c.8

source_name: skin, control

value: SkinControl


title: Psoriasis 8

description:
9464921079_L
c.8


title: Psoriasis 4

description:
9464921079_G
c.8


title: Psoriasis 14

description:
9464921080_I
c.8


title: Dm.6 [input small RNA]

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

institute: IRCCS-Policlinico San Donato

description:
Small RNA sequencing on total RNA samples.
processed data file: input_counts.txt

data_processing:
Raw reads in FASTQ files were trimmed of adapters and low quality sequences using Trimmomatic.
Trimmed successfully passing the trimming procedure were aligned to human reference genome hg19 using BWA.
Aligned reads were counted on mirBase19 using HTSeq-count.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: input_counts.txt: Tab-delimited text file containing the output from HTSeq-Counts counting procedure, one miRNA per row and one sample per column.

source_name: Biceps Brachii

extract_protocol:
Two lysis protocols were used: 1) skeletal muscle biopsies were cut into small pieces in RIP lysis buffer (Magna RIP Kit, Merck-Millipore, Burlington, MA) and homogenized by TissueLyser (Qiagen, Hilden, Germany); 2) Cultured cells were lysed with the following buffer: 150mM KCl, 25 mM TrisHCl pH 7.4, 5 mM EDTA, 0.5% NP40, 5 mM DTT, 1 mM PMSF, protease and RNase inhibitors. For both lysates, homogenates were quantified for protein content, snap frozen in liquid nitrogen and stored at -80°C until use. For both muscle tissue and cells, 50 ug of lysate were used for total RNA analysis (INPUT RNA).
Extraction and library preparation were performed following manufacturer's instructions for the TruSeq Small RNA Library Preparation Kit.

tag: disease status

value: Myotonic dystrophy-1 (DM1)

value: Biceps brachii


title: Psoriasis 17

description:
9464921080_L
c.8


title: Psoriasis 9

description:
9464921080_B
c.8


title: Psoriasis 13

description:
9464921080_H
c.8


title: SkinControl 13

description:
9440308052_K
c.8


title: Psoriasis 6

description:
9464921079_I
c.8


title: Psoriasis 15

description:
9464921080_J
c.8


title: Psoriasis 1

description:
9464921079_B
c.8


title: Psoriasis 16

description:
9464921080_K
c.8


title: SkinControl 12

description:
9440308052_J
c.8


title: Psoriasis 3

description:
9464921079_D
c.8


title: SkinControl 11

description:
9440308052_I
c.8


title: Psoriasis 2

description:
9464921079_C
c.8


title: Control.5 [input small RNA]


title: DM.4 [input small RNA]


title: Oct4 ChIP-seq, in Mbd3f/- system, Day4


title: SkinControl 10

description:
9440308052_H
c.8


title: Oct4 ChIP-seq, in Mbd3f/- system, Day2


title: DM.2 [input small RNA]


title: Control.3 [input small RNA]


title: Control.1 [input small RNA]


title: Dm.6 [RISC-IP small RNA]

description:
RNA-Seq of small RNA from RISC-IP samples.
processed data file: smallrna_riscip_counts.txt

data_processing:
Raw reads in FASTQ files were trimmed of adapters and low quality sequences using Trimmomatic.
Trimmed successfully passing the trimming procedure were aligned to human reference genome hg19 using BWA.
Aligned reads were counted on mirBase19 using HTSeq-count.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: smallrna_riscip_counts.txt: Tab-delimited text file containing the output from HTSeq-Counts counting procedure, one miRNA per row and one sample per column.

extract_protocol:
Two lysis protocols were used: 1) skeletal muscle biopsies were cut into small pieces in RIP lysis buffer (Magna RIP Kit, Merck-Millipore, Burlington, MA) and homogenized by TissueLyser (Qiagen, Hilden, Germany); 2) Cultured cells were lysed with the following buffer: 150mM KCl, 25 mM TrisHCl pH 7.4, 5 mM EDTA, 0.5% NP40, 5 mM DTT, 1 mM PMSF, protease and RNase inhibitors. For both lysates, homogenates were quantified for protein content, snap frozen in liquid nitrogen and stored at -80°C until use. For both muscle tissue and cells, 1 mg of lysate was immunoprecipitated with anti-Ago2 or control mouse IgG antibodies (RIPAb+ Ago2, Merck-Millipore, Burlington, MA), using 5 ug of antibody for 1 mg of lysate. Immunoprecipitation was performed using the Magna RIP Kit (Merck Millipore, Burlington, MA) following the manufacturer’s instructions. IgG-bound RNA (IP RNA) was extracted from magnetic beads using TRIzol reagent (Invitrogen, ThermoFisher Scientific, Waltham, MA).
Extraction and library preparation were performed following manufacturer's instructions for the TruSeq Small RNA Library Preparation Kit.


title: Control.5 [RISC-IP small RNA]

description:
RNA-Seq of small RNA from control IP samples.
processed data file: smallrna_riscip_counts.txt

value: Control mouse IgG


title: DM.4 [RISC-IP small RNA]


title: SkinControl 7

description:
9440308042_J
c.8


title: Oct4 ChIP-seq, in Mbd3f/- system, Day3

source_name: Mbd3f/- cell line, Day3 post DOX induction


title: SkinControl 2

description:
9249896027_G
c.8


title: SkinControl 4

description:
9249896027_A
c.8


title: SkinControl 8

description:
9440308042_K
c.8


title: SkinControl 6

description:
9440308042_I
c.8


title: DM.2 [RISC-IP small RNA]


title: SkinControl 1

description:
9249907024_G
c.8


title: Acute cutaneous lupus 7

description:
9440308052_B
c.8

source_name: skin, acute cutaneous

value: ACLE


title: SkinControl 5

description:
9440308042_H
c.8


title: SkinControl 3

description:
9249907024_C
c.8