title: STC9

city: Verdun

first: Nicholas

last: O'Toole

state: QC

address: 6875 Boulevard Lasalle

country: Canada

institute: Douglas Mental Health University Institute

data_processing:
BAM files were converted to FASTQ with Picard Tools
Reads were aligned to the mouse genome with STAR
Reads counts per gene were calculated with STAR
Genome_build: mm10
Supplementary_files_format_and_content: Ensembl gene Ids and read counts, tab delimited

organism: Mus musculus

source_name: Ventral Dentate Gyrus

extract_protocol:
Qiagen AllPrep RNA minikit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ventral Dentate Gyrus

tag: housing

value: Standard

tag: social defeat phenotype

value: Control


title: EEC7

status: Public on May 20 2020

type: SRA

library_source: transcriptomic

molecule: total RNA

tag: tissue

value: Enriched


title: STSUS9

value: Susceptible


title: PDTALL19 model, OMP52M51 resistant, mouse #4

type: RNA

city: Padova

first: Valentina

last: Agnusdei

state: PD

address: Via Gattamelata, 64

country: Italy

institute: Istituto Oncologico Veneto

description: Gene expression data from T-ALL cells recovered from mice treated with OMP52M51 until progression

hyb_protocol: Following fragmentation, 5.2 μg of fragmented and labeled ss-DNA were hybridized for 16 hr at 45°C on GeneChip HTA Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner GCS3000.

data_processing: Affymetrix Expression Console.  Data were preprocessed following the RMA procedure using quantile normalization

label: biotin

organism: Homo sapiens

source_name: human T-ALL cells derived from murine infiltrated spleen

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip WT PLUS Reagent KIT, 2013, Affymetrix).

growth_protocol: T-ALL cells were intravenously injected in NOD mice and leukemia growth was monitored by blood drawings and flow cytometric analysis

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

treatment_protocol: Leukemia bearing mice were intraperitoneally treated with the humanized anti-human Notch1 mAb OMP52M51 or control antibody (Rituximab) until progression of disease or in acute treatment (4 days before sacrifice). Both antibodies were administrated weekly at 20mg/Kg.

tag: cell type

value: T-acute lymphoblastic leukemia cells

tag: treatment

value: Treated with Notch1 mAb OMP52M51 until progression


title: PDTALL19 model, control group, mouse #2

description: Gene expression data from T-ALL cells recovered from mice treated with Ctrl Ab

value: Control antibody


title: PDTALL19 model, control group, mouse #5


title: PDTALL19 model, control group, mouse #4


title: PDTALL19 model, acute treated with OMP52M51, mouse #5

description: Gene expression data from T-ALL cells recovered from mice acute treated with OMP52M51

value: Acute treated with Notch1 mAb OMP52M51


title: STSUS8


title: PDTALL19 model, OMP52M51 resistant, mouse #1


title: PDTALL19 model, OMP52M51 resistant, mouse #2


title: EESUS9


title: STRES6

value: Resilient


title: GenomicDNA_ICSI_SSM_29

status: Public on May 21 2020

type: genomic

city: DIJON

first: Yannis

last: Duffourd

address: Batiment B3, 15 boulevard Maréchal de Lattre de Tassigny

country: France

institute: Inserm U1231

description: ICSI SSM sample

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium 850K Human Methylation BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: R 3.6.0, Normalisation by SWAN Method from Minfi v1.32,  DMP detection using DMPFinder from limma v3_42.0, DMR detection using DMRCate v2.2.0

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Buccal smear

label_protocol: Standard Illumina Protocol.

extract_protocol: genomic DNA was extracted and purified from smear samples using Qiagen Gentra Puregene Blood Kit Kit according to standard instructions

tag: gender

value: Female

value: ICSI

value: SSM


title: PDTALL19 model, control group, mouse #3


title: STRES2


title: EEC8


title: PDTALL19 model, control group, mouse #1


title: EESUS6


title: STRES1


title: PDTALL8 model, control group, mouse #3


title: STRES4


title: EERES9


title: STC1


title: EERES6


title: EESUS5


title: STC6


title: EEC9


title: STRES5


title: PDTALL8 model, control group, mouse #2


title: PDTALL19 model, OMP52M51 resistant, mouse #3


title: EERES3


title: EEC3


title: EESUS2


title: EEC6


title: STSUS3


title: STSUS1


title: EESUS1


title: STSUS2


title: EESUS4


title: STRES7


title: STC2


title: STC10


title: EEC1


title: pig Morula

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
Raw sequence reads were trimmed using Trim Galore (v0.6.4) to remove adapter contamination and reads with poor quality (Phred score cutoff 20); HISAT2 (v2.1.0) was used to align the reads in a splice aware manner. Data were passed through an additional filter of having a MAPQ score of 20 or more before quantitation.
The RNA-Seq pipeline of  Seqmonk was used to quantify mRNA features. Similar transcripts were merged. Log transformed (log2FPM)
Genome_build: Pig: Sscrofa11.1
Genome_build: Cow: UMD3.1
Supplementary_files_format_and_content: The RNA-Seq reports are tab-delimited and show annotated gene coordinates and their log2(FPM) values as follows: col 1: <gene name>, col2: <Chromosome>, col 3:  <Start>, col 4: <End>, col 5: <Probe strand> and then listed samples <columns 12-end>.

organism: Sus scrofa

source_name: Morula

extract_protocol:
ARCTURUS® PicoPure® RNA Isolation Kit (KIT0204, Life Technologies) was used to extract the RNA
Libraries were generated using Ovation RNA-Seq System V2 (NuGEN, Cat. 7102-08) for low amount of starting material and further amplified with NEB Next DNA Library Prep Master Mix for Illumina for 8 PCR cycles (NEB, Cat. E6040S)

value: Morula


title: STSUS7


title: GenomicDNA_Control_Control_C3

description: Control sample


title: EESUS3


title: EEC9-rep


title: STSUS4


title: STC5


title: STSUS10


title: EERES8


title: EEC2


title: EERES1


title: STSUS5


title: STC8


title: EEC5


title: STRES3


title: EERES5


title: STSUS6


title: Cold-ko-3

city: Lausanne

first: Rene

last: Dreos

state: VD

address: Ecublens

department: CIG

country: Switzerland

institute: UNIL

data_processing:
Reads were trimmed of the adapter and filtered for low complexity with reapers (-geom no-bc -3pa AGATCGGAAGAGC -qqq-check 10/10 --bcq-late -dust-suffix 20 -clean-length 20 --noqc -basename)
Reads were aligned against Mus musculus. GRCm38.86 genome using STAR
The number of red counts per gene locus was summarized with htseq-count
Genome_build: GRCm38.86
Supplementary_files_format_and_content: Tab delimited files containing gene counts

source_name: Interscapular brown adipose tissue

growth_protocol: Mice were maintained in a temperature-controlled animal facility with a 12-hour light/12-hour dark cycle and had access to standard chow (KLIBA NAFAG no.3436) and water according to Swiss Animal Protection Ordinance (OPAn).

extract_protocol:
Interscapular BAT were taken and freezed immediately in liquid nitrogen and RNA was harvested using Tri-Reagent (T9424, Sigma-Aldrich).Two RNA samples from two mice with same genotype and condition were pool together (each 250 ng) to constitute 500 ng of total RNA from biological triplicates for sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: mice were either sacrifice at room temperature or after 6 hours of cold exposure with food

value: Interscapular brown adipose tissue

tag: strain

value: cold exposure for 6 hrs with food

tag: age

value: 12 weeks old

tag: genotype

value: Cdk7 bKO


title: STC7

value: Ventral Dentate Gyrus

value: Standard


title: EERES4

value: Enriched


title: EERES7


title: Cold-ko-1


title: EESUS7

value: Susceptible


title: Cold-wt-3

value: wild type


title: EERES2


title: EESUS8


title: Cold-wt-1


title: RT-ko-6

value: room temperature


title: RT-ko-5


title: STC3

value: Control


title: RT-ko-4


title: Cold-ko-2


title: Cold-wt-2


title: CD4 cells of PB patient 2

city: Zhengzhou

first: Sha

last: Zhu

state: Henan

country: China

institute: Zhengzhou University

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

hyb_protocol: Following fragmentation,10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 30007G

data_processing: The data were analyzed with Affy package in R, RMA normalization

source_name: pure CD4 TILs from peripheral blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8ng total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

treatment_protocol: treatment naive

tag: disease state

value: triple-negative breast cancer

tag: individual

value: patient 2

value: naïve

value: peripheral blood

value: purified CD4 TILs


title: RT-wt-3


title: RT-wt-2


title: CD4 cells of PB patient 1

value: patient 1


title: RT-wt-1

value: Interscapular brown adipose tissue


title: CRE_2

city: Bethesda

first: Dinah

middle: S.

last: Singer

state: MD

address: Building 10, Room 4B-17

department: Division of Cancer Biology

country: USA

institute: National Cancer Institute

data_processing:
RNA-seq reads were aligned to mouse reference genome (mm10) with STAR aligner. Raw read counts were obtained using htseq-count.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts of sequencing reads for each sample

source_name: MEF

growth_protocol: BRD4 floxed MEF's were grown on flasks and infected with retroviral constructs with Cre-GFP for 6 days, Facs sorted and harvested for RNA

extract_protocol:
MEFs were scraped from flasks and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation


title: CRE_1


title: CD4 TILs of patient 1

source_name: pure CD4 TILs from primary tumor

value: primary tumor


title: Root apical meristems, ARR12-GFP_INPUT_rep2

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

library_source: genomic

data_processing:
Reads quality was evaluated using FastQC (version 0.11.2, Babraham Institute Cambridge, UK) tool.
Reads data were mapped using bowtie v 1.1.1 (Langmead et al., 2009) with the following setting "bowtie -m 1 -k 1 --best --strata --sam" against the genome of Arabidopsis thaliana (TAIR10).
Mapped reads in sam files were sorted and indexed with samtools.
Peaks were called by using MACS2 (version 2.1.0) program (Zhang et al., 2008) with following setting (-g 1.35e8, -B and -q 0.01).
Genome_build: TAIR10
Supplementary_files_format_and_content: bed files are generated with MACS2 using each IP sample with the matched INPUT sample

organism: Arabidopsis thaliana

source_name: Root apical meristems

growth_protocol: After 5 days of stratification, A. thaliana Col-0 and ARR12-GFP seeds were plated on squared Petri  dishes on one-half  Murashige Skoog medium and grown for three days in a vertical position in  a growth chamber at 22°C in long-day conditions.

extract_protocol:
Nuclei were extracted after formaldehyde-fixation of root meristem tissues. Nuclei were lysated and their content sonicated. Protein-DNA complexes were immuno-precipitated with anti-GFP antibody from sonicated material.
Libraries were prepared according to NuGEN's instructions accompanying the Ovation® Ultralow V2 DNA-Seq Library Preparation Kit (Part# 0344NB). Libraries were sequenced on the Illumina HiSeq2000 following the manufacturer's protocols.

tag: ecotype

value: root

tag: developmental stage

value: 3 days post germination

tag: chip antibody


title: Control_2

value: Wild type


title: Control_3


title: Root apical meristems, GFP_INPUT_rep2

value: control


title: Control_1


title: CD4 TILs of patient 2


title: Root apical meristems, ARR12-GFP_INPUT_rep1


title: Root apical meristems, GFP_INPUT_rep1


title: Root apical meristems, ARR12-GFP_IP_rep2

value: anti-GFP


title: MDA-MB-231Azacitidine

city: Baltimore

first: Michael

middle: Jonathan

last: Topper

address: 1650 Orleans St., Suite 530

department: Oncology

institute: Johns Hopkins University

description: Gene expression after 10 days of continous treatment with indicated agent or vehicle

hyb_protocol: Agilent human GE 4x 44K v2 microarrays (G4845A) were used, which contain 41,000 unique probes targeting 27,958 Entrez gene RNAs. 825 ng of each Cyanine-labeled samples was used for hybridization at 65ºC for 17 hours in a hybridization oven with rotation.

scan_protocol: Microarrays were scanned using an Agilent G2505C Scanner controlled by Agilent Scan Control 7.0 software.

data_processing: Data were extracted with Agilent Feature Extraction 9.5.3.1 software.

source_name: MDA-MB-231 cells treated with 500nM Azacitidine for 10 days

label_protocol: Sample amplification and labeling procedures were carried out by using Quick RNA Amplification and Labeling Kit (Cat# 5190-0447, Agilent Technologies) with minor modifications. Briefly, 400 ng total RNA was reverse-transcribed into cDNA by MMLV-RT using oligo dT primers (Cat# RA300A-2, System Bioscience) that incorporate T7 promoter sequence. The cDNA is then used as a template for in vitro transcription in the presence of T7 RNA polymerase and Cyanine-labeled CTP (Perkin Elmer). The labeled cRNA is purified using RNeasy mini kit (Qiagen). RNA spike-in controls (Agilent Technologies) are added to RNA samples before amplification and labeling according to manufacturer’s protocol.

growth_protocol: Cell lines were cultured in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   Cell cultures were incubated for 10 days  at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was isolated from cell pellets using Takara NucleoSpin RNA extraction kit. RNA was quantified with NanoDrop ND-1000 followed by quality assessment with 2100 Bioanalyzer (Agilent Technologies) according to manufacturer’s protocol.

treatment_protocol: Human cell lines were treated in vitro with the agents and doses indicated above for a period of 10 days

tag: Sex

value: Female

tag: cell line

tag: growth protocol

value: in-vitro cultured cell lines

value: 500nM Azacitidine for 10 days


title: HCC1806 Azacitidine

source_name: HCC1806 cells treated with 500nM Azacitidine for 10 days


title: MDA-MB-468 Azacitidine

source_name: MDA-MB-468 cells treated with 500nM Azacitidine for 10 days


title: CRE_3


title: HCC1806 Mock

source_name: HCC1806 cells treated with vehicle

value: vehicle


title: A2780 Talazoparib

source_name: A2780 cells treated with 2.5nM Talazoparib for 10 days

value: 2.5nM Talazoparib for 10 days


title: A2780 Azacitidine

source_name: A2780 cells treated with 150nM Azacitidine for 10 days

value: 150nM Azacitidine for 10 days


title: MDA-MB-468 Mock

source_name: MDA-MB-468 cells treated with vehicle


title: Root apical meristems, ARR12-GFP_IP_rep1


title: Root apical meristems, GFP_IP_rep1


title: Walker_RNA_Liver_TBT_5month_Female_biorep2

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

description: UUID:5d138846c0974420fc76239b,QC_score:3,QC_stats:Pass

data_processing:
RNA-seq and ATAC-seq were sequenced by data production centers and processed by the TaRGET II DCC with standardized data processing pipelines. Library QC was assayed based on key QC parameters. Please refer to the TaRGET II data portal for detailed pipeline description and QC standard (https://data.targetepigenomics.org).
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak output for ATAC-seq and gene count table for RNA-seq

molecule: polyA RNA

extract_protocol:
Sample collection was performed by Cheryl Walker lab at Baylor College of Medicine. 5 month mice were CO2 euthanized. Liver and blood cells from individual mouse were isolated for subsequent DNA and RNA extractions according to the standard operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.
ATAC-seq and mRNA-seq experiments were performed by Cheryl Walker lab at Baylor College of Medicine. mRNA and nuclei from 5 month mice liver and blood were isolated for subsequent ATAC-seq and mRNA-seq library preparations according to the operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.

value: 5 month

value: Liver

value: TBT (Tributyltin chloride) 0.5 mg/kg bw/d


title: Walker_RNA_Liver_TBT_5month_Female_biorep1

description: UUID:5d138845c097444041762399,QC_score:3,QC_stats:Pass


title: Walker_RNA_Liver_Ctrl_5month_Male_biorep6

description: UUID:5d138855c0974414937623c6,QC_score:3,QC_stats:Pass

value: Male

value: Control Drinking Water 0 mg/kg


title: Walker_RNA_Liver_TBT_5month_Female_biorep3

description: UUID:5d138847c09744692176239e,QC_score:3,QC_stats:Pass


title: Walker_RNA_Liver_TBT_5month_Female_biorep5

description: UUID:5d138853c09744e0c37623c0,QC_score:3,QC_stats:Pass


title: Walker_RNA_Liver_Ctrl_5month_Male_biorep5

description: UUID:5d138847c0974450b676239f,QC_score:3,QC_stats:Pass


title: MDA-MB-231 Mock

source_name: MDA-MB-231 cells treated with vehicle


title: A2780 Mock

source_name: A2780 cells treated with vehicle


title: A2780 Azacitidine+Talazoparib

source_name: A2780 cells treated with 2.5nM Talazoparib  and 150nM Azacitidine for 10 days


title: Walker_RNA_Liver_TBT_5month_Female_biorep4

description: UUID:5d13884bc0974426967623ab,QC_score:3,QC_stats:Pass


title: Walker_RNA_Liver_Ctrl_5month_Male_biorep3

description: UUID:5d13883ec09744807f762384,QC_score:3,QC_stats:Pass


title: Walker_RNA_Liver_Ctrl_5month_Male_biorep2

description: UUID:5d13883cc097440c0d762380,QC_score:3,QC_stats:Pass


title: Walker_RNA_Liver_Ctrl_5month_Female_biorep5

description: UUID:5d13884cc097446ea27623ae,QC_score:3,QC_stats:Pass


title: STC4

source_name: Ventral Dentate Gyrus

value: Ventral Dentate Gyrus

tag: housing

value: Standard

tag: social defeat phenotype

value: Control


title: Root apical meristems, GFP_IP_rep2

tag: tissue

value: root

value: 3 days post germination


title: Walker_RNA_Liver_Ctrl_5month_Female_biorep3

description: UUID:5d13883bc09744e5b376237c,QC_score:3,QC_stats:Pass

tag: treatment


title: Walker_RNA_Blood_Ctrl_5month_Male_biorep3

description: UUID:5d138839c097441b1b762377,QC_score:3,QC_stats:Pass

tag: gender

value: Blood


title: Sample 6 from KC

city: Moscow

first: Polina

last: Vishnyakova

address: Oparina 4

country: Russia

institute: National Medical Research Center for Obstetrics, Gynecology and Perinatology

description: NS_Infl_Mm_v2_C2537.rlf was used as Reporter Library File

hyb_protocol: Samples were  hybridized for 16 h at 65C according to the instructions at nCounter® XT Assay User Manual (NanoString tecnology)

scan_protocol: After hybridization samples were placed in the prep station of nCounter FLEX analysis system, there hybridized samples were purified and immobilized in a sample cartridge (cartridge ID 207846350819) according to standard protocol. Then the sample cartridge was scanned on the nCounter FLEX digital analyzer (Scanner ID 1410C0216)

data_processing: The raw data were processed in nSolver Analysis Software 4.0. We used CodeSetContent(Housekeeping) standart normalization

source_name: Kupffer cells

label_protocol: 100 ng of  total RNA was mixed with Reporter CodeSet and Capture ProbeSet from nCounter Mouse Inflammation V2 panel according to the instructions at nCounter® XT Assay User Manual (NanoString tecnology)  User Manual

extract_protocol: Sorted cells from 5 animals were pooled. The total RNA was isolated from cells by using RNeasy Plus Mini Kit (Qiagen) with additional purification and concentration with RNA Clean& Concentrator (Zymo Research).

tag: strain

value: Balb/C


title: Sample 4 from KC


title: Sample 3 from KC


title: AsPC1_Starved3

city: San Diego

first: Brian

middle: Patrick

last: James

state: CA

address: 10901 North Torrey Pines Road

department: Genomics

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Qiagen Genglobe UPX analysis primary analysis tools were used to generate gene count files  https://geneglobe.qiagen.com/us/analyze/
Qiagen Genglobe UPX analysis secondary  analysis tools were used to generate gene differential expression analysi https://geneglobe.qiagen.com/us/analyze/
Genome_build: hg19
Supplementary_files_format_and_content: normalized counts all genes

growth_protocol: AsPC-1 cells were maintained in RPMI culture media supplemented with 10% FBS, 1mM sodium pyruvate and 100 units/mL penicillin/streptomycin under 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted from cells with the PureLink RNA Mini Kit (Thermo Fisher Scientific)
RNA libraries were prepared using the QIAseq UPX 3' Transcriptome

treatment_protocol: Cell were incubated in complete media or glutamine free media supplemented with 10% dialized FBS for 24h

tag: cell type

value: pancreatic ductal adenocarcinoma (PDAC) cell line

tag: culture media

value: RPMI glutamine-free

tag: replicate number


title: AsPC1_Starved5


title: Sample 5 from KC


title: AsPC1_Starved4


title: AsPC1_Starved1


title: Walker_RNA_Liver_Ctrl_5month_Female_biorep4

description: UUID:5d13883fc097443abc762387,QC_score:3,QC_stats:Pass

tag: age

value: Female


title: AsPC1_Starved2


title: Sample 6 from MNC

source_name: blood monocytes


title: Sample 1 from KC


title: AsPC1_Ctrl4

value: RPMI complete


title: AsPC1_Ctrl5


title: Sample 5 from MNC


title: AsPC1_Ctrl3


title: Walker_RNA_Liver_Ctrl_5month_Female_biorep6

description: UUID:5d138851c09744442f7623ba,QC_score:3,QC_stats:Pass


title: 35S::HSFA9 roots Replicate 1

city: Beaucouze

first: Julia

last: Buitink

address: 42 rue Georges Morel

department: BAP

institute: INRAE

hyb_protocol: Hybridization was performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnight. Slides were washed and dried prior to scanning.

scan_protocol: Slides were scanned at 532/635nm at 2 μm resolution and high sensitivity with a Roche_NimbleGen MS200. DEVA Software v1.2.1 was used to extract pair_data files from the scanned images.

data_processing: All statistical analyses on the gene expression data were performed using R language, version 2.5.1 (R Development Core Team, 2011) and LIMMA package (Smyth G.K., 2005) from the Bioconductor project. For the processing steps, data were normalized by the lowess method in LIMMA.

organism: Medicago truncatula

label_protocol: 400ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse_transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1.5mmol of Cyanine_3 (Cy3) or Cyanine_5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean_up column kits (Macherey_Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND_1000 (Nanodrop Technologies, DE, USA). Labelled samples (30 pmol) were combined and co_hybridized to the Medtr_v1 12x135K arrays.

growth_protocol: The culture of the roots is carried out 72h in the dark (20°C, 45° tilt) then with a photoperiod of 16 hours/8 hours (20°C, 90° tilt) for approximately 1 week and finally with a photoperiod of 16 hours/8 hours (25°C, 90° tilt) for approximately 2 weeks

extract_protocol: Total RNAs were extracted from the frozen grinded seeds lots using the NucleoSpin Extract II, Total RNA Purification kit (Macherey-Nagel, GmbH & Co. KG, Germany) following manufacturer’s instructions

treatment_protocol: Radicles are transformed by Agrobacterium rhizogenes according to the Boisson-Dernier et al protocol, with slight modifications

tag: tissus

value: roots

tag: genetic background

tag: genotype

tag: phenotype

value: Wild-type

value: 3 weeks

tag: harvest date


title: Sample 3 from MNC


title: Sample 4 from MNC


title: AsPC1_Ctrl2

tag: cell line


title: 35S::HSFA9 roots Replicate 3


title: 35S::GUS roots Replicate 1


title: 35S::GUS roots Replicate 2


title: 35S::HSFA9 roots Replicate 4


title: 35S::HSFA9 roots Replicate 2


title: AsPC1_Ctrl1


title: 35S::GUS roots Replicate 4


title: AM28

city: Detroit

first: Lobelia

last: Samavati

state: Michigan

address: 3990 John R#3 Hudson, Harper University Hospital

department: Internal Medicine (H0609)

institute: Dr.

data_processing:
RNA-seq data were analyzed using the Illumina Basespace RNA express application.
The sequencing reads were aligned to the reference human genome hg19 using STAR aligner and differentially expressed (DE) genes (FDR < 5%) were identified with the DEseq2 analysis tool.
Genome_build: hg19
Supplementary_files_format_and_content: counts

source_name: Bronchoalveolar lavage (BAL)

growth_protocol: AMs were isolated from BAL samples .

extract_protocol:
mRNA was isolated from AMs  using Dynabeads mRNA isolation kit.
RNA-seq libraries were prepared using the NEBNext ultradirectional library preparation protocol (New England BioLabs, Ipswich, MA).The pooled  RNA-seq libraries were sequenced on Illumina Next-Seq 500 (75 cycles,PE)

treatment_protocol: Isolated AMs were cultured  at 37 degree C for 16h in the presence or absence of dexamethasone (100ng/mL).

tag: diagnosis

value: sarcoidosis

value: Alveolar macrophages

value: Dexa-treated


title: Sample 1 from MNC


title: AM29


title: AM27


title: AM30


title: ko-CL-2

source_name: perigonadal WAT

extract_protocol:
pgWAT were taken and freezed immediately in liquid nitrogen and RNA was harvested using Tri-Reagent (T9424, Sigma-Aldrich).Two RNA samples from two mice with same genotype and condition were pool together (each 250 ng) to constitute 500 ng of total RNA from biological triplicates for sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: mice were either sacrifice after 7 days or CL or saline treatment

value: perigonadal WAT

value: CL injection for 7 days

value: 9 weeks old

value: Cdk7 aKO


title: AM26


title: AM25


title: ko-CL-1


title: AM24


title: WGBS_WT_Rep2

city: Illkirch

last: Weber

address: 300 Bd Sebastien Brant

department: UMR7242 Biotechnology and Cell Signalling

institute: CNRS

data_processing:
Reads were cleaned to remove low quality bases as well as the first five bases of reads R1 and ten bases of reads R2 with Trim Galore v0.4.2 using the parameters --paired -q 20 --stringency 2 --clip_R1 5 --clip_R2 10. The reads were aligned to the mm10 genome and cleaned for duplicates using Bismark v0.22.1 with default parameters. Reads with signs of incomplete conversion were removed using the filter_non_conversion option in Bismark with the parameters --minimum_count 5 and --percentage_cutoff 50. Methylation calls were extracted using the Bismark methylation extractor. CGs were filtered to have a minimum sequencing depth of 5X using custom developped scripts in R.
Genome_build: mm10
Supplementary_files_format_and_content: IGV files containing methylation scores for all CGs with at least 5X sequencing depth.

source_name: E8.5 whole embryos

extract_protocol:
Genomic DNA was extracted with the AllPrep DNA/RNA Mini Kit (Qiagen).
50 ng of genomic DNA were fragmented to 350 bp using a Covaris E220 sonicator. DNA was bisulfite-converted with the EZ DNA Methylation-Gold kit (Zymo Research) and WGBS libraries were prepared using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences) according to the manufacturer's instructions with 7 PCR cycles for the final amplification. The libraries were purified using Ampure XP beads (Beckman Coulter).

tag: strain background

tag: genotype/variation

value: wild type

tag: developmental stage

value: whole embryos


title: WGBS_D1KO_Rep2

tag: tissue


title: ko-CL-3

tag: treatment


title: WGBS_DKO_Rep2

value: Dnmt3a-/- Dnmt3b-/-

tag: gender


title: ko-saline-3

tag: strain

value: saline injection for 7 days


title: Sample 2 from MNC

value: Balb/C

value: Blood


title: AM22

tag: cell type


title: ko-saline-2


title: ko-saline-1


title: wt-CL-3


title: AM21


title: AM23


title: 35S::GUS roots Replicate 3


title: AM10

value: Untreated


title: AM9


title: AM8


title: wt-saline-2


title: wt-CL-2


title: AM6


title: AM7


title: AMs from HDM-treated mouse 3

city: London

first: Clare

middle: Margaret

last: Lloyd

address: Inflammation, Repair and Development, National Heart and Lung Institute, Sir Alexander Fleming Building

department: National Heart and Lung Institute

institute: Imperial College London

data_processing:
Adapter sequences were removed and reads with mean phred scores of less than 20 by FASTQC analysis were filtered
Fitered reads were aligned to the Mm10 genome using the COBWeb aligner within StrandNGS software. A minimum 90 % sequence identity and match length of 25 base pairs, with a maximum 5 % sequence identity gap and maximum 1 novel splice event, were required for reads to align to a transcript. Reads were removed if they aligned to mouse ribosomal RNA or UniVec sequences or if both paired reads did not align to the same genomic location.
Transcripts were quantified from aligned reads using the DESeq method
Low abundance transcripts with DESeq-normalised expression < 8 in >25 % of both experimental groups were filtered
Genome_build: Mm10 2012.01.19
Supplementary_files_format_and_content: .csv file containing DESeq-normalised expression values for each sample and for each transcript detected above the lower threshold. Entrez IDs, Ensembl IDs and gene symbols are shown

source_name: Sorted airway macrophages

extract_protocol:
AMs were flow cytometry sorted and immediately lysed in QIAGEN RLT buffer supplemented with 1 % 2-mercaptoethanol. Lysates were passed through QIAShredder columns by centrifugation and RNA was extracted from lysates using the RNeasy Plus Micro Kit, as per manufacturer's instructions.
200 ng RNA per sample was polyA-purified and converted to cDNA sequencing libraries using the Illumina TruSeq Stranded mRNA v2 kit, with unique indexes per sample to allow multiplexing.

treatment_protocol: Mice were exposed to 25 ug house dust mite extract in 25 ul PBS or 25 ul PBS control by intranasal administration 5 times weekly for 3 weeks. Bronchoalveolar lavage was performed 24 hours after final HDM/PBS exposure

value: house dust mite (HDM) allergen


title: AMs from HDM-treated mouse 4


title: AM5


title: AM2


title: AMs from HDM-treated mouse 2


title: AM1


title: Sample 2 from KC

value: Liver


title: AMs from PBS-treated control mouse 5

value: PBS control


title: AMs from HDM-treated mouse 1


title: wt-saline-3


title: AMs from PBS-treated control mouse 4


title: AMs from PBS-treated control mouse 3


title: AMs from PBS-treated control mouse 2


title: AM4

value: sarcoidosis


title: AM3

value: Alveolar macrophages


title: wt-CL-1


title: qPROseq_1M_K562_Rep1

city: Ithaca

first: Julius

last: Judd

state: NY

address: 417 Biotechnology Bldg; 215 Tower Road

department: Molecular Biology and Genetics

institute: Cornell University

description:
1q
nuclear RNA
processed data file: qPROseq_1M_K562_dREGpeaks.bed

data_processing:
Library strategy: PRO-seq
Adapters were trimmed and UMIs were extracted using fastp v0.20.0.
Reads were aligned to the hg38 genome assembly using bowtie2 v2.3.5.1.
bigWig coverage tracks of 3' positions were generated using bamCoverage v3.1.3.
PCR deduplication was performed using umi_tools dedup v1.0.0.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: bigWig coverage tracks of 3' positions (raw counts, not normalized).
Supplementary_files_format_and_content: Bed files of peaks called using dREG.

source_name: lymphoblastoid cell line (K562)

growth_protocol: K562 cells were maintained in RPMI with 10% FBS at 37 °C. Biological replicates were separated by at least 3 passages.

extract_protocol:
Cells were washed with PBS, then with buffer W (10 mM Tris-Cl pH 7.5, 10 mM Kcl, 150 mM Sucrose, 5 mM MgCl2, 0.5 mM CaCl2, 0.5 mM DTT, 1X Pierce Protease inhibitors, and SUPERase-In RNase inhibitor). Cells permeabilized for 5 min on ice in buffer P (10 mM Tris-Cl pH 7.5, 10 mM Kcl, 250 mM Sucrose, 5 mM MgCl2, 1 mM EGTA, 0.5 mM DTT, 0.05% Tween-20, 1X Pierce Protease inhibitors, and SUPERase-In RNase inhibitor). Cells were washed with buffer W twice and stored in buffer F (50 mM Tris-Cl pH 8.0, 40% Glycerol, 5 mM MgCl2, 0.1 mM EDTA, 0.5 mM DTT).
PRO-seq was performed exactly as described (PMID: 27442863), using the 2-biotin-NTP option (Biotin C&U) with 1M permeabilized K562 cells as input for each replicate. qPRO-seq was performed using our new streamlined PRO-seq protocol. Briefly, we used MyOne Streptavidin C1 beads instead of M280 beads to recover biotinylated nascent RNA, which reduces non-specific binding of non-biotinylated RNAs. This allowed us to use one affinity purification instead of the three employed by the published protocol (PMID: 27442863). To achieve this, we ligated the 3' adapter to the total pool of hydrolyzed RNA isolated after the run-on reaction, bound biotinylated nascent RNA to C1 streptavadin beads, and performed 5' end repair (PNK and RppH treatment) and 5' adapter ligation with the RNA affixed to the beads. We then eluted nascent RNA from the beads using TRIzol and generated cDNA by reverse transcription using Maxima H- RT. Libraries were then PCR amplified, quantified, pooled, and sequenced on an Illumina NextSeq 500 in 37x37 paired end mode. Both PRO-seq and qPRO-seq libraries made using 1M cells were amplified for 11 PCR cycles, and qPRO-seq libraries made using 250k cells were amplified for 14 PCR cycles. Both 5' and 3' adapters for all experiments had a 6N random UMI sequence at the ligation junction to facilitate PCR deduplication.

treatment_protocol: No treatment was performed.

value: lymphoblastoid cell line

tag: number of input cells

tag: method

value: qPRO-seq


title: qPROseq_1M_K562_Rep2

description:
2q
nuclear RNA
processed data file: qPROseq_1M_K562_dREGpeaks.bed


title: qPROseq_250k_K562_Rep2

description:
2q_uli
nuclear RNA
processed data file: qPROseq_250k_K562_dREGpeaks.bed


title: qPROseq_250k_K562_Rep1

description:
1q_uli
nuclear RNA
processed data file: qPROseq_250k_K562_dREGpeaks.bed


title: wt-saline-1

value: perigonadal WAT

tag: age


title: AMs from PBS-treated control mouse 1


title: PROseq_1M_K562_Rep2

description:
2s
nuclear RNA
processed data file: PROseq_1M_K562_dREGpeaks.bed


title: PROseq_1M_K562_Rep1

description:
1s
nuclear RNA
processed data file: PROseq_1M_K562_dREGpeaks.bed


title: EEC4

city: Verdun

last: O'Toole

institute: Douglas Mental Health University Institute

data_processing:
BAM files were converted to FASTQ with Picard Tools
Reads were aligned to the mouse genome with STAR
Reads counts per gene were calculated with STAR
Genome_build: mm10
Supplementary_files_format_and_content: Ensembl gene Ids and read counts, tab delimited

extract_protocol:
Qiagen AllPrep RNA minikit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ventral Dentate Gyrus

tag: housing

value: Enriched

tag: social defeat phenotype

value: Control


title: Mutlu_RNA_Liver_PM2.5_5month_Male_biorep3

description: UUID:5b982822ee1fbd35b2292680,QC_score:3,QC_stats:Pass

extract_protocol:
Sample collection was performed by Gokhan Mutlu lab at University of Chicago. 5 month mice were CO2 euthanized. Liver and blood cells from individual mouse were isolated for subsequent DNA and RNA extractions according to the standard operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.
ATAC-seq and mRNA-seq experiments were performed by Gokhan Mutlu lab at University of Chicago. mRNA and nuclei from 5 month mice liver and blood were isolated for subsequent ATAC-seq and mRNA-seq library preparations according to the operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.

value: 5 month

value: Male


title: Mutlu_RNA_Liver_PM2.5_5month_Male_biorep2

description: UUID:5b98276dee1fbde05729267d,QC_score:3,QC_stats:Pass


title: Mutlu_RNA_Liver_PM2.5_5month_Male_biorep5

description: UUID:5b98294d767355457d8768f5,QC_score:3,QC_stats:Pass


title: Mutlu_RNA_Liver_PM2.5_5month_Male_biorep1

description: UUID:5b9826baee1fbd2b84292679,QC_score:3,QC_stats:Pass


title: Monos56

data_processing:
RNA-seq data were analyzed using the Illumina Basespace RNA express application.
The sequencing reads were aligned to the reference human genome hg19 using STAR aligner and differentially expressed (DE) genes (FDR < 5%) were identified with the DEseq2 analysis tool.

source_name: Peripheral blood

extract_protocol:
mRNA was isolated from monocytes  using Dynabeads mRNA isolation kit.
RNA-seq libraries were prepared using the NEBNext ultradirectional library preparation protocol (New England BioLabs, Ipswich, MA)

treatment_protocol: Isolated monocytes were cultured  at 37 degree C for 16h in the presence or absence of dexamethasone (100ng/mL).

tag: cells

value: Monocytes

value: Dexa-treated


title: Mutlu_RNA_Liver_PM2.5_5month_Female_biorep6

description: UUID:5b9ade1e7a654c92d1f6709a,QC_score:3,QC_stats:Pass

value: Female


title: Monos59


title: Monos58


title: Monos60


title: Mutlu_RNA_Liver_PM2.5_5month_Female_biorep5

description: UUID:5b982c95ee1fbd5f432926a0,QC_score:3,QC_stats:Pass


title: Monos57


title: Monos55


title: Mutlu_RNA_Liver_PM2.5_5month_Female_biorep3

description: UUID:5b982ba6ee1fbdf28b29269a,QC_score:3,QC_stats:Pass


title: Mutlu_RNA_Liver_PM2.5_5month_Female_biorep4

description: UUID:5b982be17673553812876908,QC_score:3,QC_stats:Pass


title: Monos54


title: Monos53


title: Monos52


title: Monos51


title: Mutlu_RNA_Liver_Ctrl_5month_Male_biorep6

description: UUID:5b982191ee1fbd7b15292659,QC_score:3,QC_stats:Pass

value: Filtered Air 0 particles/cm3/8hours/day


title: Mutlu_RNA_Liver_PM2.5_5month_Male_biorep4

description: UUID:5b98289a767355718c8768f1,QC_score:3,QC_stats:Pass


title: Monos40

value: Untreated


title: Mutlu_RNA_Liver_PM2.5_5month_Female_biorep1

description: UUID:5b982a7cee1fbdcea2292690,QC_score:3,QC_stats:Pass

value: Liver


title: Monos39


title: Mutlu_RNA_Liver_Ctrl_5month_Male_biorep5

description: UUID:5b9820de767355602b8768c9,QC_score:3,QC_stats:Pass


title: Monos38


title: Monos37


title: Mutlu_RNA_Liver_Ctrl_5month_Male_biorep1

description: UUID:5b981efeee1fbd6b9329264d,QC_score:3,QC_stats:Pass


title: Monos36


title: Monos35


title: Mutlu_RNA_Liver_Ctrl_5month_Male_biorep2

description: UUID:5b981fb2ee1fbd282029264f,QC_score:3,QC_stats:Pass


title: Mutlu_RNA_Liver_Ctrl_5month_Female_biorep6

description: UUID:5b982606ee1fbd7e9c292671,QC_score:3,QC_stats:Pass


title: Monos31


title: Monos34


title: Mutlu_RNA_Liver_Ctrl_5month_Female_biorep4

description: UUID:5b9824db767355e7078768d4,QC_score:3,QC_stats:Pass


title: Mutlu_RNA_Liver_Ctrl_5month_Female_biorep3

description: UUID:5b98242576735559f18768ce,QC_score:3,QC_stats:Pass


title: Mutlu_RNA_Liver_Ctrl_5month_Female_biorep5

description: UUID:5b982552767355fce98768d7,QC_score:3,QC_stats:Pass


title: Monos33


title: Mutlu_RNA_Liver_PM2.5_5month_Female_biorep2

description: UUID:5b982b2e76735545b0876900,QC_score:3,QC_stats:Pass


title: Monos32


title: Mutlu_RNA_Liver_Ctrl_5month_Female_biorep2

description: UUID:5b982335767355d9c48768cb,QC_score:3,QC_stats:Pass


title: Mutlu_RNA_Liver_Ctrl_5month_Female_biorep1

description: UUID:5b982246767355cf3e8768ca,QC_score:3,QC_stats:Pass


title: Mutlu_RNA_Liver_Ctrl_5month_Male_biorep4

description: UUID:5b9820a1ee1fbd70a2292653,QC_score:3,QC_stats:Pass


title: Mutlu_RNA_Blood_PM2.5_5month_Male_biorep5

description: UUID:5b9829c6ee1fbdcb87292687,QC_score:3,QC_stats:Pass

value: Blood


title: TAFRO-3 PBMCs from Remission repeat

city: Philadelphia

first: David

middle: C

last: Fajgenbaum

state: PA

address: 3620 Hamilton Walk

institute: University of Pennsylvania

data_processing:
The Cell Ranger Single Cell Software Suite was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting (http://software.10xgenomics.com/single-cell/overview/welcome). 10bp UMI tags were extracted from Read2.  Genome_build: mm10  Supplementary_files_format_and_content: mtx: count matrix in a sparse matrix format; barcodes.tsv: barcode ids for each sample; genes.tsv: gene ids for each sample
Genome_build: GRCh38
Supplementary_files_format_and_content: gene barcode matrices

source_name: PBMC

extract_protocol:
PBMCs isolated from whole blood using Ficoll and cryopreserved
Cellular suspensions were loaded on a GemCode Single Cell Instrument (10x Genomics, Pleasanton, CA) to generate single cell GEMs. Approximately ~1200 to 2800 cells were loaded per channel.  Single cell RNA-Seq libraries were prepared using GemCode Single Cell 3’ Gel Bead and Library Kit (now sold as P/N 120230, 120231, 120232, 10x Genomics) following the protocols outlined in Zheng et. al. Sequencing libraries were loaded at 2.1pM on an Illumina NextSeq500 with 2 × 75 paired-end kits using the following read length: 98bp Read1, 14bp I7 Index, 8bp I5 Index and 5bp Read2.

value: PBMC

value: iMCD

tag: disease state

value: remission

tag: technical replicate


title: Mutlu_RNA_Blood_PM2.5_5month_Male_biorep2

description: UUID:5b98285e7673554ca48768ef,QC_score:3,QC_stats:Pass


title: TAFRO-3 PBMCs from Flare repeat

tag: diagnosis

value: flare


title: Mutlu_RNA_Liver_Ctrl_5month_Male_biorep3

description: UUID:5b982029ee1fbd2e5e292651,QC_score:3,QC_stats:Pass


title: TAFRO-3 PBMCs from Flare


title: Input DNA

city: Shanghai

first: Yu

last: Liu

address: 1678 Dongfang Road, Pudong District

department: Pediatric Translational Medicine Institute

institute: Shanghai Children's Medical Center

data_processing:
The reads were aligned to the human genome (GRCh37-lite) with bwa (v0.7.12).
The multiple mapped reads and duplicated reads were removed.
Fragment length was estimated based on cross correlation plot which is generated by SPP (v1.10.1).
MACS (v2.1.1.20160309) was used to call peaks for H3K27Ac ChIP-seq data.
The results were filtered against known false positive peaks using ENCODE black list.
Genome_build: GRCh37-lite
Supplementary_files_format_and_content: Processed data were presented in bigwig format, to be visualized in  IGV (http://software.broadinstitute.org/software/igv/) or UCSC genome browser (https://genome.ucsc.edu/cgi-bin/hgGateway).

source_name: Human T-ALL cells

growth_protocol: The mononuclear cells (MNCs) isolated from the patient BM samples were engrafted into 5 irradiated NOG mice (3-4 week-old female mice, Beijing Vital River Laboratory Animal Technology Co., Ltd., Beijing, China) via intravenous (i.v.) injection. Weekly monitoring of peripheral appearance of leukemic cells (CD45+) was performed via flow cytometry analysis with retro-orbital bleeding. All the animal experiments were conducted under sterile conditions at Crown Bioscience SPF facility, and performed strictly under the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health.

extract_protocol: Cells were cross-linked with 1% formaldehyde for 10 min at room temperature and formaldehyde was then inactivated by the addition of 125 mM glycine for 5min. Sonicated DNA fragments with 100–300 bp were pre-cleared and then immunoprecipitated with Protein A+G Magnetic beads coupled with Anti-YY1 antibody (61779, active motif). After reverse crosslinking, immunoprecipitated DNAs and input DNAs were end-repaired and ligated adapters to the DNA fragments.

tag: antibody

value: NOG mice

value: 3-4 week-old

tag: Sex


title: Mutlu_RNA_Blood_PM2.5_5month_Male_biorep3

description: UUID:5b9828d6ee1fbd9daa292685,QC_score:3,QC_stats:Pass


title: Mutlu_RNA_Blood_PM2.5_5month_Male_biorep4

description: UUID:5b98294e767355cac18768f6,QC_score:3,QC_stats:Pass


title: TAFRO-3 PBMCs from Remission


title: Mutlu_RNA_Blood_PM2.5_5month_Male_biorep1

description: UUID:5b9828237673552d958768ec,QC_score:3,QC_stats:Pass


title: TAFRO-2 PBMCs from Remission


title: Mutlu_RNA_Blood_PM2.5_5month_Female_biorep6

description: UUID:5b982fdd7673558a8c876921,QC_score:3,QC_stats:Pass


title: TAFRO-2 PBMCs from Flare repeat


title: TAFRO-2 PBMCs from Flare


title: Mutlu_RNA_Blood_PM2.5_5month_Female_biorep1

description: UUID:5b982ab676735527ed8768ff,QC_score:3,QC_stats:Pass


title: Mutlu_RNA_Blood_PM2.5_5month_Female_biorep3

description: UUID:5b982cd17673552aaa87690e,QC_score:3,QC_stats:Pass


title: TAFRO-1 PBMCs from Remission repeat


title: Mutlu_RNA_Blood_PM2.5_5month_Female_biorep2

description: UUID:5b982be2ee1fbd775f29269b,QC_score:3,QC_stats:Pass


title: Mutlu_RNA_Blood_PM2.5_5month_Female_biorep4

description: UUID:5b982d4a767355c2b1876912,QC_score:3,QC_stats:Pass


title: Mutlu_RNA_Blood_Ctrl_5month_Male_biorep6

description: UUID:5b98249e76735595de8768d3,QC_score:3,QC_stats:Pass


title: TAFRO-1 PBMCs from Flare


title: TAFRO-1 PBMCs from Remission


title: TAFRO-1 PBMCs from Flare repeat


title: Mutlu_RNA_Blood_Ctrl_5month_Male_biorep5

description: UUID:5b98242676735509558768cf,QC_score:3,QC_stats:Pass


title: A549_AG14345_SMARCA4_null_DNase

city: SEATTLE

first: John

middle: A

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

data_processing:
Basecalling, RTA v1.13
Alignments to GRCh38, BWA v0.7.12
Read processing, Samtools v1.2
Read density, Bedops v2.4.15
Peak calling, Hotspot2 v2.1.1
Genome_build: hg38
Supplementary_files_format_and_content: 5% FDR peak calls as a .bed file

source_name: Human lung (carcinoma) cell line

extract_protocol:
PEG precipitation and size fractionation of DNA
Low-input single-stranded library construction protocol as per PMIDs 23493070 & 26771485

tag: cell line

tag: genotype/variation


title: Mutlu_RNA_Blood_Ctrl_5month_Male_biorep4

description: UUID:5b9823aeee1fbd824f292668,QC_score:3,QC_stats:Pass

tag: tissue

tag: treatment


title: Mutlu_RNA_Blood_Ctrl_5month_Male_biorep3

description: UUID:5b982372ee1fbd11d0292667,QC_score:3,QC_stats:Pass

tag: strain

tag: gender


title: A549_AG14317_SMARCA4_null_DNase


title: A549_AG14318_SMARCA4_null_DNase


title: A549_AG14316_SMARCA4_rescue_DNase


title: Mutlu_RNA_Blood_Ctrl_5month_Male_biorep1

description: UUID:5b982246ee1fbdc4d029265d,QC_score:3,QC_stats:Pass


title: Mutlu_RNA_Blood_Ctrl_5month_Female_biorep6

description: UUID:5b9827ab7673550bf48768e6,QC_score:3,QC_stats:Pass


title: Mutlu_RNA_Blood_Ctrl_5month_Male_biorep2

description: UUID:5b9822beee1fbd39c1292660,QC_score:3,QC_stats:Pass


title: Mutlu_RNA_Blood_Ctrl_5month_Female_biorep5

description: UUID:5b982732767355e83d8768e4,QC_score:3,QC_stats:Pass


title: TAFRO-2 PBMCs from Remission repeat

tag: cell type


title: A549_AG14262_SMARCA4_null_DNase


title: A549_AG14261_SMARCA4_rescue_DNase


title: YY1 ChIP-seq

value: YY1 (61779, active motif)


title: Mutlu_RNA_Blood_PM2.5_5month_Female_biorep5

description: UUID:5b982e75ee1fbd29ce2926a9,QC_score:3,QC_stats:Pass


title: Mutlu_RNA_Blood_Ctrl_5month_Female_biorep4

description: UUID:5b9826ba767355ef6c8768df,QC_score:3,QC_stats:Pass


title: A549_AG14257_SMARCA4_rescue_DNase


title: A549_AG14259_SMARCA4_rescue_DNase


title: A549_AG14260_SMARCA4_rescue_DNase


title: Mutlu_RNA_Blood_Ctrl_5month_Female_biorep1

description: UUID:5b98255276735500de8768d8,QC_score:3,QC_stats:Pass


title: Mutlu_RNA_Blood_Ctrl_5month_Female_biorep2

description: UUID:5b9825caee1fbd907329266e,QC_score:3,QC_stats:Pass


title: Mutlu_ATAC_Liver_PM2.5_5month_Male_biorep5

description: UUID:5bcea5328fc24509565e98f7,QC_score:9,QC_stats:Pass


title: A549_AG11292_SMARCA4_null_RNA

data_processing:
Basecalling, RTA v1.13
Alignments to GRCh38, star v2.4.2a
Annotation, cufflinks v2.2.1, GENCODE v25
Subread, featureCounts v1.5.1
Genome_build: hg38
Supplementary_files_format_and_content: combined coverage bigWig, genome alignment featureCounts outout as tsv

extract_protocol:
Ambion mirVana RNA isolation kit
Illumina TruSeq Stranded Total RNA Library Prep Kit


title: A549_AG11291_SMARCA4_null_RNA


title: A549_AG14263_SMARCA4_rescue_DNase


title: Mutlu_ATAC_Liver_PM2.5_5month_Male_biorep2

description: UUID:5bcea47df3e8134e7675955f,QC_score:9,QC_stats:Pass


title: Mutlu_ATAC_Liver_PM2.5_5month_Male_biorep3

description: UUID:5bcea4ba8fc2456c015e98f1,QC_score:10,QC_stats:Pass


title: Mutlu_ATAC_Liver_PM2.5_5month_Male_biorep4

description: UUID:5bcea4f78fc24583405e98f5,QC_score:10,QC_stats:Pass


title: A549_AG11290_SMARCA4_null_RNA


title: Mutlu_ATAC_Liver_PM2.5_5month_Male_biorep1

description: UUID:5bcea441f3e81301e675955a,QC_score:9,QC_stats:Pass


title: A549_AG11287_SMARCA4_rescue_RNA


title: Mutlu_ATAC_Liver_PM2.5_5month_Female_biorep4

description: UUID:5bcea65e4de5ef7c79c8c214,QC_score:6,QC_stats:Pass


title: Mutlu_ATAC_Liver_PM2.5_5month_Female_biorep5

description: UUID:5bcea69ad78741beeadbeac2,QC_score:9,QC_stats:Pass


title: A549_AG11289_SMARCA4_rescue_RNA


title: A549_AG11285_SMARCA4_rescue_RNA


title: Mutlu_ATAC_Liver_PM2.5_5month_Female_biorep3

description: UUID:5bcea622f9e5d783006c7b0a,QC_score:6,QC_stats:Pass


title: A549_AG11288_SMARCA4_rescue_RNA


title: Mutlu_ATAC_Liver_PM2.5_5month_Female_biorep6

description: UUID:5bcea6d6d7874129d2dbeac3,QC_score:9,QC_stats:Pass


title: A549_AG11284_SMARCA4_rescue_RNA


title: A549_AG11286_SMARCA4_rescue_RNA


title: Mutlu_RNA_Blood_Ctrl_5month_Female_biorep3

description: UUID:5b982642767355a0aa8768dd,QC_score:3,QC_stats:Pass


title: A549_AG11293_SMARCA4_null_RNA


title: Mutlu_ATAC_Liver_PM2.5_5month_Female_biorep1

description: UUID:5bcea56f4de5effc06c8c20d,QC_score:2,QC_stats:Fail


title: A549_AG15725_SMARCA4_rescue_ChIP

extract_protocol:
https://www.nature.com/articles/nprot.2018.015
Low-input single-stranded library construction protocol as per PMIDs 23493070 & 26771485


title: Mutlu_ATAC_Liver_Ctrl_5month_Male_biorep5

description: UUID:5bcea2268fc2454b5f5e98de,QC_score:6,QC_stats:Pass


title: Walker_RNA_Liver_Ctrl_5month_Male_biorep4

description: UUID:5d138843c097447ddf762392,QC_score:3,QC_stats:Pass

extract_protocol:
Sample collection was performed by Cheryl Walker lab at Baylor College of Medicine. 5 month mice were CO2 euthanized. Liver and blood cells from individual mouse were isolated for subsequent DNA and RNA extractions according to the standard operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.
ATAC-seq and mRNA-seq experiments were performed by Cheryl Walker lab at Baylor College of Medicine. mRNA and nuclei from 5 month mice liver and blood were isolated for subsequent ATAC-seq and mRNA-seq library preparations according to the operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.

value: Control Drinking Water 0 mg/kg


title: Mutlu_ATAC_Liver_Ctrl_5month_Male_biorep4

description: UUID:5bcea1e9f3e8136030759545,QC_score:6,QC_stats:Pass

value: 5 month


title: A549_AG15721_SMARCA4_rescue_ChIP

value: BRM


title: A549_AG15694_SMARCA4_null_ChIP


title: Mutlu_ATAC_Liver_Ctrl_5month_Male_biorep3

description: UUID:5bcea1ae8fc245c9065e98d7,QC_score:6,QC_stats:Pass

value: Male


title: Mutlu_ATAC_Liver_Ctrl_5month_Male_biorep2

description: UUID:5bcea172f3e81369f8759541,QC_score:6,QC_stats:Pass


title: A549_AG15720_SMARCA4_rescue_ChIP


title: Mutlu_ATAC_Liver_Ctrl_5month_Female_biorep6

description: UUID:5bcea4058fc2456c165e98ea,QC_score:10,QC_stats:Pass


title: Mutlu_ATAC_Liver_Ctrl_5month_Male_biorep1

description: UUID:5bcea1368fc2455fad5e98d4,QC_score:6,QC_stats:Pass


title: Mutlu_ATAC_Liver_PM2.5_5month_Female_biorep2

description: UUID:5bcea5a9f9e5d707bd6c7b08,QC_score:6,QC_stats:Pass


title: A549_AG15693_SMARCA4_rescue_ChIP


title: Mutlu_ATAC_Liver_Ctrl_5month_Female_biorep5

description: UUID:5bcea3c9f3e813061e759557,QC_score:9,QC_stats:Pass


title: Mutlu_ATAC_Liver_Ctrl_5month_Female_biorep4

description: UUID:5bcea3518fc2452bd15e98e6,QC_score:9,QC_stats:Pass


title: Mutlu_ATAC_Liver_Ctrl_5month_Female_biorep3

description: UUID:5bcea316f3e81375f8759550,QC_score:9,QC_stats:Pass


title: A549_AG15691_SMARCA4_rescue_ChIP


title: Mutlu_ATAC_Liver_Ctrl_5month_Female_biorep2

description: UUID:5bcea2d98fc24589c65e98e1,QC_score:8,QC_stats:Pass


title: A549_AG15692_SMARCA4_rescue_ChIP


title: Mutlu_ATAC_Liver_Ctrl_5month_Male_biorep6

description: UUID:5bcea262f3e813e148759547,QC_score:9,QC_stats:Pass


title: A549_AG15723_SMARCA4_null_ChIP


title: A549_AG15724_SMARCA4_null_ChIP


title: A549_AG15689_SMARCA4_null_ChIP


title: Mutlu_ATAC_Liver_Ctrl_5month_Female_biorep1

description: UUID:5bcea29ef3e81302bb75954c,QC_score:6,QC_stats:Pass


title: A549_AG15690_SMARCA4_null_ChIP


title: Dolinoy_RNA_Liver_Pb_5month_Male_biorep6

description: UUID:5aa80841672a763524bba52f,QC_score:3,QC_stats:Pass

extract_protocol:
Sample collection was performed by Dana Dolinoy lab at University of Michigan. 5 month mice were CO2 euthanized. Liver and blood cells from individual mouse were isolated for subsequent DNA and RNA extractions according to the standard operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.
ATAC-seq and mRNA-seq experiments were performed by Dana Dolinoy lab at University of Michigan. mRNA and nuclei from 5 month mice liver and blood were isolated for subsequent ATAC-seq and mRNA-seq library preparations according to the operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.

value: Avy

value: Pb 16ppm lead acetate


title: A549_AG15688_SMARCA4_rescue_ChIP


title: A549_AG15687_SMARCA4_rescue_ChIP


title: A549_AG15722_SMARCA4_rescue_ChIP


title: d4-Atg7 KO_rep2 [ATAC-seq]

city: Wuhan

first: Jing-Jing

last: Zhang

state: Hubei

address: 1 Lion Rock Street

department: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction

institute: Huazhong Agricultural University

description: processed data file: KO-D4.merge.bw

data_processing:
Paired-end reads for ATAC-seq were aligned to the mouse mm10 genome using Bowtie2 with the ‘‘-X 2000’’ options.
The Picard was used to remove PCR duplicates and Samtools was used to remove low quality reads (MAPQ < 30).
The MACS2 software calls the ATAC-seq peak with the “-nomodel” and “-nolambda” parameters.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files were generated using deepTools.

source_name: Embryonic Stem Cells (ESCs)

growth_protocol: ESCs were routinely cultivated on mitotically inactivated mouse embryonic fibroblasts (MEFs) in Knockout DMEM supplemented with 20% Knockout Serum Replacement, 1× Glutamine Max, 1× NEAA, 1× Pen/Strep, 0.1 mM 2-mercaptoethanol, 1000 U ml-1 LIF, 1 μM PD0325901 and 3 μM CHIR99021. MEFs were grown in DMEM high glucose supplemented with 15% FBS and 1× Pen/Strep.

extract_protocol: ATAC-Seq libraries were prepared using ATAC-seq developed by Buenrostro et al.

treatment_protocol: The EpiLCs induction were performed by seeding 1.0×10e5 ESCs into a well of a 12-well plate coated with 16.7 mg/ml human plasma fibronectin in N2B27 medium containing 20 ng/ml Activin A, 12 ng/ml bFGF, and 20% KSR. The culture medium was changed every day.

value: Atg7 KO

value: ESC to EpiLC transition

tag: time point


title: A549_AG15695_SMARCA4_null_ChIP


title: d4-Control_rep2 [ATAC-seq]

description: processed data file: CTR-D4.merge.bw

value: Control


title: Dolinoy_RNA_Liver_Pb_5month_Male_biorep5

description: UUID:5aa805ade80fac61a25b7e33,QC_score:3,QC_stats:Pass

tag: age

value: Liver


title: Dolinoy_RNA_Liver_Pb_5month_Male_biorep4

description: UUID:5aa8031ae80fac079d5b7e06,QC_score:3,QC_stats:Pass


title: A549_AG15686_SMARCA4_rescue_ChIP


title: d4-Atg7 KO_rep1 [ATAC-seq]

description: processed data file: KO-D4.merge.bw


title: d2-Atg7 KO_rep1 [ATAC-seq]

description: processed data file: KO-D2.merge.bw


title: A549_AG15685_SMARCA4_null_ChIP


title: d2-Atg7 KO_rep2 [ATAC-seq]

description: processed data file: KO-D2.merge.bw


title: d2-Control_rep2 [ATAC-seq]

description: processed data file: CTR-D2.merge.bw


title: Dolinoy_RNA_Liver_Pb_5month_Male_biorep3

description: UUID:5aa802dde80fac9e3f5b7dff,QC_score:3,QC_stats:Pass


title: ESC_rep2 [ATAC-seq]

description: processed data file: ESC.merge.bw


title: ESC_rep1 [ATAC-seq]

description: processed data file: ESC.merge.bw


title: A549_AG15683_SMARCA4_rescue_ChIP


title: Dolinoy_RNA_Liver_Pb_5month_Male_biorep2

description: UUID:5aa8022abba1a527614cc106,QC_score:3,QC_stats:Pass


title: d4-Atg7 KO_rep3 [RNA-seq]

data_processing:
Reads of RNA-seq were mapped to the mouse genome (mm10) with STAR.
Mapped reads were subsequently assembled into transcripts guided by the reference annotation (GENCODE gene models) with Stringtie.
Gene differential expression analysis using DESeq2 based on the reads count file obtained by featureCounts.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.counts.txt: Tab-delimited text files include reads count values for each Sample.

extract_protocol: Total RNA was isolated using TRIzol, and the reactions were performed with PrimeScript RT reagent Kit according to the manufacturer’s protocol.


title: Dolinoy_RNA_Liver_Pb_5month_Male_biorep1

description: UUID:5aa800c3e80fac48405b7de2,QC_score:3,QC_stats:Pass


title: A549_AG15682_SMARCA4_rescue_ChIP


title: Dolinoy_RNA_Liver_Pb_5month_Female_biorep6

description: UUID:5aa80806672a7672d7bba52c,QC_score:3,QC_stats:Pass

value: Female


title: A549_AG15681_SMARCA4_rescue_ChIP


title: d4-Control_rep1 [ATAC-seq]

description: processed data file: CTR-D4.merge.bw


title: d4-Control_rep3 [RNA-seq]


title: d4-Control_rep2 [RNA-seq]


title: Dolinoy_RNA_Liver_Pb_5month_Female_biorep5

description: UUID:5aa80535e80fac8a025b7e30,QC_score:3,QC_stats:Pass


title: A549_AG15680_SMARCA4_null_ChIP


title: Dolinoy_RNA_Liver_Pb_5month_Female_biorep4

description: UUID:5aa802a2bba1a5011c4cc111,QC_score:3,QC_stats:Pass


title: d4-Control_rep1 [RNA-seq]


title: d2-Atg7 KO_rep3 [RNA-seq]


title: d2-Atg7 KO_rep2 [RNA-seq]


title: d2-Atg7 KO_rep1 [RNA-seq]


title: d2-Control_rep1 [ATAC-seq]

description: processed data file: CTR-D2.merge.bw


title: A549_AG15684_SMARCA4_null_ChIP


title: d2-Control_rep3 [RNA-seq]


title: Dolinoy_RNA_Liver_Pb_5month_Female_biorep3

description: UUID:5aa801ee672a768216bba4a9,QC_score:3,QC_stats:Pass


title: d2-Control_rep2 [RNA-seq]


title: A549_AG15678_SMARCA4_rescue_ChIP


title: d2-Control_rep1 [RNA-seq]


title: ESC_rep3 [RNA-seq]


title: ESC_rep2 [RNA-seq]


title: KPC_shSlug2_starved5

data_processing:
Qiagen Genglobe UPX analysis primary analysis tools were used to generate gene count files  https://geneglobe.qiagen.com/us/analyze/
Qiagen Genglobe UPX analysis secondary  analysis tools were used to generate gene differential expression analysi https://geneglobe.qiagen.com/us/analyze/
Genome_build: mm10
Supplementary_files_format_and_content: normalized counts all genes

growth_protocol: All cell lines were maintained in DMEM culture media supplemented with 10% FBS and 100 units/mL penicillin/streptomycin under 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted from cells with the PureLink RNA Mini Kit (Thermo Fisher Scientific)
RNA libraries were prepared using the QIAseq UPX 3' Transcriptome

tag: strain background

value: KPC

value: pancreatic ductal adenocarcinoma (PDAC) cell line

value: Slug knockdown

tag: culture media

value: DMEM glutamine-free

tag: replicate number


title: Dolinoy_RNA_Liver_Pb_5month_Female_biorep2

description: UUID:5aa80085bba1a54d874cc0f2,QC_score:3,QC_stats:Pass

data_processing:
RNA-seq and ATAC-seq were sequenced by data production centers and processed by the TaRGET II DCC with standardized data processing pipelines. Library QC was assayed based on key QC parameters. Please refer to the TaRGET II data portal for detailed pipeline description and QC standard (https://data.targetepigenomics.org).
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak output for ATAC-seq and gene count table for RNA-seq


title: d4-Atg7 KO_rep1 [RNA-seq]


title: A549_AG15677_SMARCA4_rescue_ChIP


title: ESC_rep1 [RNA-seq]


title: Dolinoy_RNA_Liver_DEHP_5month_Male_biorep7

description: UUID:5aa808f6672a76bddfbba54c,QC_score:3,QC_stats:Pass

value: DEHP (bis (2-ethylhexyl) phthalate) 25mg DEHP/kg


title: d4-Atg7 KO_rep2 [RNA-seq]


title: KPC_shSlug2_starved4


title: Dolinoy_RNA_Liver_DEHP_5month_Male_biorep6

description: UUID:5aa808b9bba1a532d54cc157,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Liver_Ctrl_5month_Male_biorep6

description: UUID:5bce644682b0fa58ffa42856,QC_score:3,QC_stats:Pass

extract_protocol:
Sample collection was performed by Zhibin Wang lab at Johns Hopkins University. 5 month mice were CO2 euthanized. Liver and blood cells from individual mouse were isolated for subsequent DNA and RNA extractions according to the standard operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.
ATAC-seq and mRNA-seq experiments were performed by Zhibin Wang lab at Johns Hopkins University. mRNA and nuclei from 5 month mice liver and blood were isolated for subsequent ATAC-seq and mRNA-seq library preparations according to the operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.

value: Control Drinking Water 0 ppb


title: ZhibinWang_RNA_Liver_Ctrl_5month_Male_biorep4

description: UUID:5bce63ce2e6ad7eab0d6bcf3,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Liver_Ctrl_5month_Male_biorep5

description: UUID:5bce640a82b0faf1f4a42854,QC_score:3,QC_stats:Pass


title: A549_AG15679_SMARCA4_null_ChIP


title: ZhibinWang_RNA_Liver_Ctrl_5month_Male_biorep2

description: UUID:5aa7479a4b830df7d4652044,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Liver_Ctrl_5month_Male_biorep3

description: UUID:5aa74812c07a341baa722401,QC_score:2,QC_stats:Fail,Comment:Sample_failed_metadata_audit


title: Dolinoy_RNA_Liver_DEHP_5month_Male_biorep5

description: UUID:5aa807c9672a766dccbba51d,QC_score:3,QC_stats:Pass


title: KPC_shSlug2_starved2


title: KPC_shSlug2_starved1


title: Dolinoy_RNA_Liver_DEHP_5month_Male_biorep4

description: UUID:5aa80716bba1a541df4cc137,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Liver_Ctrl_5month_Male_biorep1

description: UUID:5aa7475e4b830dc2aa652043,QC_score:2,QC_stats:Fail


title: Dolinoy_RNA_Liver_Pb_5month_Female_biorep1

description: UUID:5aa8004a672a7607cbbba47d,QC_score:3,QC_stats:Pass


title: KPC_shSlug1_starved5


title: ZhibinWang_RNA_Liver_Ctrl_5month_Female_biorep4

description: UUID:5bce62de82b0fa9318a4284e,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Liver_Ctrl_5month_Female_biorep6

description: UUID:5bce635582b0fa3692a42851,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_DEHP_5month_Male_biorep3

description: UUID:5aa804bde80fac405c5b7e2d,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Liver_Ctrl_5month_Female_biorep3

description: UUID:5aa748c64b830d29e965204e,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_DEHP_5month_Male_biorep2

description: UUID:5aa801b3672a76853abba4a0,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_DEHP_5month_Male_biorep1

description: UUID:5aa80176672a769bd5bba49c,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Liver_As_5month_Male_biorep7

description: UUID:5da0e2c80a5f1e080040a7e6,QC_score:3,QC_stats:Pass

value: As (arsenite(3-)) 10ppb


title: KPC_shSlug1_starved3


title: Dolinoy_RNA_Liver_DEHP_5month_Female_biorep5

description: UUID:5aa80751bba1a56aba4cc143,QC_score:3,QC_stats:Pass

value: 5 month


title: KPC_shSlug1_starved2


title: KPC_shSlug2_starved3


title: ZhibinWang_RNA_Liver_As_5month_Male_biorep4

description: UUID:5bce622a82b0faec11a4284a,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_DEHP_5month_Female_biorep3

description: UUID:5aa804fa672a763d06bba4cb,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Liver_As_5month_Male_biorep3

description: UUID:5aa7493dc07a34205072240f,QC_score:2,QC_stats:Fail


title: KPC_shSlug1_starved4


title: ZhibinWang_RNA_Liver_Ctrl_5month_Female_biorep1

description: UUID:5aa7484e4b830d1c07652049,QC_score:3,QC_stats:Pass,Comment:Sample_failed_metadata_audit


title: KPC_shSlug1_starved1


title: ZhibinWang_RNA_Liver_As_5month_Male_biorep5

description: UUID:5bce62652e6ad72bc1d6bced,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_DEHP_5month_Female_biorep4

description: UUID:5aa8069d672a76b564bba508,QC_score:3,QC_stats:Pass


title: KPC_shLuc_starved5

value: shLuc as control


title: ZhibinWang_RNA_Liver_Ctrl_5month_Female_biorep5

description: UUID:5bce631a2e6ad7e69fd6bcf0,QC_score:3,QC_stats:Pass


title: KPC_shLuc_starved4


title: Dolinoy_RNA_Liver_DEHP_5month_Female_biorep1

description: UUID:5aa8013b672a76121bbba494,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_DEHP_5month_Female_biorep2

description: UUID:5aa80481e80fac05d45b7e2a,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Liver_As_5month_Male_biorep2

description: UUID:5aa749024b830d71b5652053,QC_score:2,QC_stats:Fail

value: Male


title: ZhibinWang_RNA_Liver_As_5month_Female_biorep5

description: UUID:5bce61ee82b0fa2d5ea42849,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Liver_As_5month_Male_biorep1

description: UUID:5aa748c5c07a349fd472240d,QC_score:2,QC_stats:Fail


title: ZhibinWang_RNA_Liver_As_5month_Female_biorep6

description: UUID:5da0e2c80a5f1eeb6d40a7e5,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Liver_Ctrl_5month_Male_biorep7

description: UUID:5da0e2c80a5f1e0a9e40a7e7,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Liver_Ctrl_5month_Female_biorep2

description: UUID:5aa7484e4b830d5f3365204a,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Liver_As_5month_Female_biorep4

description: UUID:5bce61b282b0fa87a4a42847,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_Ctrl_5month_Male_biorep6

description: UUID:5aa809e6bba1a53f8d4cc17f,QC_score:3,QC_stats:Pass

value: Avy

value: Control Diet Control


title: KPC_shLuc_starved3


title: ZhibinWang_RNA_Liver_As_5month_Female_biorep3

description: UUID:5bce61b282b0fa12c8a42848,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Liver_As_5month_Female_biorep2

description: UUID:5aa7497bce6fa7430f54ec8e,QC_score:2,QC_stats:Fail


title: ZhibinWang_RNA_Liver_As_5month_Male_biorep6

description: UUID:5bce62a182b0fa0229a4284c,QC_score:3,QC_stats:Pass


title: KPC_shLuc_starved2


title: ZhibinWang_RNA_Liver_As_5month_Female_biorep1

description: UUID:5aa7497a7a87c44b6e7b7fbd,QC_score:2,QC_stats:Fail


title: Dolinoy_RNA_Liver_Ctrl_5month_Male_biorep5

description: UUID:5aa809aabba1a59ff84cc174,QC_score:3,QC_stats:Pass


title: KPC_shLuc_starved1


title: Dolinoy_RNA_Liver_Ctrl_5month_Male_biorep4

description: UUID:5aa80662e80facff1a5b7e49,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Blood_Ctrl_5month_Male_biorep5

description: UUID:5c91bb3a3543a953eb7e6f36,QC_score:3,QC_stats:Pass

value: Blood


title: ZhibinWang_RNA_Blood_Ctrl_5month_Male_biorep3

description: UUID:5aa74ae28e8eba25df4ac5da,QC_score:2,QC_stats:Fail


title: Dolinoy_RNA_Liver_Ctrl_5month_Male_biorep3

description: UUID:5aa80446e80facde135b7e28,QC_score:3,QC_stats:Pass


title: KPC_Starved4


title: Dolinoy_RNA_Liver_Ctrl_5month_Male_biorep2

description: UUID:5aa80392bba1a584b64cc124,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Blood_Ctrl_5month_Male_biorep1

description: UUID:5aa749f1ce6fa76ee254ec94,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Blood_Ctrl_5month_Female_biorep6

description: UUID:5da0e2ca0a5f1eb86540a7ed,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_Ctrl_5month_Male_biorep1

description: UUID:5aa8000ebba1a552124cc0ea,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Blood_Ctrl_5month_Female_biorep3

description: UUID:5c91bcdd3543a96b317e6f3a,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Blood_Ctrl_5month_Female_biorep5

description: UUID:5da0e2c70a5f1e613f40a7e4,QC_score:3,QC_stats:Pass


title: KPC_Starved2


title: ZhibinWang_RNA_Blood_Ctrl_5month_Female_biorep4

description: UUID:5c91bd563543a93e1e7e6f3d,QC_score:3,QC_stats:Pass


title: KPC_Starved3


title: ZhibinWang_RNA_Blood_Ctrl_5month_Female_biorep2

description: UUID:5c91bc663543a959777e6f39,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_Ctrl_5month_Female_biorep6

description: UUID:5aa80a9ae80fac76b65b7e85,QC_score:3,QC_stats:Pass


title: KPC_Starved1


title: Dolinoy_RNA_Liver_Ctrl_5month_Female_biorep5

description: UUID:5aa80a5ee80fac9e565b7e76,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Blood_Ctrl_5month_Female_biorep1

description: UUID:5aa74b1e7a87c414967b7fcb,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Blood_As_5month_Male_biorep9

description: UUID:5da0e2cd0a5f1ece0040a7f2,QC_score:3,QC_stats:Pass


title: KPC_Ctrl5

value: DMEM complete


title: Dolinoy_RNA_Liver_Ctrl_5month_Female_biorep4

description: UUID:5aa80932672a76140ebba54e,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Blood_Ctrl_5month_Male_biorep6

description: UUID:5c91bbb23543a95c4f7e6f38,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Blood_As_5month_Male_biorep7

description: UUID:5da0e2ca0a5f1e87c340a7ec,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Blood_As_5month_Male_biorep8

description: UUID:5da0e2cb0a5f1e701c40a7ef,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Blood_Ctrl_5month_Male_biorep4

description: UUID:5c91bac13543a960aa7e6f35,QC_score:3,QC_stats:Pass


title: KPC_Ctrl4


title: KPC_Starved5


title: ZhibinWang_RNA_Blood_As_5month_Male_biorep6

description: UUID:5c91be813543a90d307e6f43,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_Ctrl_5month_Female_biorep3

description: UUID:5aa805ea672a76509dbba4ec,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Blood_Ctrl_5month_Male_biorep2

description: UUID:5aa74ae27a87c468c37b7fc9,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Blood_As_5month_Male_biorep5

description: UUID:5c91be0a3543a9a2a37e6f40,QC_score:3,QC_stats:Pass


title: KPC_Ctrl3


title: Dolinoy_RNA_Liver_Ctrl_5month_Female_biorep2

description: UUID:5aa803cebba1a57d4c4cc125,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Blood_As_5month_Male_biorep3

description: UUID:5aa74b5b8e8eba3c934ac5e4,QC_score:2,QC_stats:Fail


title: ZhibinWang_RNA_Blood_As_5month_Male_biorep4

description: UUID:5c91bdceb527563585d068fd,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Blood_As_5month_Male_biorep2

description: UUID:5aa74b5a8e8eba391d4ac5e3,QC_score:2,QC_stats:Fail


title: KPC_Ctrl2


title: KPC_Ctrl1


title: ZhibinWang_RNA_Blood_As_5month_Female_biorep6

description: UUID:5c91bfeab527561bdfd06906,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Blood_As_5month_Female_biorep5

description: UUID:5c91bf71b52756510fd06903,QC_score:3,QC_stats:Pass,Comment:Sample_failed_metadata_audit


title: ZhibinWang_RNA_Blood_As_5month_Female_biorep4

description: UUID:5c91bef9b527565a79d06900,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_Pb_5month_Male_biorep5

description: UUID:5aa80572672a760855bba4df,QC_score:3,QC_stats:Pass

value: Pb 16ppm lead acetate


title: Dolinoy_RNA_Liver_Ctrl_5month_Female_biorep1

description: UUID:5aa7ffd3bba1a574dc4cc0e0,QC_score:3,QC_stats:Pass

value: Liver


title: ZhibinWang_RNA_Blood_As_5month_Male_biorep1

description: UUID:5aa74b598e8eba5b134ac5e2,QC_score:2,QC_stats:Fail


title: ZhibinWang_RNA_Blood_As_5month_Female_biorep3

description: UUID:5aa74c0d8e8eba1b8f4ac5f0,QC_score:3,QC_stats:Pass

value: Female


title: Walker_ATAC_Liver_TBT_5month_Male_biorep6

description: UUID:5bd9db1e8105138c18820a13,QC_score:9,QC_stats:Pass

value: TBT (Tributyltin chloride) 0.5 mg/kg bw/d


title: Walker_ATAC_Liver_TBT_5month_Male_biorep5

description: UUID:5bd9db1d8ced1f231cdc7ea4,QC_score:9,QC_stats:Pass


title: Dolinoy_RNA_Blood_Pb_5month_Male_biorep4

description: UUID:5aa802debba1a569904cc113,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Blood_As_5month_Female_biorep1

description: UUID:5aa74b967a87c40ac77b7fd6,QC_score:3,QC_stats:Pass


title: ZhibinWang_RNA_Blood_As_5month_Female_biorep2

description: UUID:5aa74bd28e8eba693c4ac5ea,QC_score:3,QC_stats:Pass


title: Walker_ATAC_Liver_TBT_5month_Male_biorep4

description: UUID:5bd9daa58ced1f737edc7ea1,QC_score:2,QC_stats:Fail


title: ZhibinWang_ATAC_Liver_Ctrl_5month_Male_biorep6

description: UUID:5ccb3c522002e823f51b2f58,QC_score:0,QC_stats:Fail


title: Dolinoy_RNA_Blood_Pb_5month_Male_biorep3

description: UUID:5aa802a1e80facf6f75b7df7,QC_score:3,QC_stats:Pass


title: ZhibinWang_ATAC_Liver_Ctrl_5month_Male_biorep5

description: UUID:5c93b2e5c6f1d3ead225b847,QC_score:10,QC_stats:Pass


title: ZhibinWang_ATAC_Liver_Ctrl_5month_Male_biorep4

description: UUID:5c93b1f59b214b2956528a0b,QC_score:6,QC_stats:Pass


title: Walker_ATAC_Liver_TBT_5month_Male_biorep3

description: UUID:5bd9da2e8105138a09820a0c,QC_score:5,QC_stats:Pass


title: Dolinoy_RNA_Blood_Pb_5month_Male_biorep2

description: UUID:5aa8022bbba1a54bf34cc107,QC_score:3,QC_stats:Pass


title: ZhibinWang_ATAC_Liver_Ctrl_5month_Male_biorep2

description: UUID:5bd0955d048d0d609eb71413,QC_score:10,QC_stats:Pass


title: Walker_ATAC_Liver_TBT_5month_Male_biorep2

description: UUID:5bd9da2e8105136946820a0d,QC_score:9,QC_stats:Pass


title: ZhibinWang_ATAC_Liver_Ctrl_5month_Male_biorep3

description: UUID:5c93b17ec6f1d3dc8325b845,QC_score:8,QC_stats:Pass


title: Dolinoy_RNA_Blood_Pb_5month_Male_biorep6

description: UUID:5aa80842672a760d3dbba532,QC_score:3,QC_stats:Pass


title: ZhibinWang_ATAC_Liver_Ctrl_5month_Male_biorep1

description: UUID:5bd093b9b35d341446ea0911,QC_score:10,QC_stats:Pass


title: Walker_ATAC_Liver_TBT_5month_Male_biorep1

description: UUID:5bd9d9f28ced1f3686dc7e9b,QC_score:5,QC_stats:Pass


title: Dolinoy_RNA_Blood_Pb_5month_Female_biorep6

description: UUID:5aa807ca672a76f383bba51f,QC_score:3,QC_stats:Pass


title: ZhibinWang_ATAC_Liver_Ctrl_5month_Female_biorep5

description: UUID:5c93b44e9b214b246f528a13,QC_score:2,QC_stats:Fail


title: ZhibinWang_ATAC_Liver_Ctrl_5month_Female_biorep6

description: UUID:5c93b489c6f1d3331325b84b,QC_score:6,QC_stats:Pass


title: Walker_ATAC_Liver_TBT_5month_Female_biorep6

description: UUID:5bd9d75d810513c578820a00,QC_score:3,QC_stats:Fail


title: Dolinoy_RNA_Blood_Pb_5month_Female_biorep5

description: UUID:5aa80535672a761818bba4d5,QC_score:3,QC_stats:Pass


title: ZhibinWang_ATAC_Liver_Ctrl_5month_Female_biorep4

description: UUID:5c93b3999b214b671a528a10,QC_score:7,QC_stats:Pass


title: ZhibinWang_ATAC_Liver_Ctrl_5month_Female_biorep3

description: UUID:5bd099596801247044cab090,QC_score:10,QC_stats:Pass


title: ZhibinWang_ATAC_Liver_Ctrl_5month_Female_biorep2

description: UUID:5bd097b6b35d342ffaea0918,QC_score:10,QC_stats:Pass


title: Walker_ATAC_Liver_TBT_5month_Female_biorep4

description: UUID:5bd9d66e516538c7bf671623,QC_score:6,QC_stats:Pass


title: ZhibinWang_ATAC_Liver_As_5month_Male_biorep6

description: UUID:5c93b5f19b214ba312528a1b,QC_score:7,QC_stats:Pass


title: Walker_ATAC_Liver_TBT_5month_Female_biorep5

description: UUID:5bd9d6a981051385a48209fd,QC_score:5,QC_stats:Pass


title: Dolinoy_RNA_Blood_Pb_5month_Female_biorep4

description: UUID:5aa80266bba1a540a24cc109,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_Pb_5month_Female_biorep3

description: UUID:5aa801edbba1a5ef704cc103,QC_score:3,QC_stats:Pass


title: ZhibinWang_ATAC_Liver_As_5month_Male_biorep5

description: UUID:5c93b57ac6f1d323d525b84e,QC_score:4,QC_stats:Fail


title: ZhibinWang_ATAC_Liver_Ctrl_5month_Female_biorep1

description: UUID:5bd0964db35d34e406ea0914,QC_score:10,QC_stats:Pass


title: Dolinoy_RNA_Blood_Pb_5month_Female_biorep2

description: UUID:5aa80085bba1a542304cc0f3,QC_score:3,QC_stats:Pass


title: ZhibinWang_ATAC_Liver_As_5month_Male_biorep2

description: UUID:5bd09d19b35d343c74ea0920,QC_score:10,QC_stats:Pass


title: Walker_ATAC_Liver_TBT_5month_Female_biorep2

description: UUID:5bd9d5ba8ced1fd139dc7e9a,QC_score:8,QC_stats:Pass


title: Dolinoy_RNA_Blood_Pb_5month_Male_biorep1

description: UUID:5aa800c2e80fac3fc95b7de1,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_Pb_5month_Female_biorep1

description: UUID:5aa8004b672a76ab97bba47e,QC_score:3,QC_stats:Pass


title: ZhibinWang_ATAC_Liver_As_5month_Female_biorep5

description: UUID:5c93b759c6f1d3a79925b852,QC_score:10,QC_stats:Pass


title: ZhibinWang_ATAC_Liver_As_5month_Female_biorep6

description: UUID:5c93b796c6f1d3621125b856,QC_score:1,QC_stats:Fail


title: ZhibinWang_ATAC_Liver_As_5month_Male_biorep3

description: UUID:5bd09e81048d0d3b70b71416,QC_score:10,QC_stats:Pass


title: ZhibinWang_ATAC_Liver_As_5month_Male_biorep4

description: UUID:5c93b502c6f1d32ed725b84d,QC_score:9,QC_stats:Pass


title: ZhibinWang_ATAC_Liver_As_5month_Female_biorep4

description: UUID:5c93b6a5c6f1d345d825b850,QC_score:9,QC_stats:Pass


title: Walker_ATAC_Liver_Ctrl_5month_Male_biorep6

description: UUID:5bd9d97a516538681d671632,QC_score:5,QC_stats:Pass

value: Control Drinking Water 0 mg/kg


title: Dolinoy_RNA_Blood_DEHP_5month_Male_biorep6

description: UUID:5aa8087ebba1a5d1a34cc14f,QC_score:3,QC_stats:Pass


title: ZhibinWang_ATAC_Liver_As_5month_Female_biorep3

description: UUID:5bd0a18e65ea3d159805e694,QC_score:10,QC_stats:Pass


title: Walker_ATAC_Liver_TBT_5month_Female_biorep1

description: UUID:5bd9d5058b858c04c7610b15,QC_score:3,QC_stats:Fail


title: Dolinoy_RNA_Blood_DEHP_5month_Male_biorep7

description: UUID:5aa808babba1a56b814cc158,QC_score:3,QC_stats:Pass


title: Walker_ATAC_Liver_TBT_5month_Female_biorep3

description: UUID:5bd9d5f551653823ba671620,QC_score:5,QC_stats:Pass


title: Dolinoy_RNA_Blood_DEHP_5month_Male_biorep5

description: UUID:5aa8078e672a76019cbba511,QC_score:3,QC_stats:Pass


title: Walker_ATAC_Liver_Ctrl_5month_Male_biorep4

description: UUID:5bd9d8c6810513dc02820a06,QC_score:5,QC_stats:Pass


title: Walker_ATAC_Liver_Ctrl_5month_Male_biorep5

description: UUID:5bd9d93e8105135502820a09,QC_score:10,QC_stats:Pass


title: ZhibinWang_ATAC_Liver_As_5month_Female_biorep1

description: UUID:5bd09fae5af0253b6c688fa8,QC_score:9,QC_stats:Pass


title: Dolinoy_RNA_Blood_DEHP_5month_Male_biorep4

description: UUID:5aa806d9e80fac6b715b7e55,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_DEHP_5month_Male_biorep3

description: UUID:5aa80482e80facd42c5b7e2b,QC_score:3,QC_stats:Pass


title: Walker_ATAC_Liver_Ctrl_5month_Male_biorep2

description: UUID:5bd9d84e810513d9fb820a03,QC_score:8,QC_stats:Pass


title: Dolinoy_RNA_Blood_DEHP_5month_Male_biorep2

description: UUID:5aa801b2672a766798bba49e,QC_score:3,QC_stats:Pass


title: Biswal_ATAC_Liver_PM2.5_5month_Female_biorep8

description: UUID:5d25f41cd3d6e251a2039dc8,QC_score:6,QC_stats:Pass

extract_protocol:
Sample collection was performed by Shyam Biswal Lab at Johns Hopkins University. 5 month mice were CO2 euthanized. Liver and blood cells from individual mouse were isolated for subsequent DNA and RNA extractions according to the standard operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.
ATAC-seq and mRNA-seq experiments were performed by Shyam Biswal Lab at Johns Hopkins University. mRNA and nuclei from 5 month mice liver and blood were isolated for subsequent ATAC-seq and mRNA-seq library preparations according to the operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.


title: Biswal_ATAC_Liver_Ctrl_5month_Male_biorep8

description: UUID:5d25f415f1587205106ec98d,QC_score:5,QC_stats:Pass

value: Filtered Air NA


title: Biswal_ATAC_Liver_Ctrl_5month_Male_biorep9

description: UUID:5d25f417d3d6e2d40f039dbc,QC_score:7,QC_stats:Pass


title: Walker_ATAC_Liver_Ctrl_5month_Male_biorep3

description: UUID:5bd9d889516538152067162d,QC_score:8,QC_stats:Pass


title: Biswal_ATAC_Liver_PM2.5_5month_Female_biorep7

description: UUID:5d25f412d3d6e286fd039db5,QC_score:5,QC_stats:Pass


title: Biswal_ATAC_Liver_PM2.5_5month_Male_biorep7

description: UUID:5d25f412d3d6e2e75a039db4,QC_score:6,QC_stats:Pass


title: Biswal_ATAC_Liver_Ctrl_5month_Male_biorep7

description: UUID:5d25f414f1587230396ec98c,QC_score:5,QC_stats:Pass


title: Walker_ATAC_Liver_Ctrl_5month_Male_biorep1

description: UUID:5bd9d8115165380d6067162a,QC_score:6,QC_stats:Pass


title: Walker_ATAC_Liver_Ctrl_5month_Female_biorep6

description: UUID:5bd9d48e8ced1f80e1dc7e97,QC_score:7,QC_stats:Pass


title: Dolinoy_RNA_Blood_DEHP_5month_Male_biorep1

description: UUID:5aa80139e80fac53b25b7de8,QC_score:3,QC_stats:Pass


title: Walker_ATAC_Liver_Ctrl_5month_Female_biorep5

description: UUID:5bd9d4518ced1f3d0bdc7e94,QC_score:6,QC_stats:Pass


title: Dolinoy_RNA_Blood_DEHP_5month_Female_biorep5

description: UUID:5aa80716e80fac21065b7e61,QC_score:3,QC_stats:Pass


title: ZhibinWang_ATAC_Liver_As_5month_Female_biorep2

description: UUID:5bd0a09e5af0256d69688fac,QC_score:10,QC_stats:Pass


title: Dolinoy_RNA_Blood_DEHP_5month_Female_biorep4

description: UUID:5aa8069dbba1a564dd4cc135,QC_score:3,QC_stats:Pass


title: Biswal_ATAC_Liver_Ctrl_5month_Female_biorep8

description: UUID:5d25f416f15872697b6ec991,QC_score:6,QC_stats:Pass


title: Biswal_ATAC_Blood_PM2.5_5month_Male_biorep6

description: UUID:5ccb52a65fa153672a124689,QC_score:8,QC_stats:Pass


title: Biswal_ATAC_Liver_Ctrl_5month_Female_biorep9

description: UUID:5d25f41ad3d6e24964039dc5,QC_score:7,QC_stats:Pass


title: Biswal_ATAC_Blood_PM2.5_5month_Male_biorep4

description: UUID:5ccb52a3a6fde9b6ba6f0c63,QC_score:5,QC_stats:Pass


title: Biswal_ATAC_Blood_PM2.5_5month_Male_biorep5

description: UUID:5ccb52a4a6fde95c7e6f0c64,QC_score:0,QC_stats:Fail


title: ZhibinWang_ATAC_Liver_As_5month_Male_biorep1

description: UUID:5bd09b76b35d34c70bea091e,QC_score:10,QC_stats:Pass


title: Biswal_ATAC_Blood_PM2.5_5month_Male_biorep3

description: UUID:5ccb529c5fa1534cad12467c,QC_score:7,QC_stats:Pass


title: Biswal_ATAC_Blood_PM2.5_5month_Male_biorep2

description: UUID:5ccb529b5fa1534be612467b,QC_score:5,QC_stats:Pass


title: Walker_ATAC_Liver_Ctrl_5month_Female_biorep4

description: UUID:5bd9d4168ced1f3d2fdc7e93,QC_score:5,QC_stats:Pass


title: Walker_ATAC_Liver_Ctrl_5month_Female_biorep3

description: UUID:5bd9d3da8ced1fd0c4dc7e92,QC_score:8,QC_stats:Pass


title: Dolinoy_RNA_Blood_DEHP_5month_Female_biorep3

description: UUID:5aa804bee80fac0ff15b7e2e,QC_score:3,QC_stats:Pass


title: Biswal_ATAC_Blood_PM2.5_5month_Male_biorep1

description: UUID:5ccb52975fa1536253124672,QC_score:7,QC_stats:Pass


title: Dolinoy_RNA_Blood_DEHP_5month_Female_biorep2

description: UUID:5aa80447bba1a587714cc131,QC_score:3,QC_stats:Pass


title: Biswal_ATAC_Blood_PM2.5_5month_Female_biorep6

description: UUID:5ccb52a65fa1530ce9124687,QC_score:5,QC_stats:Pass


title: Walker_ATAC_Liver_Ctrl_5month_Female_biorep2

description: UUID:5bd9d39e8ced1f7b98dc7e91,QC_score:9,QC_stats:Pass


title: Biswal_ATAC_Blood_PM2.5_5month_Female_biorep4

description: UUID:5ccb529ba6fde9b5526f0c55,QC_score:2,QC_stats:Fail


title: Walker_ATAC_Liver_Ctrl_5month_Female_biorep1

description: UUID:5bd9d3618b858c41fa610b10,QC_score:6,QC_stats:Pass


title: Dolinoy_RNA_Blood_DEHP_5month_Female_biorep1

description: UUID:5aa800fd672a764cb0bba48d,QC_score:2,QC_stats:Fail


title: Biswal_ATAC_Blood_PM2.5_5month_Female_biorep3

description: UUID:5ccb529aa6fde97f406f0c53,QC_score:9,QC_stats:Pass


title: Biswal_ATAC_Blood_PM2.5_5month_Female_biorep2

description: UUID:5ccb52995fa153971d124676,QC_score:7,QC_stats:Pass


title: Biswal_ATAC_Liver_Ctrl_5month_Female_biorep7

description: UUID:5d25f413f1587224f96ec989,QC_score:7,QC_stats:Pass


title: Walker_ATAC_Blood_TBT_5month_Male_biorep6

description: UUID:5ccb4edf0b9dc1178a608679,QC_score:9,QC_stats:Pass


title: Biswal_ATAC_Blood_PM2.5_5month_Female_biorep1

description: UUID:5ccb5297a6fde93ae36f0c4f,QC_score:5,QC_stats:Pass


title: Dolinoy_RNA_Blood_Ctrl_5month_Male_biorep5

description: UUID:5aa8096ee80faccb6a5b7e65,QC_score:3,QC_stats:Pass


title: Walker_ATAC_Blood_TBT_5month_Male_biorep5

description: UUID:5ccb4edc5fa153c7f912465b,QC_score:9,QC_stats:Pass


title: Dolinoy_RNA_Blood_Ctrl_5month_Male_biorep4

description: UUID:5aa80626672a762f7ebba4ed,QC_score:3,QC_stats:Pass


title: Biswal_ATAC_Blood_Ctrl_5month_Male_biorep6

description: UUID:5ccb52a65fa1534c5e124688,QC_score:7,QC_stats:Pass


title: Biswal_ATAC_Blood_Ctrl_5month_Male_biorep5

description: UUID:5ccb52a55fa153448e124683,QC_score:9,QC_stats:Pass


title: Dolinoy_RNA_Blood_Ctrl_5month_Male_biorep3

description: UUID:5aa80409bba1a5cfa34cc12f,QC_score:3,QC_stats:Pass


title: Walker_ATAC_Blood_TBT_5month_Male_biorep4

description: UUID:5ccb4edc5fa1536b4912465d,QC_score:8,QC_stats:Pass


title: Walker_ATAC_Blood_TBT_5month_Male_biorep3

description: UUID:5ccb4edc5fa15339c812465c,QC_score:9,QC_stats:Pass


title: Biswal_ATAC_Blood_Ctrl_5month_Male_biorep4

description: UUID:5ccb52a15fa1535f6a12467f,QC_score:8,QC_stats:Pass


title: Biswal_ATAC_Blood_Ctrl_5month_Male_biorep1

description: UUID:5ccb5299a6fde962256f0c52,QC_score:9,QC_stats:Pass


title: Walker_ATAC_Blood_TBT_5month_Male_biorep2

description: UUID:5ccb4ed75fa1539af512464c,QC_score:7,QC_stats:Pass


title: Biswal_ATAC_Blood_Ctrl_5month_Male_biorep3

description: UUID:5ccb529e5fa15311df12467e,QC_score:5,QC_stats:Pass


title: Biswal_ATAC_Blood_Ctrl_5month_Male_biorep2

description: UUID:5ccb529a5fa1539d0712467a,QC_score:9,QC_stats:Pass


title: Dolinoy_RNA_Blood_Ctrl_5month_Male_biorep2

description: UUID:5aa80356bba1a541694cc11b,QC_score:3,QC_stats:Pass


title: Biswal_ATAC_Blood_Ctrl_5month_Female_biorep6

description: UUID:5ccb52a65fa1535a27124685,QC_score:5,QC_stats:Pass


title: Dolinoy_RNA_Blood_Ctrl_5month_Male_biorep1

description: UUID:5aa7ffd2bba1a552754cc0df,QC_score:3,QC_stats:Pass


title: Biswal_ATAC_Blood_PM2.5_5month_Female_biorep5

description: UUID:5ccb52a0a6fde9e92d6f0c5f,QC_score:8,QC_stats:Pass


title: Dolinoy_RNA_Blood_Ctrl_5month_Male_biorep6

description: UUID:5aa809aae80fac844d5b7e68,QC_score:3,QC_stats:Pass


title: Biswal_ATAC_Blood_Ctrl_5month_Female_biorep3

description: UUID:5ccb529a5fa153688e124679,QC_score:7,QC_stats:Pass


title: Dolinoy_RNA_Blood_Ctrl_5month_Female_biorep6

description: UUID:5aa80a5ebba1a55e824cc18c,QC_score:3,QC_stats:Pass


title: Walker_ATAC_Blood_TBT_5month_Female_biorep6

description: UUID:5ccb4ede0b9dc1d029608676,QC_score:10,QC_stats:Pass


title: Biswal_ATAC_Blood_Ctrl_5month_Female_biorep1

description: UUID:5ccb5298a6fde930996f0c51,QC_score:8,QC_stats:Pass


title: Dolinoy_RNA_Blood_Ctrl_5month_Female_biorep5

description: UUID:5aa80a21e80facbfe25b7e74,QC_score:3,QC_stats:Pass


title: Walker_ATAC_Blood_TBT_5month_Female_biorep5

description: UUID:5ccb4edd5fa153cf6212465e,QC_score:8,QC_stats:Pass


title: RRBS_MEF_D1cKO_d7_Tam_Rep2

data_processing:
Reads were cleaned with Trim Galore v0.4.2 using the parameters --rrbs --paired -r1 30 -r2 30 -q 20 --length 20 --stringency 5 --retain_unpaired. Reads were aligned to the mouse mm10 genome with BSMAP v2.74 using the parameters -v 2 -w 100 -r 1 -x 400 -m 30 -D C-CGG -n 1. Methylation percent values were extracted with methratio.py from BSMAP v2.74 using the parameters -z -u -g. CGs were filtered to have a minimum sequencing depth of 8X using custom developped scripts in R.
Genome_build: mm10
Supplementary_files_format_and_content: IGV files containing methylation scores for all CGs with at least 8X sequencing depth.

source_name: Mouse Embryonic Fibroblasts

extract_protocol:
Genomic DNA was extracted with the AllPrep DNA/RNA Mini Kit (Qiagen).
RRBS libraries were prepared as described in Auclair et al., Genome Biol 15:545 (2014). Briefly, we digested genomic DNA 5 hours with MspI (ThermoFisher Scientific), followed by end-repair and A-tailing with 5 U Klenow-fragment exo- (ThermoFisher Scientific) and ligation to methylated adapters overnight at 16°C with 30 U T4 DNA ligase (ThermoFisher Scientific) in Tango 1X buffer. Fragments between 150 and 400 bp were excised from a 3% agarose 0.5X TBE gel with the MinElute kit (Qiagen) and bisulfite-converted with the EpiTect Bisulfite kit (Qiagen) using two consecutive rounds of conversion. Final RRBS libraries were amplified with 14-16 cycles of PCR. The libraries were purified using Ampure XP beads (Beckman Coulter).

value: Dnmt1 L1/L1

tag: developmental stage

value: Mouse Embryonic Fibroblasts


title: RRBS_MEF_D1cKO_d7_Tam_Rep3


title: Dolinoy_RNA_Blood_Ctrl_5month_Female_biorep4

description: UUID:5aa80932bba1a5bbd74cc169,QC_score:3,QC_stats:Pass


title: RRBS_MEF_D1cKO_d7_Tam_Rep1


title: Dolinoy_RNA_Blood_Ctrl_5month_Female_biorep2

description: UUID:5aa80391bba1a5c1144cc123,QC_score:3,QC_stats:Pass


title: RRBS_MEF_D1cKO_d7_noTam_Rep2

value: Dnmt1 L2/L2


title: RRBS_MEF_D1cKO_d7_noTam_Rep1


title: Dolinoy_RNA_Blood_Ctrl_5month_Female_biorep3

description: UUID:5aa805e9e80fac48b55b7e3d,QC_score:3,QC_stats:Pass


title: RRBS_MEF_D1cKO_d7_noTam_Rep3


title: Biswal_ATAC_Blood_Ctrl_5month_Female_biorep5

description: UUID:5ccb529fa6fde9251e6f0c5e,QC_score:10,QC_stats:Pass


title: Biswal_ATAC_Blood_Ctrl_5month_Female_biorep4

description: UUID:5ccb529d5fa1538cb912467d,QC_score:7,QC_stats:Pass


title: Walker_ATAC_Blood_TBT_5month_Male_biorep1

description: UUID:5ccb4ed70b9dc1c4bd608673,QC_score:9,QC_stats:Pass


title: Walker_ATAC_Blood_TBT_5month_Female_biorep2

description: UUID:5ccb4eda5fa153489e124653,QC_score:7,QC_stats:Pass


title: RRBS_MEF_D1cKO_d5_Tam_Rep2


title: Walker_ATAC_Blood_TBT_5month_Female_biorep1

description: UUID:5ccb4ed95fa153245f124650,QC_score:8,QC_stats:Pass


title: RRBS_MEF_D1cKO_d5_Tam_Rep1


title: RRBS_MEF_D1cKO_d5_noTam_Rep2


title: RRBS_MEF_D1cKO_d5_noTam_Rep3


title: Dolinoy_ATAC_Liver_Pb_5month_Male_biorep6

description: UUID:5b75bd820331b94174afd2b3,QC_score:9,QC_stats:Pass


title: Biswal_ATAC_Blood_Ctrl_5month_Female_biorep2

description: UUID:5ccb52995fa1535fd6124675,QC_score:5,QC_stats:Pass


title: Dolinoy_RNA_Blood_Ctrl_5month_Female_biorep1

description: UUID:5aa7ff96bba1a5d3a44cc0d8,QC_score:3,QC_stats:Pass


title: Walker_ATAC_Blood_Ctrl_5month_Male_biorep6

description: UUID:5ccb4ee50b9dc1928560867e,QC_score:9,QC_stats:Pass


title: Mutlu_ATAC_Blood_PM2.5_5month_Male_biorep3

description: UUID:5d1d3d8c1657b26b476f04cf,QC_score:9,QC_stats:Pass


title: Walker_ATAC_Blood_Ctrl_5month_Male_biorep5

description: UUID:5ccb4ee25fa153984b124668,QC_score:10,QC_stats:Pass


title: Walker_ATAC_Blood_TBT_5month_Female_biorep4

description: UUID:5ccb4edd5fa153515d12465f,QC_score:9,QC_stats:Pass


title: Mutlu_ATAC_Blood_PM2.5_5month_Male_biorep5

description: UUID:5d1d3d8f1657b20b796f04d7,QC_score:8,QC_stats:Pass


title: Mutlu_ATAC_Blood_PM2.5_5month_Male_biorep2

description: UUID:5d1d3d8b1657b2d4246f04cb,QC_score:9,QC_stats:Pass


title: Dolinoy_ATAC_Liver_Pb_5month_Male_biorep3

description: UUID:5b75b8d2dbb5042bf3b01773,QC_score:9,QC_stats:Pass


title: Mutlu_ATAC_Blood_PM2.5_5month_Male_biorep4

description: UUID:5d1d3d8d1657b224276f04d1,QC_score:8,QC_stats:Pass


title: Dolinoy_ATAC_Liver_Pb_5month_Male_biorep4

description: UUID:5b75bcce0331b938f7afd2a8,QC_score:9,QC_stats:Pass


title: Dolinoy_ATAC_Liver_Pb_5month_Male_biorep2

description: UUID:5b75b45e0331b96e27afd287,QC_score:10,QC_stats:Pass


title: RRBS_MEF_D1cKO_d5_Tam_Rep3


title: Mutlu_ATAC_Blood_PM2.5_5month_Female_biorep4

description: UUID:5d1d3d8aca8f9f03f4f77cbf,QC_score:7,QC_stats:Pass


title: Walker_ATAC_Blood_Ctrl_5month_Male_biorep2

description: UUID:5ccb4ed85fa153e01212464e,QC_score:6,QC_stats:Pass


title: Mutlu_ATAC_Blood_PM2.5_5month_Female_biorep3

description: UUID:5d1d3d87ca8f9fb06df77cb5,QC_score:6,QC_stats:Pass


title: Walker_ATAC_Blood_Ctrl_5month_Male_biorep3

description: UUID:5ccb4edb5fa1534224124657,QC_score:6,QC_stats:Pass


title: Dolinoy_ATAC_Liver_Pb_5month_Male_biorep1

description: UUID:5b75b4210331b95368afd285,QC_score:9,QC_stats:Pass


title: Walker_ATAC_Blood_TBT_5month_Female_biorep3

description: UUID:5ccb4edd0b9dc17ba4608675,QC_score:10,QC_stats:Pass


title: Mutlu_ATAC_Blood_PM2.5_5month_Female_biorep1

description: UUID:5d1d3d861657b236586f04c9,QC_score:7,QC_stats:Pass


title: RRBS_MEF_D1cKO_d5_noTam_Rep1


title: Dolinoy_ATAC_Liver_Pb_5month_Male_biorep5

description: UUID:5b75bd0a0331b96609afd2ac,QC_score:9,QC_stats:Pass


title: Mutlu_ATAC_Blood_Ctrl_5month_Male_biorep3

description: UUID:5d1d3d8d1657b2469a6f04d3,QC_score:9,QC_stats:Pass

value: Filtered Air 0 particles/cm3/8hours/day


title: Walker_ATAC_Blood_Ctrl_5month_Female_biorep6

description: UUID:5ccb4ee25fa153528a124669,QC_score:8,QC_stats:Pass

value: 5 month


title: Walker_ATAC_Blood_Ctrl_5month_Male_biorep1

description: UUID:5ccb4ed70b9dc1ba9d608674,QC_score:9,QC_stats:Pass


title: Mutlu_ATAC_Blood_PM2.5_5month_Female_biorep2

description: UUID:5d1d3d87ca8f9f8743f77cb3,QC_score:2,QC_stats:Fail


title: Walker_ATAC_Blood_Ctrl_5month_Male_biorep4

description: UUID:5ccb4edb5fa1535784124656,QC_score:5,QC_stats:Pass


title: Mutlu_ATAC_Blood_Ctrl_5month_Male_biorep4

description: UUID:5d1d3d8e1657b261096f04d6,QC_score:8,QC_stats:Pass


title: Mutlu_ATAC_Blood_Ctrl_5month_Male_biorep2

description: UUID:5d1d3d8b1657b25d336f04cc,QC_score:9,QC_stats:Pass


title: Mutlu_ATAC_Blood_PM2.5_5month_Female_biorep5

description: UUID:5d1d3d8c1657b26da86f04cd,QC_score:6,QC_stats:Pass


title: Dolinoy_ATAC_Liver_Pb_5month_Female_biorep6

description: UUID:5b75bc569e0913104bf625e2,QC_score:9,QC_stats:Pass


title: Mutlu_ATAC_Blood_Ctrl_5month_Male_biorep1

description: UUID:5d1d3d861657b21e376f04c7,QC_score:9,QC_stats:Pass


title: Dolinoy_ATAC_Liver_Pb_5month_Female_biorep4

description: UUID:5b75b81d9e09136ff4f625cc,QC_score:6,QC_stats:Pass


title: Mutlu_ATAC_Blood_Ctrl_5month_Female_biorep9

description: UUID:5d9e0009b529a955f4e74b39,QC_score:9,QC_stats:Pass


title: Mutlu_ATAC_Blood_PM2.5_5month_Male_biorep1

description: UUID:5d1d3d8aca8f9f70d4f77cc0,QC_score:10,QC_stats:Pass


title: Mutlu_ATAC_Blood_Ctrl_5month_Female_biorep7

description: UUID:5d9e0008b529a950c0e74b35,QC_score:9,QC_stats:Pass


title: Dolinoy_ATAC_Liver_Pb_5month_Female_biorep3

description: UUID:5b75b7a6dbb504dd97b0176e,QC_score:6,QC_stats:Pass


title: Walker_ATAC_Blood_Ctrl_5month_Female_biorep4

description: UUID:5ccb4eda5fa1536a20124654,QC_score:8,QC_stats:Pass


title: Mutlu_ATAC_Blood_Ctrl_5month_Female_biorep6

description: UUID:5d9e0008b529a9474ce74b37,QC_score:9,QC_stats:Pass


title: Walker_ATAC_Blood_Ctrl_5month_Female_biorep3

description: UUID:5ccb4ed95fa153edf6124652,QC_score:9,QC_stats:Pass


title: Dolinoy_ATAC_Liver_Pb_5month_Female_biorep2

description: UUID:5b75b3aadbb5047704b01764,QC_score:8,QC_stats:Pass


title: Mutlu_ATAC_Blood_Ctrl_5month_Female_biorep5

description: UUID:5d9e0007b529a9895ee74b34,QC_score:9,QC_stats:Pass


title: Walker_ATAC_Blood_Ctrl_5month_Female_biorep2

description: UUID:5ccb4ed95fa153ceda124651,QC_score:10,QC_stats:Pass


title: Dolinoy_ATAC_Liver_Pb_5month_Female_biorep5

description: UUID:5b75b85adbb5040465b01771,QC_score:10,QC_stats:Pass


title: Mutlu_ATAC_Blood_Ctrl_5month_Female_biorep3

description: UUID:5d1d3d8aca8f9f5322f77cbe,QC_score:3,QC_stats:Fail


title: Walker_ATAC_Blood_Ctrl_5month_Female_biorep1

description: UUID:5ccb4ed85fa1531b5612464f,QC_score:8,QC_stats:Pass


title: Bartolomei_RNA_Liver_Ctrl_5month_Male_biorep6

description: UUID:5d37229b4b679d83bc0240eb,QC_score:3,QC_stats:Pass

extract_protocol:
Sample collection was performed by Marisa Bartolomei lab at University of Pennsylvania. 5 month mice were CO2 euthanized. Liver and blood cells from individual mouse were isolated for subsequent DNA and RNA extractions according to the standard operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.
ATAC-seq and mRNA-seq experiments were performed by Marisa Bartolomei lab at University of Pennsylvania. mRNA and nuclei from 5 month mice liver and blood were isolated for subsequent ATAC-seq and mRNA-seq library preparations according to the operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.

value: Control Diet NA


title: Mutlu_ATAC_Blood_Ctrl_5month_Female_biorep10

description: UUID:5d9e000bb529a96dbde74b3f,QC_score:9,QC_stats:Pass


title: Dolinoy_ATAC_Liver_DEHP_5month_Male_biorep7

description: UUID:5b75bc1a9e09131f89f625e1,QC_score:10,QC_stats:Pass

value: Male

value: DEHP (bis (2-ethylhexyl) phthalate) 25mg DEHP/kg


title: Walker_ATAC_Blood_Ctrl_5month_Female_biorep5

description: UUID:5ccb4edb5fa153f077124659,QC_score:10,QC_stats:Pass


title: Mutlu_ATAC_Blood_Ctrl_5month_Female_biorep1

description: UUID:5d1d3d88ca8f9f7027f77cb7,QC_score:2,QC_stats:Fail


title: Bartolomei_RNA_Liver_Ctrl_5month_Male_biorep5

description: UUID:5d37229a4b679d2b890240e9,QC_score:3,QC_stats:Pass


title: Mutlu_ATAC_Blood_Ctrl_5month_Female_biorep2

description: UUID:5d1d3d89ca8f9fe1e9f77cbb,QC_score:5,QC_stats:Pass


title: Dolinoy_ATAC_Liver_DEHP_5month_Male_biorep5

description: UUID:5b75b72e0331b938b9afd299,QC_score:10,QC_stats:Pass

value: Avy


title: Dolinoy_ATAC_Blood_Pb_5month_Male_biorep4

description: UUID:5cace1d98ad8b216055d12df,QC_score:10,QC_stats:Pass

value: Blood


title: Dolinoy_ATAC_Blood_Pb_5month_Male_biorep5

description: UUID:5cace3f56b074f27bfc08ecd,QC_score:10,QC_stats:Pass


title: Dolinoy_ATAC_Blood_Pb_5month_Male_biorep3

description: UUID:5cace072b6036d668e68c0ec,QC_score:9,QC_stats:Pass


title: Dolinoy_ATAC_Blood_Pb_5month_Male_biorep2

description: UUID:5cacdf0950bb2f7d3e743e60,QC_score:9,QC_stats:Pass