title: NXF1-iCLIP  SLBP KD-2

city: Shanghai

first: Hong

last: Cheng

address: 320 YueYang Road

department: Shanghai Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences

data_processing:
library strategy: iCLIP-seq
Briefly, custom scripts were used to demultiplex the different experimental samples by their sample barcodes. The reads containing adaptors were trimmed with cutadapt program and reads less than 18 bp were discard.
The remaining reads were then mapped to the human genome (hg19) including splicing junctions from GENCODE gene annotation (v19) with STAR. Usable reads obtained by removing potential PCR duplicates from mapped reads were used for further downstream analysis
Genome_build: hg19
Supplementary_files_format_and_content: bed

source_name: NXF1-iCLIP  SLBP KD

growth_protocol: HeLa cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (Biochrom)

extract_protocol:
Briefly, the cells for ALYREF iCLIP or NXF1-iCLIP were irradiated with UV light at 200 mJ/cm2 or 400 mJ/cm2.  After cell lysis, RNAs were partially fragmented using RNase I, followed by IPs with the ALYREF antibody immobilized on protein A Dynabeads (Life Technologies) or the Flag antibody immobilized on protein G Dynabeads (Life Technologies).  After extensive washing, immunoprecipitated RNAs were ligated at the 3’ ends to a RNA adapter and radioactively labeled by T4 polynucleotide kinase (Fermentas).  The protein-RNA complexes were then transferred to a nitrocellulose membrane.  Then, fragmented RNAs were purified from nitrocellulose membrane by PK treatment and phenol / chloroform extranction.
For iCLIP cDNA library preparation, fragmented RNAs, which were ligated with a RNA adapter (3' linker)  at the 3’ ends , reverse-transcribed with a primer containing a barcode (iCLIP RT primer).  The resulting cDNAs were purified by PAGE, circularized by single-stranded DNA ligase (Epicentre), linearized by restriction enzyme cleavage, and amplified and add P5/P3 adaptors by PCRs with (P3 and P5 solexa primer).

treatment_protocol: The ALYREF-iCLIP assay was performed in control and SLBP knock down cells using ALYREF antibody.  The NXF1-iCLIP experiments were carried out in Flag-NXF1 stable expressed cells treated with control, ALYREF and SLBP siRNAs for 72 hr using Flag antibody.

tag: cell line

value: HeLa

tag: genotype/variation

value: Flag-NXF1 stable expressed cells

tag: sirna treatment

value: SLBP knockdown

tag: antbody

value: FLAG antibody (Sigma, F3165)


title: Participant ID and visit (v) number [phchp296v1]

status: Public on Feb 27 2019

type: RNA

city: Indianapolis

first: Dr. Alexander

middle: B.

last: Niculescu

state: IN

address: 320 W. 15th Street

department: Psychiatry

country: USA

institute: Indiana University Medical School

description: Independent Test cohort blood gene expression data

hyb_protocol: Microarrays: Biotin labeled aRNA are hybridized to Affymetrix HG-U133 Plus 2.0 GeneChips according to manufacturer’s protocols http://www.affymetrix.com/support/technical/manual/expression_manual.affx. All GAPDH 3’/5’ ratios should be less than 2.0 and backgrounds under 50.

scan_protocol: Arrays are stained using standard Affymetrix protocols for antibody signal amplification and scanned on an Affymetrix GeneArray 2500 scanner with a target intensity set at 250. Present/Absent calls are determined using GCOS software with thresholds set at default values

data_processing: The AP derived and DE derived lists of genes were combined, and the gene expression data corresponding to them was used for the validation analysis. The cohorts (Validation Clinically Severe Stress, alongside the Low Stress and High Stress groups in the Discovery cohort) were assembled out of Affymetrix .cel data that was RMA normalized by gender and diagnosis. We transferred the log transformed expression data to an Excel sheet, and non-log transformed the data by taking 2 to the power of the transformed expression value. We then Z-scored the values by gender and diagnosis.  We then imported the Excel sheets with the Z-scored by gender and diagnosis expression data into Partek, and  statistical analyses were performed using a one-way ANOVA for the stepwise changed probesets, and also attempted a stringent Bonferroni corrections for all the probesets tested (Figure 1F). We also wrote an R script that automatically analyzes the data directly from the Excel sheet, and used that to confirm our calculations.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Whole Blood

label_protocol: Sample Labeling:  Sample labeling is performed using the Ambion MessageAmp II-BiotinEnhanced aRNA amplification kit. The procedure is briefly outlined below and involves the following steps:     1. Reverse Transcription to Synthesize First Strand cDNA is primed with the T7 Oligo(dT) Primer to synthesize cDNA containing a T7 promoter sequence.    2. Second Strand cDNA Synthesis converts the single-stranded cDNA into a double-stranded DNA (dsDNA) template for transcription. The reaction employs DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA.    3. cDNA Purification removes RNA, primers, enzymes, and salts that would inhibit in vitro transcription.    4. In Vitro Transcription to Synthesize aRNA with Biotin-NTP Mix generates multiple copies of biotin-modified aRNA from the double- stranded cDNA templates; this is the amplification step.    5. aRNA Purification removes unincorporated NTPs, salts, enzymes, and inorganic phosphate to improve the stability of the biotin-modified aRNA.

extract_protocol:
We used three independent cohorts: discovery (major psychiatric disorders), validation (major psychiatric disorders with clinically severe pain disorders), and testing (an independent major psychiatric disorders cohort for predicting pain state, and for predicting future ED visits for pain) (Figure 1A).
Subjects were recruited from the patient population at the Indianapolis VA Medical Center. All subjects understood and signed informed consent forms detailing the research goals, procedure, caveats and safeguards, per Indiana University IRB approved protocol. Subjects completed diagnostic assessments by an extensive structured clinical interview—Diagnostic Interview for Genetic Studies, and up to six testing visits, 3–6 months apart or whenever a new psychiatric hospitalization occurred. At each testing visit, they received a series of rating scales, including a visual analog scale (1-10) for assessing pain and the SF-36 quality of life scale, which has two pain related items (items 21 and 22), and the blood was drawn. We collected whole blood (10 ml) in two RNA-stabilizing PAXgene tubes, labeled with an anonymized ID number, and stored at -80 degrees C in a locked freezer until the time of future processing. Whole-blood RNA was extracted for microarray gene expression studies from the PAXgene tubes, as detailed below.
Whole blood (2.5 ml) RNA extraction: 2.5-5 ml of whole blood was collected into each PaxGene tube by routine venipuncture.  PaxGene tubes contain proprietary reagents for the stabilization of RNA. The cells from whole blood will be concentrated by centrifugation, the pellet washed, resuspended and incubated in buffers containing Proteinase K for protein digestion.  A second centrifugation step will be done to remove residual cell debris.  After the addition of ethanol for an optimal binding condition the lysate is applied to a silica-gel membrane/column.  The RNA bound to the membrane as the column is centrifuged and contaminants are removed in three wash steps.  The RNA is then eluted using DEPC-treated water.

tag: gender

value: Male

tag: diagnosis

value: BP

tag: test cohort pain state

value: Yes

tag: test cohort first year emergency department visits with pain

tag: test cohort all future emergency department visits with pain


title: Participant ID and visit (v) number [phchp298v2]

value: SZA


title: Participant ID and visit (v) number [phchp289v1]

value: Female

value: PTSD


title: Participant ID and visit (v) number [phchp286v3]


title: Participant ID and visit (v) number [phchp319v5]


title: Participant ID and visit (v) number [phchp286v2]


title: Participant ID and visit (v) number [phchp283v1]

value: SZ


title: NXF1-iCLIP  SLBP KD-1

type: SRA

country: China

library_source: transcriptomic


title: Participant ID and visit (v) number [phchp279v4]


title: NXF1-iCLIP  ALYREF KD-2

source_name: NXF1-iCLIP  ALYREF KD

value: ALYREF knockdown


title: Participant ID and visit (v) number [phchp277v4]


title: Participant ID and visit (v) number [phchp277v3]


title: Participant ID and visit (v) number [phchp325v2]


title: Ecrg4hetero beta-gal positive neurosphere

city: Sapporo

first: Toru

last: Kondo

address: Kita-15, Nishi-7, Kita-ku,

department: Institute for Genetic Medicine

country: Japan

institute: Hokkaido University

description: Gene expression

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

source_name: mouse neurosphere

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Both cells were cultured in DMEM/F12 containing chemicals, bFGF, EGF and heparin.

extract_protocol: Total RNA was prepared using a RNeasy Mini Kit (QIAGEN).

tag: strain

tag: tissue

value: brain

tag: age

tag: genotype

value: Ecrg4hetero beta-gal positive


title: Participant ID and visit (v) number [phchp277v5]


title: Participant ID and visit (v) number [phchp279v3]


title: Participant ID and visit (v) number [phchp279v1]


title: Participant ID and visit (v) number [phchp277v2]


title: Participant ID and visit (v) number [phchp276v3]


title: Participant ID and visit (v) number [phchp276v2]


title: Participant ID and visit (v) number [phchp277v1]


title: Participant ID and visit (v) number [phchp279v2]


title: Participant ID and visit (v) number [phchp276v4]


title: NXF1-iCLIP  Luc KD-1

source_name: NXF1-iCLIP  Luc KD

value: control


title: ALYREF-iCLIP SLBP KD-2

source_name: ALYREF-iCLIP SLBP KD

value: ALYREF antibody (ABclonal, A17974)


title: Ecrg4hetero beta-gal positive VZ/SVZ

description: Gene expression

source_name: mouse VZ/SVZ


title: ALYREF-iCLIP SLBP KD-1


title: NXF1-iCLIP  ALYREF KD-1


title: ALYREF-iCLIP Luc KD-2

source_name: ALYREF-iCLIP Luc KD


title: ALYREF-iCLIP Luc KD-1


title: NXF1-iCLIP  Luc KD-2


title: NC_6

city: tianjin

first: lili

last: tian

address: NO.154 Anshan Road

institute: tianjin medical university general hospital

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: peripheral blood mononuclear cells

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately, The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols after removing the ribosome RNA

value: blood

tag: condition

value: healthy control


title: NC_5


title: NC_4


title: NC_3


title: Participant ID and visit (v) number [phchp275v2]


title: Participant ID and visit (v) number [phchp276v1]


title: D2_2

value: acute ischemic stroke


title: D2_3


title: D2_1


title: Participant ID and visit (v) number [phchp275v3]


title: D1_5

value: subacute ischemic stroke


title: D2_6


title: Participant ID and visit (v) number [phchp274v4]


title: Participant ID and visit (v) number [phchp274v3]


title: Participant ID and visit (v) number [phchp275v1]


title: Participant ID and visit (v) number [phchp273v2]


title: Participant ID and visit (v) number [phchp273v1]


title: Participant ID and visit (v) number [phchp274v1]


title: Participant ID and visit (v) number [phchp270v4]


title: Participant ID and visit (v) number [phchp266v3]

value: MOOD


title: Participant ID and visit (v) number [phchp270v1]

value: Male


title: Participant ID and visit (v) number [phchp270v2]

value: BP


title: Participant ID and visit (v) number [phchp270v6]

value: Yes


title: Participant ID and visit (v) number [phchp270v3]


title: Participant ID and visit (v) number [phchp270v5]


title: Participant ID and visit (v) number [phchp274v2]


title: D2_4


title: D1_3


title: NC_1


title: D1_2


title: D1_4


title: D1_1


title: P0 Gjd3-CreEGFP mouse AVCS scRNA-seq library

city: Dallas

first: Gary

last: Hon

address: 5323 Harry Hines Blvd.

department: Department of Obstetrics and Gynecology

institute: UT Southwestern

data_processing:
BCL files generated by Illumina sequencing systems were demultiplexed and converted to standard FASTQ files using mkfastq function from Cell Ranger pipeline (version 2.1.0).
Reads were processed to generate expression (UMI count) matrices using Cell Ranger pipeline (version 2.1.0) with default parameters, except the parameter of expected number of cells, which was adjusted based on individual experiment.
Read1: Base 1-16 Cell barcode, 17-26 UMI
Genome_build: mm10
Supplementary_files_format_and_content: Raw UMI count matrices representing gene expression values (comma-separated) were generated as described above. Each column represents a single cell, each row represents a single gene.

molecule: polyA RNA

source_name: heart

growth_protocol: Hearts from neonatal P0 mice were dissected out, Cre+ hearts were selected based on tdTomato fluorescence expression, and AVCS was strictly microdissected guided by fluorescence reporter expression

extract_protocol:
Single cell suspension was washed with 1X PBS (0.04% BSA) before 10x Genomics procedure. The concentration of single cell suspension was adjusted to about 500 to 1000 cells/µL and was loaded on the 10x Genomics’ Chromium™ system (10x Genomics, Pleasanton, CA) with the aim of 6000 to 10000 cells per channel (Chromium™ Single Cell 3' Library & Gel Bead Kit v2, catalog number 120237).
Single cell RNA sequencing libraries were constructed following the manufacturer’s instructions (Zheng et al., 2017).

treatment_protocol: Microdissected AVCS was minced, digested, and single cell suspension was prepared using the Pierce Cardiomyocyte isolation Kit as stated in Materials and Methods section

tag: internal sample id

value: heart

tag: developmental stage


title: RNAseq in EB+48hrDox(iAscl1[bHLH:Ngn2].HA) replicate 1

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

data_processing:
Basecall conversion to fastq files was performed using Picard.
Alignment: fastq files were aligned to the mouse genome (version mm10) using tophat- 2.1.1 (Kim et al., 2013) with options “-r 100 --no-coverage-search”.
Gene counts: Rsubread (Liao et al., 2013), an R package, was used to assign reads to genes defined using Refseq (O’Leary et al., 2016) mm10 gene annotations.
Differential expression: The Wald test in the DESeq2 package (Love et al., 2014) was used for differential gene expression analysis. A q-value cutoff of less than 0.01 was used for calling differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: TXT: tab-delimited text file containing normalized RNA-seq tag counts per Refseq gene.

source_name: ES-derived embryoid bodies with induced transcription factors

growth_protocol: The inducible mESCs were grown in 2i (2-inhibitors) based medium (Advanced DMEM/F12: Neurobasal (1:1) Medium (GIBCO), supplemented with 2.5% mESC-grade fetal bovine serum (vol/vol, Corning), N2 (GIBCO), B27 (GIBCO), 2mM L-glutamine (GIBCO), 0.1 mM ß-mercaptoethanol (GIBCO), 1000 U/ml leukemia inhibitory factor (Millipore), 3mM CHIR (BioVision) and 1 mM PD0325901 (Sigma) on 0.1% gelatin (Milipore) coated plates at 37°C, 8% CO2. To obtain embryoid bodies (EBs), 60-70% confluent mESCs were dissociated by TrpLE (Gibco) and plated in AK medium (Advanced DMEM/F12: Neurobasal (1:1) Medium, 10% Knockout SR (vol/vol) (GIBCO), Pen/Strep (GIBCO), 2mM L-glutamine and 0.1mM ß-mercaptoethanol) on untreated plates for two days (day -2) at at 37°C, 8% CO2.

extract_protocol:
RNA-sseq: Cells were collected 0, 12 or 48 hours after Doxycycline TF induction and RNA was isolated by resuspending in Trizol reagent (Invitrogen, 15596026) followed by purification using Qiagen RNeasy mini kit (Qiagen, 74106).
Illumina TruSeq LS kit v2 (RS-122-2001; RS-122-2002) was used to prepare RNAseq libraries. The final quantification of the library before pooling was done with KAPA library amplification kit (Roche Lightcycler 480).

treatment_protocol: After two days, the EBs were passaged 1:2 and expression of the transgenes was induced by 3 ug/ml Doxycycline (Sigma D9891) to the AK medium. For RNA-seq experiments 2-3x10^5 cells were plated in each 100 mm untreated dishes (Corning).

tag: treatment

value: Dox induction + 48 hours

tag: cell type

value: Embryoid Bodies


title: Participant ID and visit (v) number [phchp266v1]


title: RNAseq in EB+48hrDox(iAscl1[bHLH:Ngn2].HA) replicate 2


title: RNAseq in EB+48hrDox(iAscl1.V5) replicate 4


title: RNAseq in EB+48hrDox(iAscl1.V5) replicate 5


title: RNAseq in EB+48hrDox(iFlag.Ngn2) replicate 1


title: scRNAseq in EB+48hrDox(iAscl1-v5 or iNeurog2 Tubb3::GFP)

description: A list of genotype-specific barcodes was not produced. Submitter pooled the genotypes and identified genotypes based on gene expression markers.

data_processing:
R1 is cell barcode (16bp) followed by UMI (10bp)  R2 is the RNA read (98bp)  I1 is the sample index (8bp)
Fastq files were generated by using CellRanger (version 2.1.0) mkfastq from 10X Genomics with default settings (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Feature counts: We added the transgene sequences to the reference genome manually to distinguish the two pooled cell lines: V5 (iAscl1) and GFP (iNeurog2 Tubb3::GFP) exogenous sequences were added to the end of chromosome 1 in FastA and GTF files of the mouse reference genome (mm10). A custom reference genome was generated by CellRanger mkref function by passing the modified FastA and GTF files. CellRanger count function was used to generate single cell feature counts for the library.
Downstream analysis: Downstream analysis and graph visualizations were performed in Seurat R package76 (version 2.3.4). Briefly, we removed the cells that have unique gene counts greater than 6800 (potential doublets) and less than 200. After removing the unwanted cells, we normalized the data by a global-scaling normalization method (LogNormalize) with the default scale factor (10000). Linear dimensional reduction was performed by PCA and the clustering was performed by using the statistically significant principal components (identified by jackStraw method and by standard deviation of principle components). The results were visualized by tSNE plots.
Genome_build: mm10
Supplementary_files_format_and_content: HDF5 format raw gene expression matrix from 10X Genomics cellranger count v2.1.0

extract_protocol:
Single-cell RNA-seq: Cells (iAscl1-v5 and iNeurog2 Tubb3::GFP) were collected 48 hours after Dox induction and washes were done in 1X PBS with 0.04 mg/ml BSA (Thermo Fisher Sci AM2616). Cells were strained with CellTrics 30 µM (Cat #04-004-2326) to remove cell clumps. Equal number of iA and iN Tubb3::GFP cells were pooled to have 1000 cells/ul.
10X Genomics Chromium Single Cell 3’ library kit was used to generate single cell library for a targeted cell recovery rate of 10.000 cells (120262 Chromium i7 Multiplex Kit, 120236 Chromium Single Cell 3' Chip Kit v2, 120237 Chromium Single Cell 3' Library & Gel Bead Kit v2). Fragment length distribution of the library was determined by Agilent High Sensitivity DNA D1000 Screentape (5067- 5585) system and the final quantification of the library before pooling was done with KAPA library amplification kit (Roche Lightcycler 480). The libraries were sequenced on Illumina NextSeq 500 High Output using V2.5 chemistry with 26x98 bp - 150 cycles run confirmation at the genomics core facility at NYU.

value: pooled Ainv15(iAscl1.V5) and Ainv15(iNeurog2 Tubb3::GFP)


title: RNAseq in EB+48hrDox(iAscl1.V5) replicate 3


title: Participant ID and visit (v) number [phchp259v3]

value: MDD


title: RNAseq in EB+48hrDox(iAscl1.V5) replicate 2


title: RNAseq in EB+12hrDox(iAscl1[bHLH:Ngn2].HA) replicate 2

value: Dox induction + 12 hours


title: RNAseq in EB+48hrDox(iAscl1.V5) replicate 1


title: Participant ID and visit (v) number [phchp258v2]

value: Female


title: Participant ID and visit (v) number [phchp258v3]


title: Participant ID and visit (v) number [phchp259v1]


title: Participant ID and visit (v) number [phchp265v1]

value: PTSD


title: Participant ID and visit (v) number [phchp253v2]


title: Participant ID and visit (v) number [phchp258v1]


title: Participant ID and visit (v) number [phchp266v2]


title: Participant ID and visit (v) number [phchp259v2]


title: Participant ID and visit (v) number [phchp253v1]


title: Participant ID and visit (v) number [phchp248v5]

value: SZ


title: Participant ID and visit (v) number [phchp248v2]


title: RNAseq in EB+12hrDox(iAscl1[bHLH:Ngn2].HA) replicate 1


title: Participant ID and visit (v) number [phchp248v3]


title: RNAseq in EB+48hrDox(iFlag.Ngn2) replicate 2


title: RNAseq in EB+12hrDox(iFlag.Ngn2) replicate 2


title: RNAseq in EB+12hrDox(iAscl1.V5) replicate 2


title: Participant ID and visit (v) number [phchp253v3]


title: RNAseq in EB+12hrDox(iFlag.Ngn2) replicate 1


title: Participant ID and visit (v) number [phchp247v1]


title: Participant ID and visit (v) number [phchp248v1]


title: RNAseq in EB+12hrDox(iAscl1.V5) replicate 1


title: RNAseq in EB+0hr(iFlagNgn2) replicate 1

source_name: ES-derived embryoid bodies

value: No treatment


title: RNAseq in EB+0hr(iNgn2.Isl1.Lhx3.V5) replicate 3


title: RNAseq in EB+0hr(iNgn2.Isl1.Lhx3.V5) replicate 2


title: RNAseq in EB+0hr(iNgn2.Isl1.Lhx3.V5) replicate 1


title: RNAseq in EB+0hr(iAscl1.V5) replicate 1


title: ChIPseq Onecut2 in EB+48hrDox(iFlag.Ngn2) replicate 1

description:
Onecut2_26012018_multigps_Onecut2_iNgn2_48hr.events.txt
Onecut2_26012018_multigps_Onecut2_iNgn2_48hr.bed

library_source: genomic

data_processing:
Basecall conversion to fastq files was performed using Picard.
Alignment: fastq files were aligned to the mouse genome (version mm10) using Bowtie (1.0.1) (Langmead et al., 2009) with options “-q --best --strata -m 1 --chunkmbs 1024”. Only uniquely mapped reads were considered for further analysis.
Binding event detection: MultiGPS was used to define transcription factor DNA binding events (Mahony et al., 2014). A q-value cutoff of 0.01 (assessed using binomial tests and Benjamini-Hochberg multiple hypothesis test correction), was used to call statistically significant binding events. Differential binding analysis between timepoints (12hr vs 48hr) or factor inductions (iAscl1 vs iNeurog2) was also performed using MultiGPS, which calls EdgeR (Robinson et al., 2009) internally. Differentially bound sites are defined as those that display significantly greater read enrichment levels (minimum 1.5-fold, q-value < 0.05) as determined by EdgeR’s negative binomial generalized linear models applied to MultiGPS’ per-replicate count data (TMM normalized).
Genome_build: mm10
Supplementary_files_format_and_content: MultiGPS: MultiGPS output files
Supplementary_files_format_and_content: BED: Conversion of MultiGPS output files to BED format, centered on the MultiGPS binding event location

molecule: genomic DNA

extract_protocol:
ChIP-seq: Cells were collected at 12 hours and 48 hours after TF induction and fixed with 1mM DSG (ProtoChem) followed by 1% FA (vol/vol) each for 15 min at room temperature. Pellets containing 25-30x10^6 cells were aliquoted and flash-frozen at -80°C. Cell aliquots were thawed on ice and resuspended in 5 ml of cold lysis buffer 1 (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol (vol/vol), 0.5% Igepal (vol/vol), 0.25% Triton X-100 (vol/vol)) with 1X protease inhibitors (Roche, 11697498001) and incubated at 4°C on a rotator. The samples were centrifuged for 5 min at 2300 rpm at 4°C and resuspended in 5ml of cold lysis buffer 2 (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol (vol/vol), 0.5% Igepal (vol/vol), 0.25% Triton X-100 (vol/vol)) with 1X protease inhibitors and incubated 10 min at 4°C on a rotator. Nuclear extracts were centrifuged for 5 min at 2300 rpm resuspended in cold 3 ml of sonication buffer (50mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1% Triton X-100, 0.1% sodium deoxycholate (wt/vol), 0.1% SDS (wt/vol). Sonication of the nuclear extracts was performed on ice with Branson 450 digital sonifier (Marshall Scientific, B450CC) at 20% amplitude, 18 cycles of 30s ON/60s OFF, to sheer crosslinked chromatin into average size of approximately 300 bp. Immunoprecipitation of the sonicated chromatin with Dynabeads protein-G (Thermo Fisher) conjugated antibodies were done overnight (16 hr) at 4°C on a rotator. 5 ug of following antibodies were used for immunoprecipitation.
In-house library preparation kit was used for ChIP-seq: 24ul of ChIP DNA (1:100 dilution of input DNA) was used to prepare lllumina DNA sequencing libraries. Bioo Scientific multiplexed adapters were ligated after end repair and A-tailing, and unligated adapters were removed by purification using Agencourt AmpureXP beads (Beckman Coulter). Adapter-ligated DNA was amplified by PCR using TruSeq primers (Sigma). DNA libraries between 300 and 500 bp in size were purified from agarose gel purified using Qiagen minElute columns. and the final quantification of the library before pooling was done with KAPA library amplification kit (Roche Lightcycler 480).

treatment_protocol: After two days, the EBs were passaged 1:2 and expression of the transgenes was induced by 3 ug/ml Doxycycline (Sigma D9891) to the AK medium. For ChIP-seq experiments, the seeded cell number was scaled up to 3-3.5x10^6 cells in 245 mm x 245 mm square dishes (Corning).

tag: chip target

tag: chip antibody

value: anti-Onecut2 (R&D Systems AF6294)


title: ChIPseq H3K27ac in EB+48hrDox(iFlag.Ngn2) replicate 2

value: anti-H3K27ac (Abcam ab4729)


title: ChIPseq Onecut2 in EB+48hrDox(iFlag.Ngn2) replicate 2


title: ChIPseq Ebf2 in EB+48hrDox(iFlag.Ngn2) replicate 1

description:
Ebf2_26012018_multigps_Ebf2_iNgn2_48hr.events.txt
Ebf2_26012018_multigps_Ebf2_iNgn2_48hr.bed

value: anti-Ebf2 (R&D Systems AF7006)


title: Participant ID and visit (v) number [phchp240v2]


title: Participant ID and visit (v) number [phchp242v3]


title: Participant ID and visit (v) number [phchp237v1]


title: Participant ID and visit (v) number [phchp238v2]


title: ChIPseq Brn2 in EB+48hrDox(iFlag.Ngn2) replicate 2

description:
Brn2_14112017_multigps_Brn2_iNgn2_48hr.events.txt
Brn2_14112017_multigps_Brn2_iNgn2_48hr.bed

value: anti-Brn2 (Santa Cruz SC-6029)


title: Participant ID and visit (v) number [phchp236v2]

value: Male


title: ChIPseq H3K27ac in EB+48hrDox(iFlag.Ngn2) replicate 1


title: Participant ID and visit (v) number [phchp239v3]

value: SZA


title: Participant ID and visit (v) number [phchp240v1]

value: Yes


title: Participant ID and visit (v) number [phchp239v1]


title: Participant ID and visit (v) number [phchp240v3]


title: Participant ID and visit (v) number [phchp242v1]


title: Participant ID and visit (v) number [phchp242v2]


title: Participant ID and visit (v) number [phchp241v1]

value: BP


title: ChIPseq Brn2 in EB+48hrDox(iFlag.Ngn2) replicate 1

value: Dox induction + 48 hours


title: Participant ID and visit (v) number [phchp239v2]


title: Participant ID and visit (v) number [phchp237v2]


title: Participant ID and visit (v) number [phchp238v3]


title: Participant ID and visit (v) number [phchp236v3]


title: Participant ID and visit (v) number [phchp238v1]


title: ChIPseq Onecut2 in EB+48hrDox(iAscl1.V5) replicate 2

description:
Onecut2_26012018_multigps_Onecut2_iAscl1_48hr.events.txt
Onecut2_26012018_multigps_Onecut2_iAscl1_48hr.bed

value: Embryoid Bodies


title: ChIPseq Neurog2 in EB+48hrDox(iFlag.Ngn2) replicate 1

description:
Ascl1_Ngn2_12_and_48_14112017_EB+48hr_iN_Ngn2.events.txt
Ascl1_Ngn2_12_and_48_14112017_EB+48hr_iN_Ngn2.bed

value: anti-Neurog2 (Santa Cruz SC-19233)


title: ChIPseq Ebf2 in EB+48hrDox(iFlag.Ngn2) replicate 2


title: Participant ID and visit (v) number [phchp236v1]

value: MDD


title: ChIPseq Neurog2 in EB+48hrDox(iFlag.Ngn2) replicate 2


title: ChIPseq H3K27ac in EB+48hrDox(iAscl1.V5) replicate 2


title: ChIPseq Brn2 in EB+48hrDox(iAscl1.V5) replicate 2

description:
Brn2_14112017_multigps_Brn2_iAscl1_48hr.events.txt
Brn2_14112017_multigps_Brn2_iAscl1_48hr.bed


title: ChIPseq Ebf2 in EB+48hrDox(iAscl1.V5) replicate 1

description:
Ebf2_26012018_multigps_Ebf2_iAscl1_48hr.events.txt
Ebf2_26012018_multigps_Ebf2_iAscl1_48hr.bed


title: ChIPseq Ebf2 in EB+48hrDox(iAscl1.V5) replicate 2


title: ChIPseq H3K27ac in EB+48hrDox(iAscl1.V5) replicate 1


title: Participant ID and visit (v) number [phchp234v3]


title: Participant ID and visit (v) number [phchp235v1]


title: Participant ID and visit (v) number [phchp235v2]


title: Participant ID and visit (v) number [phchp234v2]


title: Participant ID and visit (v) number [phchp235v3]


title: ChIPseq Ascl1 in EB+48hrDox(iAscl1.V5) replicate 2

description:
Ascl1_Ngn2_12_and_48_14112017_EB+48hr_iA_Ascl1.events.txt
Ascl1_Ngn2_12_and_48_14112017_EB+48hr_iA_Ascl1.bed

value: anti-Ascl1 (Abcam ab74065)


title: ChIPseq Ascl1 in EB+48hrDox(iAscl1.V5) replicate 1


title: ChIPseq in EB+12hrDox(iAscl1[bHLH:Ngn2].HA) input-DNA

value: input

value: Dox induction + 12 hours


title: ChIPseq Brn2 in EB+48hrDox(iAscl1.V5) replicate 1


title: ChIPseq A[N]bHLH.HA in EB+12hrDox(iAscl1[bHLH:Ngn2].HA) replicate 1

description:
Ascl1_Ngn2_06042017_EB+12hr_iA[N]_Ascl1[Ngn2].events.txt
Ascl1_Ngn2_06042017_EB+12hr_iA[N]_Ascl1[Ngn2].bed

value: A[N]bHLH

value: anti-HA (Abcam ab9110)


title: ChIPseq A[N]bHLH.HA in EB+12hrDox(iAscl1[bHLH:Ngn2].HA) replicate 2


title: ChIPseq in EB+12hrDox(iFlag.Ngn2) input-DNA


title: Participant ID and visit (v) number [phchp234v1]


title: Participant ID and visit (v) number [phchp228v1]

value: PTSD


title: Participant ID and visit (v) number [phchp229v1]


title: Participant ID and visit (v) number [phchp232v2]

value: Female


title: ChIPseq Neurog2 in EB+12hrDox(iFlag.Ngn2) replicate 2

description:
Ascl1_Ngn2_06042017_EB+12hr_iN_Ngn2.events.txt
Ascl1_Ngn2_06042017_EB+12hr_iN_Ngn2.bed


title: Participant ID and visit (v) number [phchp232v1]


title: Participant ID and visit (v) number [phchp227v3]


title: Participant ID and visit (v) number [phchp227v1]


title: Participant ID and visit (v) number [phchp227v2]


title: ChIPseq Ascl1 in EB+12hrDox(iAscl1.V5) input-DNA


title: ChIPseq Ascl1 in EB+12hrDox(iAscl1.V5) replicate 3

description:
Ascl1_Ngn2_06042017_EB+12hr_iA_Ascl1.events.txt
Ascl1_Ngn2_06042017_EB+12hr_iA_Ascl1.bed


title: ChIPseq Ascl1 in EB+12hrDox(iAscl1.V5) replicate 1


title: ChIPseq Ascl1 in EB+12hrDox(iAscl1.V5) replicate 2


title: Participant ID and visit (v) number [phchp231v1]


title: ChIPseq Neurog2 in EB+12hrDox(iFlag.Ngn2) replicate 3


title: ChIPseq Neurog2 in EB+12hrDox(iFlag.Ngn2) replicate 1


title: ATACseq in EB replicate 2

data_processing:
Basecall conversion to fastq files was performed using Picard.
Alignment: ATAC-seq data was mapped to the mouse genome (version mm10) using bowtie2-2.2.2 (Robinson et al., 2009) using “-q --very-sensitive” options.
Domain-finding: Enriched domains were identified using the DomainFinder module in SeqCode: (https://github.com/seqcode/seqcode-core/blob/master/src/org/seqcode/projects/seed/DomainFinder.java). Briefly, contiguous 50bp genomic bins with significantly higher read enrichment compared to normalized input were identified (binomial test, p-value < 0.05). Further, contiguous blocks within 200bp were joined together to call enriched domains.
Genome_build: mm10
Supplementary_files_format_and_content: BED: Domains displaying significant enrichment of ATAC-seq reads

extract_protocol:
ATAC-seq: 50.000 cells were harvested and washed twice in cold 1X PBS. Cells were resuspended in 10mM Tris pH 7.4, 10mM NaCl, 3mM MgCl2, and 0.1% NP-40 and centrifuged immediately at 4°C. The pellet was resuspended in 25 ul of 2x TD buffer, 2.5 ul TDE1 (Nextera DNA sample preparation kit, FC-121-1030) followed by incubation for 30 min at 37C. The reaction was then cleaned by Min-elute PCR purification kit (Qiagen, 28004). The optimal number of PCR cycles were determined to be the 1/3 of the maximum fluorescence measured by qPCR reaction with 1X SYBR Green (Invitrogen), custom designed primers (Buenrostro et al., 2013) and 2X NEB MasterMix (New England Labs, M0541). Following PCR enrichment, the library was cleaned with min-elute PCR kit and quantified using Qubit (Life Technologies, Q32854).
Nextera DNA sample preparation kit, FC-121-1030 was used for ATAC-seq. The fragment length distribution of the library was determined by Agilent High Sensitivity DNA D1000 Screentape (5067- 5585) system and the final quantification of the library before pooling was done with KAPA library amplification kit (Roche Lightcycler 480).

treatment_protocol: After two days, the EBs were passaged 1:2 and expression of the transgenes was induced by 3 ug/ml Doxycycline (Sigma D9891) to the AK medium. For ATAC-seq experiments, 2-3x10^5 cells were plated in each 100 mm untreated dishes (Corning).

value: No treatment


title: Participant ID and visit (v) number [phchp232v3]


title: Participant ID and visit (v) number [phchp226v3]


title: Participant ID and visit (v) number [phchp226v2]


title: Participant ID and visit (v) number [phchp222v3]

value: SZ


title: Participant ID and visit (v) number [phchp219v2]

value: Male


title: Participant ID and visit (v) number [phchp219v3]


title: Participant ID and visit (v) number [phchp226v1]


title: Participant ID and visit (v) number [phchp225v1]

value: PSYCH


title: ATACseq in EB+48hrDox(iAscl1[bHLH:Ngn2].HA) replicate 2

description: iAscl1[bHLH-Neurog2]_48h.atac-domains.p0.05.bed


title: ATACseq in EB+48hrDox(iAscl1[bHLH:Ngn2].HA) replicate 1


title: Participant ID and visit (v) number [phchp224v1]

value: Yes


title: ChIPseq Onecut2 in EB+48hrDox(iAscl1.V5) replicate 1

value: anti-Onecut2 (R&D Systems AF6294)


title: ATACseq in EB+48hrDox(iFlag.Ngn2) replicate 2

value: Dox induction + 48 hours


title: ATACseq in EB+48hrDox(iFlag.Ngn2) replicate 1

value: Embryoid Bodies


title: ATACseq in EB replicate 1


title: ATACseq in EB+12hrDox(iAscl1[bHLH:Ngn2].HA) replicate 2

description: iAscl1[bHLH-Neurog2]_12h.atac-domains.p0.05.bed


title: ATACseq in EB+48hrDox(iAscl1.V5) replicate 2


title: Participant ID and visit (v) number [phchp222v2]


title: ATACseq in EB+48hrDox(iAscl1.V5) replicate 1


title: Participant ID and visit (v) number [phchp219v1]

value: BP


title: Participant ID and visit (v) number [phchp216v3]

value: MOOD


title: ATACseq in EB+12hrDox(iFlag.Ngn2) replicate 2


title: ATACseq in EB+12hrDox(iAscl1[bHLH:Ngn2].HA) replicate 1


title: ATACseq in EB+12hrDox(iAscl1.V5) replicate 2


title: ATACseq in EB+12hrDox(iFlag.Ngn2) replicate 1


title: ATACseq in EB+12hrDox(iAscl1.V5) replicate 1


title: Participant ID and visit (v) number [phchp217v1]


title: Participant ID and visit (v) number [phchp216v2]


title: Participant ID and visit (v) number [phchp213v3]


title: MDA-MB-231-AdipoR1-KO-R3

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: Cells treated with AdipoR1-KO CRISPR

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

growth_protocol: Cell medium was composed as follow: DMEM 1X (Thermo Fisher), 10%  serum (Corning), 1X glutamine (Life Technologies), 1X penicillin/streptomycin (Life  Technologies), cells were grown in a CO2 incubator (5% CO2) at 37˚C

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit

value: breast cancer cell

tag: passages

value: Low passages (6-10)


title: MDA-MB-231-AdipoR1-KO-R1

description: Cells treated with AdipoR1-KO CRISPR


title: Participant ID and visit (v) number [phchp213v1]

tag: gender


title: MDA-MB-231-AdipoR1-WT-R3

description: Parental cell


title: Participant ID and visit (v) number [phchp212v2]

tag: diagnosis

value: MDD


title: MDA-MB-231-AdipoR1-KO-R2

description: Cells treated with AdipoR1-KO CRISPR


title: Participant ID and visit (v) number [phchp213v2]

tag: test cohort pain state


title: MDA-MB-231-AdipoR1-WT-R2

description: Parental cell


title: MDA-MB-231-AdipoR1-WT-R1

description: Parental cell


title: Participant ID and visit (v) number [phchp211v1]

tag: test cohort first year emergency department visits with pain


title: Participant ID and visit (v) number [phchp208v2]

tag: test cohort all future emergency department visits with pain


title: Participant ID and visit (v) number [phchp207v1]


title: Participant ID and visit (v) number [phchp208v1]


title: Participant ID and visit (v) number [phchp211v2]


title: MDA-MB-231-SET-KO-Clone2-R1

description: Cells treated with SET1B-SETKO gRNA

tag: strain


title: Participant ID and visit (v) number [phchp212v1]


title: MDA-MB-231-SET-KO-Clone1-R2

description: Cells treated with SET1B-SETKO gRNA


title: MDA-MB-231-SET-KO-Clone2-R2

description: Cells treated with SET1B-SETKO gRNA


title: Participant ID and visit (v) number [phchp198v4]


title: MDA-MB-231-SET-KO-Clone1-R1

description: Cells treated with SET1B-SETKO gRNA


title: Participant ID and visit (v) number [phchp204v1]


title: Participant ID and visit (v) number [phchp200v2]


title: Participant ID and visit (v) number [phchp199v1]


title: Participant ID and visit (v) number [phchp200v3]


title: Participant ID and visit (v) number [phchp199v3]


title: Participant ID and visit (v) number [phchp211v3]


title: MDA-MB-231-SET-WT-R1

description: Parental cell


title: Participant ID and visit (v) number [phchp204v2]


title: Participant ID and visit (v) number [phchp208v3]


title: MDA-MB-231-SET-WT-R2

description: Parental cell


title: HS083 SC-/-

city: Chilly Mazarin

first: Veeranagouda

last: Yaligara

address: Sanofi R&D

country: France

institute: Sanofi

description:
obese woman
C707_S11_001

data_processing:
Raw read QC
First and last 10 bases were trimmed and mapped Reference Human.B38 with GeneModel RefGene20170606
Count data generated using GeneModel RefGene20170606
Normalization by DESeq using count data (Gene IDs having at least 10 count or reads in any three samples were kept).
Log2 conversion (0   replaced with 1) using DESeq data (Log2DESeq)
Genome_build: Human.B38
Supplementary_files_format_and_content: Log2 DESeq

source_name: adipose tissue progenitor

growth_protocol: Native progenitor cells were sorted from human adipose tissue stromal vascular fraction after collagenase digestion without culture/treatment

extract_protocol:
Sorted progenitor cells were immediatly put in RNAprotect and frozen.
For AmpliSeq transcriptome sequencing library construction,  AmpliSeq™ Library PLUS, AmpliSeq Transcriptome Human Gene Expression Panel and AmpliSeq CD indexes SetA kits were purchased from Illumina and sequencing libraries were constructed as described in AmpliSeq for Illumina Transcriptome Human Gene Expression Panel reference guide (Illumina).
AmpliSeq Transcriptome Human Gene Expression Panel

tag: patient id

tag: subtype

value: subcutaneous

tag: sorted cells

value: subcutaneous -/-


title: HS083 VISC MSCA1+

description:
obese woman
C709_S13_001

value: visceral

value: visceral MSCA1+


title: HS083 SC -/CD271+

description:
obese woman
C706_S10_001

value: subcutaneous -/CD271+


title: HS083  VISC -/CD271+

description:
obese woman
C710_S14_001

value: visceral -/CD271+


title: HS083 VISC -/-

description:
obese woman
C711_S15_001

value: visceral -/-


title: Participant ID and visit (v) number [phchp200v1]

value: Male


title: HS083 SC MSCA1+

description:
obese woman
C705_S9_001

value: subcutaneous MSCA1+


title: Participant ID and visit (v) number [phchp197v2]

value: SZ

value: Yes


title: Participant ID and visit (v) number [phchp197v3]


title: BH056 VISC -/-

description:
obese woman
C703_S7_001


title: Participant ID and visit (v) number [phchp204v3]

value: Female


title: Participant ID and visit (v) number [phchp198v1]


title: BH056 VISC -/CD271+

description:
obese woman
C702_S6_001


title: BH056 VISC MSCA1+

description:
obese woman
C701_S5_001


title: BH056 SC -/-

description:
obese woman
C699_S3_001


title: Participant ID and visit (v) number [phchp197v1]


title: Participant ID and visit (v) number [phchp198v2]


title: Participant ID and visit (v) number [phchp196v1]


title: Participant ID and visit (v) number [phchp196v3]


title: Participant ID and visit (v) number [phchp195v3]


title: BH056 SC -/CD271+

description:
obese woman
C698_S2_001


title: Participant ID and visit (v) number [phchp197v4]


title: LD179 VISC -/-

description:
obese woman
C695_S23_001


title: BH056 SC MSCA1+

description:
obese woman
C697_S1_001


title: Participant ID and visit (v) number [phchp195v1]


title: Participant ID and visit (v) number [phchp194v2]


title: LD179 VISC MSCA1+

description:
obese woman
C693_S21_001


title: LD179 SC -/CD271+

description:
obese woman
C690_S18_001


title: Participant ID and visit (v) number [phchp199v2]


title: LD179  SC -/-

description:
obese woman
C691_S19_001


title: Participant ID and visit (v) number [phchp194v3]


title: Participant ID and visit (v) number [phchp193v4]

value: BP


title: Participant ID and visit (v) number [phchp196v2]


title: LD179  VISC -/CD271+

description:
obese woman
C694_S22_001


title: Participant ID and visit (v) number [phchp195v2]


title: ZV089  VISC -/CD271+

description:
obese woman
C686_S14_001


title: ZV089 SC -/-

description:
obese woman
C683_S11_001


title: LD179 SC MSCA1+

description:
obese woman
C689_S17_001


title: ZV089 VISC MSCA1+

description:
obese woman
C685_S13_001


title: ZV089 VISC -/-

description:
obese woman
C687_S15_001


title: ZV089 SC -/CD271+

description:
obese woman
C682_S10_001


title: Participant ID and visit (v) number [phchp194v1]


title: SM010 VISC -/-

description:
obese woman
C679_S7_001


title: Participant ID and visit (v) number [phchp193v1]


title: Participant ID and visit (v) number [phchp190v3]


title: Participant ID and visit (v) number [phchp190v2]


title: Participant ID and visit (v) number [phchp188v3]

value: PSYCH


title: Participant ID and visit (v) number [phchp190v1]


title: SM010 VISC -/CD271+

description:
obese woman
C678_S6_001


title: Participant ID and visit (v) number [phchp193v3]


title: Participant ID and visit (v) number [phchp190v4]


title: Participant ID and visit (v) number [phchp216v1]

value: MOOD


title: ZV089 SC MSCA1+

description:
obese woman
C681_S9_001


title: SM010 SC -/-

description:
obese woman
C675_S3_001


title: SM010 SC MSCA1+

description:
obese woman
C673_S1_001


title: SM010 VISC MSCA1+

description:
obese woman
C677_S5_001


title: Participant ID and visit (v) number [phchp188v1]


title: SM010  SC-/CD271+

description:
obese woman
C674_S2_001


title: Participant ID and visit (v) number [phchp188v2]


title: Rec-1_ChIPseq_input_GSI_rep2

city: Philadelphia

first: YEQIAO

last: ZHOU

address: 421 Curie Boulevard

department: Pathology

institute: University of Pennsylvania

data_processing:
Reads from all ChIP-seq experiments were aligned to the Ensembl GRCh37.75 primary assembly including chromosome 1-22, chrX, chrY, chrM and contigs using BWA (version 0.7.13) with parameters bwa aln -q 5 -l 32 -k 2 -t 6. Reads mapped to contigs, ENCODE blacklist and marked as duplicates by Picard (version 2.1.0) were discarded and the remaining reads were used in downstream analyses and visualization.
Bedgraph of reads normalized to reads per million (RPM) were generated with bedtools (version 2.25.0) genomecov. Uploadable bigWig files were generated with UCSC bedGraphToBigWig (version 329).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files for genome browser viewing

source_name: Rec-1 cell line

growth_protocol: Rec-1 (male) cells were grown in RPMI 1640 (Corning, cat# 10-040-CM) supplemented with 10% fetal bovine serum (Hyclone, cat# SH30070.03), 2 mM L-glutamine (Corning, cat# 25-005-CI), 100 U/mL and 100 μg/mL penicillin/streptomycin (Corning, cat# 30-002-CI), 100 mM nonessential amino acids (Gibco, cat# 11140-050), 1mM sodium pyruvate (Gibco, cat#11360-070) and 0.1mM of 2-mercaptoethanol (Sigma, cat# M6250).

extract_protocol:
ChIP-seq was performed as previously described (Ryan et al., 2017). Briefly, chromatin samples prepared from appropriate number of fixed cells (10^7 for histone modifications and 4 x 10^7 for transcription factors) were sonicated and cleared with recombinant protein G–conjugated Agarose beads (Invitrogen, cat# 15920-010) and subsequently immunoprecipitated with antibodies recognizing Notch1 (Wang et al., 2014), RBPJ (D10A4) (CST, cat# 5313), H3K27ac (Active Motif, cat# 39133), H3K27me3 (EMD Millipore cat# 07-449), H3K4me1 (Abcam, cat# ab8895), Smc1a (Bethyl, cat# A300-055A) and CTCF (EMD Millipore cat# 07-729). Antibody-chromatin complexes were captured with recombinant protein G–conjugated Agarose beads, washed with Low Salt Wash Buffer, High Salt Wash Buffer, LiCl Wash Buffer and TE buffer with 50mM NaCl and eluted. Input sample was prepared by the same approach without immunoprecipitation. After reversal of cross-linking, RNase and Proteinase K (Invitrogen, cat# 25530-049) treatment were performed and DNA was purified with QIAquick PCR Purification Kit (Qiagen, cat# 28106).
Libraries were then prepared using the NEBNext Ultra II DNA library Prep Kit for Illumina (NEB, cat# E7645S). Two replicates were performed for each condition. Indexed libraries were validated for quality and size distribution using a TapeStation 2200 (Agilent). Single end sequencing (75 bp) or Paired-end sequencing (38 bp+38 bp) was performed on a NextSeq 550.

treatment_protocol: Cells were treated with the GSI compound E (1 μM, Calbiochem cat# 565790) for 72 hours, washed, and then cultured for 5 hours in media containing 1μM GSI (mock washout) or DMSO (washout) as previously described (Weng et al., 2006).

tag: cell line

value: Mantle cell lymphoma cell line

value: input

tag: drug treatment

value: GSI-mock-washout


title: Rec-1_ChIPseq_input_WO_rep2

value: GSI-washout


title: Participant ID and visit (v) number [phchp186v3]


title: Participant ID and visit (v) number [phchp186v4]


title: Rec-1_ChIPseq_input_DMSO_rep2

value: untreated


title: Participant ID and visit (v) number [phchp186v1]


title: Rec-1_ChIPseq_input_GSI_rep1


title: Rec-1_ChIPseq_input_DMSO_rep1


title: Rec-1_GSI_H3K27ac_ChIPseq_rep2


title: Participant ID and visit (v) number [phchp186v2]


title: Participant ID and visit (v) number [phchp184v3]


title: Participant ID and visit (v) number [phchp187v1]


title: Participant ID and visit (v) number [phchp186v5]


title: Rec-1_ChIPseq_input_WO_rep1


title: Participant ID and visit (v) number [phchp184v1]


title: Participant ID and visit (v) number [phchp183v2]


title: Participant ID and visit (v) number [phchp187v2]


title: Participant ID and visit (v) number [phchp180v3]


title: Participant ID and visit (v) number [phchp180v2]


title: Participant ID and visit (v) number [phchp181v1]


title: Rec-1_GSI_H3K27ac_ChIPseq_rep1


title: Participant ID and visit (v) number [phchp178v1]


title: Participant ID and visit (v) number [phchp180v1]


title: Participant ID and visit (v) number [phchp184v2]


title: Participant ID and visit (v) number [phchp183v1]


title: Rec-1_WO_H3K27ac_ChIPseq_rep1

extract_protocol:
ChIP-seq was performed as previously described (Ryan et al., 2017). Briefly, chromatin samples prepared from appropriate number of fixed cells (107 for histone modifications and 4 x 107 for transcription factors) were sonicated and cleared with recombinant protein G–conjugated Agarose beads (Invitrogen, cat# 15920-010) and subsequently immunoprecipitated with antibodies recognizing Notch1 (Wang et al., 2014), RBPJ (D10A4) (CST, cat# 5313), H3K27ac (Active Motif, cat# 39133), H3K27me3 (EMD Millipore cat# 07-449), H3K4me1 (Abcam, cat# ab8895), Smc1a (Bethyl, cat# A300-055A) and CTCF (EMD Millipore cat# 07-729). Antibody-chromatin complexes were captured with recombinant protein G–conjugated Agarose beads, washed with Low Salt Wash Buffer, High Salt Wash Buffer, LiCl Wash Buffer and TE buffer with 50mM NaCl and eluted. Input sample was prepared by the same approach without immunoprecipitation. After reversal of cross-linking, RNase and Proteinase K (Invitrogen, cat# 25530-049) treatment were performed and DNA was purified with QIAquick PCR Purification Kit (Qiagen, cat# 28106).
Libraries were then prepared using the NEBNext Ultra II DNA library Prep Kit for Illumina (NEB, cat# E7645S). Two replicates were performed for each condition. Indexed libraries were validated for quality and size distribution using a TapeStation 2200 (Agilent). Single end sequencing (75 bp) or Paired-end sequencing (38 bp+38 bp) was performed on a NextSeq 550.


title: Participant ID and visit (v) number [phchp177v1]


title: Participant ID and visit (v) number [phchp177v2]


title: Rec-1_GSI_H3K27me3_ChIPseq_rep2


title: Participant ID and visit (v) number [phchp181v3]


title: Participant ID and visit (v) number [phchp175v1]

value: SZA


title: Participant ID and visit (v) number [phchp174v1]

value: MDD


title: Rec-1_WO_H3K27me3_ChIPseq_rep1


title: Participant ID and visit (v) number [phchp173v3]


title: Rec-1_WO_H3K27me3_ChIPseq_rep2


title: DND41_GSI_RNAseq_rep3

data_processing:
RNA-seq data was aligned to Ensembl GRCh37.75 primary assembly including chromosome 1-22, chrX, chrY, chrM and contigs using STAR (version 2.5) with parameters --outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignIntronMax 100000 --outSAMstrandField intronMotif --outSAMunmapped Within --chimSegmentMin 25  --chimJunctionOverhangMin 25.
Strand-specific read counts were quantified using Subread (version 1.5.1) featureCounts with parameters -t exon -g gene_id -s 1 -T 6 and used as input to differential gene expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with read count; bigWig files for genome browser viewing

source_name: DND41 cell line

growth_protocol: DND41 (male) cells were grown in RPMI 1640 (Corning, cat# 10-040-CM) supplemented with 10% fetal bovine serum (Hyclone, cat# SH30070.03), 2 mM L-glutamine (Corning, cat# 25-005-CI), 100 U/mL and 100 μg/mL penicillin/streptomycin (Corning, cat# 30-002-CI), 100 mM nonessential amino acids (Gibco, cat# 11140-050), 1mM sodium pyruvate (Gibco, cat#11360-070) and 0.1mM of 2-mercaptoethanol (Sigma, cat# M6250).

extract_protocol:
Cells from GSI and washout conditions were washed with 1 x PBS (Corning, cat# 21031CV) and lysed with 350 μl RLT Plus buffer (Qiagen) supplemented with 10% 2-mercaptoethanol (Sigma, cat# M6250), vortexed briefly, snap-frozen on dry ice, and stored at -80°C. Subsequently, total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen, cat# 74034).
RNA integrity numbers were determined using TapeStation 2200 (Agilent), and all samples used for RNA-seq library preparation had RIN numbers greater than 9.5. 800 ng of total RNA was used and libraries were prepared using the SMARTer Standard Total RNA Sample Prep Kit-HI Mammalian (Clontech, cat# 634873). Libraries were single-end sequenced (75 bp) on a NextSeq 550.

value: T-ALL cell line


title: Rec-1_WO_H3K27ac_ChIPseq_rep2


title: DND41_GSI_RNAseq_rep2


title: DND41_GSI_RNAseq_rep1


title: Rec-1_GSI_H3K27me3_ChIPseq_rep1


title: DND41_WO_RNAseq_rep3


title: HCC1599_GSI_RBPJ_ChIPseq_rep1

source_name: HCC1599 cell line

growth_protocol: HCC1599 (female) cells were grown in RPMI 1640 (Corning, cat# 10-040-CM) supplemented with 10% fetal bovine serum (Hyclone, cat# SH30070.03), 2 mM L-glutamine (Corning, cat# 25-005-CI), 100 U/mL and 100 μg/mL penicillin/streptomycin (Corning, cat# 30-002-CI), 100 mM nonessential amino acids (Gibco, cat# 11140-050), 1mM sodium pyruvate (Gibco, cat#11360-070) and 0.1mM of 2-mercaptoethanol (Sigma, cat# M6250).

value: Triple-negative breast cancer cell line

value: RBPJ


title: HCC1599_ChIPseq_input_GSI


title: HCC1599_ChIPseq_input_DMSO


title: Participant ID and visit (v) number [phchp173v2]

value: Male


title: HCC1599_GSI_RBPJ_ChIPseq_rep2


title: Participant ID and visit (v) number [phchp172v3]


title: Participant ID and visit (v) number [phchp172v1]


title: Participant ID and visit (v) number [phchp170v2]


title: Participant ID and visit (v) number [phchp169v1]


title: Participant ID and visit (v) number [phchp168v3]


title: Participant ID and visit (v) number [phchp173v1]


title: HCC1599_WO_RBPJ_ChIPseq_rep2


title: HCC1599_GSI_NICD1_ChIPseq_rep2


title: DND41_WO_RNAseq_rep2


title: DND41_WO_RNAseq_rep1


title: Participant ID and visit (v) number [phchp170v3]


title: HCC1599_WO_RBPJ_ChIPseq_rep1


title: Participant ID and visit (v) number [phchp170v1]


title: HCC1599_ChIPseq_input_WO


title: Participant ID and visit (v) number [phchp168v1]


title: Participant ID and visit (v) number [phchp166v6]


title: Participant ID and visit (v) number [phchp168v2]


title: Participant ID and visit (v) number [phchp166v4]


title: Participant ID and visit (v) number [phchp166v3]


title: HCC1599_GSI_NICD1_ChIPseq_rep1


title: Participant ID and visit (v) number [phchp166v5]


title: HCC1599_WO_NICD1_ChIPseq_rep2


title: HCC1599_GSI_H3K27me3_ChIPseq_rep1


title: HCC1599_GSI_H3K27me3_ChIPseq_rep2


title: HCC1599_WO_NICD1_ChIPseq_rep1


title: HCC1599_WO_H3K27me3_ChIPseq_rep1


title: Participant ID and visit (v) number [phchp165v2]

value: SZ


title: HCC1599_GSI_H3K4me1_ChIPseq_rep1


title: HCC1599_WO_H3K27me3_ChIPseq_rep2


title: Participant ID and visit (v) number [phchp166v1]

value: Yes


title: Participant ID and visit (v) number [phchp167v1]


title: Participant ID and visit (v) number [phchp165v3]


title: Participant ID and visit (v) number [phchp162v2]


title: Participant ID and visit (v) number [phchp161v2]


title: Participant ID and visit (v) number [phchp157v3]


title: Participant ID and visit (v) number [phchp165v1]


title: Participant ID and visit (v) number [phchp157v1]


title: Participant ID and visit (v) number [phchp166v2]


title: Participant ID and visit (v) number [phchp161v3]


title: Participant ID and visit (v) number [phchp162v3]


title: Participant ID and visit (v) number [phchp162v1]


title: HCC1599_WO_H3K4me1_ChIPseq_rep2


title: Participant ID and visit (v) number [phchp161v1]


title: HCC1599_WO_H3K4me1_ChIPseq_rep1


title: HCC1599_GSI_H3K4me1_ChIPseq_rep2


title: HCC1599_WO_H3K27ac_ChIPseq_rep2


title: HCC1599_GSI_H3K27ac_ChIPseq_rep2


title: HCC1599_GSI_H3K27ac_ChIPseq_rep1


title: HCC1599_GSI_RNAseq_rep1


title: HCC1599_GSI_RNAseq_rep2


title: HCC1599_GSI_RNAseq_rep3


title: HCC1599_WO_H3K27ac_ChIPseq_rep1


title: Participant ID and visit (v) number [phchp157v2]


title: HCC1599_WO_RNAseq_rep1


title: HCC1599_WO_RNAseq_rep2


title: Participant ID and visit (v) number [phchp152v1]


title: Participant ID and visit (v) number [phchp156v1]

value: Female


title: Participant ID and visit (v) number [phchp150v3]


title: Participant ID and visit (v) number [phchp150v1]


title: Participant ID and visit (v) number [phchp150v2]


title: Participant ID and visit (v) number [phchp149v2]


title: Participant ID and visit (v) number [phchp149v3]


title: Participant ID and visit (v) number [phchp143v2]

value: BP


title: Participant ID and visit (v) number [phchp144v1]


title: HCC1599_WO_RNAseq_rep3


title: Participant ID and visit (v) number [phchp132v5]


title: Participant ID and visit (v) number [phchp132v3]


title: Participant ID and visit (v) number [phchp143v1]


title: Participant ID and visit (v) number [phchp143v3]


title: Participant ID and visit (v) number [phchp149v1]


title: Participant ID and visit (v) number [phchp139v1]


title: Participant ID and visit (v) number [phchp138v3]


title: Participant ID and visit (v) number [phchp127v1]


title: Participant ID and visit (v) number [phchp132v6]


title: Participant ID and visit (v) number [phchp132v4]


title: Participant ID and visit (v) number [phchp119v3]


title: Participant ID and visit (v) number [phchp127v2]


title: Participant ID and visit (v) number [phchp128v1]


title: Participant ID and visit (v) number [phchp122v2]


title: Participant ID and visit (v) number [phchp132v2]


title: Participant ID and visit (v) number [phchp118v4]


title: Participant ID and visit (v) number [phchp120v1]


title: Participant ID and visit (v) number [phchp138v2]


title: Participant ID and visit (v) number [phchp127v3]


title: Participant ID and visit (v) number [phchp124v2]


title: Participant ID and visit (v) number [phchp120v2]


title: Participant ID and visit (v) number [phchp118v2]


title: Participant ID and visit (v) number [phchp130v1]


title: Participant ID and visit (v) number [phchp124v1]


title: Participant ID and visit (v) number [phchp130v3]


title: Participant ID and visit (v) number [phchp132v1]


title: MB157_WO_RNAseq_rep3

source_name: MB157 cell line

growth_protocol: MB157 (female) cells were grown in DMEM (Corning, cat# 10-013-CV) supplemented with 10% fetal bovine serum (Hyclone, cat# SH30070.03) and 100 U/mL and 100 μg/mL penicillin/streptomycin (Corning, cat# 30-002-CI). When passaged cells were detached with 0.25% trypsin, EDTA-free (Gibco, cat# 15090-046) to avoid activation of Notch signaling.


title: Participant ID and visit (v) number [phchp128v2]


title: MB157_GSI_RNAseq_rep1


title: MB157_WO_RNAseq_rep2


title: Participant ID and visit (v) number [phchp120v3]


title: MB157_GSI_RNAseq_rep3


title: MB157_GSI_RNAseq_rep2


title: Participant ID and visit (v) number [phchp122v1]


city: TORONTO

first: Haiyang

last: Guo

state: Ontario

address: 101 College Street, 11-601D, TMDT, 11-601D, TMDT

department: Princess Margaret Cancer Centre

country: Canada

institute: UNIV HEALTH NETWORK

description:
LNCaP_RNA-Seq_Flag-OC2_Overexpression_Hypoxia_rep2
LNCaP_RNA-seq_RPKM_OC2_Overexpression.txt
H-OC2-2

data_processing:
The trimmed reads were aligned to human genome hg19 with STAR (version 2.4.2a) and gene expression was then quantified using the reads per kilobase per million mapped reads (RPKM) method by Cufflinks (version 2.1.1) with GENCODE v24 GRCh37 GTF file
Genome_build: hg19
Supplementary_files_format_and_content: txt files contain the gene expression matrices

source_name: LNCaP cells

growth_protocol: LNCaP and PC3 cell lines were obtained from the American Type Culture Collection (ATCC). All prostate cancer cell lines were cultured as recommended by ATCC. No mycoplasma contamination was detected in these cell lines using MycoAlert™ Mycoplasma Detection Kit (LT07-118, Lonza).

extract_protocol:
Total RNA of PC3 and LNCaP cells was extracted using RNeasy Mini Kit (74106, Qiagen) following manufacturer’s procedure.
Whole transcriptome sequencing libraries were prepared using TruSeq® Stranded mRNA Library Prep Kit (RS-122-2101, Illumina, San Diego, CA, USA) by following the manufacturer’s instructions.

treatment_protocol: For hypoxia treatment, cells were incubated in hypoxia chamber at 0.2% O2.

tag: tumor type

value: prostate cancer

value: LNCaP

tag: protocol


title: LNCaP_RNA-Seq_Empty_Vector_Hypoxia_rep1

description:
LNCaP_RNA-Seq_Empty_Vector_Hypoxia_rep1
LNCaP_RNA-seq_RPKM_OC2_Overexpression.txt
H-EV-1


description:
LNCaP_RNA-Seq_Flag-OC2_Overexpression_Hypoxia_rep1
LNCaP_RNA-seq_RPKM_OC2_Overexpression.txt
H-OC2-1


title: LNCaP_RNA-Seq_Empty_Vector_Hypoxia_rep2

description:
LNCaP_RNA-Seq_Empty_Vector_Hypoxia_rep2
LNCaP_RNA-seq_RPKM_OC2_Overexpression.txt
H-EV-2


title: MB157_WO_RNAseq_rep1

tag: cell type


description:
LNCaP_RNA-Seq_Flag-OC2_Overexpression_Normoxia_rep2
LNCaP_RNA-seq_RPKM_OC2_Overexpression.txt
N-OC2-2


description:
LNCaP_RNA-Seq_Flag-OC2_Overexpression_Normoxia_rep1
LNCaP_RNA-seq_RPKM_OC2_Overexpression.txt
N-OC2-1


description:
LNCaP_RNA-Seq_Empty_Vector_Normoxia_rep2
LNCaP_RNA-seq_RPKM_OC2_Overexpression.txt
N-EV-2


description:
LNCaP_RNA-Seq_Empty_Vector_Normoxia_rep1
LNCaP_RNA-seq_RPKM_OC2_Overexpression.txt
N-EV-1


title: SMAD3_ChIP-HIF2A_reChIP-Seq_in_PC3_Hypoxia

data_processing:
All ChIP-Seq data were aligned using Bowtie2 (version 2.2.1) to the human genome of build version NCBI37/HG19
MACS2 was used for peak calling with the parameter “--SPMR” on and and --keep-dup=1.
For re-ChIP-Seq analysis, after reads alignment, the primary ChIP-Seq bam file was used as the control for re-ChIP-Seq bam file in the peak calling by MACS2. To generate normalized bedgraph files of re-ChIP-Seq data, re-ChIP-Seq bedgraph file and primary ChIP-Seq bedgraph file were subjected to MASC2 bdgcmp sub-command with the option "--method=FE".
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated by UCSC bedGraphToBigWig tool from resultant bedgraph files.

source_name: PC3 cells

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-enriched DNA was used for library creation with the Rubicon ThruPLEX-FD kit and sequenced (75 bp single-end reads).

value: Hypoxia

value: PC3 cells

tag: antibody

value: SMAD3 and HIF2A


title: SMAD3_ChIP-HIF1A_reChIP-Seq_in_PC3_Hypoxia

value: SMAD3 and HIF1A


title: Participant ID and visit (v) number [phchp138v1]

description: Independent Test cohort blood gene expression data

source_name: Whole Blood

value: MOOD


title: Participant ID and visit (v) number [phchp118v1]

value: SZA


title: Participant ID and visit (v) number [phchp119v2]


title: Participant ID and visit (v) number [phchp117v3]


title: Participant ID and visit (v) number [phchp117v1]


title: Participant ID and visit (v) number [phchp115v1]


title: Participant ID and visit (v) number [phchp115v3]


title: Flag-OC2_ChIP-Seq_in_PC3_Normoxia

value: Normoxia

value: Flag


title: Participant ID and visit (v) number [phchp116v1]


title: Participant ID and visit (v) number [phchp112v2]


title: Participant ID and visit (v) number [phchp113v1]


title: Participant ID and visit (v) number [phchp112v1]


title: HIF1A_ChIP-Seq_in_PC3_Hypoxia_siSMAD3


title: Flag-OC2_ChIP-Seq_in_PC3_Hypoxia


title: Participant ID and visit (v) number [phchp117v2]


title: SMAD3_ChIP-Seq_in_PC3_Hypoxia


title: HIF1A_ChIP-Seq_in_PC3_Hypoxia_siCtrl


title: Participant ID and visit (v) number [phchp112v3]


title: Participant ID and visit (v) number [phchp108v3]


title: Participant ID and visit (v) number [phchp115v2]


title: HIF2A_ChIP-Seq_in_PC3_Hypoxia


title: HCC1143_shRNA-screen

city: Gunma

first: Reika

last: Kawabata-Iwakawa

address: 3-39-22, Showa-Machi, Maebashi

institute: Gunma University

data_processing:
Library strategy: shRNA screen
Data processing was performed in accordance to the manufacture's protocol (http://dharmacon.gelifesciences.com/uploadedFiles/Resources/lentiviral-pooled-library-bioinfomatic-analysis-protocol.pdf).
FASTQ files were trimmed the adapter sequences and aligned to the reference shRNA sequences by using bowtie2.
The Bowtie output files were converted into count files through a python script "countBowtieHits.py" and “RTable.py” obtained from the manufacture's protocol.
TCC-edgeR was used for normalization and statistical analysis.
Genome_build: reference shRNA sequences
Supplementary_files_format_and_content: tab-delimited text files include idl, sample name, normalized count values for each sample, statistics value obtained by TCC-edgeR.

source_name: Breast cancer cell line

growth_protocol: Cells were cultured in PRMI 1640 medium supplemented with 100 U/mL of penicillin, 100 U/mL of streptomycin, and 10% fetal bovine serum in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol: Thirty cycles of PCR with primers on the shRNA vector (forward primer : ATTTCTTGGCTTTATATATCTTGTGGAAAG, reverse primer : TGTGGATGAATACTGCCATTTGTCTC) were performed on 3 micro-g genomic DNAs. Sequencing adaptors (Bioo Sciences) were ligated to the PCR amplicons with 8 cycles of PCR.

treatment_protocol: Lenti-Plex v1.5 (Sigma) is a genome-wide shRNA library which covers approximately 15,000 genes with 80,000 shRNA clones. In order to identify shRNAs targeting genes which specifically kill 3 TNBC cell lines compared to the non-TNBC cell lines, mixture of lenti-viral particles were introduced to breast cancer cell lines of non-TNBC (MCF7, T-47D, BT474) and TNBC (MDA-MB468, HCC70, HCC1143) subtype at MOI that produce 30-50% infected cells. The infected cells were subsequently selected by Puromycin for 7 days and genomic DNA with integrated shRNA was isolated from the cell lines.

value: Basal-like TNBC


title: Participant ID and visit (v) number [phchp114v1]


title: T47D_shRNA-screen

value: Luminal (non-TNBC)


title: MDA-MB-468_shRNA-screen


title: HCC70_shRNA-screen


title: MCF7_shRNA-screen


title: BT474_shRNA-screen


title: MDA-MB-468_RNA-seq

data_processing:
Data processing and analyses were performed using the TopHat Alignment, Cufflinks Assembly, and Differential Expression apps (Illumina, San Diego, CA, USA).
The reads were filtered, trimmed, and aligned in the UCSC reference human genome 19 (hg19) using the Tophat2 (v2.0.7) and Bowtie1 (0.12.9) pipelines.
Assembly of transcripts was performed using the Cufflinks 2.1.1.
Differentially expressed transcripts were detected using the Cuffdiff 2.1.1.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include gene symbol, sample name (nonTNBC or TNBC), mean of RPKM values for each sample, stastics value obtained by cuffdiff.

extract_protocol:
Total RNA was extracted using NucleoSpin RNA (TaKaRa Bio, Shiga, Japan/MACHEREY-NAGEL, Düren, Germany). The quality of RNA was assessed with RNA integrity number (RIN) using Agilent RNA6000 Pico Kit and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Samples used for transcrptome analysis had on average a RIN value of 9.4 and a minimum RIN value of 8.9.
Library preparation was performed using TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) from 1 µg of total RNA according to the manufacturer’s protocol.


title: T47D_RNA-seq


title: BT474_RNA-seq


title: Participant ID and visit (v) number [phchp103v1]

extract_protocol:
We used three independent cohorts: discovery (major psychiatric disorders), validation (major psychiatric disorders with clinically severe pain disorders), and testing (an independent major psychiatric disorders cohort for predicting pain state, and for predicting future ED visits for pain) (Figure 1A).
Subjects were recruited from the patient population at the Indianapolis VA Medical Center. All subjects understood and signed informed consent forms detailing the research goals, procedure, caveats and safeguards, per Indiana University IRB approved protocol. Subjects completed diagnostic assessments by an extensive structured clinical interview—Diagnostic Interview for Genetic Studies, and up to six testing visits, 3–6 months apart or whenever a new psychiatric hospitalization occurred. At each testing visit, they received a series of rating scales, including a visual analog scale (1-10) for assessing pain and the SF-36 quality of life scale, which has two pain related items (items 21 and 22), and the blood was drawn. We collected whole blood (10 ml) in two RNA-stabilizing PAXgene tubes, labeled with an anonymized ID number, and stored at -80 degrees C in a locked freezer until the time of future processing. Whole-blood RNA was extracted for microarray gene expression studies from the PAXgene tubes, as detailed below.
Whole blood (2.5 ml) RNA extraction: 2.5-5 ml of whole blood was collected into each PaxGene tube by routine venipuncture.  PaxGene tubes contain proprietary reagents for the stabilization of RNA. The cells from whole blood will be concentrated by centrifugation, the pellet washed, resuspended and incubated in buffers containing Proteinase K for protein digestion.  A second centrifugation step will be done to remove residual cell debris.  After the addition of ethanol for an optimal binding condition the lysate is applied to a silica-gel membrane/column.  The RNA bound to the membrane as the column is centrifuged and contaminants are removed in three wash steps.  The RNA is then eluted using DEPC-treated water.

value: Male


title: Participant ID and visit (v) number [phchp099v3]

value: SZ


title: Participant ID and visit (v) number [phchp102v1]

value: Yes


title: Participant ID and visit (v) number [phchp108v1]


title: Participant ID and visit (v) number [phchp108v2]


title: MCF7_RNA-seq


title: Participant ID and visit (v) number [phchp102v3]


title: Participant ID and visit (v) number [phchp101v1]


title: Participant ID and visit (v) number [phchp099v2]


title: HCC1143_RNA-seq


title: Participant ID and visit (v) number [phchp099v1]


title: Participant ID and visit (v) number [phchp098v1]


title: Participant ID and visit (v) number [phchp102v2]


title: HCC70_RNA-seq


title: Participant ID and visit (v) number [phchp097v1]

value: Female


title: Participant ID and visit (v) number [phchp096v3]


title: No Ab control, sequencing run 1

city: Boston

first: Martha

last: Bulyk

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham & Women's Hospital

data_processing:
Base calls were performed using Casava v1.8
Reads were trimmed to 36 nt to remove lower quality 3’ end base calls using fastx-trimmer v0.0.13.
Reads were then aligned to hg38 using bowtie v1.1.1 (bowtie -n 2 -m 1).
Aligned reads from replicate sequencing runs were pooled either within biological replicates or across all replicates. Peaks were then called on pooled aligned reads, using MACS2 v2.1.1.20160309, with the no antibody sample as a control (macs2 callpeak -g hs -bw 400).
Genome_build: hg38
Supplementary_files_format_and_content: Processed data are in narrowPeak format and correspond to all peak calls for pooled replicates A and B against the no antibody control

source_name: HepG2 cells

growth_protocol: HepG2 cells were purchased from ATCC (HB-8065). Cells were cultured in DMEM with High Glucose and 4.0 mM L-Glutamine, without Sodium Pyruvate (HyClone SH30022.01) supplemented with 10% heat inactivated FBS (Gibco 10082139) and 1% penicillin/streptomycin.

extract_protocol:
Cross-linking and harvest of cells for ChIP: To prepare material for ChIP-seq, cells were grown on 15 cm culture dishes, with two independent passages maintained simultaneously. Plates were removed from the incubator and placed at room temperature. Formaldehyde (Sigma F87750) was added directly to the culture media to a final concentration of 1%. Plates were incubated at room temperature for 10 minutes, with swirling every 2.5 minutes. Cross-linking was quenched by adding 2.5 M stock glycine to a final concentration of 0.125 M and plates were swirled to mix. Media was then aspirated and cells were washed once in 1X PBS. Eight milliliters of cold lysis buffer (5mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40 substitute, prepared fresh and sterile filtered) was then added directly to cells on the dish. Cells were then scraped, transferred to a 15 cm conical tube, and spun at 2000 rpm for 5 minutes at 4 C. The supernatant was then removed and flash frozen in liquid nitrogen at a concentration of 2e7 cells/mL for storage at -80 C. Sonication of cross-linked material for ChIP: Sonication time was determined empirically by sonicating aliquots of cross-linked material across multiple 10-cycle intervals of 30 seconds on and 30 seconds off using a Biorupter Twin with a circulating water bath in a 4 C environmental chamber. For HepG2 cells, intervals tested were from 2 10-cycle intervals, up to 6 10-cycle intervals, settling on 5 10-cycle intervals after evaluating sonication completion by agarose gel electrophoresis. Final sonication conditions are as follows: A 1 mL aliquot of cells was thawed and gently resuspended before being passed through a 20 gauge needle 20 times. Crude nuclear prep was then collected by spinning the lysate at 2000 rpm for 5 minutes at 4 C. The resulting pellet was resuspended in 300 uL RIPA buffer and then processed in a Biorupter Twin circulating bath sonicator for 50 cycles of 30 seconds on and 30 seconds off at the high setting in a 4 C environmental chamber. Following sonication, samples were spun at 16,000 rcf for 15 minutes at 4 C and the supernatant was either snap frozen and stored at -80 C or used as input for immunoprecipitation. Prior to immunoprecipitation, the total protein concentration of a sample was measured using a Bradford assay, and all sample concentrations were normalized to 1.75 mg/mL with 1X RIPA buffer and split into 1 mL aliquots. Immunoprecipitation: Sixty microliters of Protein G Sepharose beads (Sigma P3296) were used per sample. Beads were washed twice by spinning at 2500 rcf for 1 minute, removing the supernatant and adding an equal volume of 1X PBS. Beads were then resuspended in 1X PBS to 60 uL. Thirty microliters of washed beads were blocked by adding 9 uL of 0.3 mg/mL salmon sperm DNA and 12 uL 1 mg/mL BSA and incubating at 4 C for 1 hour on a rotisserie. The remaining 30 uL was added directly to a 1 mL sonicated cell aliquot and incubated for 1 hour at 4 C on a rotisserie to pre-clear. Following clearing, the sample was spun at 2500 rcf for 1 minute and 950 uL of supernatant was transferred to a new tube. Ten micrograms of antibody (Abgent AP19255B) and 30 uL of blocked bead slurry was then added and samples were incubated at 4 C overnight with rotation on a rotisserie. A no antibody control sample was also prepared from a paired aliquot by incubating overnight with 30 uL of blocked bead slurry, without addition of the primary antibody. Approximately 18 hours later, samples were washed by spinning at 2.5k rcf at 1 minute, adding 1 mL of the following buffers, incubating for 1 minute, and repeating. All washes were carried out at 4 C. Washes began with 2 1X PBS washes, 4 washes with IP wash buffer (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40 substitute, and 1% sodium deoxycholate), and 1 wash with PBS-RIPA buffer (1X PBS, 1% NP-40 substitute, 0.5% sodium deoxycholate, and 0.1% SDS). Immunoprecipitated material was eluted off the beads by adding 200 uL elution buffer (70 mM Tris-Cl pH 8.0, 1 mM EDTA, 1.5% SDS), and incubating at 65 C for 10 minutes with vortexing every 2 minutes. Samples were then spun at 2500 rcf for 2 minutes and the supernatant was transferred to a new tube. Reversal of cross-links:To each sample (Antibody or no antibody), 13 uL of 4 M NaCl (200 mM final) was added, and samples were incubated at 65 C for 18 hours. The next morning, 20 ug of Proteinase K was added to each sample and incubated at 45 C for 60 minutes. Five volumes of Qiagen Buffer PB (QIAquick PCR purification kit) was then added to one volume of sample. This material was then processed according to the manufacturer’s instructions for the QIAquick PCR purification kit, eluting twice with 30 uL volumes of pre-warmed Qiagen Buffer EB.
Libraries for sequencing with Illumina high-throughput sequencing chemistry were prepared using the NEBNext Ultra II DNA Library Prep Kit (NEB E7645) with adaptors from the NEBNext Singleplex Oligos for Illumina Kit (NEB E7350) according to manufacturer’s instructions. A final cycle number of 12 cycles of amplification was required during the PCR step. Libraries were multiplexed at equal concentrations based on integration under TapeStation D1000 tape traces and sequenced on an Illumina NextSeq instrument at the The Bauer Core Facility at Harvard University.


title: Replicate B, sequencing run 2

value: Abgent AP19255B


title: Participant ID and visit (v) number [phchp097v3]

data_processing: The AP derived and DE derived lists of genes were combined, and the gene expression data corresponding to them was used for the validation analysis. The cohorts (Validation Clinically Severe Stress, alongside the Low Stress and High Stress groups in the Discovery cohort) were assembled out of Affymetrix .cel data that was RMA normalized by gender and diagnosis. We transferred the log transformed expression data to an Excel sheet, and non-log transformed the data by taking 2 to the power of the transformed expression value. We then Z-scored the values by gender and diagnosis.  We then imported the Excel sheets with the Z-scored by gender and diagnosis expression data into Partek, and  statistical analyses were performed using a one-way ANOVA for the stepwise changed probesets, and also attempted a stringent Bonferroni corrections for all the probesets tested (Figure 1F). We also wrote an R script that automatically analyzes the data directly from the Excel sheet, and used that to confirm our calculations.


title: Replicate B, sequencing run 1


title: Replicate A, sequencing run 2


title: No Ab control, sequencing run 2


title: Participant ID and visit (v) number [phchp096v4]


title: Replicate A, sequencing run 1


title: Participant ID and visit (v) number [phchp097v2]


title: Participant ID and visit (v) number [phchp094v1]

value: BP


title: Participant ID and visit (v) number [phchp093v6]


title: Participant ID and visit (v) number [phchp096v1]


title: Participant ID and visit (v) number [phchp130v2]

value: MDD


title: Participant ID and visit (v) number [phchp093v5]


title: Participant ID and visit (v) number [phchp105v1]


title: Participant ID and visit (v) number [phchp092v3]


title: Participant ID and visit (v) number [phchp093v1]


title: Participant ID and visit (v) number [phchp093v4]


title: Participant ID and visit (v) number [phchp092v2]


title: Participant ID and visit (v) number [phchp091v2]


title: STING-/- with R284S_Doxorubicin

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

description: STING-/- MEF cells reconstituted with STING R284S variant were treated with Doxorubicin.

hyb_protocol: Fragmented and Labeled products were hybridized to GeneChip Mouse Gene 2.0 ST Arrays (Affymetrix part# 902500). Washing and staining of arrays took place on the GeneChip Fluidics Station 450

scan_protocol: GeneChips were scanned with GeneChip Scanner 3000 7G system

data_processing: Raw .CEL files were were analyzed with in the Affymetrix Expression Console software v.1.3.1.187 using rma-sketch normalization with Affymetrix default analysis settings to generate .CHP files.

label: biotin

label_protocol: 300ng of Total RNA per sample was prepared using the GeneChip WT PLUS Reagent Kit (Affymetrix part#902280) and yielded cDNA product for fragmentation and labeling

growth_protocol: STING-/- MEF cells were cultured in DMEM containing 10% FBS.

extract_protocol: RNeasy Mini Kit (Qiagen)

treatment_protocol: The MEF cells were treated with AMPK inhibitors for 9 hours.

value: Primary MEF cells


title: STING-/- with R284S_GSK 690693

description: STING-/- MEF cells reconstituted with STING R284S variant were treated with GSK 690693 .


title: STING-/- MEF_hSTING_dsDNA

description: STING-/- MEF cells reconstituted with hSTING were treated with dsDNA

treatment_protocol: The MEF cells were treated with double strand DNA using Lipofectamine 2000 for 9 hours.


title: STING-/- MEF_N154S_dsDNA

description: STING-/- MEF cells reconstituted with N154S were treated with dsDNA


title: STING-/- with R284S_Compound C

description: STING-/- MEF cells reconstituted with STING R284S variant were treated with Compound C.


title: Participant ID and visit (v) number [phchp087v3]


title: Participant ID and visit (v) number [phchp093v2]


title: Participant ID and visit (v) number [phchp091v1]


title: Participant ID and visit (v) number [phchp093v3]


title: Participant ID and visit (v) number [phchp091v3]


title: Participant ID and visit (v) number [phchp087v2]


title: STING-/- with R284S_Vehicle

description: STING-/- MEF cells reconstituted with STING R284S variant.


title: Participant ID and visit (v) number [phchp087v1]


title: STING-/- MEF_R284S _dsDNA

description: STING-/- MEF cells reconstituted with R284S were treated with dsDNA


title: Participant ID and visit (v) number [phchp089v4]


title: Participant ID and visit (v) number [phchp086v3]


title: Participant ID and visit (v) number [phchp092v1]


title: STING-/- MEF_N154S_control

description: STING-/- MEF cells reconstituted with N154S


title: Participant ID and visit (v) number [phchp086v2]


title: Participant ID and visit (v) number [phchp086v1]


title: Participant ID and visit (v) number [phchp085v3]


title: STING-/- with R284S_Tofacitinib

description: STING-/- MEF cells reconstituted with STING R284S variant were treated with Tofacitinib.


title: Input, Day four

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

country: Switzerland

institute: CHUV

description: Liver homogenate of mice

data_processing:
Alignment: Both paired-ends were first mapped individually on the mouse genome version Mm10, allowing up to 50 multiple matches. The paired reads were then reassembled using an inhouse script. When the alignment revealed multiple possible fragments for a tag pair, all possible fragments up to a length of 1 kb were kept and given a weight corresponding to the ratio of the times the fragment was sequenced divided by the number of matches on the genome. Fragments sequenced more than once were counted a maximum of three times.
Scores were computed as the log2-ratio between counts in paired ChIPs and Input samples to which a pseudocount value of 10 was added. The counts were assigned to all the Pol2 TSS from the Gencode gene list for mouse genome Mm10, taking into account a distance from minus 250 to plus 250 around the TSS.
Genome_build: Mouse genome Mm10
Supplementary_files_format_and_content: Associated Bedgraph files were generated for all the Pol2 TSS described above. ChIPseq bedgraph files contain the fragment count accumulation per genomic position around the Pol2 TSS. The pseudocounts have not been included in those files, but all samples have been normalized to a total fragment count of 10'000'000.

source_name: Liver

growth_protocol: Females and littermate males were housed four to five per cage at 23°C, with a 12:12 hour light-dark cycle and ad libitum access to water and food. Tamoxifen treatment and all tissue collections were performed at ZT2–3 where ZT0 is the start of the light period

extract_protocol:
ChIP-seq was performed with the ‘MicroPlex Library Preparation’ kit, from Diagenode
10 ng of immunoprecipitated material was used for sequencing library preparation. Total input was also prepared for sequencing at each time point and replicate. Paired-end sequencing libraries were prepared with the ‘MicroPlex Library Preparation’ kit, from Diagenode, following the instructions of the manufacturer (Diagenode, catalog no C05010011).  No size selection was performed and the chromatin was amplified with 14 cycles of PCR. 100 nucleotides at the fragment ends were sequenced with paired-end sequencing technology from HiSeq 2500 (Illumina).

treatment_protocol: Control female Hcfc1 lox/+ and male Hcfc1 lox/Y, and test female Alb-Cre-ERT2tg ; Hcfc1 lox/+ and male Alb-Cre-ERT2tg ; Hcfc1 131 lox/Y mice (10 to 14 weeks old) were administered intraperitoneal injections of 1 mg/mouse tamoxifen [100 μl of 10 mg/ml (1:10 ethanol:corn oil); Sigma-Aldrich CAS # 10540-29-1] three times at 24 hr intervals from Day 0 to Day 2.

tag: tissue

value: liver

tag: Sex

value: male

value: Hcfc1 hepKO/Y

tag: experiment

value: Input

tag: age (weeks)

tag: time

value: day 4

tag: chip antibody


title: ChIP-seq HCF1, Day four

description: Liver homogenate of mice

value: ChIP-Seq


title: Input, Day zero

description: Liver homogenate of mice

value: day 0


title: ChIP-seq HCF1, Day zero

description: Liver homogenate of mice


title: Male_KO_D09_Rep2

description:
Liver homogenate
DS063

data_processing:
RNA-seq reads were aligned to the Mouse mm9 genome assembly and transcriptome using TopHat version 2.0.13 with Bowtie version 1.1.2. Counts per gene were calculated using the Rsubreads R package and transformed in RPKM. Normalization was done via the edgeR R package using TMM. The cutoff for genes considered as non-transcribed was calculated according to the method described in https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-778.
Genome_build: UCSC Mm9
Supplementary_files_format_and_content: Matrix table with processed log2 FPKM for all samples

extract_protocol:
Liver tissue from 10-14 week old mice maintained on a breeder chow diet was harvested and freeze-clamped in liquid nitrogen.
Poly(A)-containing RNA from individual livers was used for RNA-seq. RNA was extracted with RNeasy kit (Qiagen cat. # 74104). The disruption and homogenization was done with TissueLyser II. Samples were quantified with MySpec machine and 200μg (in 100μl) of RNA sample was used for further analysis. Strand-specific libraries were prepared with the TruSeq Stranded mRNA Library Prep kit (Illumina catalog # RS-122-9004DOC). The fragment ends (50 nucleotides) were sequenced with single-end sequencing technology from HiSeq 2500 (Illumina).

value: Liver

tag: genotype

tag: time after tamoxifen injection, in days


title: Male_WT_D09_Rep2

description:
Liver homogenate
DS062


title: Male_KO_D09_Rep1

description:
Liver homogenate
DS061


title: Participant ID and visit (v) number [phchp085v2]

tag: gender

tag: diagnosis

value: SZA

tag: test cohort first year emergency department visits with pain

tag: test cohort all future emergency department visits with pain


title: STING-/- MEF_pBabe_dsDNA

description: STING-/- MEF cells reconstituted with pBabe vector were treated with dsDNA


title: Male_WT_D09_Rep1

description:
Liver homogenate
DS060

value: Male


title: Male_KO_D08_Rep2

description:
Liver homogenate
DS059


title: Male_WT_D08_Rep2

description:
Liver homogenate
DS058


title: STING-/- MEF_R284S _control

description: STING-/- MEF cells reconstituted with R284S


title: Participant ID and visit (v) number [phchp084v3]


title: STING-/- MEF_hSTING_control

description: STING-/- MEF cells reconstituted with hSTING


title: Participant ID and visit (v) number [phchp084v4]

tag: test cohort pain state


title: Participant ID and visit (v) number [phchp084v1]


title: Participant ID and visit (v) number [phchp080v1]


title: Male_WT_D07_Rep2

description:
Liver homogenate
DS056


title: Participant ID and visit (v) number [phchp083v3]

value: SZ


title: Participant ID and visit (v) number [phchp085v1]

value: Yes


title: Participant ID and visit (v) number [phchp084v2]

value: Female


title: Participant ID and visit (v) number [phchp083v1]


title: Participant ID and visit (v) number [phchp079v5]


title: STING-/- MEF_pBabe_control

description: STING-/- MEF cells reconstituted with pBabe vector


title: Participant ID and visit (v) number [phchp081v1]


title: Participant ID and visit (v) number [phchp083v2]


title: Participant ID and visit (v) number [phchp079v2]


title: Male_WT_D06_Rep2

description:
Liver homogenate
DS054


title: Male_KO_D05_Rep2

description:
Liver homogenate
DS053


title: Participant ID and visit (v) number [phchp079v4]


title: Participant ID and visit (v) number [phchp081v2]


title: Male_KO_D06_Rep2

description:
Liver homogenate
DS055


title: Participant ID and visit (v) number [phchp079v6]


title: Male_WT_D05_Rep2

description:
Liver homogenate
DS052


title: Participant ID and visit (v) number [phchp079v3]


title: Male_WT_D04_Rep2

description:
Liver homogenate
DS050


title: Male_WT_D03_Rep2

description:
Liver homogenate
DS048


title: Male_KO_D02_Rep2

description:
Liver homogenate
DS047


title: Male_WT_D02_Rep2

description:
Liver homogenate
DS046


title: Male_KO_D04_Rep2

description:
Liver homogenate
DS051


title: Male_KO_D02_Rep1

description:
Liver homogenate
DS045


title: Male_KO_D01_Rep2

description:
Liver homogenate
DS043


title: Male_WT_D02_Rep1

description:
Liver homogenate
DS044


title: Male_WT_D01_Rep2

description:
Liver homogenate
DS042


title: Participant ID and visit (v) number [phchp079v1]


title: Male_WT_D00_Rep2

description:
Liver homogenate
DS040


title: Male_KO_D00_Rep2

description:
Liver homogenate
DS041


title: Participant ID and visit (v) number [phchp076v2]


title: Male_KO_D03_Rep2

description:
Liver homogenate
DS049


title: Participant ID and visit (v) number [phchp075v2]


title: Participant ID and visit (v) number [phchp075v1]


title: Participant ID and visit (v) number [phchp076v3]


title: Participant ID and visit (v) number [phchp076v1]


title: Participant ID and visit (v) number [phchp074v3]


title: Participant ID and visit (v) number [phchp074v2]


title: Male_KO_D14_Rep1

description:
Liver homogenate
DS038


title: Participant ID and visit (v) number [phchp074v1]


title: Participant ID and visit (v) number [phchp073v3]


title: Participant ID and visit (v) number [phchp072v2]


title: Participant ID and visit (v) number [phchp072v3]


title: Participant ID and visit (v) number [phchp070v6]


title: Participant ID and visit (v) number [phchp070v5]


title: Participant ID and visit (v) number [phchp075v3]


title: Participant ID and visit (v) number [phchp073v2]


title: Participant ID and visit (v) number [phchp073v1]


title: Participant ID and visit (v) number [phchp072v1]


title: Male_WT_D14_Rep1

description:
Liver homogenate
DS037


title: Male_KO_D13_Rep1

description:
Liver homogenate
DS036


title: Participant ID and visit (v) number [phchp070v4]


title: Female_Het_D13_Rep1

description:
Liver homogenate
DS035


title: Male_KO_D14_Rep2

description:
Liver homogenate
DS039


title: Male_WT_D13_Rep1

description:
Liver homogenate
DS034


title: Male_KO_D12_Rep1

description:
Liver homogenate
DS033


title: Female_Het_D12_Rep1

description:
Liver homogenate
DS032


title: Participant ID and visit (v) number [phchp070v3]


title: Male_KO_D11_Rep1

description:
Liver homogenate
DS030


title: Male_WT_D12_Rep1

description:
Liver homogenate
DS031


title: Female_Het_D11_Rep1

description:
Liver homogenate
DS029


title: Male_KO_D10_Rep1

description:
Liver homogenate
DS027


title: Male_WT_D11_Rep1

description:
Liver homogenate
DS028


title: Female_Het_D10_Rep1

description:
Liver homogenate
DS026


title: Female_Het_D08_Rep1

description:
Liver homogenate
DS023


title: Male_WT_D08_Rep1

description:
Liver homogenate
DS022


title: Male_KO_D07_Rep1

description:
Liver homogenate
DS021


title: Male_KO_D08_Rep1

description:
Liver homogenate
DS024


title: Male_WT_D10_Rep1

description:
Liver homogenate
DS025


title: Participant ID and visit (v) number [phchp068v3]


title: Participant ID and visit (v) number [phchp070v1]


title: Participant ID and visit (v) number [phchp068v1]


title: Participant ID and visit (v) number [phchp070v2]


title: Female_Het_D07_Rep1

description:
Liver homogenate
DS020


title: Participant ID and visit (v) number [phchp068v2]


title: Participant ID and visit (v) number [phchp069v2]


title: Participant ID and visit (v) number [phchp062v2]


title: Participant ID and visit (v) number [phchp067v1]


title: Participant ID and visit (v) number [phchp069v1]


title: Participant ID and visit (v) number [phchp065v3]


title: Participant ID and visit (v) number [phchp065v2]


title: Participant ID and visit (v) number [phchp067v3]


title: Participant ID and visit (v) number [phchp069v3]


title: Participant ID and visit (v) number [phchp062v1]


title: Participant ID and visit (v) number [phchp062v3]


title: Participant ID and visit (v) number [phchp061v3]


title: Female_Het_D06_Rep1

description:
Liver homogenate
DS017


title: Male_KO_D06_Rep1

description:
Liver homogenate
DS018


title: Male_WT_D06_Rep1

description:
Liver homogenate
DS016


title: Male_KO_D05_Rep1

description:
Liver homogenate
DS015


title: Male_WT_D07_Rep1

description:
Liver homogenate
DS019


title: Participant ID and visit (v) number [phchp065v1]


title: Participant ID and visit (v) number [phchp060v1]


title: Female_Het_D05_Rep1

description:
Liver homogenate
DS014


title: Participant ID and visit (v) number [phchp061v1]


title: Female_Het_D04_Rep1

description:
Liver homogenate
DS011


title: Male_KO_D04_Rep1

description:
Liver homogenate
DS012


title: Male_WT_D04_Rep1

description:
Liver homogenate
DS010


title: Female_Het_D03_Rep1

description:
Liver homogenate
DS008


title: Male_KO_D03_Rep1

description:
Liver homogenate
DS009


title: Male_WT_D03_Rep1

description:
Liver homogenate
DS007


title: Participant ID and visit (v) number [phchp061v2]


title: Female_Het_D01_Rep1

description:
Liver homogenate
DS005


title: Male_WT_D05_Rep1

description:
Liver homogenate
DS013


title: Male_WT_D01_Rep1

description:
Liver homogenate
DS004


title: Participant ID and visit (v) number [phchp058v2]


title: Female_Het_D00_Rep1

description:
Liver homogenate
DS002


title: Male_KO_D00_Rep1

description:
Liver homogenate
DS003


title: Participant ID and visit (v) number [phchp057v1]


title: Participant ID and visit (v) number [phchp055v1]


title: Participant ID and visit (v) number [phchp058v3]


title: Participant ID and visit (v) number [phchp053v3]


title: Participant ID and visit (v) number [phchp058v1]


title: Participant ID and visit (v) number [phchp053v2]


title: Male_KO_D01_Rep1

description:
Liver homogenate
DS006


title: Participant ID and visit (v) number [phchp051v1]


title: Participant ID and visit (v) number [phchp055v3]


title: Participant ID and visit (v) number [phchp053v1]


title: Participant ID and visit (v) number [phchp049v2]


title: Participant ID and visit (v) number [phchp049v1]