title: VCaP_DMSO_H2BK5ac

value: prostate cancer


title: ChIP_AsPC1_RELA_TNFa_Rep1

status: Public on Jun 26 2025

type: SRA

city: Stuttgart

first: Steven

middle: A

last: Johnsen

address: Auerbachstrasse 112

country: Germany

institute: Robert Bosch Center for Tumor Diseases

library_source: genomic

data_processing:
Paired or single end sequencing reads were mapped to the reference genome assembly hg38 using bowtie2/2.5.0. PCR duplicates were removed with samtools markdup and replicates were merged using samtools merge (samtools/1.18). Bigwig files for individual and merged bam files were generated removing blacklist regions using reads per genomic content (RPGC) normalization with bamCoverage (deeptools/3.3.2) . MACS2 callpeak (python/3.10.7) was used to call the significant peaks with --broad cutoff 0.05 for histone marks and non-broad cutoff of 0.05 for transcription factors while using input files from respective conditions as background.
Assembly: hg38
Supplementary files format and content: merged bigiwg file for each conditiion
Supplementary files format and content: 3 column bed file

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: AsPC1 (RPMI, 10% FBS, 1% Pen-Strep) and L36pl (phenol red free MEM, 10% FBS, 1% Pen-Strep) were maintained in humidified 5% CO2 incubator at 37C.

extract_protocol:
Chromatin immunoprecipitation was performed by crosslinking cells with 1% formaldehyde for 20 min and quenched by 1.25 M glycine for 5 min. Cells were lysed with lysis buffer (150 mM NaCl, 20 mM EDTA, 50 mM Tris-HCl, 0.5% v/v NP-40, 1% v/v Triton X-100, 10 mM NaF). Nuclear pellets were resuspended and sonicated in sonication buffer (150 mM NaCl, 20 mM EDTA, 50 mM Tris-HCl, 1% v/v NP-40, 0.5% v/v sodium deoxycholate, 10 mM NaF, 0.1% SDS) using a Bioruptor Pico (Diagenode) and a cycle setting of 30 sec on/off until fragment sizes around 200-500 bp was reached. Protease and phosphatase inhibitors were added to both lysis and sonication buffers. Samples were precleared by 50% slurry of sepharose resuspended in sonication buffer. Antibodies were added and incubated rotating overnight. Sepharose beads coupled with Protein A (rabbit antibodies) or Protein G (mouse or goat antibodies) were added to samples and incubated for 2 hr, washed, de-crosslinked, RNAse A and proteinase K treated, and DNA was extracted. For GATA6 and Pol II ChIP of PDX tumors, 5 mm3 samples were thawed on ice in a petri dish, washed three times with PBS, cut into small pieces and transferred to a 15 mL falcon. Samples were fixed with 1% formaldehyde rotating on wheel for 20 min and quenched with 1.25 M glycine for 5 min. Samples were washed three times with PBS, resuspended in RPMI 1640 with 210 µg liberase TH per sample and transferred to gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec) and incubated (step 1: spin 50 rpm 20 min; step 2: spin 1000 rpm 30 min; step 3: spin -1000 rpm 30 min). Samples were centrifuged and transferred to a new tube and washed three times with lysis buffer, resuspending the nuclear pellet each time. ChIP was continues as described above for cell lines. For H3K27ac ChIP of PDX tumors, 5 mm3 samples were homogenized on dry ice using the Sciences BioMasher II Micro Tissue Homogenizer. ChIP was carried out for the powdered tissue as described for cell lines.
ChIP DNA was quantified with Qubit using the Qubit 1X dsDNA High Sensitivity Kit and libraries were prepped per supplier’s protocol using the MicroPlex Library Preparatioin Kit v3 (Diagenode, C05010001). The library fragment size was determined by TapeStation using the High Sensitivity D1000 Sample Buffer and High Sensitivity D1000 ScreenTape.

tag: cell line

tag: cell type

value: PDAC


title: VCaP_GNE_4h_FOXA1

city: Ann Arbor

first: Arul

last: Chinnaiyan

state: MI

address: 1500 East Medical Center Dr

department: MCTP

country: USA

institute: University of Michigan

data_processing:
Trimmomatic version 0.39 (settings TruSeq3-PE-2.fa:2:30:10, minlen 50)
Reads were aligned to hg38 (GRCh38) using bwa (“bwa mem” command with options -5SP -T0, version 0.7.17-r1198-dirty).
Alignments were then filtered using both samtools (quality score cutoff of 20) and picard MarkDuplicates (removed duplicates).
Peak calling was performed using MACS2
Removed blacklisted regions of the genome from the peaks list (From encode's file ENCFF356LFX.bed)
Assembly: hg38
Supplementary files format and content: bigwigs, peak beds

source_name: VCaP

growth_protocol: LNCaP cells were grown in Gibco RPMI-1640 + 10% FBS. VCaP cells were grown in Gibco DMEM Glutamax + 10% FBS

extract_protocol:
Chromatin immunoprecipitation experiments were carried out using the ideal ChIP-seq kit for transcription Factors and histone (Diagenode) as per the manufacturer’s protocol. Chromatin from 2×106 cells was used for each ChIP reaction with 4μg of the target protein antibody. In brief, cells were trypsinized and washed twice with 1× PBS, followed by cross-linking for 10 min in 1% formaldehyde solution. Crosslinking was terminated by the addition of 1/10 volume 1.25 M glycine for 5 min at room temperature followed by cell lysis and sonication (Bioruptor, Diagenode), resulting in an average chromatin fragment size of 200 bp. Fragmented chromatin was then used for immunoprecipitation using various antibodies, with overnight incubation at 4 °C. ChIP DNA was de-crosslinked and purified using the standard protocol.
Purified DNA was then prepared for sequencing as per the manufacturer’s instructions (Illumina). ChIP samples (1–10 ng) were converted to blunt-ended fragments using T4 DNA polymerase, Escherichia coli DNA polymerase I large fragment (Klenow polymerase), and T4 polynucleotide kinase (New England BioLabs (NEB)). A single adenine base was added to fragment ends by Klenow fragment (3′ to 5′ exo minus; NEB), followed by ligation of Illumina adaptors (Quick ligase, NEB). The adaptor-ligated DNA fragments were enriched by PCR using the Illumina Barcode primers and Phusion DNA polymerase (NEB). PCR products were size selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (Qiagen). Libraries were quantified and quality checked using the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2500 Sequencer (125-nucleotide read length).

treatment_protocol: The cells were treated with 100nM CBPD, 1uM GNE or 1uM CCS for 4hrs

value: VCaP

tag: chip antibody

value: FOXA1 (Thermo Fisher Scientific:PA5-27157)

tag: treatment


title: Female Adrenal Gland, 100 mg/kg/day PFHxSA, Animal r93

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

institute: U.S. Environmental Protection Agency

description:
Library name: p02_10105_r93_a
etap_pfhxsa_adrenal_female_counts.csv

library_source: transcriptomic

data_processing:
Raw sequencing reads (FASTQ files) were aligned to known probe sequences listed in the TempO-Seq probe manifest using HISAT2 to compute a matrix of read counts for each probe in each sample.
Assembly: TempO-seq Rat S1500+ v1.2
Supplementary files format and content: Count table CSV files contain a row for each known probe and a column for each sample. Each cell contains the number of reads from a single cell uniquely aligned to a single probe sequence
Supplementary files format and content: Probe manifest CSV file contains a row for each known probe with the probe name, sequence, and target gene

molecule: total RNA

organism: Rattus norvegicus

source_name: Adrenal Gland

growth_protocol: Male and female Sprague Dawley (Crl:CD IGS, Charles River Laboratory) rats are purchased at 6 – 8 weeks of age. Upon receipt, the animals are placed on a standard, purified laboratory diet and reverse osmosis treated drinking water ad libitum. The specific brand and type of food and source of the water should be noted in Appendix II (Detailed Animal Study Report) of the individual assessment. After a 7- to 14-day quarantine and acclimation period, the animals are weighed and randomly assigned by weight to chemical exposure and control groups. Only clinically healthy animals are used in the study. The target age for initiating exposure is 8 - 10 weeks.

extract_protocol:
Treated and control animals are necropsied approximately 24 hours after the last exposure. Carbon dioxide asphyxiation is used as the method of euthanasia, with death confirmed by a secondary method such as exsanguination or cervical dislocation. The following tissues were dissected from each animal: kidney, liver, adrenal gland, brain, heart, lung, ovary (females), spleen, testis (males), thyroid, thymus, and uterus (females). Tissue samples were collected within ten minutes of termination. The left liver lobe, right kidney, left lung, both testis, uterus, heart, spleen, thymus and whole brain were sectioned into 5mm^3 pieces. Samples from these larger tissues were then individually divided into at least 3 cryovials. At least two of the samples from each tissue in each animal were preserved in RNAlater™ (Thermo Fisher Scientific) at 4°C overnight and then frozen at approximately -20°C for up to 3 weeks before transferring to approximately -80°C. At least one sample from each larger tissue is frozen immediately in liquid nitrogen and stored at approximately -80°C.   The smaller bilateral tissues: adrenal glands, thyroid gland, and ovaries (female) are placed into two cryovials and preserved in RNALater with the left side of the tissue or gland going into the first cryovial and the right side going into the second cryovial. The first tube of RNALater preserved tissue is submitted for sequencing. For each tissue undergoing transcriptomic analysis, total RNA is extracted from one of the aliquots stored in RNAlater™.
The isolated total RNA is used to perform targeted RNA sequencing (RNA-seq) using the BioSpyder TempO-Seq rat S1500+ assay (v1.2) according to manufacturer’s instructions. No specific RNA purity or integrity criteria are applied to the RNA samples as the TempO-Seq assay has been designed to provide high quality gene expression measurements on whole cell lysates, purified RNA, and formalin-fixed paraffin embedded tissue.

treatment_protocol: For oral gavage studies, at least four male and four female rats per dose group receive the vehicle alone or test article in vehicle via gavage (5 or 10 ml/kg) for five days. Animals are weighed daily prior to administration and are observed twice daily, once during administration and once in the late afternoon, at least six hours apart, for assessment of moribundity and mortality. Formal clinical observations are performed on the first day post-dosing and prior to necropsy. Moribund animals or animals exhibiting overt clinical toxicity are removed from the study. The temperature in the experimental animal room is maintained at a target of 22°C (± 3°C) with a relative humidity that is ideally between 50-60% but is at least 30% and preferably not to exceed 70% other than during room cleaning. Lighting is artificial with a sequence of 12 hours light, 12 hours dark. Animals are housed individually or caged in small groups of no more than three animals of the same sex in accordance with local institutional animal care and use requirements.

tag: Sex

value: Female

tag: tissue

value: Adrenal Gland

tag: strain

value: Sprague Dawley

tag: age

value: 8-10 weeks

value: 100 mg/kg/day PFHxSA, 5-day repeat exposure, oral gavage

tag: treatment (dose)

value: 100 mg/kg/day

tag: treatment (dose_group)

tag: treatment (chemical_name)

value: Perflurohexanesulfonamide (PFHxSA)

tag: treatment (route_of_exposure)

value: Oral gavage

tag: sample qc_issue

value: No Issue


title: ChIP_AsPC1_RELA_EGF_Rep3


title: Female Adrenal Gland, 100 mg/kg/day PFHxSA, Animal r92

description:
Library name: p02_10105_r92_a
etap_pfhxsa_adrenal_female_counts.csv


title: ChIP_AsPC1_RELA_EGF_Rep1


title: Female Adrenal Gland, 30 mg/kg/day PFHxSA, Animal r91

description:
Library name: p02_10105_r91_a
etap_pfhxsa_adrenal_female_counts.csv

value: 30 mg/kg/day PFHxSA, 5-day repeat exposure, oral gavage

value: 30 mg/kg/day


title: VCaP_DMSO_FOXA1

value: DMSO


title: ChIP_AsPC1_FOSL1_siRELATE_Rep3


title: ChIP_AsPC1_FOSL1_siRELATE_Rep2


title: VCaP_CBPD_4h_FOXA1


title: Female Adrenal Gland, 30 mg/kg/day PFHxSA, Animal r90

description:
Library name: p02_10105_r90_a
etap_pfhxsa_adrenal_female_counts.csv


title: VCaP_CBPD_4h_AR

value: AR (Millipore:06-680)


title: VCaP_GNE_4h_AR

value: prostate cancer


title: ChIP_AsPC1_FOSL1_siRELATE_Rep1

value: PDAC


title: ChIP_AsPC1_RELA_Vehicle_Rep2


title: VCaP_DMSO_AR

value: VCaP


title: Female Adrenal Gland, 30 mg/kg/day PFHxSA, Animal r89

description:
Library name: p02_10105_r89_a
etap_pfhxsa_adrenal_female_counts.csv


title: Female Adrenal Gland, 100 mg/kg/day PFHxSA, Animal r94

description:
Library name: p02_10105_r94_a
etap_pfhxsa_adrenal_female_counts.csv


title: Female Adrenal Gland, 30 mg/kg/day PFHxSA, Animal r88

description:
Library name: p02_10105_r88_a
etap_pfhxsa_adrenal_female_counts.csv


title: ChIP_AsPC1_FOSL1_siFOSL1TE_Rep3


title: ChIP_AsPC1_RELA_EGF_Rep2


title: ChIP_AsPC1_FOSL1_siFOSL1TE_Rep2


title: VCaP_CCS_4h_H3K27ac

value: H3K27ac (Diagenode:C15410196)


title: ChIP_AsPC1_FOSL1_siFOSL1TE_Rep1


title: ChIP_AsPC1_RELA_Vehicle_Rep3


title: ChIP_AsPC1_RELA_Vehicle_Rep1


title: ChIP_AsPC1_FOSL1_siNT5TE_Rep3


title: ChIP_AsPC1_FOSL1_siNT5TE_Rep2


title: VCaP_GNE_4hrs_H3K27ac


title: Female Adrenal Gland, 30 mg/kg/day PFHxSA, Animal r87

description:
Library name: p02_10105_r87_a
etap_pfhxsa_adrenal_female_counts.csv

value: Female


title: ChIP_AsPC1_FOSL1_siNT5TE_Rep1


title: Female Adrenal Gland, 10 mg/kg/day PFHxSA, Animal r86

description:
Library name: p02_10105_r86_a
etap_pfhxsa_adrenal_female_counts.csv

value: Adrenal Gland

value: 10 mg/kg/day PFHxSA, 5-day repeat exposure, oral gavage

value: 10 mg/kg/day


title: ChIP_AsPC1_FOSL1_siNT5_Rep2


title: VCaP_CBPD_4hrs_H3K27ac


title: ChIP_AsPC1_FOSL1_Dex_TNFaEGF_Rep3


title: Female Adrenal Gland, 10 mg/kg/day PFHxSA, Animal r84

description:
Library name: p02_10105_r84_a
etap_pfhxsa_adrenal_female_counts.csv

value: Sprague Dawley

value: 8-10 weeks


title: Dog_6_normal_4

city: Davis

first: Stephanie

last: Goldschmidt

state: CA

address: one shields ave

department: VSR

institute: UC-Davis

description: Library name: DSP-1001660022200-F-D11

data_processing:
Raw FASTQ sequence reads were processed through the GeoMx NGS Pipeline Software for conversion to digital counts (DCC files) and subsequent downstream analyses with the GeoMx DSP Data Analysis Suite.
Assembly: Canine Cancer Atlas probe
Supplementary files format and content: Cf_R_NGS_CA_v1.0.pkc contains information about the probes and barcodes used in GeoMx assays (allows to map probe barcode to gene name)
Supplementary files format and content: dcc files contain raw counts of the probe barcodes detected in a ROI.
Library strategy: Spatial Transcriptomics

organism: Canis lupus familiaris

source_name: Caudal mandible

growth_protocol: This study consisted of 9 formalin-fixed paraffin embedded (FFPE) samples from dogs with spontaneously occurring canine oral squamous cell carcinoma (COSCC)

extract_protocol:
GeoMx DSP analysis was performed according to NanoString’s standard procedures for NGS readout. Briefly, semi-automated slide preparation was conducted on a Leica BOND RX stainer for deparaffinization, epitope retrieval, and proteinase K treatment to expose RNA targets. The GeoMx Canine Cancer Atlas probe set was hybridized in situ to the tissue sections by overnight incubation at 37C. Subsequently, tissue sections were stained with fluor-conjugated morphology marker antibodies specific for pan-cytokeratin (PanCK; Alexa 532, Cy3/568nm channel), CD45 (Alexa 594, Texas Red/615nm channel), CD3 (Alexa 647,  Cy5/666 nm channel), and the SYTO-13 nucleic acid stain (FITC/525nm channel, for instrument focus).  Morphology markers facilitated selection of regions of interest (ROIs) containing approximately 300 cells, as defined by the nuclear stain. Four ROIs were selected for each phenotype (5 phenotypes: surface normal, surface tumor, surface peri-tumoral dysplasia, deep invasive tumor, tumor microenvironment), leading to a total of approximately 20 ROIs per patient.
indexed libraries were prepared from the DSP DNA oligonucleotides using high-fidelity PCR with GeoMx Seq Code Illumina-compatible primers.
Validated libraries (i.e., expected amplicon size of 162 bp) were sequenced on an Illumina NovaSeq X Plus Sequencing System

treatment_protocol: Within this study the pathologic specimens were serially sectioned every 5 millimeters (mm). Thus, selecting these patients allowed us to select slides that had surface of the tumor, its deep invasive front, the TMS, peritumoral dysplasia, and normal on a single block. Spatial transcriptomic analysis of COSCC and non-malignant tissues was performed on the NanoString GeoMx Digital Spatial Profiler (DSP) platform utilizing the GeoMx Canine Cancer Atlas.

value: Caudal mandible

tag: tumor variant

value: Conventional

tag: tumor size


title: Dog_6_normal_3

description: Library name: DSP-1001660022200-F-D10


title: Female Adrenal Gland, 10 mg/kg/day PFHxSA, Animal r85

description:
Library name: p02_10105_r85_a
etap_pfhxsa_adrenal_female_counts.csv

value: Perflurohexanesulfonamide (PFHxSA)

value: Oral gavage

value: No Issue


title: ChIP_AsPC1_FOSL1_siNT5_Rep1


title: ChIP_AsPC1_FOSL1_Dex_TNFaEGF_Rep1


title: ChIP_AsPC1_FOSL1_Dex_TNFaEGF_Rep2


title: ChIP_AsPC1_FOSL1_BI_TNFaEGF_Rep3


title: ChIP_AsPC1_FOSL1_BI_TNFaEGF_Rep1


title: Female Adrenal Gland, 10 mg/kg/day PFHxSA, Animal r83

description:
Library name: p02_10105_r83_a
etap_pfhxsa_adrenal_female_counts.csv


title: Dog_6_normal_2

description: Library name: DSP-1001660022200-F-D09


title: ChIP_AsPC1_FOSL1_TNFaEGF_Rep3


title: Female Adrenal Gland, 10 mg/kg/day PFHxSA, Animal r82

description:
Library name: p02_10105_r82_a
etap_pfhxsa_adrenal_female_counts.csv


title: ChIP_AsPC1_FOSL1_TNFaEGF_Rep2


title: ChIP_AsPC1_FOSL1_BI_TNFaEGF_Rep2


title: Female Adrenal Gland, 3 mg/kg/day PFHxSA, Animal r80

description:
Library name: p02_10105_r80_a
etap_pfhxsa_adrenal_female_counts.csv

value: 3 mg/kg/day PFHxSA, 5-day repeat exposure, oral gavage

value: 3 mg/kg/day


title: Female Adrenal Gland, 3 mg/kg/day PFHxSA, Animal r81

description:
Library name: p02_10105_r81_a
etap_pfhxsa_adrenal_female_counts.csv


title: Female Adrenal Gland, 3 mg/kg/day PFHxSA, Animal r79

description:
Library name: p02_10105_r79_a
etap_pfhxsa_adrenal_female_counts.csv


title: ChIP_AsPC1_FOSL1_TNFa_Rep2


title: Dog_6_normal_1

description: Library name: DSP-1001660022200-F-D08


title: ChIP_AsPC1_FOSL1_TNFa_Rep3


title: ChIP_AsPC1_FOSL1_TNFa_Rep1


title: ChIP_AsPC1_FOSL1_siNT5_Rep3


title: VCaP_DMSO_H3K27ac

value: prostate cancer

value: DMSO


title: ChIP_AsPC1_FOSL1_EGF_Rep3

value: PDAC


title: Female Adrenal Gland, 3 mg/kg/day PFHxSA, Animal r78

description:
Library name: p02_10105_r78_a
etap_pfhxsa_adrenal_female_counts.csv


title: ChIP_AsPC1_FOSL1_TNFaEGF_Rep1


title: ChIP_AsPC1_FOSL1_EGF_Rep2


title: Dog_6_dysplasia_2

description: Library name: DSP-1001660022200-F-D05


title: ChIP_AsPC1_FOSL1_EGF_Rep1


title: Female Adrenal Gland, 3 mg/kg/day PFHxSA, Animal r77

description:
Library name: p02_10105_r77_a
etap_pfhxsa_adrenal_female_counts.csv


title: ChIP_AsPC1_FOSL1_Vehicle_Rep1


title: ChIP_AsPC1_FOSL1_Vehicle_Rep2


title: ChIP_AsPC1_FOSL1_Vehicle_Rep3


title: ChIP_AsPC1_H3K27ac_siRELATE_Rep3


title: ChIP_AsPC1_H3K27ac_siRELATE_Rep1


title: ChIP_AsPC1_H3K27ac_siRELATE_Rep2


title: Dog_6_surface_4

description: Library name: DSP-1001660022200-F-D03


title: Female Adrenal Gland, 1 mg/kg/day PFHxSA, Animal r75

description:
Library name: p02_10105_r75_a
etap_pfhxsa_adrenal_female_counts.csv

value: 1 mg/kg/day PFHxSA, 5-day repeat exposure, oral gavage

value: 1 mg/kg/day


title: Dog_6_surface_3

description: Library name: DSP-1001660022200-F-D02


title: ChIP_AsPC1_H3K27ac_siFOSL1TE_Rep3


title: Female Adrenal Gland, 1 mg/kg/day PFHxSA, Animal r74

description:
Library name: p02_10105_r74_a
etap_pfhxsa_adrenal_female_counts.csv

value: Female

value: Adrenal Gland


title: Dog_6_dysplasia_4

description: Library name: DSP-1001660022200-F-D07


title: Dog_6_surface_1

description: Library name: DSP-1001660022200-F-C12


title: ChIP_AsPC1_H3K27ac_siNT5TE_Rep2


title: Female Adrenal Gland, 1 mg/kg/day PFHxSA, Animal r76

description:
Library name: p02_10105_r76_a
etap_pfhxsa_adrenal_female_counts.csv


title: Dog_6_TMS_3

description: Library name: DSP-1001660022200-F-C10


title: Female Adrenal Gland, 0.3 mg/kg/day PFHxSA, Animal r70

description:
Library name: p02_10105_r70_a
etap_pfhxsa_adrenal_female_counts.csv

value: 0.3 mg/kg/day PFHxSA, 5-day repeat exposure, oral gavage

value: 0.3 mg/kg/day


title: Female Adrenal Gland, 1 mg/kg/day PFHxSA, Animal r73

description:
Library name: p02_10105_r73_a
etap_pfhxsa_adrenal_female_counts.csv

value: Sprague Dawley

value: 8-10 weeks


title: ChIP_AsPC1_H3K27ac_siFOSL1TE_Rep1


title: ChIP_AsPC1_H3K27ac_Dex_TNFaEGF_Rep2


title: Dog_6_surface_2

description: Library name: DSP-1001660022200-F-D01

value: Caudal mandible

value: Conventional


title: Female Adrenal Gland, 0.3 mg/kg/day PFHxSA, Animal r68

description:
Library name: p02_10105_r68_a
etap_pfhxsa_adrenal_female_counts.csv

value: Perflurohexanesulfonamide (PFHxSA)

value: Oral gavage


title: ChIP_AsPC1_H3K27ac_siFOSL1TE_Rep2


title: Dog_6_dysplasia_3

description: Library name: DSP-1001660022200-F-D06


title: ChIP_AsPC1_H3K27ac_BI_TNFaEGF_Rep3


title: Female Adrenal Gland, 0.3 mg/kg/day PFHxSA, Animal r69

description:
Library name: p02_10105_r69_a
etap_pfhxsa_adrenal_female_counts.csv

value: No Issue


title: ChIP_AsPC1_H3K27ac_BI_TNFaEGF_Rep2


title: ChIP_AsPC1_H3K27ac_siNT5TE_Rep3


title: ChIP_AsPC1_H3K27ac_siNT5TE_Rep1


title: Dog_6_TMS_4

description: Library name: DSP-1001660022200-F-C11


title: Female Adrenal Gland, 1 mg/kg/day PFHxSA, Animal r72

description:
Library name: p02_10105_r72_a
etap_pfhxsa_adrenal_female_counts.csv


title: Dog_6_dysplasia_1

description: Library name: DSP-1001660022200-F-D04


title: Dog_6_deep_3

description: Library name: DSP-1001660022200-F-C06


title: Female Adrenal Gland, 0.3 mg/kg/day PFHxSA, Animal r71

description:
Library name: p02_10105_r71_a
etap_pfhxsa_adrenal_female_counts.csv


title: ChIP_AsPC1_H3K27ac_siNT5_Rep3


title: ChIP_AsPC1_H3K27ac_siNT5_Rep2


title: ChIP_AsPC1_H3K27ac_TNFaEGF_Rep3


title: Female Adrenal Gland, 0.1 mg/kg/day PFHxSA, Animal r66

description:
Library name: p02_10105_r66_a
etap_pfhxsa_adrenal_female_counts.csv

value: 0.1 mg/kg/day PFHxSA, 5-day repeat exposure, oral gavage

value: 0.1 mg/kg/day


title: Dog_6_TMS_2

description: Library name: DSP-1001660022200-F-C09


title: ChIP_AsPC1_H3K27ac_siNT5_Rep1


title: ChIP_AsPC1_H3K27ac_Dex_TNFaEGF_Rep1


title: Dog_6_TMS_1

description: Library name: DSP-1001660022200-F-C08


title: Dog_6_deep_4

description: Library name: DSP-1001660022200-F-C07


title: ChIP_AsPC1_H3K27ac_BI_TNFaEGF_Rep1


title: Female Adrenal Gland, 0.1 mg/kg/day PFHxSA, Animal r65

description:
Library name: p02_10105_r65_a
etap_pfhxsa_adrenal_female_counts.csv


title: Female Adrenal Gland, 0.3 mg/kg/day PFHxSA, Animal r67

description:
Library name: p02_10105_r67_a
etap_pfhxsa_adrenal_female_counts.csv


title: ChIP_AsPC1_H3K27ac_TNFa_Rep3


title: ChIP_AsPC1_H3K27ac_TNFa_Rep1


title: Female Adrenal Gland, 0.1 mg/kg/day PFHxSA, Animal r64

description:
Library name: p02_10105_r64_a
etap_pfhxsa_adrenal_female_counts.csv


title: ChIP_AsPC1_H3K27ac_EGF_Rep2


title: ChIP_AsPC1_H3K27ac_EGF_Rep1


title: ChIP_AsPC1_H3K27ac_Dex_TNFaEGF_Rep3


title: ChIP_AsPC1_H3K27ac_TNFaEGF_Rep2


title: Dog_6_deep_2

description: Library name: DSP-1001660022200-F-C05


title: ChIP_AsPC1_H3K27ac_TNFaEGF_Rep1


title: ChIP_AsPC1_H3K27ac_TNFa_Rep2


title: Dog_6_deep_1

description: Library name: DSP-1001660022200-F-C04


title: ChIP_AsPC1_H3K27ac_EGF_Rep3


title: Dog_4_normal_4

description: Library name: DSP-1001660022200-F-C03

source_name: Rostral maxilla

value: Rostral maxilla

value: PapillaryCPV


title: Dog_4_normal_3

description: Library name: DSP-1001660022200-F-C02


title: Dog_4_normal_2

description: Library name: DSP-1001660022200-F-C01


title: ChIP_AsPC1_H3K27ac_Vehicle_Rep2

value: PDAC


title: Dog_4_normal_1

description: Library name: DSP-1001660022200-F-B12


title: Female Adrenal Gland, 0.01 mg/kg/day PFHxSA, Animal r60

description:
Library name: p02_10105_r60_a
etap_pfhxsa_adrenal_female_counts.csv

value: 0.01 mg/kg/day PFHxSA, 5-day repeat exposure, oral gavage

value: 0.01 mg/kg/day


title: C17_WAPLAID_C8,TACL-OFF_IAA,FLAG,rep1

city: Utrecht

first: Peter

last: Krijger

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: C17_WAPLAID_C8_TACL-OFF_IAA_FLAG_rep1_rep2.pval.bigwig

data_processing:
Reads were mapped and processed using the 4DN ChIP-seq data processing pipeline (https://github.com/4dn-dcic/chip-seq-pipeline2)
Assembly: hg38
Supplementary files format and content: pval bigWig and IDR narrowPeaks

growth_protocol: eHap1 cells were cultured in Iscove's Modified Dulbecco's Medium (IMDM) medium supplemented with Glutamax (Thermofisher), 25mM Hepes, 10% FBS, and 1% Penicillin-Streptomycin following standard procedures. Cells were routinely checked and sorted for haploidy.

extract_protocol:
100 million cells were crosslinked with 1% formaldehyde for 10min. Cells were subsequently quenched with 125mM glycine for 10min and washed twice with cold PBS. Cells were scraped from culture dishes and cell pellets were subsequently lysed in LB1 buffer (50mM Hepes, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100), washed in LB2 buffer (10mM Tris, 200mM NaCl, 1mM EDTA, 0.5mM EGTA), and resuspended in LB3 buffer (10mM Tris, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine) prior sonication. Chromatin was sonicated using Bioruptor Pico (Diagnode) with a setting of 30s on, 30s off for 8 cycles. Fragmented chromatin was then incubated with 6ug of antibodies pre-coupled to Dynabeads protein G beads (Thermofisher) overnight at 4oC. Beads-bound chromatin was then washed 10x with RIPA buffer (50mM Hepes, 500mM LiCl, 1mM EDTA, 1% NP40, 0.7% sodium deoxycholate), once with TBS buffer, and decrosslinked in elution buffer (50mM Tris, 10mM EDTA, 1% SDS) at 65oC for 18h. Eluted DNA was then treated with protease K and RNAse A, and subsequently purified with phenol/chloroform/isoamyl alcohol 25:24:1.
Purified DNA was either assessed with qPCR or continued with ChIP-seq NGS sequencing library preparation. Sequencing libraries was constructed using NEBnext Ultra II DNA library prep kit (NEB) following the manufacture’s protocol. Briefly, DNA was end-repaired and poly-A tailed, ligated to NEBnext adapters, and digested with USER enzyme. Annealed libraries were then purified with AMPure XP beads (Beckman Coulter) and PCR amplified with indexing primers for 4-12 cycles. Sequencing libraries were checked with Bioanalyzer HS DNA chip (Agilent).

treatment_protocol: To release TetR from the TetO platform, cells were treated with doxycycline for 1h.To deplete factors, cells were treated with auxin (5-Ph-IAA, BioAcademia)for 2 (RAD21) or 3h (STAG2, WAPL, CTCF, PDS5A).

tag: genotype

tag: protein

value: FLAG

tag: replicate

tag: antibody

value: anti-FLAG (F1804, Merck)


title: Dog_3_dysplasia_4

description: Library name: DSP-1001660022200-F-B11


title: C17_WAPLAID_C8,TACL-ON_IAA,FLAG,rep2

description: C17_WAPLAID_C8_TACL-ON_IAA_FLAG_rep1_rep2.pval.bigwig

tag: cell line


title: Female Adrenal Gland, 0.01 mg/kg/day PFHxSA, Animal r59

description:
Library name: p02_10105_r59_a
etap_pfhxsa_adrenal_female_counts.csv

value: Female

value: Adrenal Gland

tag: treatment


title: ChIP_AsPC1_H3K27ac_Vehicle_Rep3

tag: cell type


title: C17_WAPLAID_C8,TACL-OFF_IAA,FLAG,rep2


title: Dog_3_dysplasia_3

description: Library name: DSP-1001660022200-F-B10

tag: tissue


title: Female Adrenal Gland, 0.1 mg/kg/day PFHxSA, Animal r63

description:
Library name: p02_10105_r63_a
etap_pfhxsa_adrenal_female_counts.csv

tag: Sex

tag: strain

value: Sprague Dawley

value: 8-10 weeks


title: Female Adrenal Gland, 0.01 mg/kg/day PFHxSA, Animal r58

description:
Library name: p02_10105_r58_a
etap_pfhxsa_adrenal_female_counts.csv

tag: age

tag: treatment (dose)


title: C17_WAPLAID_C8,TACL-OFF,WAPL,rep1

value: TACL-OFF

value: WAPL

value: anti-WAPL (sc-365189, Santa Cruz)


title: ChIP_AsPC1_H3K27ac_Vehicle_Rep1


title: C17_WAPLAID_C8,TACL-OFF,FLAG,rep2

description: C17_WAPLAID_C8_TACL-OFF_FLAG_rep1_rep2.pval.bigwig


title: Dog_3_dysplasia_2

description: Library name: DSP-1001660022200-F-B09

value: Caudal mandible


title: C17_WAPLAID_C8,TACL-ON_IAA,FLAG,rep1


title: C17_WAPLAID_C8,TACL-OFF,FLAG,rep1


title: C17_WAPLAID_C8,TACL-ON,WAPL,rep1

value: TACL-ON


title: Female Adrenal Gland, 0.01 mg/kg/day PFHxSA, Animal r57

description:
Library name: p02_10105_r57_a
etap_pfhxsa_adrenal_female_counts.csv

tag: treatment (dose_group)

tag: treatment (chemical_name)

value: Perflurohexanesulfonamide (PFHxSA)

value: Oral gavage

value: No Issue


title: Dog_3_dysplasia_1

description: Library name: DSP-1001660022200-F-B08

value: PapillaryCPV


title: C17_WAPLAID_C8,TACL-ON,FLAG,rep1

description: C17_WAPLAID_C8_TACL-ON_FLAG_rep1_rep2.pval.bigwig


title: Dog_3_TMS_4

description: Library name: DSP-1001660022200-F-B07


title: Female Adrenal Gland, Vehicle Control, Animal r55

description:
Library name: p02_10105_r55_a
etap_pfhxsa_adrenal_female_counts.csv

value: Corn oil control, 5-day repeat exposure, oral gavage

value: 0 mg/kg/day

tag: treatment (route_of_exposure)

tag: sample qc_issue


title: C17_V5-MAU2,mCherry,V5,rep1

value: mCherry

value: anti-V5 (R960-25, Thermo fisher)


title: Dog_3_TMS_3

description: Library name: DSP-1001660022200-F-B06

tag: tumor variant

tag: tumor size


title: Female Adrenal Gland, 0.01 mg/kg/day PFHxSA, Animal r61

description:
Library name: p02_10105_r61_a
etap_pfhxsa_adrenal_female_counts.csv

value: Female

value: 0.01 mg/kg/day PFHxSA, 5-day repeat exposure, oral gavage

value: 0.01 mg/kg/day


title: Female Adrenal Gland, Vehicle Control, Animal r56

description:
Library name: p02_10105_r56_a
etap_pfhxsa_adrenal_female_counts.csv

value: Adrenal Gland

value: Sprague Dawley

value: 8-10 weeks


title: Female Adrenal Gland, Vehicle Control, Animal r54

description:
Library name: p02_10105_r54_a
etap_pfhxsa_adrenal_female_counts.csv


title: C17_WAPLAID_C8,TACL-ON,FLAG,rep2

tag: genotype

tag: protein

value: FLAG

value: anti-FLAG (F1804, Merck)


title: Dog_3_TMS_2

description: Library name: DSP-1001660022200-F-B05

value: Caudal mandible


title: C17_V5-MAU2,TACL-ON,V5,rep1

value: TACL-ON

tag: replicate

tag: antibody


title: C17_V5-MAU2,TACL-ON,NIPBL,rep1

tag: cell line

tag: treatment

value: NIPBL

value: anti-NIPBL (A301-779A, Bethyl)


title: Female Adrenal Gland, Vehicle Control, Animal r53

description:
Library name: p02_10105_r53_a
etap_pfhxsa_adrenal_female_counts.csv

tag: tissue

value: Perflurohexanesulfonamide (PFHxSA)

value: Oral gavage

value: No Issue


title: Female Adrenal Gland, Vehicle Control, Animal r52

description:
Library name: p02_10105_r52_a
etap_pfhxsa_adrenal_female_counts.csv

tag: Sex

value: Corn oil control, 5-day repeat exposure, oral gavage

value: 0 mg/kg/day


title: C17_V5-MAU2,TACL-ON,Input,rep1

value: Input


title: C17_STAG2AID_C2,TACL-ON_IAA,SMC1,rep1

value: Anti-SMC1 (A300-055A, Bethyl)


title: Dog_3_surface_4

description: Library name: DSP-1001660022200-F-B03

value: PapillaryCPV


title: C17_STAG2AID_C2,TACL-ON_IAA,NIPBL,rep1


title: C17_STAG2AID_C2,TACL-ON_IAA,STAG1,rep1

value: anti-STAG1 (A302-579A, Bethyl)


title: Dog_3_TMS_1

description: Library name: DSP-1001660022200-F-B04


title: Female Adrenal Gland, Vehicle Control, Animal r51

description:
Library name: p02_10105_r51_a
etap_pfhxsa_adrenal_female_counts.csv

value: Female

value: Adrenal Gland

tag: strain

value: Sprague Dawley


title: C17_STAG2AID_C2,TACL-ON_IAA,FLAG,rep2

description: C17_STAG2AID_C2_TACL-ON_IAA_FLAG_rep1_rep2.pval.bigwig

value: FLAG

value: anti-FLAG (F1804, Merck)


title: Dog_3_surface_3

description: Library name: DSP-1001660022200-F-B02

value: Caudal mandible


title: C17_WAPLAID_C8,TACL-ON,Input,rep1

value: TACL-ON


title: C17_STAG2AID_C2,TACL-ON_IAA,FLAG,rep1


title: C17_STAG2AID_C2,TACL-OFF,STAG1,rep1

value: TACL-OFF


title: Dog_3_surface_2

description: Library name: DSP-1001660022200-F-B01


title: Female Adrenal Gland, Vehicle Control, Animal r49

description:
Library name: p02_10105_r49_a
etap_pfhxsa_adrenal_female_counts.csv

tag: age

value: 8-10 weeks

value: Perflurohexanesulfonamide (PFHxSA)


title: C17_STAG2AID_C2,TACL-OFF,FLAG,rep2

description: C17_STAG2AID_C2_TACL-OFF_FLAG_rep1_rep2.pval.bigwig


title: C17_V5-MAU2,mCherry,NIPBL,rep1

value: mCherry

value: NIPBL

value: anti-NIPBL (A301-779A, Bethyl)


title: C17_V5-MAU2,mCherry,Input,rep1

value: Input


title: Dog_3_surface_1

description: Library name: DSP-1001660022200-F-A12


title: Dog_2_normal_4

description: Library name: DSP-1001660022200-F-A11

source_name: Rostral mandible

value: Rostral mandible

value: Conventional


title: Male Adrenal Gland, 100 mg/kg/day PFHxSA, Animal r47

description:
Library name: p01_10105_r47_a
etap_pfhxsa_adrenal_male_counts.csv

value: Male

value: 100 mg/kg/day PFHxSA, 5-day repeat exposure, oral gavage

tag: treatment (dose)

value: 100 mg/kg/day

value: Oral gavage

value: No Issue


title: Male Adrenal Gland, 100 mg/kg/day PFHxSA, Animal r48

description:
Library name: p01_10105_r48_a
etap_pfhxsa_adrenal_male_counts.csv

value: Adrenal Gland

value: Sprague Dawley

tag: treatment (dose_group)


title: C17_STAG2AID_C2,TACL-ON,FLAG,rep1

description: C17_STAG2AID_C2_TACL-ON_FLAG_rep1_rep2.pval.bigwig

value: TACL-ON

value: FLAG

value: anti-FLAG (F1804, Merck)


title: Dog_2_normal_3

description: Library name: DSP-1001660022200-F-A10


title: Male Adrenal Gland, 100 mg/kg/day PFHxSA, Animal r46

description:
Library name: p01_10105_r46_a
etap_pfhxsa_adrenal_male_counts.csv

value: 8-10 weeks

tag: treatment (chemical_name)

value: Perflurohexanesulfonamide (PFHxSA)


title: C17_STAG2AID_C2,TACL-ON,FLAG,rep2


title: Dog_2_normal_2

description: Library name: DSP-1001660022200-F-A09


title: Female Adrenal Gland, Vehicle Control, Animal r50

description:
Library name: p02_10105_r50_a
etap_pfhxsa_adrenal_female_counts.csv

value: Female

value: Corn oil control, 5-day repeat exposure, oral gavage

value: 0 mg/kg/day

tag: treatment (route_of_exposure)


title: Dog_2_normal_1

description: Library name: DSP-1001660022200-F-A08

value: Rostral mandible


title: Male Adrenal Gland, 100 mg/kg/day PFHxSA, Animal r45

description:
Library name: p01_10105_r45_a
etap_pfhxsa_adrenal_male_counts.csv

tag: sample qc_issue


title: C17_RAD21AID_SC6,mCherry_IAA,SMC1,rep1

value: Anti-SMC1 (A300-055A, Bethyl)


title: C17_RAD21AID_SC6,mCherry_IAA,Input,rep1

value: Input


title: C17_RAD21AID_SC6,mCherry_IAA,NIPBL,rep1

value: NIPBL

value: anti-NIPBL (A301-779A, Bethyl)


title: Male Adrenal Gland, 100 mg/kg/day PFHxSA, Animal r44

description:
Library name: p01_10105_r44_a
etap_pfhxsa_adrenal_male_counts.csv

value: Male

value: 100 mg/kg/day PFHxSA, 5-day repeat exposure, oral gavage

value: 100 mg/kg/day

value: Oral gavage


title: C17_RAD21AID_SC6,mCherry,SMC1,rep1

description: C17_RAD21AID_SC6_mCherry_SMC1_rep1_rep2.pval.bigwig

value: mCherry


title: Dog_2_surface_4

description: Library name: DSP-1001660022200-F-A07

tag: tumor variant

value: Conventional


title: C17_RAD21AID_SC6,mCherry,RAD21,rep1

value: anti-RAD21 (05-908, Merck)


title: C17_STAG2AID_C2,TACL-ON,STAG1,rep1

value: TACL-ON

value: anti-STAG1 (A302-579A, Bethyl)


title: Male Adrenal Gland, 30 mg/kg/day PFHxSA, Animal r43

description:
Library name: p01_10105_r43_a
etap_pfhxsa_adrenal_male_counts.csv

value: Adrenal Gland

value: Sprague Dawley

value: 8-10 weeks

value: 30 mg/kg/day PFHxSA, 5-day repeat exposure, oral gavage

value: 30 mg/kg/day

value: Perflurohexanesulfonamide (PFHxSA)

value: No Issue


title: C17_RAD21AID_SC6,mCherry,Input,rep1

value: Input


title: C17_STAG2AID_C2,TACL-ON,Input,rep1


title: Male Adrenal Gland, 30 mg/kg/day PFHxSA, Animal r42

description:
Library name: p01_10105_r42_a
etap_pfhxsa_adrenal_male_counts.csv

value: Male


title: Dog_2_dysplasia_3

description: Library name: DSP-1001660022200-F-A06

value: Rostral mandible

tag: tumor size


title: Dog_2_dysplasia_2

description: Library name: DSP-1001660022200-F-A05


title: C17_RAD21AID_SC6,mCherry,NIPBL,rep1

tag: genotype

value: NIPBL

value: anti-NIPBL (A301-779A, Bethyl)


title: C17_STAG2AID_C2,TACL-OFF,FLAG,rep1

value: TACL-OFF

tag: protein

value: FLAG

value: anti-FLAG (F1804, Merck)


title: Male Adrenal Gland, 30 mg/kg/day PFHxSA, Animal r41

description:
Library name: p01_10105_r41_a
etap_pfhxsa_adrenal_male_counts.csv

value: Oral gavage


title: Male Adrenal Gland, 30 mg/kg/day PFHxSA, Animal r40

description:
Library name: p01_10105_r40_a
etap_pfhxsa_adrenal_male_counts.csv


title: C17_RAD21AID_SC1,TACL-ON,RAD21,rep1

value: TACL-ON

tag: replicate

value: anti-RAD21 (05-908, Merck)


title: C17_RAD21AID_SC1,TACL-ON,MAU2,rep1

tag: antibody

value: anti-SCC4/MAU2 (ab183033, Abcam)


title: C17_RAD21AID_D8,mCherry_IAA,MAU2,rep1

tag: cell line


title: Dog_2_dysplasia_1

description: Library name: DSP-1001660022200-F-A04

value: Conventional


title: C17_RAD21AID_SC1,TACL-ON_IAA,RAD21,rep1

tag: treatment


title: C17_RAD21AID_D8,mCherry,MAU2,rep1

value: mCherry


title: Dog_2_surface_3

description: Library name: DSP-1001660022200-F-A03

tag: tissue


title: Male Adrenal Gland, 30 mg/kg/day PFHxSA, Animal r39

description:
Library name: p01_10105_r39_a
etap_pfhxsa_adrenal_male_counts.csv

tag: Sex

value: Adrenal Gland

value: Sprague Dawley

value: 8-10 weeks

value: 30 mg/kg/day PFHxSA, 5-day repeat exposure, oral gavage

value: 30 mg/kg/day


title: C17_PDS5AAID_B10,TACL-ON_IAA,NIPBL,rep1


title: Dog_2_dysplasia_4

description: Library name: DSP-1001660022200-F-A02

value: Rostral mandible


title: C17_PDS5AAID_B10,TACL-ON_IAA,FLAG,rep2

description: C17_PDS5AAID_B10_TACL-ON_IAA_FLAG_rep1_rep2.pval.bigwig


title: Male Adrenal Gland, 10 mg/kg/day PFHxSA, Animal r38

description:
Library name: p01_10105_r38_a
etap_pfhxsa_adrenal_male_counts.csv

value: Male

tag: strain

value: 10 mg/kg/day PFHxSA, 5-day repeat exposure, oral gavage

value: 10 mg/kg/day

value: Perflurohexanesulfonamide (PFHxSA)

value: No Issue


title: NTC-plate2

description: Library name: DSP-1001660022200-F-A01


title: C17_PDS5AAID_B10,TACL-ON_IAA,FLAG,rep1

value: FLAG

value: anti-FLAG (F1804, Merck)


title: Male Adrenal Gland, 10 mg/kg/day PFHxSA, Animal r37

description:
Library name: p01_10105_r37_a
etap_pfhxsa_adrenal_male_counts.csv

tag: age

value: Oral gavage


title: C17_PDS5AAID_B10,TACL-OFF,FLAG,rep2

description: C17_PDS5AAID_B10_TACL-OFF_FLAG_rep1_rep2.pval.bigwig

value: TACL-OFF


title: C17_PDS5AAID_B10,TACL-OFF,NIPBL,rep1

value: NIPBL

value: anti-NIPBL (A301-779A, Bethyl)


title: C17_RAD21AID_SC1,TACL-ON_IAA,MAU2,rep1

value: anti-SCC4/MAU2 (ab183033, Abcam)


title: Dog_2_surface_2

description: Library name: DSP-1001660022199-E-H12

value: Conventional


title: Male Adrenal Gland, 10 mg/kg/day PFHxSA, Animal r36

description:
Library name: p01_10105_r36_a
etap_pfhxsa_adrenal_male_counts.csv

value: Adrenal Gland

value: Sprague Dawley

value: 8-10 weeks

tag: treatment (dose)


title: C17_PDS5AAID_B10,TACL-ON,NIPBL,rep1

value: TACL-ON


title: Dog_2_surface_1

description: Library name: DSP-1001660022199-E-H11

value: Rostral mandible


title: C17_PDS5AAID_B10,TACL-ON,Input,rep1

value: Input


title: Male Adrenal Gland, 10 mg/kg/day PFHxSA, Animal r35

description:
Library name: p01_10105_r35_a
etap_pfhxsa_adrenal_male_counts.csv

value: Male

value: 10 mg/kg/day PFHxSA, 5-day repeat exposure, oral gavage

value: 10 mg/kg/day

tag: treatment (dose_group)


title: Male Adrenal Gland, 10 mg/kg/day PFHxSA, Animal r34

description:
Library name: p01_10105_r34_a
etap_pfhxsa_adrenal_male_counts.csv

tag: treatment (chemical_name)

value: Perflurohexanesulfonamide (PFHxSA)

value: No Issue


title: Male Adrenal Gland, 3 mg/kg/day PFHxSA, Animal r33

description:
Library name: p01_10105_r33_a
etap_pfhxsa_adrenal_male_counts.csv

value: 3 mg/kg/day PFHxSA, 5-day repeat exposure, oral gavage

value: 3 mg/kg/day

tag: treatment (route_of_exposure)

value: Oral gavage


title: C17_PDS5AAID_B10,TACL-ON,FLAG,rep2

description: C17_PDS5AAID_B10_TACL-ON_FLAG_rep1_rep2.pval.bigwig

value: FLAG

value: anti-FLAG (F1804, Merck)


title: C17_CTCFAID_C22,TACL-ON_IAA,FLAG,rep2

description: C17_CTCFAID_C22_TACL-ON_IAA_FLAG_rep1_rep2.pval.bigwig


title: Male Adrenal Gland, 3 mg/kg/day PFHxSA, Animal r32

description:
Library name: p01_10105_r32_a
etap_pfhxsa_adrenal_male_counts.csv

tag: sample qc_issue


title: Dog_2_TMS_4

description: Library name: DSP-1001660022199-E-H10

tag: tumor variant

value: Conventional


title: F044_single_nucleotide_mutagenesis_library_frog_oocyte_progesterone_7h_Tail_seq

city: Cambridge

first: David

last: Bartel

address: 455 Main Street

institute: Whitehead Institute

description: Libraries enriched by antisese oligos before ligaion, followed by reverse transcription and PCR amplification with library-specific primers

library_source: other

data_processing:
To build a reference sequence for the N60(LC)-PASmos library, sequencing reads (read 1) of the 0 h post progesterone sample (uninjected) from AVITI were trimmed down to 81 nt from 5ʹ ends. Trimmed reads were examined for the presence of the constant region in the 3ʹ UTR of mRNA poly(A) tail-length standards (ACCAGCCTCAAGAACACCCGAATGG) with 7 allowed mismatches in the first 25 nt, allowing positional offsets between –3 and +3 nt. The remaining reads were examined for the expected constant sequence AATAAAGAAATTGATTTGTCT at position 61–81, allowing positional offsets between –3 and +3 nt. Reads with a 21-nt sequence that had no more than six mismatches to the constant sequence at any allowed positions were retained. Retained reads that had a non-zero positional offset were modified to make the offset value zero: “N” bases were added to the beginning of the read if the offset value was negative, while the first few bases at the start of the read were removed if the offset value is positive. Then the modified reads were collapsed using UMICollapse. Clusters with more than 100 reads were kept. The primary sequence of each cluster was used as the reference sequence for the N60(LC)-PASmos library. The sequencing run performed on HiSeq 2500 for the N60(LC)-PASmos and the single-nucleotide mutagenesis libraries stuttered at cycle 26 in read 1 and reported the same bases for cycle 26 and cycle 27. As a result, the base at cycle 27 was removed from all sequencing reads before downstream analysis. For the N60(LC)-PASmos libraries, sequencing reads (read 1) from the HiSeq run were mapped to the reference sequence using STAR (v2.7.1) with the parameters ‘--outFilterMultimapNmax 1 --alignEndsType Local –clip3pNbases 199 --outSAMattributes All --outSAMtype BAM SortedByCoordinate’. Poly(A)-tail lengths of the mapped reads were determined the same way as those of the N60-PASmos libraries described in our previous study1. For the single-nucleotide mutagenesis libraries, sequencing reads (read 1) from the HiSeq run were mapped to the reference sequence (the last 100 nt wild-type sequence of the 3ʹ UTR of ten selected frog oocyte mRNAs) using STAR (v2.7.1) with the parameters ‘--outFilterMultimapNmax 1 --outFilterMismatchNmax 1 --alignEndsType EndToEnd –clip3pNbases 180 --outSAMattributes All --outSAMtype BAM SortedByCoordinate’. After mapping, the CIGAR label in the bam file was used to determine the type of mutation for each variant. Poly(A)-tail lengths of the mapped reads were determined the same way as those of the N60(LC)-PASmos libraries, except that the starting position of the poly(A) tail was set at 101 of the read 1. Only the wild-type and single-nucleotide substitution mutants were kept. For each retained variant, poly(A) tags (read clusters) that contained the same read 2 (serving as a unique molecular identifier) sequences were grouped and collapsed, and the median tail length of the grouped poly(A) tags was used as the poly(A)-tail length of the collapsed tag.
Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4, primary assembly. Xenopus laevis: v10.1 assembly.
Supplementary files format and content: For the N60(LC)-PASmos library sequenced with HiSeq2500, tab-delimited text files with columns indicating 1) unique id for a variant in the library; 2) sequence of the variable region; 3) median tail length; 4) number of reads; 5–8) tail lengths at quantile 10, 25, 75, and 90. For the single-nucleotide mutagenesis library (F044), tab-delimited text files with columns indicating 1) unique id for the mRNA that was used to derive mutants; 2) the type of the variant or wild-type; 3) UMI; 4) number of UMIs collapsed; 5) poly(A)-tail length. For the N60(LC)-PASmos library sequenced with AVITI, one is a fasta file and the other is a tab-delimited text file indicating 1) sequence of the variable region; 2) number of reads.
Library strategy: gene-specific Tail-seq

molecule: other

organism: Xenopus laevis

source_name: oocyte

extract_protocol:
Frog oocytes (100 as a group) were collected at the indicated time after progesterone treatment. OR-2 buffer was removed and oocytes were washed three times with ice-cold buffer RL (20 mM HEPES pH 7.5, 100 mM KCl, 5 mM MgCl2, 1% (v/v) Triton X-100, 100 µg/ml cycloheximide, cOmplete protease inhibitor cocktail [MilliporeSigma, 11836170001, 1 tablet per 10 ml buffer], 10 µl/oocyte). After removing all wash buffer, oocytes were lysed in buffer RL (10 µl per oocyte) supplemented with 200 units/ml SUPERase•In (10 µl/oocyte) by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was mixed with 3x volume TRIzol LS (Thermo Fisher, 10296010). Note that the “0 h post progesterone treatment” sample was prepared by collecting the supernatant of the lysate of untreated oocytes and combining it with the uninjected mRNA library before the Tri-Reagent was added to the mix. All RNAs isolated with the TRIzol-LS were performed with Phasemaker tubes (Thermo Fisher, A33248) according to the manufacturer’s protocol. Total RNAs were resuspended in 40 µl water (0.4 µl/oocyte).
Total RNAs (10 µl, ~30 µg) isolated from injected oocytes were combined with 10 amol with reporter mRNA poly(A) tail-length standard mix and then mixed with 8 pmol KXSH009, 8 pmol KXSH010, and 2x SSC (0.3 M NaCl, 30 mM sodium citrate pH 7.0) in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads (Thermo Fisher, 65002) and incubated for 20 min at 23°C on a thermal mixer, shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 µl 1xB&W buffer (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1 M NaCl) and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined, precipitated with ethanol, and resuspended in 6.5 µl water. The anti-sense oligo-enriched RNA was ligated to a pre-adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS347a, 50 mM HEPES pH 7.5, 10 mM MgCl2, 10 mM dithiothreitol, 1 unit/µl T4 RNA ligase 1 (New England Biolabs, M0204S). The ligation reaction was incubated at 23°C for 150 min. After ligation, RNA was extracted with phenol/chloroform, precipitated with ethanol, and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS348 and 1 µl 10 mM dNTPs in a total volume of 13 µl, incubated at 65°C for 5 min, and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x SSIV Buffer, 5 mM dithiothreitol, 1 unit/µl SUPERase•In, and 200 units SuperScript IV Reverse Transcriptase (ThermoFisher, 18090050) at 55°C for 15 min. After reverse transcription, RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min followed by neutralization with 24 µl 1 M HEPES pH 7.5. The cDNA library was ethanol-precipitated, resuspended in water, and amplified in a 50 µl PCR reaction with KXS037 and a barcoded primer (KXS057) that hybridized to a constant region of the library using the KAPA HiFi HotStart Kits following the manufacturer’s suggested protocol for 11~14 cycles. The PCR-amplified library was cleaned up twice with AMPure XP beads (Beckman Coulter, A63881) with a beads-to-sample ratio of 1.2. Sequencing was performed on an Illumina HiSeq 2500, with a custom run of two reads. The first read was sequenced with the primer KXS067 for 281 cycles. The second read was sequenced in the same direction with a standard TruSeq sequencing primer for 10 cycles. Additionally, to build a reference sequence, the N60(LC)-PASmos library made from the 0 h post progesterone sample (uninjected) was also sequenced on AVITI, with a custom run of two reads in the same direction for 299 cycles and 10 cycles respectively, using the same primers as those for the HiSeq.

treatment_protocol: Frog oocytes used for the injection were obtained from Xenopus1 (12005). Healthy Stage V and VI oocytes were hand-picked and transferred to OR-2 buffer (5 mM HEPES pH 7.6, 82.5 mM NaCl, 2.5 mM KCl, 1 mM MgCl2, 1 mM CaCl2, 1 mM Na2HPO4) supplemented with 100 µg/ml Gentamicin (Thermo Fisher, 15750060) at 18°C overnight (> 16 hr) for recovery before injections. Injections were performed at 23°C with PLI-100 Plus Pico-Injector. For the N60(LC)-PASmos library, 4 nl mRNA (0.1 pmol/µl) was injected per oocyte.  Frog oocytes were matured in vitro in OR-2 buffer supplemented with 10 µg/ml progesterone (Millipore Sigma, P0130) diluted from a 10 mg/ml stock in ethanol. The time it took for frog oocytes to mature varied between different batches. In most cases, 50% of oocytes reached GVBD (displaying a white spot in the animal pole) between 3 hr and 5 hr and 100% of oocytes reached GVBD by 7 hr after incubation with progesterone.

value: oocyte

value: 10 µM progesterone for 7 h


title: C17_PDS5AAID_B10,TACL-ON,FLAG,rep1


title: Dog_2_TMS_3

description: Library name: DSP-1001660022199-E-H09

tag: tumor size


title: C17_CTCFAID_C22,TACL-OFF,FLAG,rep2

description: C17_CTCFAID_C22_TACL-OFF_FLAG_rep1_rep2.pval.bigwig

tag: genotype

value: TACL-OFF


title: C17_CTCFAID_C22,TACL-OFF_IAA,FLAG,rep2

description: C17_CTCFAID_C22_TACL-OFF_IAA_FLAG_rep1_rep2.pval.bigwig

tag: protein


title: C17_PDS5AAID_B10,TACL-OFF,FLAG,rep1

tag: replicate


title: Female Adrenal Gland, 0.1 mg/kg/day PFHxSA, Animal r62

description:
Library name: p02_10105_r62_a
etap_pfhxsa_adrenal_female_counts.csv

value: Female

value: Adrenal Gland

value: Sprague Dawley

value: 8-10 weeks

value: 0.1 mg/kg/day PFHxSA, 5-day repeat exposure, oral gavage

value: 0.1 mg/kg/day


title: F044_single_nucleotide_mutagenesis_library_frog_oocyte_uninjected_Tail_seq


title: Dog_2_TMS_2

description: Library name: DSP-1001660022199-E-H08

value: Rostral mandible


title: C17_CTCFAID_C22,TACL-ON_IAA,FLAG,rep1

tag: antibody


title: Dog_2_TMS_1

description: Library name: DSP-1001660022199-E-H07


title: C17_CTCFAID_C22,TACL-OFF_IAA,FLAG,rep1

tag: cell line


title: Male Adrenal Gland, 3 mg/kg/day PFHxSA, Animal r30

description:
Library name: p01_10105_r30_a
etap_pfhxsa_adrenal_male_counts.csv

value: Male

tag: treatment

value: Perflurohexanesulfonamide (PFHxSA)

value: No Issue


title: N60_LC_CPEmos_library_frog_oocyte_progesterone_7hr_Tail_seq

tag: tissue


title: C17_CTCFAID_C22,TACL-OFF,FLAG,rep1


title: Dog_2_deep_4

description: Library name: DSP-1001660022199-E-H06


title: C17_CTCFAID_C22,TACL-ON,Input,rep1

value: TACL-ON

value: Input


title: Male Adrenal Gland, 3 mg/kg/day PFHxSA, Animal r29

description:
Library name: p01_10105_r29_a
etap_pfhxsa_adrenal_male_counts.csv

tag: Sex

value: 3 mg/kg/day PFHxSA, 5-day repeat exposure, oral gavage

value: 3 mg/kg/day

value: Oral gavage


title: Dog_2_deep_2

description: Library name: DSP-1001660022199-E-H04

value: Conventional


title: VCaP_CBPD_4h_BRD4_Diagenode

description: Library name: SI_35551_VCaP_CBPD_4h_BRD4_Diagenode.

data_processing:
Reads were first processed using Trimmomatic version 0.39 (settings TruSeq3-PE-2.fa:2:30:10, minlen 50) followed by alignment with bwa (“bwa mem”, options -5SP -T0, version 0.7.17-r1198-dirty) to mm10 (GRCm38) genome reference or hg38 (GRCh38) reference. After alignment the reads were filtered using Markduplicates from Picard then by quality score of >20 via samtools. MACS2 was used to call peaks which were then filtered using bedtools and converted to bigwigs with UCSC wigtoBigwig. Cistrome overlap analysis were performed in R (v3.6.0) using ChipSeekAnno (v3.0.0) and ChipSeeker (v1.29.1). Enrichment heatmaps were generated using Deeptools. HOMER was used to perform motif enrichment analysis. Motif dot plot summaries were created in R (v3.6.0) using Sushi.
Assembly: hg38
Supplementary files format and content: .bed: peak locations from macs bed calling with blacklist removed; .bw: signal files

source_name: prostate

growth_protocol: Gibco RPMI-1640 + 10% FBS (ThermoFisher) were used for LNCaP,  PC-3, and DU145 cells, VCaP was grown in Gibco DMEM Glutamax + 10% FBS

extract_protocol:
1-2 million cells were used per ChIP reaction with 2 or 4ug of antibody. Briefly, cells were crosslinked for 10 minutes in a 1% formaldehyde solution, followed by termination with 1/10th the volume of 1.25M glycine for 5 minutes at room temperature. Following this, the cells were lysed and sonicated (Bioruptor Pico, Diagenode) with a desired chromatin size of about 200bp. Sheared chromatin was then incubated with desired antibodies overnight at 4 °C. Next day, the ChIP-DNA was de-crosslinked and purified using the Diagenode iPure Kit V3, following the manufacturer's protocol.
Utilizing the manufacturer’s instructions (Illumina), purified DNA was prepared for sequencing. About 1-10ng of ChIP DNA were converted to blunt-ended fragments using T4 DNA polymerase, Escherichia coli DNA polymerase I large fragment (Klenow polymerase), and T4 polynucleotide kinase (New England BioLabs (NEB)). Klenow fragment (3′ to 5′ exo minus; NEB) was used to add a single adenine base to fragment ends, followed by ligation of Illumina adaptors (Quick ligase, NEB). PCR enriched the adaptor-ligated DNA fragments using the Illumina Barcode primers and Phusion DNA polymerase (NEB). PCR products were size-selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (Qiagen). Quantified libraries quality-checked using the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2500 Sequencer (125-nucleotide read length).

treatment_protocol: The cells were treated with DMSO, 100nM CBPD-409 or 1uM GNE-049 for 4hrs and 24hrs

value: prostate

value: VCAP

tag: cell type

value: mixed


title: Dog_2_deep_1

description: Library name: DSP-1001660022199-E-H03


title: Male Adrenal Gland, 1 mg/kg/day PFHxSA, Animal r28

description:
Library name: p01_10105_r28_a
etap_pfhxsa_adrenal_male_counts.csv

value: Adrenal Gland

tag: strain

value: Sprague Dawley

tag: age

value: 1 mg/kg/day PFHxSA, 5-day repeat exposure, oral gavage

value: 1 mg/kg/day


title: C17_CTCFAID_C22,TACL-ON,FLAG,rep1

description: C17_CTCFAID_C22_TACL-ON_FLAG_rep1_rep2.pval.bigwig

value: FLAG

value: anti-FLAG (F1804, Merck)


title: Male Adrenal Gland, 3 mg/kg/day PFHxSA, Animal r31

description:
Library name: p01_10105_r31_a
etap_pfhxsa_adrenal_male_counts.csv

value: Male

value: 8-10 weeks

tag: treatment (dose)

tag: treatment (dose_group)

value: Perflurohexanesulfonamide (PFHxSA)


title: C17,TACL-ON_CRISPRi-WAPL,Input,rep1

value: Input


title: VCaP_DMSO_BRD4

description: Library name: SI_35550_VCaP_DMSO_BRD4_

value: dmso


title: Dog_7_normal_3

description: Library name: DSP-1001660022199-E-H01

source_name: Rostral-caudal mandible

value: Rostral-caudal mandible


title: Male Adrenal Gland, 1 mg/kg/day PFHxSA, Animal r26

description:
Library name: p01_10105_r26_a
etap_pfhxsa_adrenal_male_counts.csv

tag: treatment (chemical_name)

tag: treatment (route_of_exposure)

value: Oral gavage

value: No Issue


title: Male Adrenal Gland, 1 mg/kg/day PFHxSA, Animal r25

description:
Library name: p01_10105_r25_a
etap_pfhxsa_adrenal_male_counts.csv

tag: sample qc_issue


title: PC3_H2BK16ac_abcam

description: Library name: SI_39925_PC3_H2BK16ac_abcam

value: prostate

value: No treatment


title: Male Adrenal Gland, 1 mg/kg/day PFHxSA, Animal r24

description:
Library name: p01_10105_r24_a
etap_pfhxsa_adrenal_male_counts.csv


title: Dog_7_normal_4

description: Library name: DSP-1001660022199-E-H02

tag: tumor variant

value: Conventional

tag: tumor size


title: Dog_2_deep_3

description: Library name: DSP-1001660022199-E-H05

value: Rostral mandible


title: Dog_7_normal_1

description: Library name: DSP-1001660022199-E-G11


title: Male Adrenal Gland, 0.3 mg/kg/day PFHxSA, Animal r23

description:
Library name: p01_10105_r23_a
etap_pfhxsa_adrenal_male_counts.csv

value: Adrenal Gland

value: Sprague Dawley

value: 0.3 mg/kg/day PFHxSA, 5-day repeat exposure, oral gavage

value: 0.3 mg/kg/day


title: DU145_H2BK16ac_abcam

description: Library name: SI_39924_DU145_H2BK16ac_abcam

value: mixed


title: C17,mCherry,STAG2,rep1

tag: genotype

value: mCherry

tag: protein

value: anti-STAG2 (A300-159A, Bethyl)


title: Dog_7_normal_2

description: Library name: DSP-1001660022199-E-G12


title: C17,mCherry,WAPL,rep1

value: WAPL

tag: replicate

tag: antibody

value: anti-WAPL (sc-365189, Santa Cruz)


title: VCaP_H2BK16ac_abcam

description: Library name: SI_39922_VCaP_H2BK16ac_abcam

tag: cell line

value: VCAP

tag: treatment


title: Dog_7_dysplasia_4

description: Library name: DSP-1001660022199-E-G10

tag: tissue

value: Rostral-caudal mandible


title: C17_CTCFAID_C22,TACL-ON,FLAG,rep2

value: TACL-ON

value: FLAG

value: anti-FLAG (F1804, Merck)


title: C17,TACL-ON_CRISPRi-Ctrl,Input,rep1

value: Input


title: C17,mCherry,STAG1,rep1

value: anti-STAG1 (A302-579A, Bethyl)


title: Male Adrenal Gland, 0.3 mg/kg/day PFHxSA, Animal r22

description:
Library name: p01_10105_r22_a
etap_pfhxsa_adrenal_male_counts.csv

tag: Sex

value: Male

value: 8-10 weeks

value: Perflurohexanesulfonamide (PFHxSA)

value: Oral gavage

value: No Issue


title: PC3_H2BK20ac_CST

description: Library name: SI_39917_PC3_H2BK20ac_CST

value: prostate

tag: cell type

value: mixed

value: No treatment


title: N60_LC_CPEmos_library_frog_oocyte_uninjected_Tail_seq

description: Libraries enriched by antisese oligos before ligaion, followed by reverse transcription and PCR amplification with library-specific primers

value: oocyte


title: Male Adrenal Gland, 1 mg/kg/day PFHxSA, Animal r27

description:
Library name: p01_10105_r27_a
etap_pfhxsa_adrenal_male_counts.csv

value: Adrenal Gland

tag: strain

value: Sprague Dawley

tag: age

value: 1 mg/kg/day PFHxSA, 5-day repeat exposure, oral gavage

value: 1 mg/kg/day


title: DU145_H2BK20ac_CST

description: Library name: SI_39916_DU145_H2BK20ac_CST


title: Male Adrenal Gland, 0.3 mg/kg/day PFHxSA, Animal r21

description:
Library name: p01_10105_r21_a
etap_pfhxsa_adrenal_male_counts.csv

value: 0.3 mg/kg/day PFHxSA, 5-day repeat exposure, oral gavage

tag: treatment (dose)

value: 0.3 mg/kg/day

tag: treatment (dose_group)


title: C17,mCherry,SMC1,rep3

description:
C17_mCherry_SMC1_rep2_rep3.pval.bigwig
C17_mCherry_SMC1_rep2_rep3.idr.optimal_peak.regionPeak.bb

value: mCherry

value: Anti-SMC1 (A300-055A, Bethyl)


title: VCaP_H2BK20ac_CST

description: Library name: SI_39914_VCaP_H2BK20ac_CST

value: VCAP


title: Dog_7_dysplasia_3

description: Library name: DSP-1001660022199-E-G09

value: Rostral-caudal mandible

value: Conventional


title: Dog_7_dysplasia_2

description: Library name: DSP-1001660022199-E-G08


title: C17,mCherry,SMC1,rep2


title: Male Adrenal Gland, 0.3 mg/kg/day PFHxSA, Animal r20

description:
Library name: p01_10105_r20_a
etap_pfhxsa_adrenal_male_counts.csv

value: Male

value: 8-10 weeks

tag: treatment (chemical_name)

value: Perflurohexanesulfonamide (PFHxSA)

tag: treatment (route_of_exposure)

value: Oral gavage


title: AU15330_FOXA1

value: VCaP

value: prostate cancer

tag: chip antibody

value: FOXA1 (Thermo Fisher Scientific:PA5-27157)


title: AU15330_AR

value: AR (Millipore:06-680)


title: Male Adrenal Gland, 0.3 mg/kg/day PFHxSA, Animal r19

description:
Library name: p01_10105_r19_a
etap_pfhxsa_adrenal_male_counts.csv

value: Adrenal Gland

value: Sprague Dawley

tag: sample qc_issue

value: No Issue


title: Dog_7_deep_4

description: Library name: DSP-1001660022199-E-G06

tag: tumor variant

tag: tumor size


title: Dog_7_dysplasia_1

description: Library name: DSP-1001660022199-E-G07


title: C17,mCherry,PDS5A,rep1

tag: genotype

tag: protein

tag: replicate

value: anti-PDS5A (A300-089A, Bethyl)


title: Dog_7_deep_3

description: Library name: DSP-1001660022199-E-G05


title: Male Adrenal Gland, 0.1 mg/kg/day PFHxSA, Animal r18

description:
Library name: p01_10105_r18_a
etap_pfhxsa_adrenal_male_counts.csv

tag: treatment

value: 0.1 mg/kg/day PFHxSA, 5-day repeat exposure, oral gavage

value: 0.1 mg/kg/day


title: DMSO_FOXA1

tag: cell line

value: DMSO


title: Dog_7_deep_2

description: Library name: DSP-1001660022199-E-G04

tag: tissue

value: Rostral-caudal mandible


title: C17,mCherry,NIPBL,rep2

value: mCherry

value: NIPBL

tag: antibody

value: anti-NIPBL (A301-779A, Bethyl)


title: Male Adrenal Gland, 0.1 mg/kg/day PFHxSA, Animal r16

description:
Library name: p01_10105_r16_a
etap_pfhxsa_adrenal_male_counts.csv

tag: Sex

value: Male

tag: strain

value: 8-10 weeks

value: Perflurohexanesulfonamide (PFHxSA)


title: C17,mCherry,Input,rep4

value: Input


title: C17,mCherry,MAU2,rep2

value: anti-SCC4/MAU2 (ab183033, Abcam)


title: CBPD409_4h_rep2

data_processing:
The program bwa mem was run for alignment.
Alignments were then filtered using both samtools (quality score cutoff of 20) and picard MarkDuplicates (removed duplicates and chrM).
Peaks were called using macs2 (with options: -g hs -f BAMPE -B -q 0.001 --nolambda --SPMR 2).
Assembly: hg38
Supplementary files format and content: macs peak beds, bigwigs

growth_protocol: Cells were cultured in ATCC-formulated RPMI with 10% FBS and penicillin.streptomycin except NCI-H929, which using ATCC-formulated RPMI with 0.05mM 2-mercaptoethanol, 10% FBS and penicillin

extract_protocol:
ATAC-seq was performed as previously described in Buenrostro et al. 2013 Nat Methods. In brief, 50,000 cancer cells were washed in cold PBS and resuspended in cytoplasmic lysis buffer (CER-I from the NE-PER kit, Invitrogen, cat. no. 78833). This single-cell suspension was incubated on ice for 5 min. The lysate was centrifuged at 1,300g for 5 min at 4 °C. Nuclei were resuspended in 50μl of 1× TD buffer, then incubated with 0.5-3μl Tn5 enzyme (depending on the cell line) for 30 min at 37 °C (Nextera DNA Library Preparation Kit; cat. no. FC-121-1031). Samples were immediately purified by Qiagen minElute column and PCR-amplified with the NEBNext High-Fidelity 2X PCR Master Mix (NEB; cat. no. M0541L) following the original protocol27. qPCR was used to determine the optimal PCR cycles to prevent over-amplification. The amplified library was further purified by Qiagen minElute column and SPRI beads (Beckman Coulter; cat. no. A63881).
The tagmented adapter-ligated DNA was immediately purified by Qiagen minElute column and PCR-amplified with the NEBNext High-Fidelity 2X PCR Master Mix (NEB; cat. no. M0541L) following the original protocol. qPCR was used to determine the optimal PCR cycles to prevent over-amplification. The amplified library was further purified by Qiagen minElute column and SPRI beads (Beckman Coulter; cat. no. A63881). ATAC-seq libraries were sequenced on the Illumina HiSeq 2500 (125-nucleotide read length, paired end).

treatment_protocol: Cell were plated at 70-80% confluence in a 6-well plate and treated with CDBP-409 or AU-15330 dissolved in DMSO at 100nM or 1uM concentration, respectively, for labeled durations.

value: VCaP

tag: cell type

value: Prostate cancer


title: Dog_7_deep_1

description: Library name: DSP-1001660022199-E-G03

value: Conventional


title: Male Adrenal Gland, 0.1 mg/kg/day PFHxSA, Animal r15

description:
Library name: p01_10105_r15_a
etap_pfhxsa_adrenal_male_counts.csv

value: Adrenal Gland

value: Sprague Dawley

tag: age

tag: treatment (dose)

tag: treatment (dose_group)

value: Oral gavage

value: No Issue


title: CBPD409_4h_rep1


title: Dog_7_TMS_4

description: Library name: DSP-1001660022199-E-G02


title: DMSO_24h_rep2

value: DMSO


title: Male Adrenal Gland, 0.1 mg/kg/day PFHxSA, Animal r14

description:
Library name: p01_10105_r14_a
etap_pfhxsa_adrenal_male_counts.csv

value: 0.1 mg/kg/day PFHxSA, 5-day repeat exposure, oral gavage

value: 0.1 mg/kg/day

tag: treatment (chemical_name)

tag: treatment (route_of_exposure)


title: Dog_7_TMS_3

description: Library name: DSP-1001660022199-E-G01

value: Rostral-caudal mandible

tag: tumor variant


title: C17,mCherry,RAD21,rep3

description:
C17_mCherry_RAD21_rep1_rep3.pval.bigwig
C17_mCherry_RAD21_rep1_rep3.idr.optimal_peak.regionPeak.bb

value: mCherry

value: anti-RAD21 (05-908, Merck)


title: C17,mCherry,H3K4me3,rep1

description: C17_mCherry_H3K4me3_rep1_rep2.pval.bigwig

value: anti-H3K4me3 (39060, Active motif)


title: DMSO_24h_rep1


title: Dog_7_TMS_1

description: Library name: DSP-1001660022199-E-F11

tag: tumor size


title: Male Adrenal Gland, 0.01 mg/kg/day PFHxSA, Animal r12

description:
Library name: p01_10105_r12_a
etap_pfhxsa_adrenal_male_counts.csv

value: Male

value: 8-10 weeks

value: 0.01 mg/kg/day PFHxSA, 5-day repeat exposure, oral gavage

value: 0.01 mg/kg/day

value: Perflurohexanesulfonamide (PFHxSA)

tag: sample qc_issue


title: DMSO_AR

value: VCaP

value: prostate cancer

tag: chip antibody

value: AR (Millipore:06-680)


title: Male Adrenal Gland, 0.1 mg/kg/day PFHxSA, Animal r17

description:
Library name: p01_10105_r17_a
etap_pfhxsa_adrenal_male_counts.csv

value: Adrenal Gland

value: Sprague Dawley

value: Oral gavage


title: AU15330_4h

value: Prostate cancer


title: C17,mCherry,H3K27ac,rep2

description: C17_mCherry_H3K27ac_rep1_rep2.pval.bigwig

tag: genotype

tag: protein

tag: replicate

value: anti-H3K27ac (39133, Active motif)


title: Male Adrenal Gland, 0.01 mg/kg/day PFHxSA, Animal r11

description:
Library name: p01_10105_r11_a
etap_pfhxsa_adrenal_male_counts.csv

tag: tissue

tag: treatment

value: No Issue


title: C17,mCherry,H3K27ac,rep1

tag: cell line

value: mCherry

tag: antibody


title: Dog_7_surface_5

description: Library name: DSP-1001660022199-E-F10

value: Rostral-caudal mandible

value: Conventional


title: C17,mCherry,CTCF,rep1

value: CTCF

value: anti-CTCF (ab128873, Abcam)


title: Male Adrenal Gland, 0.01 mg/kg/day PFHxSA, Animal r10

description:
Library name: p01_10105_r10_a
etap_pfhxsa_adrenal_male_counts.csv

tag: Sex

value: Male

tag: strain

value: 8-10 weeks

value: 0.01 mg/kg/day PFHxSA, 5-day repeat exposure, oral gavage


title: ChIP_L3.6pl_RELA_TNFaEGF_Rep2

tag: cell type

value: PDAC


title: Dog_7_surface_4

description: Library name: DSP-1001660022199-E-F09


title: Male Adrenal Gland, 0.01 mg/kg/day PFHxSA, Animal r09

description:
Library name: p01_10105_r09_a
etap_pfhxsa_adrenal_male_counts.csv

tag: age

tag: treatment (dose)

value: 0.01 mg/kg/day

tag: treatment (dose_group)

value: Perflurohexanesulfonamide (PFHxSA)


title: C17,TACL-OFF,STAG2,rep1

value: TACL-OFF

value: anti-STAG2 (A300-159A, Bethyl)


title: DMSO

value: VCaP

value: DMSO


title: Dog_7_surface_3

description: Library name: DSP-1001660022199-E-F08

tag: tumor variant


title: C17,TACL-OFF,STAG1,rep1

value: anti-STAG1 (A302-579A, Bethyl)


title: Male Adrenal Gland, 0.01 mg/kg/day PFHxSA, Animal r13

description:
Library name: p01_10105_r13_a
etap_pfhxsa_adrenal_male_counts.csv

value: Adrenal Gland

value: Sprague Dawley

tag: treatment (chemical_name)

tag: treatment (route_of_exposure)

value: Oral gavage

value: No Issue


title: Male Adrenal Gland, Vehicle Control, Animal r08

description:
Library name: p01_10105_r08_a
etap_pfhxsa_adrenal_male_counts.csv

value: Corn oil control, 5-day repeat exposure, oral gavage

value: 0 mg/kg/day

tag: sample qc_issue


title: ChIP_L3.6pl_H3K27ac_TNFaEGF_Rep3


title: Dog_7_surface_2

description: Library name: DSP-1001660022199-E-F07

value: Rostral-caudal mandible

value: Conventional

tag: tumor size


title: C17,TACL-OFF,SMC1,rep3

description:
C17_TACL-OFF_SMC1_rep2_rep3.pval.bigwig
C17_TACL-OFF_SMC1_rep2_rep3.idr.optimal_peak.regionPeak.bb

tag: genotype

tag: protein

value: Anti-SMC1 (A300-055A, Bethyl)


title: Dog_7_TMS_2

description: Library name: DSP-1001660022199-E-F12

tag: tissue


title: Male Adrenal Gland, Vehicle Control, Animal r07

description:
Library name: p01_10105_r07_a
etap_pfhxsa_adrenal_male_counts.csv

value: Male

value: 8-10 weeks

tag: treatment


title: ChIP_L3.6pl_H3K27ac_TNFaEGF_Rep2

tag: cell line

value: PDAC


title: C17,TACL-OFF,SMC1,rep2

value: TACL-OFF

tag: replicate

tag: antibody


title: ChIP_L3.6pl_H3K27ac_TNFa_Rep3


title: ChIP_L3.6pl_H3K27ac_TNFaEGF_Rep1


title: Dog_8_normal_4

description: Library name: DSP-1001660022199-E-F05

value: Rostral mandible


title: Dog_8_normal_3

description: Library name: DSP-1001660022199-E-F04


title: C17,TACL-OFF,RAD21,rep3

value: anti-RAD21 (05-908, Merck)


title: Male Adrenal Gland, Vehicle Control, Animal r05

description:
Library name: p01_10105_r05_a
etap_pfhxsa_adrenal_male_counts.csv

tag: Sex

tag: strain

value: Perflurohexanesulfonamide (PFHxSA)


title: Male Adrenal Gland, Vehicle Control, Animal r06

description:
Library name: p01_10105_r06_a
etap_pfhxsa_adrenal_male_counts.csv

tag: age


title: ChIP_L3.6pl_RELA_TNFaEGF_Rep1

tag: cell type


title: C17_RAD21AID_SC6,mCherry_IAA,RAD21,rep1


title: ChIP_L3.6pl_H3K27ac_TNFa_Rep2


title: Male Adrenal Gland, Vehicle Control, Animal r04

description:
Library name: p01_10105_r04_a
etap_pfhxsa_adrenal_male_counts.csv

tag: treatment (dose)

tag: treatment (dose_group)


title: ChIP_L3.6pl_H3K27ac_TNFa_Rep1


title: Male Adrenal Gland, Vehicle Control, Animal r03

description:
Library name: p01_10105_r03_a
etap_pfhxsa_adrenal_male_counts.csv

tag: treatment (chemical_name)


title: Dog_8_normal_1

description: Library name: DSP-1001660022199-E-F02

tag: tumor variant


title: C17,TACL-OFF,Input,rep2

value: Input


title: Dog_8_normal_2

description: Library name: DSP-1001660022199-E-F03


title: C17,TACL-OFF,MAU2,rep2

value: anti-SCC4/MAU2 (ab183033, Abcam)


title: Male Adrenal Gland, Vehicle Control, Animal r02

description:
Library name: p01_10105_r02_a
etap_pfhxsa_adrenal_male_counts.csv

value: Adrenal Gland

value: Sprague Dawley

tag: treatment (route_of_exposure)

tag: sample qc_issue


title: ChIP_L3.6pl_H3K27ac_EGF_Rep3


title: Dog_8_dysplasia_4

description: Library name: DSP-1001660022199-E-F01

tag: tumor size


title: C17,TACL-OFF,H3K4me3,rep2

description: C17_TACL-OFF_H3K4me3_rep1_rep2.pval.bigwig

tag: genotype

tag: protein

value: anti-H3K4me3 (39060, Active motif)


title: C17,mCherry,H3K4me3,rep2

description: C17_mCherry_H3K4me3_rep1_rep2.pval.bigwig

tag: treatment

value: mCherry


title: Male Adrenal Gland, Vehicle Control, Animal r01

description:
Library name: p01_10105_r01_a
etap_pfhxsa_adrenal_male_counts.csv

tag: tissue

value: Corn oil control, 5-day repeat exposure, oral gavage

value: 0 mg/kg/day

value: Oral gavage

value: No Issue


title: C17,TACL-OFF,H3K4me3,rep1

tag: cell line

tag: replicate


title: ChIP_L3.6pl_H3K27ac_EGF_Rep2


title: Dog_8_dysplasia_3

description: Library name: DSP-1001660022199-E-E12

value: Conventional


title: Dog_7_surface_1

description: Library name: DSP-1001660022199-E-F06

value: Rostral-caudal mandible


title: kidney, RP105-/- CLP3

city: wuhan

first: Hong

last: Duo

address: No. 169 East Lake Road, Wuchang District

country: China

institute: Zhongnan Hospital of Wuhan University

description:
Library name: SAMPLE6
FPKM.KOCLP3

data_processing:
Raw reads were filtered using fastp to remove adapter sequences, low-quality reads, and reads with >10% N bases.
Clean reads were mapped to the Mus musculus reference genome (GRCm38/mm10) using HISAT2.
Transcript assembly and quantification were performed using StringTie.
Gene expression levels were normalized as FPKM (fragments per kilobase per million reads).
Differential expression analysis was conducted using the DESeq2 package in R. Genes with adjusted P-value < 0.05 were considered differentially expressed.
Assembly: GRCm38/mm10
Supplementary files format and content: A gene expression matrix in tab-delimited text format was provided. Rows represent genes, columns represent samples, and values are normalized expression levels (FPKM).
Supplementary files format and content: A CSV file includes FPKM values for each sample. Rows represent genes, and columns represent individual samples.

organism: Mus musculus

source_name: kidney

growth_protocol: Mice were housed under specific pathogen-free (SPF) conditions with a 12-hour light/dark cycle and free access to food and water.

extract_protocol:
Total RNA was extracted from kidney tissue using TRIzol reagent (Invitrogen) following the manufacturer’s protocol. RNA purity and integrity were assessed using NanoDrop and Agilent 2100 Bioanalyzer.
Poly(A)+ RNA was enriched using oligo(dT) magnetic beads and fragmented. First- and second-strand cDNA synthesis was performed, followed by end repair, A-tailing, adapter ligation, and PCR amplification. Libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit (NEB) and sequenced on an Illumina NovaSeq 6000 platform.

treatment_protocol: Mice were randomly assigned to experimental groups and subjected to cecal ligation and puncture (CLP) or sham surgery. RP105 knockout mice were generated by CRISPR/Cas9. Kidney tissues were collected 24 hours after surgery.

value: kidney

value: RP105 knockout

value: CLP

tag: batch


title: ChIP_L3.6pl_H3K27ac_EGF_Rep1

value: PDAC


title: Dog_8_dysplasia_2

description: Library name: DSP-1001660022199-E-E11

value: Rostral mandible


title: kidney, RP105-/- CLP2

description:
Library name: SAMPLE5
FPKM.KOCLP2


title: Dog_8_dysplasia_1

description: Library name: DSP-1001660022199-E-E10


title: ChIP_L3.6pl_H3K27ac_Vehicle_Rep3


title: C17,TACL-OFF,H3K27ac,rep2

description: C17_TACL-OFF_H3K27ac_rep1_rep2.pval.bigwig

value: TACL-OFF

tag: antibody

value: anti-H3K27ac (39133, Active motif)


title: C17,TACL-OFF,NIPBL,rep2

value: NIPBL

value: anti-NIPBL (A301-779A, Bethyl)


title: ChIP_L3.6pl_H3K27ac_Vehicle_Rep2


title: Dog_8_surface_3

description: Library name: DSP-1001660022199-E-E08


title: C17,TACL-ON,WAPL,rep1

value: TACL-ON

value: WAPL

value: anti-WAPL (sc-365189, Santa Cruz)


title: Dog_8_surface_4

description: Library name: DSP-1001660022199-E-E09


title: ChIP_L3.6pl_H3K27ac_Vehicle_Rep1


title: SOD1-Tg model_cortex

city: Freiburg

first: Chintan

last: Chhatbar

address: Breisacher strasse 64

department: Department of Neuropathology

institute: Uniklinikum Freiburg

description: Library name: SOD1_Tg_cortex

library_source: transcriptomic single cell

data_processing:
The demultiplexing was carried out using in-built Illumina software on Next-seq machines.
Barcode processing, gene counting and aggregation were made using the Cell Ranger software
Assembly: GRCm39 M33 release date 07.2023
Supplementary files format and content: h5 matrix files containing counts data

molecule: polyA RNA

source_name: brain

extract_protocol:
mice were perfused with cold HBSS and CNS was extracted and flash frozen. A small portion of CNS regions of interest was excised from the CNS tissue and enriched for myeloid cells with modified Frankenstein’s protocol. Briefly, CNS tissue was homogenized in Nuclei EZ lysis buffer (Millipore Sigma) and upon incubation was filtere through 70µm filter. The suspension was centrifuged at 600g for 5 min at 4°C. The pellet was washed with nuclei wash and resuspension buffer (1x PBS, 1.0% BSA, 0.2 U/μl RNase Inhibitor) and centrifuged at 600g for5min at 4°C.Following this, Nuclei were stained for DAPI, NeuN and Olig 2 markers and sorted by Flow cytometry.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: brain


title: kidney, CLP 3

description:
Library name: SAMPLE3
FPKM.WTCLP3

value: WT


title: kidney, CLP 2

description:
Library name: SAMPLE2
FPKM.WTCLP2


title: kidney, CLP 1

description:
Library name: SAMPLE1
FPKM.WTCLP1


title: Dog_8_surface_2

description: Library name: DSP-1001660022199-E-E07


title: C17,TACL-ON,SMC1,rep3

description:
C17_TACL-ON_SMC1_rep2_rep3.pval.bigwig
C17_TACL-ON_SMC1_rep2_rep3.idr.optimal_peak.regionPeak.bb

value: Anti-SMC1 (A300-055A, Bethyl)


title: C17,TACL-ON,STAG1,rep1

value: anti-STAG1 (A302-579A, Bethyl)


title: SOD1-Tg model cortex_control

description: Library name: SOD1_control_cortex


title: SOD1-Tg model spinal cord

description: Library name: SOD1_Tg_spinal_cord


title: C17,TACL-ON,STAG2,rep1

value: anti-STAG2 (A300-159A, Bethyl)


title: Dog_8_surface_1

description: Library name: DSP-1001660022199-E-E06

value: Conventional


title: MEF cells, Med23 WT, VSV, rep3

city: Shanghai

first: zhang

last: yiyang

address: 2005 Songhu Road, Yangpu District, Shanghai, China

institute: Fudan

data_processing:
RNA-seq raw reads were obtained from an Illumina NovaSeq 6000 sequence analyzer.
Cutadapt was used to remove sequencing adapters and poor-quality base trimming, retaining only reads with a quality score greater than 30 and discarding reads shorter than 50 bp or 75 bp for SE100 or PE150 reads, respectively.
the filtered clean reads were mapped to the human reference genome mm10 with tophat2, and gene quantification and differential expression analysis were performed by cuffdiff with parameters -b -u.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: MEF

growth_protocol: MEFs were maintained in complete DMEM with 10% FBS and 1% penicillin-streptomycin. Bone marrow cells were isolated from mouse femurs and cultured at 37°C in RPMI1640 containing 10% FBS and 1% penicillin-streptomycin, with M-CSF (10 ng/ml, Peprotech) for BMDM differentiation.

extract_protocol:
RNA was harvested using trizol. 1.3 ug of total RNA was used for the construction of sequencing libraries.
We used a commercial RNA library kit to prepare the RNA-seq library with the manufacturer’s specifications.

treatment_protocol: BMDMs or MEFs were infected with VSV for 4h.MEF cells were infected with VSV for 8h.

value: MEF

value: mouse embryonic fibroblasts

value: VSV


title: kidney, RP105-/- CLP1

description:
Library name: SAMPLE4
FPKM.KOCLP1

value: kidney

value: RP105 knockout

value: CLP


title: MEF cells, Med23 WT, VSV, rep2


title: Dog_8_TMS_4

description: Library name: DSP-1001660022199-E-E05

value: Rostral mandible


title: Dog_8_TMS_3

description: Library name: DSP-1001660022199-E-E04


title: C17,TACL-OFF,H3K27ac,rep1

value: TACL-OFF

value: anti-H3K27ac (39133, Active motif)


title: C17,TACL-OFF,FLAG,rep2

value: FLAG

value: anti-FLAG (F1804, Merck)


title: FAD_40_week_Hippocampus

description: Library name: FAD_40_week

value: brain


title: MEF cells, Med23 WT, Mock, rep3

value: WT

value: DMSO


title: Dog_8_TMS_2

description: Library name: DSP-1001660022199-E-E03


title: C17,TACL-ON,SMC1,rep2

value: TACL-ON

value: Anti-SMC1 (A300-055A, Bethyl)


title: MEF cells, Med23 WT, VSV, rep1


title: SOD1-Tg model spinal cord control

description: Library name: SOD1_control_spinal_cord


title: FAD_40_week_control_Hippocampus

description: Library name: FAD_40_week_control


title: C17,TACL-ON,RAD21,rep3

description:
C17_TACL-ON_RAD21_rep1_rep3.pval.bigwig
C17_TACL-ON_RAD21_rep1_rep3.idr.optimal_peak.regionPeak.bb

value: anti-RAD21 (05-908, Merck)


title: Dog_8_TMS_1

description: Library name: DSP-1001660022199-E-E02

value: Conventional


title: Dog_8_deep_4

description: Library name: DSP-1001660022199-E-E01


title: FAD_16_week_Hippocampus

description: Library name: FAD_16_week


title: C17,TACL-ON,PDS5A,rep1

value: anti-PDS5A (A300-089A, Bethyl)


title: C17,TACL-ON,NIPBL,rep2

value: NIPBL

value: anti-NIPBL (A301-779A, Bethyl)


title: FAD_16_week_control_Hippocampus

description: Library name: FAD_16_week_control


title: MEF cells, Med23 WT, Mock, rep1

value: MEF

value: mouse embryonic fibroblasts


title: C17,TACL-ON,MAU2,rep2

value: anti-SCC4/MAU2 (ab183033, Abcam)


title: MEF cells, Med23 KO, VSV, rep3

value: Med23 KO

value: VSV


title: Cuprizone model remylination phase

description: Library name: Cup_RE


title: C17,TACL-ON,Input,rep6

value: Input


title: Dog_8_deep_2

description: Library name: DSP-1001660022199-E-D11

value: Rostral mandible


title: Cuprizone model demylination phase

description: Library name: Cup_DE

value: brain


title: MEF cells, Med23 KO, VSV, rep2


title: MEF cells, Med23 KO, VSV, rep1


title: Dog_8_deep_1

description: Library name: DSP-1001660022199-E-D10


title: C17,TACL-ON,H3K4me3,rep2

description: C17_TACL-ON_H3K4me3_rep1_rep2.pval.bigwig

value: anti-H3K4me3 (39060, Active motif)


title: Dog_5_TMS_4

description: Library name: DSP-1001660022199-E-D09

value: Caudal mandible


title: Cuprizone model control

description: Library name: Cup_control

value: WT


title: APP_23

description: Library name: APP_23_Hip

value: APP23 transgenic


title: Dog_5_TMS_3

description: Library name: DSP-1001660022199-E-D08


title: C17,TACL-ON,Input,rep5

value: TACL-ON


title: C17,TACL-ON,H3K4me3,rep1


title: MEF cells, Med23 KO, Mock, rep3

value: DMSO


title: C17,TACL-ON,H3K27ac,rep2

description: C17_TACL-ON_H3K27ac_rep1_rep2.pval.bigwig

value: anti-H3K27ac (39133, Active motif)


title: S. aureus, planktonic 3

city: Newark

first: Dane

last: Parker

state: NJ

address: 205 South Organge Ave, G-1208

department: Pathology, Immunology and Laboratory Medicine

institute: Rutgers New Jersey Medical School

description: Library name: SA3

data_processing:
Sequencing files were processed in Partek Flow
Assembly: STAR 2.7.8a with hg38 for human
Assembly: STAR 2.7.8a with SA-000013465 for S. aureus
Supplementary files format and content: xls file with normalized counts and expression differences

organism: Staphylococcus aureus

source_name: Staphylococcus aureus

extract_protocol:
Direct-zol micro RNA extraction kit (Zyzmo)
Ribozero plus (Illumina)

value: Staphylococcus aureus

value: Growth in vitro


title: MEF cells, Med23 WT, Mock, rep2

value: MEF


title: MEF cells, Med23 KO, Mock, rep1

value: mouse embryonic fibroblasts


title: MEF cells, Med23 KO, Mock, rep2


title: Dog_5_TMS_1

description: Library name: DSP-1001660022199-E-D06

value: Conventional


title: Dog_5_TMS_2

description: Library name: DSP-1001660022199-E-D07


title: S. aureus, planktonic 2

description: Library name: SA2


title: Dog_8_deep_3

description: Library name: DSP-1001660022199-E-D12


title: C17,TACL-ON,H3K27ac,rep1


title: BMDM cells, Med23 WT, VSV, rep3

source_name: BMDM

value: BMDM

value: Bone marrow-derived macrophages


title: Dog_5_normal_4

description: Library name: DSP-1001660022199-E-D05


title: BMDM cells, Med23 WT, VSV, rep2

value: VSV


title: C17,TACL-ON,FLAG,rep2

description:
C17_TACL-ON_FLAG_rep1_rep2.pval.bigwig
C17_TACL-ON_FLAG_rep1_rep2.idr.optimal_peak.regionPeak.bb

value: FLAG

value: anti-FLAG (F1804, Merck)


title: Dog_5_normal_3

description: Library name: DSP-1001660022199-E-D04


title: S. aureus, planktonic 1

description: Library name: SA1


title: C17,TACL-ON,CTCF,rep1

value: CTCF

value: anti-CTCF (ab128873, Abcam)


title: Dog_5_normal_2

description: Library name: DSP-1001660022199-E-D03

value: Caudal mandible


title: 30/C

city: Balice

first: Anna

middle: Dominika

last: Steg

address: Krakowska 1

department: Department of Animal Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

description: Library name: Sample 30

data_processing:
Quality control (fastQC)
Processing fastq files with the QuantSeq Data Analysis Pipeline on BlueBee® Genomics
Filtration of low raw reads number samples. Minimal counts of reads set to 10 mln, and only samples that reach that condition are submitted.
Assembly: Sus Scrofa 11.1
Supplementary files format and content: Processed data files are in txt format providing read counts

organism: Sus scrofa

source_name: liver

extract_protocol:
RNA was isolated with A&A Biotechnology Total RNA Mini kit
Libraries were prepared using  QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) according to the manufacturer recommendations.

value: liver

value: Polish Large White sows covered with a Landrace boars

value: C (10000 U vit. D3/kg of feed)


title: N/TERT-2G cells, hFWE KO Clone #11, replicate 3

city: Omaha

first: Laura

middle: A.

last: Hansen

state: NE

address: 2500 California Plaza

institute: Creighton University

description: Sample A15

data_processing:
Adapter trimming using Trim Galore
Read alignment using STAR
Transcript quantification using Salmon
Variance stabalizing transformation of normalized counts using DESeq2
Assembly: GRCh38
Supplementary files format and content: tsv file containing variance-stabalized expression values for each sample

growth_protocol: Cell culture inserts in a 24wells carrier plate (Nunc, Thermo Fisher Scientific, 141002) were coated using 100µg/mL rat tail collagen (Sigma–Aldrich, C3867) for 1hour at 4°C. After phosphate–buffered saline(PBS) washing the filters, 150,000cells were seeded and submerged in CnT–prime medium (CELLnTEC, CnT–PR) at the lowest insert stand. After 72hours, the medium was switched to differentiation medium (40% Dulbecco’s modified Eagle’s Medium (Sigma–Aldrich, D6546) and 60% 3D barrier medium (CELLnTEC, CnT–PR–3D)) and the ORGANOIDs were lifted to the highest stand, air–exposed.  Medium was refreshed every other day until end of the culture

extract_protocol:
Total RNA was isolated from epidermal organoids after 10 days of air liquid interface culture using the Favorprep total tissue RNA kit (Favorgen Biotech, Tung, Taiwan) according to manufacturer’s instructions.
To prepare sequencing libraries, a total RNA input of 500 ng was used for library preparation with the NEBNext Ultra II Directional RNA Library Prep kit for Illumina along with NEBNext Poly(A) mRNA Magnetic Isolation Module (both New England BioLabs Inc.) according to the manufacturer’s protocol. The library quality and quantity of RNA were assessed using RNA ScreenTape Assay (Agilent) and Agilent 4200 TapeStation System following the manufacturer’s protocol. Libraries were pooled equimolar for sequencing to a final concentration of 3 nM. The pooled libraries were sequenced on the Illumina NextSeq 2000 system (Illumina) using NextSeq 1000/2000 P2 Reagent Cartridge 100 cycles and P2 Flow Cell (Illumina).

value: Immortalized epidermal keratinocyte

value: hFWE KO

value: Epidermal Organoid Culture


title: S. aureus, planktonic 4

description: Library name: SA4

value: Staphylococcus aureus

value: Growth in vitro


title: BMDM cells, Med23 WT, Mock, rep3

value: WT

value: DMSO


title: 28/A

description: Library name: Sample 28

value: A (control)


title: Dog_5_normal_1

description: Library name: DSP-1001660022199-E-D02

value: Conventional


title: N/TERT-2G cells, hFWE KO Clone #11, replicate 2

description: Sample A14


title: 27/C

description: Library name: Sample 27


title: N/TERT-2G cells, hFWE KO Clone #11, replicate 1

description: Sample A13


title: BMDM cells, Med23 WT, Mock, rep1

value: BMDM

value: Bone marrow-derived macrophages


title: BMDM cells, Med23 KO, VSV, rep3

value: Med23 KO

value: VSV


title: Dog_5_dysplasia_3

description: Library name: DSP-1001660022199-E-C12

value: Caudal mandible


title: Dog_5_dysplasia_4

description: Library name: DSP-1001660022199-E-D01


title: 24/B

description: Library name: Sample 24

value: liver

value: B (5000 U vit. D3/kg of feed)


title: Dog_5_dysplasia_2

description: Library name: DSP-1001660022199-E-C11


title: BMDM cells, Med23 KO, VSV, rep2


title: 23/A

description: Library name: Sample 23

value: Polish Large White sows covered with a Landrace boars


title: 25/B

description: Library name: Sample 25


title: N/TERT-2G cells, hFWE KO Clone #8, replicate 1

description: Sample A10

value: Immortalized epidermal keratinocyte


title: N/TERT-2G cells, hFWE KO Clone #5, replicate 3

description: Sample A9

value: hFWE KO


title: BMDM cells, Med23 KO, VSV, rep1


title: BMDM cells, Med23 WT, VSV, rep1


title: 22/A

description: Library name: Sample 22


title: Dog_5_dysplasia_1

description: Library name: DSP-1001660022199-E-C10


title: Dog_9_normal_4

description: Library name: DSP-1001660022199-E-C09

value: Rostral maxilla


title: BMDM cells, Med23 KO, Mock, rep3


title: BMDM cells, Med23 WT, Mock, rep2


title: N/TERT-2G cells, hFWE KO Clone #5, replicate 1

description: Sample A7

value: Epidermal Organoid Culture


title: Dog_9_normal_3

description: Library name: DSP-1001660022199-E-C08


title: Dog_9_normal_2

description: Library name: DSP-1001660022199-E-C07


title: BMDM cells, Med23 KO, Mock, rep2


title: N/TERT-2G cells, hFWE KO Pool, replicate 3

description: Sample A6


title: 19/B

description: Library name: Sample 19


title: BMDM cells, Med23 KO, Mock, rep1


title: 18/B

description: Library name: Sample 18


title: 21/C

description: Library name: Sample 21

value: C (10000 U vit. D3/kg of feed)


title: N/TERT-2G cells, hFWE KO Clone #8, replicate 2

description: Sample A12


title: Dog_9_normal_1

description: Library name: DSP-1001660022199-E-C06


title: 16/A

description: Library name: Sample 16


title: Dog_9_dysplasia_4

description: Library name: DSP-1001660022199-E-C05


title: N/TERT-2G cells, hFWE KO Pool, replicate 1

description: Sample A4


title: N/TERT-2G cells, hFWE KO Pool, replicate 2

description: Sample A5


title: N/TERT-2G cells, hFWE WT, replicate 3

description: Sample A3

value: hFWE WT


title: 15/B

description: Library name: Sample 15


title: 3rd slice

city: Dallas

first: Elnaz

last: Ghotbi

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

data_processing:
Raw sequencing data were processed using 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings with manual alignement
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Skin

extract_protocol: Sequencing libraries were prepared following the manufacturer’s instructions (document number CG000239_VisiumSpatialGeneExpression).

treatment_protocol: The mice were induced by 4-hydroxytamoxifen at P2

value: Skin

value: R26-tdTomato; Krox20-CreERT


title: 2nd slice


title: 4th slice


title: N/TERT-2G cells, hFWE KO Clone #5, replicate 2

description: Sample A8


title: Dog_9_dysplasia_2

description: Library name: DSP-1001660022199-E-C03

value: Conventional


title: N/TERT-2G cells, hFWE WT, replicate 2

description: Sample A2


title: Dog_9_dysplasia_1

description: Library name: DSP-1001660022199-E-C02


title: 14/A

description: Library name: Sample 14

value: A (control)


title: 1st slice


title: N/TERT-2G cells, hFWE WT, replicate 1

description: Sample A1


title: 12/B

description: Library name: Sample 12


title: mouse_D11_10X

first: Helle

last: Jorgensen

address: Papworth Road

department: Cardiorespiratory section

country: United Kingdom

institute: University of Cambridge

description: Single-cell RNA seq, 10X Chromium

data_processing:
Sample 1 and 2: Cell Ranger pipeline v.3.1.0 was used to align raw sequencing reads to a custom genome (based on the GRCm38 mouse genome, including the open reading frame encoding EYPF (Srinivas et al., 2001). Quality control (QC), normalization and gene expression analysis was performed using the CRAN R package Seurat v.3.1.2 (Butler et al., 2018; Stuart et al., 2019) in R v.3.6.2. Cells with <5,000 UMI counts (healthy) or <3500 UMI counts (injury), <2,000 genes detected (healthy) or <1500 genes detected (injury) and >5% mitochondrial reads (both) were excluded. Normalization was performed using SCTransform (Hafemeister and Satija, 2019) v.0.2.1 implemented in Seurat.
Sample 3-6: Sequencing data was aligned to a 10X-supplied human reference genome (GRCh38-3.0.0) using Space Ranger (v.1.0). Downstream analysis was performed with R (v.4.0.3). The Spaniel R package (v.1.2.0) was used to import the data into SingleCellExperiment objects and was also used to create spot images. Any spots with fewer than 200 UMIs were removed. The SingleCellExperiment objects were then converted into SeuratObjects for downstream analysis using Seurat (v.3.1.3). Individual replicates were normalised using the “NormaliseData” function followed by the identification of the top 200 highly variable genes using the “FindVariableFeatures” function.
Assembly: Sample 1 and 2: Custom genome based on the GRCm38 mouse genome, including the open reading frame encoding EYFP (Srinivas et al., 2001)
Assembly: Sample 3-6: 10X-supplied human reference genome (GRCh38-3.0.0)
Supplementary files format and content: barcodes.tsv.gz: barcodes of detected cells (single-cell RNA-seq) or capture spots (spatial RNA-seq)
Supplementary files format and content: features.tsv.gsz: IDs of detected genes
Supplementary files format and content: mtx files containing matrix of raw count values
Supplementary files format and content: scalefactors_json.json:scale factors
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the image
Supplementary files format and content: tissue_positions_list.csv: list of capture spot barcodes and coordinates
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and capture spots
Supplementary files format and content: tissue_hires_image.png: hi-res image of the tissues
Supplementary files format and content: tissue_lowres_image.png: low-res image of the tissue

source_name: Carotid artery

extract_protocol:
Sample 1 and 2: Datasets of lineage-labelled VSMCs from healthy and injured mouse carotid arteries were generated as described (Worssam et al. 2023) after pooling cells from 5 Myh11eYFP animals 11 days post-ligation (D11) or 2 control Myh11eYFP animals that did not undergo surgery (NS). After carotid artery harvest and dissection, arteries were incubated for 6 minutes in collagenase type IV (1 mg/mL, Life Technologies) and porcine pancreatic elastase (1 U/mL, Worthington) in DMEM. After removing the adventitia, the medial samples from each animal cohort were pooled and digested in collagenase type IV (2.5 mg/mL, Life Technologies) and porcine pancreatic elastase (2.5 U/mL, Worthington) in DMEM for 90 minutes. Medial cell suspensions were filtered through a 40 µm filter and singlet cells expressing eYFP isolated by fluorescence-activated cell sorting (FACS, Aria-Fusion flow cytometer, BD Bioscience) into PBS with 0.05% BSA and 5 µL/mL recombinant RNAse inhibitor (Sigma). Isolation of single cells was verified with a haemocytometer. Sorted cells (10,000) were pelleted, resuspended in 47 µL of PBS with 0.05% BSA and loaded for Drop-Seq using the 10X Chromium system. Amplified cDNA libraries were sequenced on a HiSeq 4000 system.
Sample 3-6: A plaque-containing aortic sample from a 54 year old male organ donor was snap-frozen by fully submerging in an isopentane bath cooled by dry ice until frozen, embedded in OCT (2-8°C), sectioned and analysed using VISIUM technology (cat 1000184) according to manufacturer's instructions (10X).
Sample 1 and 2: A total of 10,000 EYFP+ cells were loaded onto a Chromium system (10x Genomics) and amplified cDNA libraries generated using the 3’ Gene Expression v3.0 kit (10x Genomics) were sequenced using 150 cycle paired end protocol (NovaSeq, Illumina).
Sample 3-6: Frozen sections were processed using the Visium Spatial Gene Expression protocol (10x Genomics), and spatially resolved transcriptomic libraries were constructed and sequenced using a 150-cycle paired-end protocol (NovaSeq, Illumina).

value: Carotid artery

tag: background


title: Dog_9_TMS_4

description: Library name: DSP-1001660022199-E-C01