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

description:
Library name: p06_10105_r75_h
etap_pfhxsa_heart_female_counts.csv


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

status: Public on Jun 26 2025

type: SRA

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

country: USA

institute: U.S. Environmental Protection Agency

description:
Library name: p06_10105_r74_h
etap_pfhxsa_heart_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: Heart

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: Heart

tag: strain

value: Sprague Dawley

tag: age

value: 8-10 weeks

tag: treatment

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

tag: treatment (dose)

value: 1 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: 1154DNA01

city: San Francisco

first: Charles

last: Langelier

state: CA

address: HSE 401, 513 Parnassus Ave

department: Medicine

institute: University of California San Francisco

data_processing:
Kallisto
Assembly: HG38
Supplementary files format and content: Genecounts table

organism: Homo sapiens

source_name: Whole blood

extract_protocol:
KingFisher
NEBNext UltraII

value: Whole blood


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

description:
Library name: p06_10105_r73_h
etap_pfhxsa_heart_female_counts.csv


title: 1141DNA01

value: Male


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

description:
Library name: p06_10105_r77_h
etap_pfhxsa_heart_female_counts.csv

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

value: 3 mg/kg/day


title: 1132DNA01


title: 1131DNA01


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

description:
Library name: p06_10105_r72_h
etap_pfhxsa_heart_female_counts.csv


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

description:
Library name: p06_10105_r71_h
etap_pfhxsa_heart_female_counts.csv

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

value: 0.3 mg/kg/day


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

description:
Library name: p06_10105_r70_h
etap_pfhxsa_heart_female_counts.csv


title: 1128DNA01


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

description:
Library name: p06_10105_r69_h
etap_pfhxsa_heart_female_counts.csv


title: 1127DNA01


title: 1125DNA01


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

description:
Library name: p06_10105_r67_h
etap_pfhxsa_heart_female_counts.csv


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

description:
Library name: p06_10105_r66_h
etap_pfhxsa_heart_female_counts.csv

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

value: 0.1 mg/kg/day


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

description:
Library name: p06_10105_r68_h
etap_pfhxsa_heart_female_counts.csv

value: Female


title: 1134DNA01


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

description:
Library name: p06_10105_r65_h
etap_pfhxsa_heart_female_counts.csv

value: Heart


title: 1119DNA01


title: 1117DNA01


title: 1116DNA01


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

description:
Library name: p06_10105_r63_h
etap_pfhxsa_heart_female_counts.csv

value: Sprague Dawley


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

description:
Library name: p06_10105_r64_h
etap_pfhxsa_heart_female_counts.csv

value: 8-10 weeks


title: 1130DNA01


title: 1106DNA01


title: 1101DNA01


title: 1110DNA01


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

description:
Library name: p06_10105_r62_h
etap_pfhxsa_heart_female_counts.csv


title: 1112DNA01


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

description:
Library name: p06_10105_r60_h
etap_pfhxsa_heart_female_counts.csv

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

value: 0.01 mg/kg/day


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

description:
Library name: p06_10105_r59_h
etap_pfhxsa_heart_female_counts.csv

value: Perflurohexanesulfonamide (PFHxSA)


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

description:
Library name: p06_10105_r61_h
etap_pfhxsa_heart_female_counts.csv

value: Oral gavage


title: 1100DNA01


title: Female Heart, Vehicle Control, Animal r56

description:
Library name: p06_10105_r56_h
etap_pfhxsa_heart_female_counts.csv

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

value: 0 mg/kg/day

value: No Issue


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

description:
Library name: p06_10105_r57_h
etap_pfhxsa_heart_female_counts.csv


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

description:
Library name: p06_10105_r58_h
etap_pfhxsa_heart_female_counts.csv


title: 1087DNA01

value: Whole blood


title: 1088DNA01


title: 1121DNA01


title: 1085DNA01


title: Female Heart, Vehicle Control, Animal r55

description:
Library name: p06_10105_r55_h
etap_pfhxsa_heart_female_counts.csv


title: 1083DNA01


title: Female Heart, Vehicle Control, Animal r53

description:
Library name: p06_10105_r53_h
etap_pfhxsa_heart_female_counts.csv


title: 1133DNA01

value: Male


title: 1082DNA01


title: 1079DNA01


title: Female Heart, Vehicle Control, Animal r52

description:
Library name: p06_10105_r52_h
etap_pfhxsa_heart_female_counts.csv


title: 1078DNA01


title: Female Heart, Vehicle Control, Animal r51

description:
Library name: p06_10105_r51_h
etap_pfhxsa_heart_female_counts.csv


title: 1072DNA01


title: Female Heart, Vehicle Control, Animal r50

description:
Library name: p06_10105_r50_h
etap_pfhxsa_heart_female_counts.csv


title: 1070DNA11


title: 1066DNA01


title: Female Heart, Vehicle Control, Animal r49

description:
Library name: p06_10105_r49_h
etap_pfhxsa_heart_female_counts.csv


title: 1068DNA01


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

description:
Library name: p05_10105_r47_h
etap_pfhxsa_heart_male_counts.csv

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

value: 100 mg/kg/day


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

description:
Library name: p05_10105_r45_h
etap_pfhxsa_heart_male_counts.csv


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

description:
Library name: p05_10105_r46_h
etap_pfhxsa_heart_male_counts.csv

value: Outlier sample removed


title: 1063DNA01


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

description:
Library name: p05_10105_r48_h
etap_pfhxsa_heart_male_counts.csv


title: 1056DNA01


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

description:
Library name: p05_10105_r43_h
etap_pfhxsa_heart_male_counts.csv

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

value: 30 mg/kg/day


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

description:
Library name: p05_10105_r44_h
etap_pfhxsa_heart_male_counts.csv

value: Heart


title: 1062DNA01

value: Female


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

description:
Library name: p05_10105_r42_h
etap_pfhxsa_heart_male_counts.csv

value: Sprague Dawley

value: 8-10 weeks


title: Female Heart, Vehicle Control, Animal r54

description:
Library name: p06_10105_r54_h
etap_pfhxsa_heart_female_counts.csv


title: 1054DNA01


title: 1055DNA01


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

description:
Library name: p05_10105_r41_h
etap_pfhxsa_heart_male_counts.csv


title: 1053DNA01


title: 1051DNA01


title: 1050DNA01


title: 1049DNA01


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

description:
Library name: p05_10105_r39_h
etap_pfhxsa_heart_male_counts.csv


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

description:
Library name: p05_10105_r38_h
etap_pfhxsa_heart_male_counts.csv

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

value: 10 mg/kg/day


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

description:
Library name: p05_10105_r37_h
etap_pfhxsa_heart_male_counts.csv

value: Perflurohexanesulfonamide (PFHxSA)

value: Oral gavage


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

description:
Library name: p05_10105_r36_h
etap_pfhxsa_heart_male_counts.csv


title: 1061DNA01


title: 1045DNA01


title: 1043DNA01


title: 1046DNA01


title: 1042DNA01


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

description:
Library name: p05_10105_r33_h
etap_pfhxsa_heart_male_counts.csv

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

value: 3 mg/kg/day


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

description:
Library name: p05_10105_r32_h
etap_pfhxsa_heart_male_counts.csv

value: No Issue


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

description:
Library name: p05_10105_r30_h
etap_pfhxsa_heart_male_counts.csv

value: Male


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

description:
Library name: p05_10105_r29_h
etap_pfhxsa_heart_male_counts.csv


title: 1026DNA01

value: Whole blood


title: 1029DNA01


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

description:
Library name: p05_10105_r28_h
etap_pfhxsa_heart_male_counts.csv

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

value: 1 mg/kg/day


title: 1039DNA01


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

description:
Library name: p05_10105_r34_h
etap_pfhxsa_heart_male_counts.csv


title: 1022DNA01


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

description:
Library name: p05_10105_r27_h
etap_pfhxsa_heart_male_counts.csv


title: 1031DNA01


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

description:
Library name: p05_10105_r40_h
etap_pfhxsa_heart_male_counts.csv

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


title: 1017DNA01


title: 1047DNA01


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

description:
Library name: p05_10105_r25_h
etap_pfhxsa_heart_male_counts.csv


title: 1016DNA01


title: 1015DNA01


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

description:
Library name: p05_10105_r23_h
etap_pfhxsa_heart_male_counts.csv

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

value: 0.3 mg/kg/day


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

description:
Library name: p05_10105_r24_h
etap_pfhxsa_heart_male_counts.csv

value: Heart


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

description:
Library name: p05_10105_r26_h
etap_pfhxsa_heart_male_counts.csv

value: Sprague Dawley


title: 1118DNA01

value: Female


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

description:
Library name: p05_10105_r35_h
etap_pfhxsa_heart_male_counts.csv

value: 8-10 weeks

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


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

description:
Library name: p05_10105_r22_h
etap_pfhxsa_heart_male_counts.csv

value: Perflurohexanesulfonamide (PFHxSA)


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

description:
Library name: p05_10105_r31_h
etap_pfhxsa_heart_male_counts.csv

value: Oral gavage

value: Outlier sample removed


title: 1014DNA01


title: 1012DNA01


title: 1005DNA01


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

description:
Library name: p05_10105_r21_h
etap_pfhxsa_heart_male_counts.csv


title: 1004DNA01


title: 1002DNA01


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

description:
Library name: p05_10105_r18_h
etap_pfhxsa_heart_male_counts.csv

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

value: 0.1 mg/kg/day


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

description:
Library name: p05_10105_r16_h
etap_pfhxsa_heart_male_counts.csv

value: Male

value: No Issue


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

description:
Library name: p05_10105_r17_h
etap_pfhxsa_heart_male_counts.csv


title: C17,mCherry,RAD21,rep1

city: Utrecht

first: Peter

last: Krijger

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

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

library_source: genomic

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

molecule: genomic DNA

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: cell line

tag: genotype

value: mCherry

tag: protein

tag: replicate

tag: antibody

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


title: C17,mCherry,MAU2,rep1

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


title: C17,TACL-ON,RAD21,rep1

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

value: TACL-ON


title: C17,TACL-ON,MAU2,rep1


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

description:
Library name: p05_10105_r15_h
etap_pfhxsa_heart_male_counts.csv


title: C17,TACL-OFF,Input,rep1

value: TACL-OFF

value: Input


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

description:
Library name: p05_10105_r14_h
etap_pfhxsa_heart_male_counts.csv

value: Heart

value: Sprague Dawley


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

description:
Library name: p05_10105_r13_h
etap_pfhxsa_heart_male_counts.csv

value: 8-10 weeks

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

value: 0.01 mg/kg/day


title: C17,TACL-ON,Input,rep4


title: human_ST_Section_D_10X

city: Cambridge

first: Helle

last: Jorgensen

address: Papworth Road

department: Cardiorespiratory section

country: United Kingdom

institute: University of Cambridge

description: Spatial transcriptome sequencing (Visium, 10X Genomics)

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
Library strategy: spatial RNA-seq

source_name: Plaque section from human aorta

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: Plaque section from human aorta

value: Anonymous

tag: background


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

description:
Library name: p05_10105_r10_h
etap_pfhxsa_heart_male_counts.csv

value: Perflurohexanesulfonamide (PFHxSA)

value: Oral gavage


title: human_ST_Section_C_10X


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

description:
Library name: p05_10105_r09_h
etap_pfhxsa_heart_male_counts.csv

value: Male


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

description:
Library name: p05_10105_r19_h
etap_pfhxsa_heart_male_counts.csv

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

value: 0.3 mg/kg/day

value: No Issue


title: Male Heart, Vehicle Control, Animal r08

description:
Library name: p05_10105_r08_h
etap_pfhxsa_heart_male_counts.csv

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

value: 0 mg/kg/day


title: thrombin_20F

data_processing:
Raw data reads were trimmed with Trim Galore v.0.6.7, and aligned to the human genome (GRCh38) with Kallisto v.0.46.2.
Count files were generated from transcript level estimates using tximport v.
Trimmed Mean of M-values (TMM) normalization was conducted and GSEA performed (Subramanian et al, 2005).
Assembly: GRCh38
Supplementary files format and content: unnormalized count files

molecule: polyA RNA

source_name: aortic VSMC

growth_protocol: VSMCs were established from human aortic explants. Following outgrowth, cells were maintained in promocell smooth muscle cell growth medium 2

extract_protocol:
RNA extracted with qiagen Rneasy extraction kit
Libraries were prepared from oligo-dT-purified mRNA and sequenced on an Illumina Novaseq 6000 (150 bp paired end reads).

treatment_protocol: Bulk RNA-seq was conducted on total RNA isolated from of 3 different hVSMC isolates following 24 hours serum starvation in serum free media with or without 2U / mL thrombin.

value: aortic VSMC

value: primary cells

tag: cell type

value: VSMC

value: serum starved with thrombin (2U / mL) for 24 hrs

value: female


title: thrombin_77F

tag: Sex


title: human_ST_Section_A_10X

tag: tissue


title: thrombin_45F


title: Male Heart, Vehicle Control, Animal r03

description:
Library name: p05_10105_r03_h
etap_pfhxsa_heart_male_counts.csv

value: Heart

tag: strain

value: Sprague Dawley

value: 8-10 weeks

value: Outlier sample removed


title: Male Heart, Vehicle Control, Animal r06

description:
Library name: p05_10105_r06_h
etap_pfhxsa_heart_male_counts.csv

tag: age

value: Perflurohexanesulfonamide (PFHxSA)


title: Male Heart, Vehicle Control, Animal r02

description:
Library name: p05_10105_r02_h
etap_pfhxsa_heart_male_counts.csv

tag: treatment

value: Oral gavage


title: Male Heart, Vehicle Control, Animal r01

description:
Library name: p05_10105_r01_h
etap_pfhxsa_heart_male_counts.csv

value: Male

tag: treatment (dose)


title: ctrl_45F

value: serum starved for 24 hours


title: Male Heart, Vehicle Control, Animal r07

description:
Library name: p05_10105_r07_h
etap_pfhxsa_heart_male_counts.csv

tag: treatment (dose_group)


title: Female Brain, 100 mg/kg/day PFHxSA, Animal r96

description:
Library name: p04_10105_r96_b
etap_pfhxsa_brain_female_counts.csv

source_name: Brain

value: Female

value: Brain

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

value: 100 mg/kg/day

tag: treatment (chemical_name)


title: CRC with liver metastasis Sample AOI 40

city: cheonan

first: Dongjun

last: Jeong

state: Chungcheongnam-do

address: 25, Bongjeong-ro, Dongnam-gu

country: South Korea

institute: Soonchunhayng Unvi.

description: Nanostring GeoMX

data_processing:
Raw sequencing data were processed using the Nanostring GeoMX pipleline to generate FASTQ files
Assembly: mm10
Supplementary files format and content: JeongLABAllDataWTA.xlsx
Library strategy: Spatial Transcriptomics

molecule: nuclear RNA

source_name: FFPE

extract_protocol:
TMA FFPE slide was sectioned at a thickness of 5 µm.
Spatial transcriptome sequencing libraries were prepared with Nanostring GeoMX

value: Liver

value: CRC with liver metastasis


title: ctrl_77F

value: aortic VSMC

value: primary cells

value: VSMC


title: Male Heart, Vehicle Control, Animal r05

description:
Library name: p05_10105_r05_h
etap_pfhxsa_heart_male_counts.csv

value: Heart

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

value: 0 mg/kg/day

tag: treatment (route_of_exposure)

value: No Issue


title: CRC with liver metastasis Sample AOI 38

description: Nanostring GeoMX


title: CRC with liver metastasis Sample AOI 39

description: Nanostring GeoMX


title: CRC with liver metastasis Sample AOI 37

description: Nanostring GeoMX


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

description:
Library name: p05_10105_r11_h
etap_pfhxsa_heart_male_counts.csv

value: Sprague Dawley

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: Female Brain, 100 mg/kg/day PFHxSA, Animal r95

description:
Library name: p04_10105_r95_b
etap_pfhxsa_brain_female_counts.csv

value: Female

value: Brain

value: Oral gavage


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

description:
Library name: p05_10105_r20_h
etap_pfhxsa_heart_male_counts.csv

value: Male

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

value: 0.3 mg/kg/day


title: human_ST_Section_B_10X

value: Plaque section from human aorta

value: Anonymous


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

description:
Library name: p05_10105_r12_h
etap_pfhxsa_heart_male_counts.csv

value: Heart


title: CRC with liver metastasis Sample AOI 35

description: Nanostring GeoMX

value: Liver

value: CRC with liver metastasis


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

description:
Library name: p04_10105_r94_b
etap_pfhxsa_brain_female_counts.csv

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

value: 100 mg/kg/day

value: No Issue


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

description:
Library name: p04_10105_r93_b
etap_pfhxsa_brain_female_counts.csv

value: Sprague Dawley

value: 8-10 weeks


title: CRC with liver metastasis Sample AOI 34

description: Nanostring GeoMX


title: CRC with liver metastasis Sample AOI 33

description: Nanostring GeoMX


title: Male Heart, Vehicle Control, Animal r04

description:
Library name: p05_10105_r04_h
etap_pfhxsa_heart_male_counts.csv

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

value: 0 mg/kg/day

value: Perflurohexanesulfonamide (PFHxSA)


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

description:
Library name: p04_10105_r92_b
etap_pfhxsa_brain_female_counts.csv

value: Female

value: Brain

value: Oral gavage


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

description:
Library name: p04_10105_r90_b
etap_pfhxsa_brain_female_counts.csv

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

value: 30 mg/kg/day


title: ctrl_20F

value: aortic VSMC

tag: cell line

value: primary cells

value: VSMC

value: serum starved for 24 hours

value: female


title: CRC with liver metastasis Sample AOI 32

description: Nanostring GeoMX

value: Liver

value: CRC with liver metastasis


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

description:
Library name: p04_10105_r89_b
etap_pfhxsa_brain_female_counts.csv

value: Sprague Dawley

value: No Issue


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

description:
Library name: p04_10105_r88_b
etap_pfhxsa_brain_female_counts.csv

value: 8-10 weeks


title: CRC with liver metastasis Sample AOI 30

description: Nanostring GeoMX


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

description:
Library name: p04_10105_r86_b
etap_pfhxsa_brain_female_counts.csv

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

value: 10 mg/kg/day


title: CRC with liver metastasis Sample AOI 29

description: Nanostring GeoMX


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

description:
Library name: p04_10105_r84_b
etap_pfhxsa_brain_female_counts.csv

value: Female

value: Perflurohexanesulfonamide (PFHxSA)


title: Normal colon Sample AOI 27

description: Nanostring GeoMX

value: Sigmoid colon

value: Normal colon


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

description:
Library name: p04_10105_r85_b
etap_pfhxsa_brain_female_counts.csv

value: Brain

value: Oral gavage


title: Normal colon Sample AOI 25

description: Nanostring GeoMX


title: Normal colon Sample AOI 24

description: Nanostring GeoMX


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

description:
Library name: p04_10105_r82_b
etap_pfhxsa_brain_female_counts.csv


title: CRC with liver metastasis Sample AOI 36

description: Nanostring GeoMX


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

description:
Library name: p04_10105_r83_b
etap_pfhxsa_brain_female_counts.csv


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

description:
Library name: p04_10105_r81_b
etap_pfhxsa_brain_female_counts.csv

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

value: 3 mg/kg/day


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

description:
Library name: p04_10105_r80_b
etap_pfhxsa_brain_female_counts.csv


title: Normal colon Sample AOI 22

description: Nanostring GeoMX


title: Normal colon Sample AOI 23

description: Nanostring GeoMX


title: Normal colon Sample AOI 21

description: Nanostring GeoMX


title: Normal colon Sample AOI 28

description: Nanostring GeoMX


title: Normal colon Sample AOI 26

description: Nanostring GeoMX


title: CRC with liver metastasis Sample AOI 31

description: Nanostring GeoMX


title: Primary colon cancer Sample AOI 20

description: Nanostring GeoMX

value: Cecum

value: Primary colon cancer


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

description:
Library name: p04_10105_r78_b
etap_pfhxsa_brain_female_counts.csv


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

description:
Library name: p04_10105_r87_b
etap_pfhxsa_brain_female_counts.csv

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

value: 30 mg/kg/day


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

description:
Library name: p04_10105_r77_b
etap_pfhxsa_brain_female_counts.csv

value: Sprague Dawley


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

description:
Library name: p04_10105_r76_b
etap_pfhxsa_brain_female_counts.csv

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

value: 1 mg/kg/day

value: No Issue


title: Primary colon cancer Sample AOI 18

description: Nanostring GeoMX


title: Primary colon cancer Sample AOI 19

description: Nanostring GeoMX


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

description:
Library name: p04_10105_r74_b
etap_pfhxsa_brain_female_counts.csv

value: 8-10 weeks


title: Primary colon cancer Sample AOI 16

description: Nanostring GeoMX


title: Primary colon cancer Sample AOI 17

description: Nanostring GeoMX


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

description:
Library name: p04_10105_r73_b
etap_pfhxsa_brain_female_counts.csv

value: Female


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

description:
Library name: p04_10105_r72_b
etap_pfhxsa_brain_female_counts.csv

value: Perflurohexanesulfonamide (PFHxSA)


title: Primary colon cancer Sample AOI 15

description: Nanostring GeoMX


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

description:
Library name: p04_10105_r75_b
etap_pfhxsa_brain_female_counts.csv


title: Primary colon cancer Sample AOI 11

description: Nanostring GeoMX

value: Ascending colon


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

description:
Library name: p04_10105_r69_b
etap_pfhxsa_brain_female_counts.csv

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

value: 0.3 mg/kg/day


title: Japanese quail, Juvenile, Pituitary Gland, Short Photoperiod, Sample 3

city: Glasgow

first: Tyler

last: Stevenson

address: Jarret Building

department: School of Biodiversity, One Health, and Comparative Medicine

institute: University of Glasgow

description: Library name: Juvenile Pituitary 8L 425

data_processing:
Raw reads were demultiplexed and basealled using guppy basecaller
Porechop was used to trim adapters
Filtlong used to select long reads (>25bp reads)
Minimap2 used to align reads to Coturnix japonica (2.0) genome
Transcript expression levels generated using Salmon
Assembly: GCF_001577835.1
Supplementary files format and content: Comma Separated Values Files with expressed gene transcripts for each sample

organism: Coturnix japonica

source_name: Pituitary Gland

extract_protocol:
RNA was extracted using TRIzol reagent according to manufacturer instructions and cleaned using a Qiagen RNEasy MinElute Cleanup Kit
RNA was processed into cDNA libraries using the SQK PCB 109 cDNA Barcoding Kit (Oxford Nanopore Technologies) according to manufacturer instructions

value: Pituitary Gland

value: Short Photoperiod (8L:16D)


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

description:
Library name: p04_10105_r70_b
etap_pfhxsa_brain_female_counts.csv

value: Brain

value: Oral gavage


title: Japanese quail, Juvenile, Pituitary Gland, Short Photoperiod, Sample 4

description: Library name: Juvenile Pituitary 8L 421


title: Japanese quail, Juvenile, Pituitary Gland, Short Photoperiod, Sample 1

description: Library name: Juvenile Pituitary 8L 422


title: Japanese quail, Juvenile, Pituitary Gland, Short Photoperiod, Sample 2

description: Library name: Juvenile Pituitary 8L 424


title: F044_single_nucleotide_mutagenesis_library_frog_oocyte_uninjected_AVITI

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


title: Japanese quail, Juvenile, Pituitary Gland, Long Photoperiod, Sample 4

description: Library name: Juvenile Pituitary 16L 406

value: Long Photoperiod (16L:8D)


title: Primary colon cancer Sample AOI 10

description: Nanostring GeoMX

value: Primary colon cancer


title: Primary colon cancer Sample AOI 13

description: Nanostring GeoMX


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

description:
Library name: p04_10105_r79_b
etap_pfhxsa_brain_female_counts.csv

value: Sprague Dawley

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

value: 3 mg/kg/day


title: Japanese quail, Juvenile, Pituitary Gland, Long Photoperiod, Sample 3

description: Library name: Juvenile Pituitary 16L 405


title: Japanese quail, Juvenile, Pituitary Gland, Short Photoperiod, Sample 5

description: Library name: Juvenile Pituitary 8L 423


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

description:
Library name: p04_10105_r66_b
etap_pfhxsa_brain_female_counts.csv

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

value: 0.1 mg/kg/day

value: No Issue


title: Japanese quail, Juvenile, Pituitary Gland, Long Photoperiod, Sample 1

description: Library name: Juvenile Pituitary 16L 403


title: Japanese quail, Adult, Pituitary Gland, Short Photoperiod, Sample 5

description: Library name: Adult Pituitary 8L 261


title: Primary colon cancer Sample AOI 9

description: Nanostring GeoMX


title: Japanese quail, Adult, Pituitary Gland, Short Photoperiod, Sample 4

description: Library name: Adult Pituitary 8L 259


title: Japanese quail, Juvenile, Pituitary Gland, Long Photoperiod, Sample 2

description: Library name: Juvenile Pituitary 16L 404


title: Normal colon Sample AOI 7

description: Nanostring GeoMX

value: Normal colon


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

description:
Library name: p04_10105_r65_b
etap_pfhxsa_brain_female_counts.csv

value: Female

value: 8-10 weeks

value: Perflurohexanesulfonamide (PFHxSA)


title: Primary colon cancer Sample AOI 14

description: Nanostring GeoMX

value: Ascending colon


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

description:
Library name: p04_10105_r71_b
etap_pfhxsa_brain_female_counts.csv

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

value: 0.3 mg/kg/day


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

description:
Library name: p04_10105_r68_b
etap_pfhxsa_brain_female_counts.csv

value: Brain

value: Oral gavage


title: Japanese quail, Adult, Pituitary Gland, Long Photoperiod, Sample 4

description: Library name: Adult Pituitary 16L 148

value: Pituitary Gland

value: Long Photoperiod (16L:8D)


title: Japanese quail, Adult, Pituitary Gland, Short Photoperiod, Sample 2

description: Library name: Adult Pituitary 8L 262

value: Short Photoperiod (8L:16D)


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

description:
Library name: p04_10105_r64_b
etap_pfhxsa_brain_female_counts.csv

value: Sprague Dawley


title: Normal colon Sample AOI 4

description: Nanostring GeoMX


title: Japanese quail, Adult, Pituitary Gland, Long Photoperiod, Sample 5

description: Library name: Adult Pituitary 16L 150


title: Japanese quail, Adult, Pituitary Gland, Short Photoperiod, Sample 1

description: Library name: Adult Pituitary 8L 257


title: Normal colon Sample AOI 5

description: Nanostring GeoMX


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

description:
Library name: p04_10105_r62_b
etap_pfhxsa_brain_female_counts.csv


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

description:
Library name: p04_10105_r61_b
etap_pfhxsa_brain_female_counts.csv

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

value: 0.01 mg/kg/day


title: Japanese quail, Adult, Pituitary Gland, Long Photoperiod, Sample 3

description: Library name: Adult Pituitary 16L 149


title: Japanese quail, Adult, Pituitary Gland, Long Photoperiod, Sample 1

description: Library name: Adult Pituitary 16L 146


title: Normal colon Sample AOI 3

description: Nanostring GeoMX


title: Huntington’s model

city: Freiburg

first: Chintan

last: Chhatbar

address: Breisacher strasse 64

department: Department of Neuropathology

country: Germany

institute: Uniklinikum Freiburg

description: Library name: Huntingtons_Model

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

organism: Mus musculus

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

tag: genotype


title: Huntington’s model control

description: Library name: Huntingtons_Model_control

value: WT


title: Japanese quail, Adult, Pituitary Gland, Short Photoperiod, Sample 3

description: Library name: Adult Pituitary 8L 258


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

description:
Library name: p04_10105_r60_b
etap_pfhxsa_brain_female_counts.csv

value: No Issue


title: Normal colon Sample AOI 1

description: Nanostring GeoMX

value: Normal colon


title: Normal colon Sample AOI 2

description: Nanostring GeoMX


title: C17,TACL-OFF

data_processing:
Hi-C data was processed using the distiller pipeline (https://github.com/open2c/distiller-nf). The reads were mapped to the human reference genome assembly hg38 with bwa mem. The alignments were parsed and filtered for duplicates using the pairtools package (https://github.com/open2c/pairtools). Filtered reads pairs were aggregated into genomic bins of different sizes using the cooler package (https://github.com/open2c/cooler). The resulting Hi-C matrices were normalized using the iterative correction procedure.
Assembly: hg38
Supplementary files format and content: contact matrices in .MCOOL and .HIC formats

extract_protocol:
Hi-C template preparation was performed as described in Rao et al (2014). In brief, ten million cells per sample were crosslinked with 2% formaldehyde followed by quenching by glycine at final concentration of 0.2 M. Four-cutter restriction enzyme DpnII was used for in situ digestion. Digested DNA were repaired with biotin-14–dATP in a Klenow end-filling reaction. End-repaired, ligated, and reverse-crosslinked DNA was subsequently purified using isopropanol and magnetic beads. Purified DNA was sheared to 300-500 bp with Covaris and subsequently size-selected by AMPure XP. Appropriately-sized ligation fragments marked by biotin were pulled down with MyOne Streptavidin C1 DynaBeads (Invitrogen) and prepped for Illumina sequencing.
Hi-C library preparation was performed as described in Rao et al (2014). In brief, appropriately-sized ligation fragments marked by biotin were pulled down with MyOne Streptavidin C1 DynaBeads (Invitrogen) and prepped for Illumina sequencing.

treatment_protocol: To release TetR from the TetO platform, cells were treated with doxycycline for 1h.

value: TACL-OFF


title: C17,TACL-ON

value: TACL-ON


title: C17,cherry

value: mCherry


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

description:
Library name: p04_10105_r63_b
etap_pfhxsa_brain_female_counts.csv

value: Female

value: 8-10 weeks

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

value: 0.1 mg/kg/day

value: Perflurohexanesulfonamide (PFHxSA)


title: Japanese quail, Adult, Pituitary Gland, Long Photoperiod, Sample 2

description: Library name: Adult Pituitary 16L 147

value: Pituitary Gland

value: Long Photoperiod (16L:8D)


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

description:
Library name: p04_10105_r91_b
etap_pfhxsa_brain_female_counts.csv

value: Brain

value: Sprague Dawley

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

value: 30 mg/kg/day

value: Oral gavage


title: eHAP1, C17_WAPL-AID, TACL-ON, rep1

data_processing:
4C-seq reads were mapped to the hg38 reference genome and processed using pipe4C ( https://github.com/deLaatLab/pipe4C).
Normalized 4C coverage was calculated separately for each TetO integration site using R (r-project.org). Counts at non-blind fragments within a 20 MB region (10 MB upstream and downstream of the viewpoint) were adjusted to 1 million mapped reads after exclusion of the two highest-count fragments. Count data was smoothed using a running mean with a window size of 21 fragments using the R package caTools v 1.18.2.
To systematically annotate the TACL domains induced by the recruitment of cohesin to the TetO platforms, we developed a Hidden Markov Model (HMM). The HMM was implemented using the Python package hmmlearn (https://github.com/hmmlearn/hmmlearn). We created an HMM with the states 'TACL_domain' and 'no_change'. The normalised 4C-seq signals for TACL-ON and Cherry conditions were binarised into two observations: "TACL_domain" (4C-seq signal difference between TACL-ON and Cherry greater than 25) and "no_change" (4C-seq signal difference less than or equal to 25). The emission probabilities were estimated using manually defined TACL domains. The probability of the "TACL_domain" state was calculated as the fraction of restriction fragments with 4C-seq signal greater than 25 in the manually defined TACL domains and set to 0.6. The probability of the "no_change" state was calculated as the fraction of restriction fragments with 4C-seq signal less than or equal to 25 in the flanking regions of the manually defined TACL domains and was set to 0.98. The transition probability was set to 10-6. The estimated "TACL_domain" and "no_change" states were then subjected to several additional filters. First, restriction fragments belonging to stretches of more than 20 consecutive "TACL_domain" states were retained. Second, restriction fragments with consecutive "TACL_domain" states within 100 kb of each other were merged. Third, merged regions containing at least 40 restriction fragments were retained and further merged within 1.5 Mb of each other to draft TACL domains. Finally, if TetO was outside of the drafted TACL domain, the closest domain segment on the other side of the domain with respect to the TetO location was added to obtain TACL domains.
Assembly: hg38
Supplementary files format and content: wig, bed
Library strategy: 4C-seq

extract_protocol:
4C templates preparation was performed as described in PMID: 31351925. In brief, ten million cells per sample were crosslinked with 2% formaldehyde, followed by quenching by glycine at final concentration of 0.125 M. Four-cutter restriction enzyme MboI (New England BioLabs) was used for in situ digestion (300U/10 million cells). Digested DNA fragments were ligated, reverse-crosslinked and subsequently purified through isopropanol and magnetic beads (Macherey-Nagel NucleoMag PCR Beads). Four-cutter restriction enzyme Csp6I (CviQI, ThermoFisher ER0211, 50U/sample) was used for template trimming.
Indexed Illumina sequencing adapters were introduced to ligation fragments of interest with a two-step PCR strategy using ELT PCR System (Roche, cat. no. 11681842001).
To prevent PCR amplification and sequencing of TetO repeats due to tandem ligation of two or more TetO DpnII fragments in a given 4C circle, an in vitro digestion of 4C templates was performed as in PMID: 31932773, with the following modifications: two sgRNA were used to target Cas9 into the TetO repeats between viewpoint primers; pre-incubation of Cas9 protein and sgRNA template at room temperature. In brief, two sgRNA templates were obtained using the Megashortscript T7 transcription kit (Invitrogen) followed by 4x AMPure XP (Agencourt) purification. Purified Cas9 protein (generated by Hubrecht protein facility) was pre-incubated with the sgRNAs for 30min at room temperature. 4C templates were subsequently added to the pre-incubated Cas9/sgRNA complexed for overnight digestion at 37°C. Cas9 protein was inactivated by incubating at 70 °C for 5 min. Resulting products were purified with 1x AMPure XP and used as PCR template for TetO dedicated 4C.


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

description:
Library name: p04_10105_r57_b
etap_pfhxsa_brain_female_counts.csv

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

value: 0.01 mg/kg/day

value: No Issue


title: H1975-RT, Rep3

city: Fukuoka

first: Naoki

last: Haratake

state: Please Select

address: 3-1-1 Maidashi, Higashi-ku

country: Japan

institute: Graduate School of Medical Sciences, Kyushu University

data_processing:
Raw sequencing reads were aligned to the human genome (GRCh38.74) using STAR.
Raw feature counts were normalized and differential expression analysis using DESeq2.
Differential expression rank order was utilized for subsequent Gene Set Enrichment Analysis (GSEA), performed using the fgsea (v1.8.0) package in R.
Gene sets queried included those from the Hallmark Gene Sets available through the Molecular Signatures Database (MSigDB).
Assembly: hg38
Supplementary files format and content: TPM

source_name: lung

growth_protocol: H1975, H1975-OR, H1975-RT cells (American Type Culture Collection (ATCC), Manassas, VA, USA) were cultured in RPMI1640 medium (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% fetal bovine serum (FBS; GEMINI Bio-Products, West Sacramento, CA, USA) and Insulin.

extract_protocol:
Total RNA from cells cultured in triplicates was isolated using RNeasy Plus Mini Kit.
TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) was used for library preparation.

treatment_protocol: MUC1shRNA (MISSION shRNA TRCN0000122938; Sigma, St. Louis, MO, USA)  was inserted into the pLKO-tet-puro vector (Plasmid #21915; Addgene, Cambridge, MA, USA) . Vector-transduced cells were selected for growth in 1–2 μg/ml puromycin. Cells were treated with 0.1% DMSO as the vehicle control or 500 ng/ml doxycycline (DOX; Millipore Sigma).

value: lung

value: Lung Cancer

value: OSIMERTINIB→DMSO


title: eHAP1, C17_WAPL-AID, TACL-ON_IAA, rep1


title: eHAP1, C17_STAG2-AID, TACL-ON, rep1

value: TACL-ON


title: H1975-RT, Rep2


title: H1975-RT, Rep1


title: eHAP1, C17_RAD21-AID, TACL-ON, rep1


title: eHAP1, C17_PDS5A-AID, TACL-ON_IAA, rep1


title: Female Brain, Vehicle Control, Animal r56

description:
Library name: p04_10105_r56_b
etap_pfhxsa_brain_female_counts.csv

value: Female

value: 8-10 weeks

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

value: 0 mg/kg/day


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

description:
Library name: p04_10105_r59_b
etap_pfhxsa_brain_female_counts.csv

value: Perflurohexanesulfonamide (PFHxSA)


title: eHAP1, C17_STAG2-AID, TACL-ON_IAA, rep1


title: eHAP1, C17_RAD21-AID, TACL-ON_IAA, rep1


title: eHAP1, C17_CTCF-AID, TACL-ON_IAA, rep1


title: H1975-OR, Rep3

value: OSIMERTINIB→OSIMERTINIB


title: eHAP1, C17_CTCF-AID, TACL-ON, rep2


title: eHAP1, C17_PDS5A-AID, TACL-ON, rep1


title: Female Brain, Vehicle Control, Animal r55

description:
Library name: p04_10105_r55_b
etap_pfhxsa_brain_female_counts.csv

value: Brain

value: Sprague Dawley


title: eHAP1, C17, TACL-ON, rep1


title: Female Brain, Vehicle Control, Animal r54

description:
Library name: p04_10105_r54_b
etap_pfhxsa_brain_female_counts.csv


title: eHAP1, C17_CTCF-AID, TACL-ON, rep1


title: Female Brain, Vehicle Control, Animal r51

description:
Library name: p04_10105_r51_b
etap_pfhxsa_brain_female_counts.csv


title: H1975-OR Rep2

value: OSIMERTINIB


title: C17,TmCherry,rep3, BrU-seq

data_processing:
BrU-seq reads were mapped to the hg38 human reference genome assembly using STAR v2.7.9a (PMID: 23104886) with GENCODE v44 gene annotation.
Uniquely mapped reads with MAPQ > 10 were selected and split by strand using SAMtools v1.12 (PMID: 19505943). Forward strand reads were extracted by using -f 16 FLAG, reverse strand reads were extracted by using -F 16 FLAG.
Gene counts were obtained using the ”htseq-count” function from HTSeq v0.13.5 (PMID: 25260700). Counts were calculated separately for genes from forward and reverse strands with the parameters “--stranded no”, “--nonunique all”, “--order pos”, and “--type gene”.
Differentially expressed genes were identified using the DESeq2 v1.30.1 (PMID: 25516281). Low expressed genes were filtered by requiring the samples to have gene counts greater than 10. The “nbinomWaldTest” function with default parameters was used to test contrasts. Genes with FDR < 0.05 and absolute log2-fold-change > 1 were considered significant.
For downstream analyses, the genes were overlapped with annotated TACL domains and split into groups depending on their relative distance and position to the TetO platforms using bioframe v0.3.0.
Assembly: hg38
Supplementary files format and content: tsv (raw counts), tsv (DESeq2 output)
Library strategy: BrU-seq

extract_protocol:
Cultured cells were incubated with 2mM Bromouridine (BrU, Merck) for 10min and subsequently lysed in TRIzol reagent (Thermofisher). RNA was isolated following the manufacture’s protocol. Briefly, lysed cells were mixed with chloroform and centrifuged for 15min. The aqueous phase was transferred to a new tube and mixed with isopropanol. After centrifugation, RNA pellet was washed once with 70% ethanol and dissolved in DEPC water. To capture BrU-labelled nascent RNA, 6ug anti-BrdU antibodies (BD biosciences) pre-coupled with Dynabeads protein G beads (Thermofisher) were incubated with the total RNA for 1h at room temperature. Beads were then washed 3x with PBS/0.1% Tween-20/RNaseOUT. To purify the beads-bound RNA, TRIzol reagent was directly added to the beads and RNA was purified as described above.
NGS sequencing libraries were generated using NEBnext Ultra II directional RNA library prep kit (NEB) following manufacture’s protocol. Briefly, RNA was fragmented to about 200bp in size. First strand and second strand cDNA were synthesized. Double strand cDNA was then end repaired, 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 7 cycles.

treatment_protocol: To release TetR from the TetO platform, cells were treated with doxycycline for 2h.

value: TmCherry


title: C17,TmCherry,rep2, BrU-seq


title: H1975-OR Rep1


title: Female Brain, Vehicle Control, Animal r52

description:
Library name: p04_10105_r52_b
etap_pfhxsa_brain_female_counts.csv

value: Oral gavage


title: eHAP1, C17, TACL-OFF, rep1

value: TACL-OFF


title: C17,TACL-OFF,rep3, BrU-seq


title: H1975-OR Rep3


title: H1975 Rep3

value: DMSO


title: C17,TACL-ON,rep3, BrU-seq


title: eHAP1, C17, mCherry, rep1

value: mCherry


title: Normal colon Sample AOI 8

description: Nanostring GeoMX

value: Ascending colon

value: Normal colon


title: Normal colon Sample AOI 6

description: Nanostring GeoMX


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

description:
Library name: p03_10105_r47_b
etap_pfhxsa_brain_male_counts.csv

value: Male

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

value: 100 mg/kg/day

value: No Issue


title: H1975-OR, Rep1

value: lung

value: Lung Cancer


title: C17,TACL-ON,rep1, BrU-seq

value: TACL-ON


title: C17,TACL-ON,rep2

data_processing:
ATAC-seq reads were mapped to the hg38 human reference genome assembly using bwa mem v0.7.17-r1188 (PMID: 19451168).
Uniquely mapped reads in proper read pairs (-f 2) with MAPQ > 10 were selected using SAMtools v1.15 (PMID: 19505943)
Duplicate reads were filtered out using the Picard v2.25.6 “MarkDuplicates” function (https://broadinstitute.github.io/picard/).
Bigwig coverage tracks were generated using the “bamCoverage” function from the deepTools v3.4.2 (PMID: 27079975) with the “--effectiveGenomeSize” parameter set to 2913022398 and “--normalizeUsing” parameter set to RPGC.
Peaks were called using MACS2 v2.2.6 (PMID: 18798982) for pooled data and replicates in a narrowPeak mode, with mappable genome size set to hs, q-value cutoff of 0.05, “--keep-dup” parameter set to all, and “--nomodel” parameter. The consensus peak list was obtained by overlapping the peaks called for pooled data with peaks from replicates. Only the peaks from canonical chromosomes outside of the blacklist regions (PMID: 31249361) that had an overlap of at least 50% with peaks from both replicates were retained.
ATAC-seq and H3K27ac peaks from the TACL-ON, TACL-OFF and Cherry conditions were pooled into one set for differential occupancy analysis. Peak counts were obtained using the “intersect” function from BEDTools v2.27.1 (PMID: 20110278) with “-c -wa” parameters.
Differential ATAC-seq peaks were identified using the DESeq2 v1.30.1 (PMID: 25516281). The “nbinomWaldTest” function with default parameters was used to test contrasts. Peaks with FDR < 0.05 and absolute log2-fold-change > 0.5 were considered significant.
Assembly: hg38
Supplementary files format and content: bigwig (coverage), bed (peaks), tsv (DESeq2 analyis)

extract_protocol:
ATAC-seq was conducted following the Omni-ATAC protocol. In summary, 200,000 cells were lysed using a solution containing 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin, then incubated with a homemade Tagment DNA Enzyme for 30 minutes at 37 °C.
DNA purification was carried out using the QIAGEN MinElute Reaction Cleanup Kit. Library fragments were amplified with Phusion High-Fidelity PCR Master Mix with HF Buffer (Thermo Fisher Scientific, catalog no. F531S) and custom primers featuring unique single or dual indexes. Purification of the libraries was performed using AMPure XP beads (Beckman Coulter, catalog no. A63881), following the manufacturer’s guidelines. The quality of the constructed libraries was assessed using the Agilent Bioanalyzer 2100 with the DNA 7500 kit (catalog no. 5067-1504).


title: Female Brain, Vehicle Control, Animal r49

description:
Library name: p04_10105_r49_b
etap_pfhxsa_brain_female_counts.csv

value: Female

value: Brain

value: 8-10 weeks

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

value: 0 mg/kg/day

value: Perflurohexanesulfonamide (PFHxSA)


title: Primary colon cancer Sample AOI 12

description: Nanostring GeoMX

value: Primary colon cancer


title: Female Brain, Vehicle Control, Animal r50

description:
Library name: p04_10105_r50_b
etap_pfhxsa_brain_female_counts.csv

value: Sprague Dawley

value: Oral gavage


title: H1975-OR, Rep2

value: OSIMERTINIB→OSIMERTINIB


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

description:
Library name: p04_10105_r67_b
etap_pfhxsa_brain_female_counts.csv

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

value: 0.3 mg/kg/day


title: Female Brain, Vehicle Control, Animal r53

description:
Library name: p04_10105_r53_b
etap_pfhxsa_brain_female_counts.csv


title: C17,TACL-ON,rep1


title: VCaP_EUseq_100nM_CBPD_4h_rep2

city: Ann Arbor

first: Arul

last: Chinnaiyan

state: MI

address: 1500 East Medical Center Dr

department: MCTP

institute: University of Michigan

data_processing:
Files were first processed using FastQC for quality check then run through kallisto quant.
Individual samples were combined into one TPM table using tidyverse in R and the hg38 transcript to gene key. R package edgeR was then used to generate the cpm table.
Additional downstream analysis was performed in R using packages limma, edgeR, gsea.
Assembly: hg38
Supplementary files format and content: A single combined CPM table in csv format has been generated for all regular samples.
Supplementary files format and content: EU set has a counts and a tpm table in csv format.

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:
Total RNA was extracted from cells using QIAzol Lysis Reagent (QIAGEN). Initially, 1x10^6 cells were lysed with 700 µL of QIAzol. The lysates were incubated at room temperature for 5 minutes to dissociate nucleoproteins, then mixed with 140 µL chloroform and centrifuged at 12,000 g for 15 minutes at 4°C to achieve phase separation. The aqueous phase was then mixed with 1.5x volume of ethanol and applied to a RNeasy Mini spin column (QIAGEN) for RNA purification, following the miRNeasy Mini Kit protocol. The RNA was then eluted in RNase-free water and its concentration and purity assessed using a NanoDrop spectrophotometer. Cells were treated with or without CBPD-409 for 2 and 4 hours, with 0.5mM 5-Ethynyl Uridine (EU) added to the medium 45 minutes before cell harvest. After treatment, cells were washed with PBS, harvested, and lysed with the kit's lysis buffer. RNA isolation was performed using QIAzol reagent and RNeasy Mini spin column (Qiagen), following previously described methods. For ribosomal RNA depletion, 5μg of total RNA were processed using the Ribominus™ Eukaryote System v2 (ThermoFisher). The rRNA-depleted, EU-labeled RNA (250-500ng) was then incubated with 0.25mM biotin azide in the Click-iT® reaction cocktail for 30 minutes with gentle vortexing. Biotin-conjugated EU-RNA was precipitated using UltraPure™ Glycogen (1 μL, ThermoFisher), 7.5 M ammonium acetate (50 μL, Sigma-Aldrich), and chilled 100% ethanol (700 μL) at –70°C overnight. The sample was then centrifuged at 13,000 × g for 20 minutes at 4°C, and the RNA pellet was washed with 75% ethanol. Finally, 100-200ng of the purified EU-RNA was used for library preparation and sequencing, as detailed in the RNA-seq section.
Following extraction, ribosomal RNA (rRNA) was depleted from the total RNA samples using the RiboErase module of the KAPA RNA HyperPrep Kit (Roche). The rRNA-depleted RNA was then applied for library preparation. The procedure was conducted following the protocol provided with the KAPA RNA HyperPrep Kit. The prepared libraries were validated for quality using the Agilent 2100 Bioanalyzer. The libraries were then sequenced on an Illumina HiSeq 2500, utilizing a paired-end sequencing strategy (2 × 100 nucleotide read length with sequence coverage to 15–20M paired reads).

treatment_protocol: The cells were treated with 100nM CBPD, 1uM GNE or 1uM CCS for 4hrs, 12hrs or 24hrs

value: VCaP

value: prostate cancer


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

description:
Library name: p03_10105_r45_b
etap_pfhxsa_brain_male_counts.csv

value: Male

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

value: 100 mg/kg/day

value: No Issue


title: VCaP_EUseq_100nM_CBPD_4h_rep1


title: C17,TACL-OFF,rep1, BrU-seq

value: TACL-OFF


title: C17,TACL-OFF,rep2, BrU-seq


title: C17,cherry,rep2

value: mCherry


title: VCaP_EUseq_100nM_CBPD_2h_rep2


title: H1975 Rep2

value: lung

value: Lung Cancer

value: DMSO


title: C17,TACL-ON,rep2, BrU-seq

value: TACL-ON


title: L36pl_48hr_TNFaEGF_Rep3

city: Stuttgart

first: Steven

middle: A

last: Johnsen

address: Auerbachstrasse 112

institute: Robert Bosch Center for Tumor Diseases

data_processing:
Paired end sequencing reads were mapped to the reference genome assembly hg38 using STAR (star/2.7.9a). Reverse (sense strand) reads were quantified using htseq-count (htseq/0.9.1).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: AsPC1 (RPMI, 10% FBS, 1% Pen-Strep), HPAFII and L36pl (phenol red free MEM, 10% FBS, 1% Pen-Strep), PaTu8988s (DMEM, 20% FBS, 1% Pen-Strep) were maintained in humidified 5% CO2 incubator at 37C. PDX models were generated as described in PMID: 36889906.

extract_protocol:
Cells were washed twice with PBS after removing cell culture medium and total RNA was extracted from cells by adding 700 µL of QIAzol, incubated for 5 min on rocker, scraped and transferred to a new tube. 140 µL chloroform was added to the samples, vortexed for 15 sec, incubated for 3 min at room temperature, and centrifuged. Aqueous phase was transferred to a new tube and mixed with an equal volume of isopropanol. Samples were incubated at -20°C overnight and centrifuged. RNA pellet was washed twice with 70% ethanol and the pellet was air-dried at room temperature for 5-10 min. 50 µL of RNAse-free water was used to resuspend the pellet.
Before RNA-sequencing, RNA integrity was validated by gel electrophoresis and libraries were prepped using 500 ng following supplier’s protocol TruSeq Stranded mRNA Library Prep Kit (Illumina, 20020595). The library fragment size was determined by TapeStation.
cDNA_oligo_dT

value: PDAC


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

description:
Library name: p03_10105_r46_b
etap_pfhxsa_brain_male_counts.csv

value: Brain

value: Sprague Dawley

value: 8-10 weeks

value: Perflurohexanesulfonamide (PFHxSA)

value: Oral gavage


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

description:
Library name: p03_10105_r48_b
etap_pfhxsa_brain_male_counts.csv


title: L36pl_48hr_TNFa_Rep3


title: C17,TACL-OFF,rep2


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

description:
Library name: p03_10105_r41_b
etap_pfhxsa_brain_male_counts.csv

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

value: 30 mg/kg/day


title: C17,TmCherry_Dox2h,rep3, BrU-seq


title: C17,TACL-OFF,rep1


title: L36pl_48hr_EGF_Rep3


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

description:
Library name: p03_10105_r44_b
etap_pfhxsa_brain_male_counts.csv

value: Male

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


title: LNCaP_R1881_GNE_12h_rep2

source_name: LNCaP

value: LNCaP

value: prostate cancer


title: C17,cherry,rep1

value: mCherry


title: H1975 Rep1

value: lung


title: L36pl_48hr_Vehicle_Rep3


title: LNCaP_R1881_GNE_12h_rep1


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

description:
Library name: p03_10105_r38_b
etap_pfhxsa_brain_male_counts.csv

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

value: 10 mg/kg/day

value: No Issue


title: L36pl_48hr_Vehicle_Rep2

value: PDAC


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

description:
Library name: p03_10105_r43_b
etap_pfhxsa_brain_male_counts.csv

value: Brain


title: L36pl_48hr_TNFaEGF_Rep2


title: VCaP_Euseq_100nM_CBPD_2h_rep1

value: VCaP


title: L36pl_48hr_TNFaEGF_Rep1


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

description:
Library name: p03_10105_r42_b
etap_pfhxsa_brain_male_counts.csv

value: Sprague Dawley

value: 8-10 weeks


title: VCaP_EUseq_DMSO_rep2

value: DMSO


title: AsPC1_48hr_TNFaEGF_Rep3


title: AsPC1_48hr_TNFaEGF_Rep2


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

description:
Library name: p03_10105_r36_b
etap_pfhxsa_brain_male_counts.csv

value: Perflurohexanesulfonamide (PFHxSA)

value: Oral gavage


title: L36pl_48hr_TNFa_Rep2


title: L36pl_48hr_TNFa_Rep1


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

description:
Library name: p03_10105_r40_b
etap_pfhxsa_brain_male_counts.csv

value: Male

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

value: 30 mg/kg/day


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

description:
Library name: p03_10105_r39_b
etap_pfhxsa_brain_male_counts.csv


title: L36pl_48hr_EGF_Rep2


title: L36pl_48hr_EGF_Rep1


title: LNCaP_R1881_rep1

value: LNCaP

value: prostate cancer


title: L36pl_48hr_Vehicle_Rep1


title: LNCaP_R1881_CBPD_12h_rep2


title: LNCaP_CD_medium_GNE_12h_rep2


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

description:
Library name: p03_10105_r37_b
etap_pfhxsa_brain_male_counts.csv


title: AsPC1_48hr_EGF_Rep1


title: LNCaP_R1881_CBPD_12h_rep1


title: AsPC1_48hr_Vehicle_Rep2


title: AsPC1_48hr_TNFaEGF_Rep1


title: LNCaP_CD_medium_GNE_12h_rep1


title: AsPC1_48hr_TNFa_Rep3


title: LNCaP_R1881_rep2


title: AsPC1_48hr_TNFa_Rep2


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

description:
Library name: p03_10105_r34_b
etap_pfhxsa_brain_male_counts.csv


title: AsPC1_30min_TNFaEGF_Rep3


title: VCaP_EUseq_DMSO_rep1


title: AsPC1_30min_TNFaEGF_Rep1


title: LNCaP_CD_medium_CBPD_12h_rep1


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

description:
Library name: p03_10105_r30_b
etap_pfhxsa_brain_male_counts.csv

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

value: 3 mg/kg/day


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

description:
Library name: p03_10105_r35_b
etap_pfhxsa_brain_male_counts.csv

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

value: 10 mg/kg/day


title: AsPC1_48hr_TNFa_Rep1

value: PDAC


title: AsPC1_30min_TNFa_Rep3


title: AsPC1_48hr_EGF_Rep3


title: AsPC1_30min_TNFa_Rep2


title: AsPC1_48hr_Vehicle_Rep3


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

description:
Library name: p03_10105_r33_b
etap_pfhxsa_brain_male_counts.csv

value: Brain

value: No Issue


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

description:
Library name: p03_10105_r32_b
etap_pfhxsa_brain_male_counts.csv

value: Sprague Dawley


title: VCaP_CCS_24h_rep2

source_name: VCAP

value: VCAP


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

description:
Library name: p03_10105_r28_b
etap_pfhxsa_brain_male_counts.csv

value: 8-10 weeks

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

value: 1 mg/kg/day


title: AsPC1_30min_TNFa_Rep1


title: AsPC1_30min_EGF_Rep2


title: LNCaP_CD_medium_CBPD_12h_rep2


title: AsPC1_48hr_EGF_Rep2


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

description:
Library name: p03_10105_r27_b
etap_pfhxsa_brain_male_counts.csv

value: Male

value: Perflurohexanesulfonamide (PFHxSA)

value: Oral gavage


title: AsPC1_30min_TNFaEGF_Rep2


title: LNCaP_CSS_medium__rep2

value: LNCaP

value: DMSO


title: AsPC1_48hr_Vehicle_Rep1


title: AsPC1_30min_EGF_Rep3


title: LNCaP_CSS_medium__rep1

value: prostate cancer


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

description:
Library name: p03_10105_r29_b
etap_pfhxsa_brain_male_counts.csv

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

value: 3 mg/kg/day


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

description:
Library name: p03_10105_r31_b
etap_pfhxsa_brain_male_counts.csv


title: ChIP_L3.6pl_FOSL1_TNFaEGF_Rep2

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

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.


title: AsPC1_30min_Vehicle_Rep3


title: VCaP_CBPD_24h_rep2


title: AsPC1_30min_Vehicle_Rep1


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

description:
Library name: p03_10105_r26_b
etap_pfhxsa_brain_male_counts.csv

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

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.


title: VCaP_CCS_24h_rep1


title: AsPC1_30min_Vehicle_Rep2


title: AsPC1_30min_EGF_Rep1


title: ChIP_L3.6pl_FOSL1_TNFaEGF_Rep1


title: VCaP_GNE_24h_rep1


title: ChIP_AsPC1_Pol2_siRELATE_Rep3


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

description:
Library name: p03_10105_r24_b
etap_pfhxsa_brain_male_counts.csv


title: ChIP_AsPC1_Pol2_siRELATE_Rep2


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

description:
Library name: p03_10105_r22_b
etap_pfhxsa_brain_male_counts.csv

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

value: 0.3 mg/kg/day


title: ChIP_AsPC1_Pol2_siRELATE_Rep1

value: PDAC


title: VCaP_CCS_4h_rep2


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

description:
Library name: p03_10105_r23_b
etap_pfhxsa_brain_male_counts.csv

value: Brain

value: No Issue


title: ChIP_AsPC1_Pol2_siFOSL1TE_Rep3


title: ChIP_AsPC1_Pol2_siNT5TE_Rep2


title: ChIP_AsPC1_Pol2_siNT5TE_Rep1


title: ChIP_AsPC1_Pol2_siFOSL1TE_Rep2


title: ChIP_AsPC1_Pol2_siFOSL1TE_Rep1


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

description:
Library name: p03_10105_r25_b
etap_pfhxsa_brain_male_counts.csv

value: Sprague Dawley


title: VCaP_GNE_24h_rep2

value: VCAP


title: ChIP_AsPC1_Pol2_siNT5TE_Rep3


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

description:
Library name: p03_10105_r20_b
etap_pfhxsa_brain_male_counts.csv

value: 8-10 weeks


title: VCaP_CBPD_24h_rep1


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

description:
Library name: p03_10105_r21_b
etap_pfhxsa_brain_male_counts.csv


title: VCaP_CCS_4h_rep1


title: ChIP_AsPC1_Pol2_siNT5_Rep3


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

description:
Library name: p03_10105_r19_b
etap_pfhxsa_brain_male_counts.csv


title: ChIP_AsPC1_Pol2_siNT5_Rep2


title: ChIP_AsPC1_Pol2_Dex_TNFaEGF_Rep2


title: VCaP_GNE_4h_rep2


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

description:
Library name: p03_10105_r18_b
etap_pfhxsa_brain_male_counts.csv

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

value: 0.1 mg/kg/day


title: ChIP_AsPC1_Pol2_Dex_TNFaEGF_Rep3


title: ChIP_AsPC1_Pol2_siNT5_Rep1


title: VCaP_GNE_4h_rep1


title: ChIP_AsPC1_Pol2_Dex_TNFaEGF_Rep1


title: VCaP_CBPD_4h_rep2


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

description:
Library name: p03_10105_r17_b
etap_pfhxsa_brain_male_counts.csv

value: Male

value: Perflurohexanesulfonamide (PFHxSA)


title: ChIP_AsPC1_Pol2_BI_TNFaEGF_Rep3


title: ChIP_AsPC1_Pol2_BI_TNFaEGF_Rep2


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

description:
Library name: p03_10105_r16_b
etap_pfhxsa_brain_male_counts.csv

value: Oral gavage


title: VCaP_CBPD_4h_rep1


title: VCaP_DMSO_rep2

value: DMSO


title: ChIP_AsPC1_Pol2_BI_TNFaEGF_Rep1


title: ChIP_AsPC1_Pol2_TNFaEGF_Rep3


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

description:
Library name: p03_10105_r15_b
etap_pfhxsa_brain_male_counts.csv


title: ChIP_AsPC1_Pol2_TNFaEGF_Rep2


title: VCaP_DMSO_rep1

value: prostate cancer


title: ChIP_AsPC1_Pol2_TNFaEGF_Rep1


title: ChIP_AsPC1_Pol2_TNFa_Rep3


title: VCaP_DMSO_D28_ERG_CST

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

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: ERG (Cell Signaling Technology:97249S)


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

description:
Library name: p03_10105_r13_b
etap_pfhxsa_brain_male_counts.csv

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

value: 0.01 mg/kg/day


title: ChIP_AsPC1_Pol2_TNFa_Rep2

value: PDAC


title: ChIP_AsPC1_Pol2_TNFa_Rep1


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

description:
Library name: p03_10105_r12_b
etap_pfhxsa_brain_male_counts.csv

value: Brain


title: ChIP_AsPC1_Pol2_EGF_Rep1


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

description:
Library name: p03_10105_r11_b
etap_pfhxsa_brain_male_counts.csv

value: No Issue


title: VCaP_CBPD_4hrs_H3K18ac

value: H3K18ac (Active Motif:39755)


title: VCaP_DMSO_H3K18ac


title: ChIP_AsPC1_Pol2_Vehicle_Rep2


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

description:
Library name: p03_10105_r10_b
etap_pfhxsa_brain_male_counts.csv

value: Sprague Dawley


title: ChIP_AsPC1_Pol2_Vehicle_Rep1


title: ChIP_AsPC1_RELA_siRELATE_Rep3


title: VcaP_GNE_4h_Pol2

value: RNA Pol II (Active motif:39097)


title: ChIP_AsPC1_RELA_siRELATE_Rep1


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

description:
Library name: p03_10105_r09_b
etap_pfhxsa_brain_male_counts.csv

value: 8-10 weeks


title: ChIP_AsPC1_RELA_siRELATE_Rep2


title: ChIP_AsPC1_RELA_siFOSL1TE_Rep3


title: ChIP_AsPC1_RELA_siFOSL1TE_Rep2


title: Male Brain, Vehicle Control, Animal r08

description:
Library name: p03_10105_r08_b
etap_pfhxsa_brain_male_counts.csv

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

value: 0 mg/kg/day


title: Male Brain, Vehicle Control, Animal r07

description:
Library name: p03_10105_r07_b
etap_pfhxsa_brain_male_counts.csv

value: Male

value: Perflurohexanesulfonamide (PFHxSA)


title: VcaP_DMSO_Pol2

value: DMSO


title: VCaP_MED1_AM

value: prostate cancer

value: MED1 (Active motif:61065);


title: ChIP_AsPC1_Pol2_EGF_Rep3


title: ChIP_AsPC1_Pol2_EGF_Rep2


title: ChIP_AsPC1_RELA_siNT5TE_Rep2


title: ChIP_AsPC1_RELA_siNT5TE_Rep3


title: Male Brain, Vehicle Control, Animal r05

description:
Library name: p03_10105_r05_b
etap_pfhxsa_brain_male_counts.csv

value: Oral gavage


title: ChIP_AsPC1_RELA_siNT5_Rep3


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

description:
Library name: p03_10105_r14_b
etap_pfhxsa_brain_male_counts.csv

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

value: 0.1 mg/kg/day


title: ChIP_AsPC1_RELA_siFOSL1TE_Rep1

value: PDAC


title: ChIP_AsPC1_Pol2_Vehicle_Rep3


title: ChIP_AsPC1_RELA_siNT5_Rep2


title: VCaP_GNE_4hrs_H3K18ac

value: VCaP


title: Male Brain, Vehicle Control, Animal r04

description:
Library name: p03_10105_r04_b
etap_pfhxsa_brain_male_counts.csv

value: Brain

value: No Issue


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

description:
Library name: p04_10105_r58_b
etap_pfhxsa_brain_female_counts.csv

value: Female

value: Sprague Dawley

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

value: 0.01 mg/kg/day


title: VCaP_P300


title: VCaP_GNE_4hrs_H2BK20ac

value: H2BK20ac (Cell Signaling Technology:34156S)


title: Male Brain, Vehicle Control, Animal r03

description:
Library name: p03_10105_r03_b
etap_pfhxsa_brain_male_counts.csv

value: Male

value: 8-10 weeks

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

value: 0 mg/kg/day


title: ChIP_AsPC1_RELA_siNT5_Rep1


title: VCaP_CBPD_4hrs_H2BK20ac

value: prostate cancer


title: Male Brain, Vehicle Control, Animal r06

description:
Library name: p03_10105_r06_b
etap_pfhxsa_brain_male_counts.csv

value: Perflurohexanesulfonamide (PFHxSA)

value: Oral gavage


title: VcaP_CBPD_4h_Pol2

value: RNA Pol II (Active motif:39097)


title: ChIP_AsPC1_RELA_Dex_TNFaEGF_Rep2

value: PDAC


title: VCaP_DMSO_BRD4

value: VCaP

value: BRD4 (Diagenode:C15410337)

value: DMSO


title: VCaP_DMSO_H2BK20ac


title: Male Brain, Vehicle Control, Animal r02

description:
Library name: p03_10105_r02_b
etap_pfhxsa_brain_male_counts.csv

value: Brain

value: No Issue


title: ChIP_AsPC1_RELA_BI_TNFaEGF_Rep3


title: ChIP_AsPC1_RELA_siNT5TE_Rep1


title: Male Brain, Vehicle Control, Animal r01

description:
Library name: p03_10105_r01_b
etap_pfhxsa_brain_male_counts.csv

value: Sprague Dawley


title: ChIP_AsPC1_RELA_Dex_TNFaEGF_Rep1


title: ChIP_AsPC1_RELA_TNFaEGF_Rep3


title: ChIP_AsPC1_RELA_BI_TNFaEGF_Rep2


title: ChIP_AsPC1_RELA_BI_TNFaEGF_Rep1


title: VCaP_GNE_4hrs_H2BK5ac

value: H2BK5ac (Cell Signaling Technology:12799S)


title: ChIP_AsPC1_RELA_TNFaEGF_Rep2


title: Female Adrenal Gland, 100 mg/kg/day PFHxSA, Animal r96

description:
Library name: p02_10105_r96_a
etap_pfhxsa_adrenal_female_counts.csv

source_name: Adrenal Gland

value: Female

value: Adrenal Gland

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

value: 100 mg/kg/day


title: ChIP_AsPC1_RELA_TNFaEGF_Rep1


title: VCaP_CBPD_4hrs_H2BK5ac


title: Female Adrenal Gland, 100 mg/kg/day PFHxSA, Animal r95

description:
Library name: p02_10105_r95_a
etap_pfhxsa_adrenal_female_counts.csv

value: 8-10 weeks


title: ChIP_AsPC1_RELA_TNFa_Rep3


title: ChIP_AsPC1_RELA_Dex_TNFaEGF_Rep3


title: ChIP_AsPC1_RELA_TNFa_Rep2