title: HCT116_control_replication1

city: Seoul

first: Sanghee

last: Han

state: Dongdaemun-gu

address: 26, Kyungheedae-ro, Dongdaemun-gu, Seoul, Republic of Korea

institute: Kyunghee university

description:
Library name: con1
HCT116_control_replication1

data_processing:
QuantSeq 3' mRNA-Seq reads were aligned to the genome and transcriptome using Bowtie2. The alignment file was processed to assemble transcripts, estimate abundances, and identify differentially expressed genes (DEGs). Read counts were analyzed using EdgeR with TMM+CPM normalization for differential expression analysis. Gene classification and pathway enrichment analysis were performed using DAVID and Medline databases. Data mining and visualization were conducted using ExDEGA (Ebiogen Inc., Korea).
Assembly: GRCh38 (Genome Reference Consortium Human Build 38).
Supplementary files format and content: Processed data are provided in CSV format, containing normalized gene expression values (TMM+CPM), differential expression analysis results (fold changes, p-values), and gene classifications based on functional annotations.

growth_protocol: HCT116 colorectal cancer cells were cultured in RPMI-1640 medium supplemented with 10% FBS and 1% penicillin-streptomycin at 37°C in a 5% CO₂ humidified incubator.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.
Libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Austria) according to the manufacturer’s instructions. Briefly, total RNA (1 µg) was used as the starting material, and poly(A)-tailed RNA was selectively enriched. First-strand cDNA synthesis was performed using an oligo-dT primer with an Illumina-compatible sequence. Second-strand synthesis was initiated by a random primer with an Illumina-compatible linker sequence. The resulting double-stranded library was purified using magnetic beads and amplified to add complete adapter sequences required for sequencing on the Illumina NextSeq 550 platform.

treatment_protocol: Cells were treated with PSY ethanolic extract (50 µg/ml) for 24 hours, while control cells were treated with DMSO under the same conditions.

value: Cancer cell

value: Wild type

value: DMSO (Control)

value: Batch 1


title: KO_ZT2b

status: Public on Jan 05 2026

type: RNA

city: Lübeck

first: Leonardo

last: de Assis

address: Marie Curie

country: Germany

institute: University of Lübeck

hyb_protocol: Genome-wide expression analyses utilized Clariom S arrays (Thermo Fisher Scientific) with 100 ng RNA per sample, as per the manufacturer’s recommendations (WT Plus Kit, Thermo Fisher).

scan_protocol: Affymetrix

data_processing: Data analysis was conducted with Transcriptome Analyses Console (Thermo Fisher, version 4.0) with results expressed in log2 values. Microarray data from wild-type mice were obtained from a previous publication (GSE199998). Gene expression data were processed by averaging repeated probes, and lowly expressed genes were filtered out using a log2 expression threshold of less than 3.8, corresponding to the 25th percentile. Only gene names associated with ENSEMBL codes were included in the analysis. After removing duplicates, a total of 14,456 genes were retained for further analysis.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: liver

extract_protocol: Total RNA was extracted following the manufacturer’s instructions using TRIzol (Thermo Fisher, USA).

treatment_protocol: Three- to eight-month-old male ADQ-WT and ADQ-KO mice were group-housed under a 12-hour light, 12-hour dark (LD, ~300 lux in the light phase) cycle at 22 ± 2 °C and a relative humidity of 60 ± 5 % with ad libitum access to standard chow and water. Mice were culled by cervical dislocation at 4-hour intervals, tissues were kept on dry ice and stored at −80 °C.

tag: tissue

value: liver

tag: genotype

value: Adiponectin global KO

tag: timepoint


title: KO_ZT14a

label_protocol: Genome-wide expression analyses utilized Clariom S arrays (Thermo Fisher Scientific) with 100 ng RNA per sample, as per the manufacturer’s recommendations (WT Plus Kit, Thermo Fisher).


title: KO_ZT2c


title: Unmated, FACS-sorted esg+ cells, Replicate 2

type: SRA

city: Salt Lake City

first: Tahmineh

last: Kandelouei

state: Utah

address: 1950 Circle of Hope Dr.

country: USA

institute: Huntsman Cancer Institute

description: Library name: 19966X6

library_source: transcriptomic

data_processing:
The sample reads were aligned to the latest genome assembly (BDGP 6.94) using the STAR Aligner.
The aligned reads were then assigned to genes using HTSeq in 'Union' mode.
Raw scores derived from this process were then used for differential expression analysis using the DESeq2 algorithm.
Genes that met the criteria of an absolute log2 fold change ≥1 and an adjusted p-value <0.05 were identified as significantly differentially expressed.
Assembly: dm6
Supplementary files format and content: tab-delimited text files include raw counts for each sample.

organism: Drosophila melanogaster

source_name: gut

extract_protocol:
RNAwas extracted from dissected midguts using RNAqueous®-Micro Total RNA Isolation Kit.
NEBNext® Ultra™ II Directional RNA Library Prep with polyA mRNA isolation.

value: gut

tag: cell type

value: esg+ progenitor cells


title: KO_ZT6a


title: Unmated, FACS-sorted esg+ cells, Replicate 1

description: Library name: 19966X5


title: KO_ZT2d


title: Unmated, FACS-sorted esg+ cells, Replicate 3

description: Library name: 19966X7


title: KO_ZT2a


title: HCT116_control_replication2

country: South Korea

description:
Library name: con2
HCT116_control_replication2

organism: Homo sapiens

tag: cell line

tag: treatment

tag: batch


title: HCT116_psy treated_replication2

description:
Library name: psy2
HCT116_psy treated_replication2

value: PSY (50µg/mL)


title: HCT116_psy treated_replication1

description:
Library name: psy1
HCT116_psy treated_replication1


title: Unmated, FACS-sorted esg+ cells, Replicate 4

description: Library name: 19966X8


title: Mated, FACS-sorted esg+ cells, Replicate 4

description: Library name: 19966X4


title: Mated,Whole gut, Replicate 4

description: Library name: 19464X4


title: Mated,Whole gut, Replicate 1

description: Library name: 19464X1


title: Mated, FACS-sorted esg+ cells, Replicate 1

description: Library name: 19966X1


title: Mated, FACS-sorted esg+ cells, Replicate 3

description: Library name: 19966X3


title: Mated, FACS-sorted esg+ cells, Replicate 2

description: Library name: 19966X2


title: Unmated, Whole gut, Replicate 4

description: Library name: 19464X8


title: Mated,Whole gut, Replicate 3

description: Library name: 19464X3


title: Unmated, Whole gut, Replicate 3

description: Library name: 19464X7


title: Mated,Whole gut, Replicate 2

description: Library name: 19464X2


title: Dicer1+/+ cells, cultured in DMEM/F12 with 10% FBS, passage 27

city: Vancouver

first: David

last: Huntsman

state: BC

address: 675 W 10th Ave

department: Molecular Oncology

country: Canada

institute: BC Cancer Research Centre

description: Library name: hdt1119_cell_p27_dmem

data_processing:
Paired-end reads were processed with the nf-core rnaseq pipeline, version 3.14.0 and aligned to mm10. The trimmer was parameter was set to ‘trimgalore’ and the aligner to ‘star_salmon’, with extra salmon quant arguments supplied as ‘--seqBias –gcBias’.
Following alignment and quantification, the counts were imported with tximport version 1.26.1 and differential expression between the Dicer1 mutant and control samples was assessed within each media type using DESeq2 version 1.38.3. Genes with fewer than 10 counts in at least 3 samples were excluded from analysis.
Assembly: mm10
Supplementary files format and content: Transcript level counts and normalised counts in .sf format and the corresponding transcript to gene mapping used to collapse transcript counts to gene counts.

molecule: polyA RNA

source_name: kidney

growth_protocol: The whole kidneys from Hic1CreERT2/CreERT2:Rosa26LSL-tdTomato and Hic1CreERT2/CreERT2:Dicerfl/fl-D1693N;Rosa26LSL-tdTomato GEMM mice 4 weeks post tamoxifen treatment, which occurred when mice were 3-weeks-old, were minced with forceps to small chunks pipette-able by a 5mL serological pipette. Tumour chunks were then incubated in Gibco HBSS (no calcium, magnesium, phenol red, Catalog #14175103) and Stemcell 10X Collagenase/hyaluronidase in DMEM (Catalog # 07912), in a glass flask at 37oC on a hot plate, until everything was dissolved, usually takes between 30-45min. Enzymatic digestion was stopped with Advanced DMEM/F-12 (Catalog #12634010). Cells and tumour chunks were spun at 1000rpm for 5min. Pellets were resuspended in Gibco 0.25% Trypsin-EDTA (Catalog #25200072) for 5min at 37oC, followed by filtering through a Falcon 70μm cell strainer (Catalog #08-771-2). Cells were pelleted and resuspended in Stemcell Mouse MesenCult™ Expansion media (Catalog #05513). tdTomato positive cells were enriched by FACS and subsequently cultured in Mesencult media or DMEM/F12 media supplemented with 10%FBS.

extract_protocol:
RNA from frozen cell pellets was extracted using the Zymo Quick-RNA Miniprep Kit (Zymo cat# R1054). Total RNA integrity is assessed with the TapeStation 4200 (Agilent Technologies; RNA Assay Cat No.5067-5576) and quantified with the Qubit RNA HS assay (ThermoFisher; Cat No. Q32852).  Total RNA is used as input to enrich for mRNA with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB; Cat No. E7490).
Strand-specific libraries are prepared using the DNBSEQ Fast RNA Library Prep kit (Complete Genomics; Cat No. 940-001522-00) and sequenced at Vancouver Prostate Centre. Library quality and size are checked with the TapeStation 4200 (Agilent Technologies; D1000 Assay Cat No. 5067-5582) and then quantified using the Qubit dsDNA HS Assay (ThermoFisher; Cat No. Q32854). The libraries are sequenced using a Complete Genomics DNBSEQ-G400RS High-throughput Sequencer to generate 30 million 100-bp paired-end reads per library.

value: kidney

value: Hic1+ mesenchymal cells


title: Unmated, Whole gut, Replicate 1

description: Library name: 19464X5


title: Dicer1+/+ cells, cultured in Mesencult, passage 23

description: Library name: hdt1119_cell_p23_mesencult

value: Mesencult


title: Dicer1+/+ cells, cultured in DMEM/F12 with 10% FBS, passage 23

description: Library name: hdt1119_cell_p23_dmem


title: Dicer1+/D1693N cells, cultured in Mesencult, passage 22

description: Library name: hdt1056_cell_p22_mesencult


title: Dicer1+/D1693N cells, cultured in DMEM/F12 with 10% FBS, passage 20

description: Library name: hdt1056_cell_p20_dmem


title: Dicer1+/+ cells, cultured in Mesencult, passage 27

description: Library name: hdt1119_cell_p27_mesencult


title: Dicer1+/+ cells, cultured in Mesencult, passage 22

description: Library name: hdt1119_cell_p22_mesencult


title: Dicer1+/+ cells, cultured in DMEM/F12 with 10% FBS, passage 22

description: Library name: hdt1119_cell_p22_dmem


title: Dicer1+/D1693N cells, cultured in DMEM/F12 with 10% FBS, passage 18

description: Library name: hdt1056_cell_p18_dmem


title: Dicer1+/D1693N cells, cultured in Mesencult, passage 18

description: Library name: hdt1056_cell_p18_mesencult


title: FeCAS_1

city: Oeiras

first: Catarina

last: Pimentel

state: Lisboa

address: Av. da República

department: MOSTMICRO

country: Portugal

institute: ITQB NOVA

data_processing:
The quality of the RNA-Seq raw data was analysed using the FastQC tool. Reads were mapped against Candida albicans genome (GCA_000182965.3 downloaded from NCBI genome database) using Bowtie2. The mapping files were sorted by genomic position using Samtools and the quantification of the transcripts expression was done using the FeatureCounts software.
Assembly: GCA_000182965.3
Supplementary files format and content: Tab delimited .txt file containing feature counts for each sample

organism: Candida albicans SC5314

growth_protocol: Overnight cultures from isolated colonies were diluted in fresh medium to an initial OD600 0.2 and grown to exponential phase (OD600 0.8) at 30 ºC with shaking at 180 rpm in synthetic complete (SC) citrate medium pH 6.5 (SC citrate: MP CSM 0.77 g/L; yeast nitrogen base w/o amino acids and ammonium sulphate 1.7 g/L; ammonium sulphate 5.4 g/L; glucose 2%; citrate buffer: 5 mM).

extract_protocol:
RNA was isolated following cell lysis (lysis buffer: 0.1 M LiCl; 0.01M Na2EDTA; 0.01M Tris-HCl pH 7.4; 0.2% SDS, dissolved in bi-distillated sterile water) using the glass bead method and phenol:chloroform extraction. Samples were then vortexed 10 minutes at 4ºC and centrifugation at 14000 rpm to separate the organic from the aqueous fraction. The aqueous fraction was transferred to a microcentrifuge tube, ethanol 100% was added and RNA was precipitated overnight at -20ºC. RNA was collected by centrifugation at 14000 rpm for 15 minutes and the pellet was resuspended in RNAse free water and incubated 15 minutes at 65ºC to help the solubilisation of the pellet. RNA samples were treated with DNAse (TURBO DNAse Ambion) according to manufacturer’s instructions, at 37ºC for 40 minutes. RNA samples were then purified using RNeasy Mini Kit (QIAGEN).The integrity of RNA samples was evaluated by agarose gel electrophoresis.
RNA libraries were prepared for sequencing by the Genomics Facility of the Gulbenkian Institute of Science, Oeiras, Portugal, using the SMART-SEQ2 protocol.

treatment_protocol: Cells were harvested by centrifugation at 3600 g for 5 min and left untreated or treated with 5 mM FeSO4 4, 0.375 μg/mL caspofungin or both compounds for 2 hours.

tag: strain

value: 5 mM FeSO4 and 0.375 μg/mL caspofungin for 2 h


title: FeCAS_2


title: CAS_1

value: 0.375 μg/mL caspofungin for 2 h


title: Dicer1+/D1693N cells, cultured in Mesencult, passage 15

description: Library name: hdt1056_cell_p15_mesencult


title: Untreated_2

value: untreated


title: FeCAS_3


title: CAS_3


title: Dicer1+/D1693N cells, cultured in DMEM/F12 with 10% FBS, passage 15

description: Library name: hdt1056_cell_p15_dmem


title: Fe_1

value: 5 mM FeSO4 for 2 h


title: Untreated_3


title: Fe_2


title: CAS_2


title: CS_109

city: New York City

first: Yee Hoon

last: Foong

state: NY

address: NYU Grossman School of Medicine

department: Department of Medicine

institute: New York University

description:
Library name: 109
Archival FFPE tissue

data_processing:
The demultiplexed raw data is input into the 10X Space Ranger Software (version 3.1.2) using the Loupe Browser to automatically or manually align the tissue slide to the gene expression data.
Assembly: hg38
Supplementary files format and content: aligned_fiducials_CS.jpg: aligned fiducials of the tissue image
Supplementary files format and content: aligned_tissue_image_CS.jpg: aligned tissue image
Supplementary files format and content: detected_tissue_image_CS.jpg: image of the tissue and spots
Supplementary files format and content: scalefactors_json_CS.json: scale factors in json format
Supplementary files format and content: tissue_hires_image_CS.png: hi-res image of the tissue
Supplementary files format and content: tissue_lowres_image_CS.png: low-res image of the tissue
Supplementary files format and content: tissue_positions_CS.csv: list of spatial barcodes and the spot coordinates
Library strategy: Spatial Transcriptomics

source_name: Heart

extract_protocol:
Archival FFPE tissue was retrieved for patients identified by electronic health records as having a CS diagnosis. Blocks and regions of interest for 10X Genomics Visium sequencing were chosen by a pathologist based on the presence of inflammation, normal appearance or fibrosis
Spatial transcriptome sequencing libraries were  prepared according to the 10X Genomics Visium Cytassist Tissue Preparation Guide (CG000518). The libraries were sequenced on the Illumina Novaseq X-Plus system using one lane of the 10B 100 cycle flow cell. The sequencing metrics are executed as paired-end 50 bases with dual 10 base pair index reads.

value: Heart

value: No Immunosuppression


title: Untreated_1


title: CS_108-1

description:
Library name: 108-1
Archival FFPE tissue

value: Immunosuppression


title: CS_103

description:
Library name: 103
Archival FFPE tissue


title: CS_102-2

description:
Library name: 102-2
Archival FFPE tissue


title: CS_108-2

description:
Library name: 108-2
Archival FFPE tissue


title: Fe_3


title: CS_100

description:
Library name: 100
Archival FFPE tissue


title: CS_106

description:
Library name: 106
Archival FFPE tissue


title: BO112-SARC-012_surgery-1

city: Stanford

first: Anusha

last: Kalbasi

state: CA

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford

description:
Library name: BO112-SARC-012_surgery
10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x genomics cellranger-7.0.1.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz files

source_name: Tumor

extract_protocol:
Tumor samples were minced and up to 1 gram of tumor was placed in a GentleMACS C tube with RPMI, Collagenase D (1mg/mL), and DNase I (0.3mg/mL) and dissociated using a GentleMACS Octo Dissociator for 1hr at 37C. Cells were washed and filtered through a 100-micron strainer to obtain a single cell suspension. Cells were treated with RBC lysis buffer (BD) for 5 mins at room temperature. Live cells were isolated using a magnetic column based live cell isolation kit. For one tumor (RT-001), CD45+ and CD45- cells were further isolated using an antibody based magnetic isolation.
Single cell gene expression libraries were created using Chromium Next GEM Single Cell 3' (v3.1 Chemistry) (10x Genomics), Chromium Next GEM Chip G Single Cell Kit (10x Genomics), and Single Index Kit T Set A (10x Genomics) according to the manufacturer’s instructions. Briefly, cells were loaded to target 10,000 cells to form GEMs and barcode individual cells. GEMs were then cleaned cDNA and libraries were also created according to manufacturer’s instructions. Library quality was assessed using 4200 TapeStation System and D1000 ScreenTape (both from Agilent) and Qubit 2.0 (Invitrogen) for concentration and size distribution. Samples were sequenced using NextSeq500 (Illumina) with 75 PE reads.  Samples were demultiplexed with Cell Ranger mkfastq (10x Genomics).

value: Tumor

value: surgery

tag: sorted population

value: live cell tumor digest

tag: patient

value: Patient 012

value: Cohort -2 (preoperative RT, BO-112, resection)


title: RT-003_200122_tumor-1

description:
Library name: RT-003_200122_tumor
10X Genomics

value: Radiation only-003

value: pre-operative RT, resection


title: BO112-SARC-012_Baseline-1

description:
Library name: BO112-SARC-012_Baseline
10X Genomics

value: baseline


title: BO112-SARC-010_surgery-1

description:
Library name: BO112-SARC-010_surgery
10X Genomics

value: Patient 010


title: CS_107

description:
Library name: 107
Archival FFPE tissue


title: CS_104

description:
Library name: 104
Archival FFPE tissue


title: BO112-SARC-004_baseline-1

description:
Library name: BO112-SARC-004_baseline
10X Genomics

value: Patient 004


title: CS_101-2

description:
Library name: 101-2
Archival FFPE tissue


title: ISG20_rep_2, HFF/ISG20, biological replicate 2

city: Ulm

first: Thomas

last: Stamminger

address: Albert Einstein Allee 11

institute: Institute of Virology, Ulm University

description:
Library name: Sample 5
ISG.0hpi.4sU.B

data_processing:
SLAM-seq data were processed using the GRAND-SLAM pipeline (v3.0.7.a)
Reads were aligned to rRNA (U13369.1) and Mycoplasma databases with Bowtie2 (v2.3.0), followed by alignment to a combined human and HCMV genome using STAR (v2.7.10b) with the following parameters: --outFilterMismatchNmax 20, --outFilterScoreMinOverLread 0.4, --outFilterMatchNminOverLread 0.4, and --alignEndsType Extend5pOfReads12.
Aligned reads were converted, corrected, and merged using GEDI (Bam2CIT, CorrectCIT, and MergeCIT) [62]. GRAND-SLAM  (-trim5p 15 -modelall -intronic) and Grand3 (-auto -D - profile) were then used to generate read counts and new-to-total ratios (NTRs) at the gene level. Downstream analyses were performed using the grandR package (v0.2.5)
Genes were filtered with FilterGenes() and normalized with Normalize()
4sU dropout was evaluated using Plot4sUDropoutAll(), and half-lives were estimated with FitKineticsSnapshot()
Assembly: GRCh38
Supplementary files format and content: tab separated values (tsv) with read counts per gene and sample; ISG20_2.tsv was generated with GRAND-SLAM
Supplementary files format and content: tab separated values (tsv) with read counts per gene and sample; data_SLAM.tsv was generated with Grand3

source_name: connective tissue

growth_protocol: Primary human foreskin fibroblasts (HFF) cells were cultivated in 5% CO2 in minimal essential medium containing 7% fetal calf serum, 1% GlutaMAX (Gibco) and penicillin-streptomycin. After lentiviral transduction culturing was performed in the presence of 500 µg/ml geneticin (InvivoGen).

extract_protocol:
Total RNA was isolated using the Direct-zol Miniprep (Zymo Research) according to the manufacturer's instructions including an extended on-column Dnase digestion for 30 min; The 4sU alkylation reaction was performed by incubating 2 to 5 µg total RNA in 1x RNase-free PBS (pH 8) containing 50% dimethyl sulfoxide (DMSO) and 10 mM iodoacetamide (IAA) at 50oC for 15 min. The reaction was quenched with 100 mM DTT and incubated for 5 min on ice, before the RNA was purified using the RNeasy MinElute Cleanup Kit (Qiagen).
Library construction was performed by Novogene (Cambridge, UK). Including mRNA enrichment.

treatment_protocol: Cells were treated with doxycycline (500 ng/ml) for 24 h before total RNA was isolated; 4sU treatment (400 µM) was performed for 1 h prior to RNA isolation

value: connective tissue

value: primary human foreskin fibroblasts

value: ISG20 overexpression

value: 400 µM 4sU


title: ISG20_no4SU, HFF/ISG20, without 4sU treatment

description:
Library name: Sample 6
ISG.0hpi.no4sU.A

value: without 4sU treatment


title: CS_101-1

description:
Library name: 101-1
Archival FFPE tissue

value: Heart

value: No Immunosuppression


title: BO112-SARC-011_baseline-1

description:
Library name: BO112-SARC-011_baseline
10X Genomics

value: Tumor

value: Patient 011


title: RT-001_190612_CD45neg-1

description:
Library name: RT-001_190612_CD45neg
10X Genomics

value: surgery

value: live CD45 negative cell tumor digest

value: Radiation only-001


title: M5_rep2

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

country: China

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

description: Library name: Sample 4

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (https://ftp.ensembl.org/pub/release-112/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.13.5 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file: https://ftp.ensembl.org/pub/release-112/gtf/homo_sapiens/Homo_sapiens.GRCh38.112.gtf.gz.
Assembly: GRCh38
Supplementary files format and content: File include Count and FPKM values for each sample

source_name: SKIN

growth_protocol: The HaCaT cells were purchased from the Shanghai Cell Bank of Chinese Academy of Sciences (Shanghai, China). The HaCaT cell lines were cultured in DMEM medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 U/mL streptomycin and 0.03% glutamine at 37 oC in 5% CO2.

extract_protocol:
After M5 treatment for 72 hours, HaCaT cells were collected into Trizol for RNA extraction. Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The HaCaTcell lines were seeded into 6-well plates and grown overnight. The next day, when the cell plating density reached 50%, cells were treated with PBS and M5 respectively. After 72 hours, cells were harvested for RNA sequencing.

value: SKIN

value: HaCaT

value: keratinocyte

value: 25 μM DAC treatment


title: CTRL_no4SU, HFF/CTRL, without 4sU treatment

description:
Library name: Sample 3
Control.0hpi.no4sU.A

value: WT


title: RT-001_190612_CD45pos-1

description:
Library name: RT-001_190612_CD45pos
10X Genomics

value: live CD45 positive cell tumor digest

value: pre-operative RT, resection


title: M5_rep1

description: Library name: Sample 3


title: BO112-SARC-011_surgery-1

description:
Library name: BO112-SARC-011_surgery
10X Genomics

value: live cell tumor digest

value: Cohort -2 (preoperative RT, BO-112, resection)


title: PBS_rep1

description: Library name: Sample 1

value: negative control


title: P. microspora-inoculated leaves, 6 days post-inoculation, rep3

city: Gifu

first: Afdholiatus

last: Syafaah

address: Yanagido 1-1

department: UGSAS

country: Japan

institute: Gifu University

description: Library name: GT1_d6I3

data_processing:
Raw reads were pre-processed using Fastp v0.23.4. The clean data were subsequently mapped to the Hevea brasiliensis genome sequence by STAR (https://github.com/alexdobin/STAR, version 2.7.11a) with default parameter. The expression values were obtained with featureCounts v2.0.6
Data for the two conditions (inoculated vs mock) with three biological replicates
Assembly: Hevea brasiliensis
Supplementary files format and content: csv file includes gene counts value for each sample

organism: Hevea brasiliensis

source_name: leaf

growth_protocol: Rubber plants, a Pestalotiopsis-susceptible clone, GT-1, were cultivated in a greenhouse with day and night temperatures maintained at 25 °C. For the experiment, the rubber leaf was cut off in the mature stage immediately before experiments.

extract_protocol:
Leaf samples for each treatment were pooled, snap-frozen in liquid nitrogen, ground into a fine powder, and stored at -80 °C. Total RNA was isolated using the CTAB buffer method. RNA concentration, purity, and integrity were assesed using a spectrophotometer (Eppendorf BioSpectrometer Basic), electrophoresis in 1% agarose gel. At least 400 ng of total RNA was used to RNA-Seq.
The oligo dT beads was used to enrich mRNA with poly A tail. The fragments mRNA was synthesized into first strand cDNA using random primers and the second strand cDNA was synthesized with dUTP instead of dTTP. The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments.

treatment_protocol: The detached rubber leaf washed with running ion-exchanged water was inoculated by puncturing the adaxial surface with sterilized syringe needles, creating six clustered inoculation spots. For the pathogen-inoculated samples (inoculated), mycelial plugs measuring 6 mm in diameter were cut from the actively growing edge of a single-spore colony of P. microspora using a sterile cork borer. These plugs were then placed upside-down at the inoculation sites, ensuring that the mycelial surface was in direct contact with the leaf. A plug from potato sucrose agar (PSA) was used for the uninfected control samples, after carefully abrading the lower epidermis at a defined site (mock). Leaf tissue surrounding each inoculation site was collected at 2-, 4-, and 6- days post-inoculation (dpi)

value: leaf

value: GT1 clone

value: inoculated


title: RT-002_200226_tumor-1

description:
Library name: RT-002_200226_tumor
10X Genomics

value: Tumor

value: Radiation only-002


title: P. microspora-inoculated leaves, 6 days post-inoculation, rep1

description: Library name: GT1_d6I1


title: P. microspora-inoculated leaves, 6 days post-inoculation, rep2

description: Library name: GT1_d6I2


title: CS_102-1

description:
Library name: 102-1
Archival FFPE tissue

value: Heart

value: No Immunosuppression


title: P. microspora-inoculated leaves, 4 days post-inoculation, rep3

description: Library name: GT1_d4I3


title: BO112-SARC-010_baseline-1

description:
Library name: BO112-SARC-010_baseline
10X Genomics

value: baseline

value: Patient 010


title: BO112-SARC-004_surgery-1

description:
Library name: BO112-SARC-004_surgery
10X Genomics

value: surgery

value: Patient 004


title: ISG20_rep_1, HFF/ISG20, biological replicate 1

description:
Library name: Sample 4
ISG.0hpi.4sU.A

value: connective tissue

value: primary human foreskin fibroblasts

value: ISG20 overexpression

value: 400 µM 4sU


title: P. microspora-inoculated leaves, 2 days post-inoculation, rep3

description: Library name: GT1_d2I3


title: P. microspora-inoculated leaves, 2 days post-inoculation, rep2

description: Library name: GT1_d2I2


title: mock inoculation (control), 6 days post-inoculation, rep2

description: Library name: GT1_d6M2

value: mock


title: CTRL_rep_1, HFF/CTRL, biological replicate 1

description:
Library name: Sample 1
Control.0hpi.4sU.A

value: WT


title: CTRL_rep_2, HFF/CTRL, biological replicate 2

description:
Library name: Sample 2
Control.0hpi.4sU.B


title: PBS_rep2

description: Library name: Sample 2

value: SKIN

value: HaCaT

value: keratinocyte

value: negative control


title: mock inoculation (control), 4 days post-inoculation, rep3

description: Library name: GT1_d4M3

value: leaf

value: GT1 clone


title: mock inoculation (control), 2 days post-inoculation, rep3

description: Library name: GT1_d2M3


title: P. microspora-inoculated leaves, 4 days post-inoculation, rep1

description: Library name: GT1_d4I1

value: inoculated


title: DN-190 PV

city: Cleveland

first: Han

last: Sun

state: OH

address: 9500 Euclid Ave

department: QHS

institute: Cleveland Clinic

data_processing:
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.  We performed quality control procedures using the R Seurat package. We filtered spots that have unique feature counts less than 200, and spots that have greater than 10% mitochondrial counts. To normalize the feature counts and account for the variance of the tissue spatial relationship, We applied sctransform (Hafemeister and Satija, Genome Biology 2019 ), which fit regularized negative binomial models of gene expression in order to account for technical artifacts while preserving biological variance.
Supplementary files format and content: h5 files and .jpg files for spatial data
Supplementary files format and content: GRCH38

source_name: pulmonary vein

extract_protocol: Human frozen tissues were sectioned, placed on 10X Genomics Visium sldies and processed for RNAseq by spatial region.

tag: tissue system

value: pulmonary vein

tag: Sex

value: male

value: donor heart


title: mock inoculation (control), 6 days post-inoculation, rep3

description: Library name: GT1_d6M3


title: DL-6 PV

value: donor lung


title: P. microspora-inoculated leaves, 2 days post-inoculation, rep1

description: Library name: GT1_d2I1


title: mock inoculation (control), 4 days post-inoculation, rep2

description: Library name: GT1_d4M2


title: DL-8 PV biol rep 2

value: female


title: DL-1 PV bio rep 2


title: mock inoculation (control), 4 days post-inoculation, rep1

description: Library name: GT1_d4M1


title: mock inoculation (control), 2 days post-inoculation, rep2

description: Library name: GT1_d2M2


title: mock inoculation (control), 6 days post-inoculation, rep1

description: Library name: GT1_d6M1


title: P. microspora-inoculated leaves, 4 days post-inoculation, rep2

description: Library name: GT1_d4I2


title: DN-192 LA

source_name: left atrial appendage

value: left atrial appendage


title: mock inoculation (control), 2 days post-inoculation, rep1

description: Library name: GT1_d2M1


title: DL-4 PV


title: 18-16_PDX

city: Sherbrooke

first: Alexis

last: Perreault

state: Quebec

address: 3001 12e avenue Nord

institute: Université de Sherbrooke

description:
Library name: Sample 4
Column name in raw_counts_All_Samples.txt: 18-16_PDX

data_processing:
The resulting libraries underwent a total of 11 amplification cycles and were purified using 0.9X Ampure XP beads (Beckman Boulter, Mississauga, ON, Canada, cat#A63881).
Quality and size of fragments were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Mississauga, ON, Canada).
Libraries were then quantified with a Qubit fluorometer (Thermo Fisher Scientific, Mississauga, ON, Canada, cat#Q32866), pooled at equimolar concentrations, diluted to 1.8 pM, and sequenced on an Illumina NextSeq 500 (illumina, San Diego, CA, USA, cat#SY-515-1001) using the NextSeq 500/550 High Output Kit v2.5 (75 cycles) (illumina, cat#20024907) with a 2 × 43 bp paired-end run configuration. RNA preparation and sequencing were performed by the Plateforme RNomique de l’Université de Sherbrooke.
Reads were trimmed using Trimmomatic, and their quality was assessed using FastQC22. Kallisto was used to pseudo-align the reads to the transcriptome and quantify transcript abundance23.
A combined transcriptome reference was generated using gffread from Ensembl v109 annotations and genome file for the human genome (GRCh38)24. Transcript- level abundances were summarized to gene-level counts using the tximport package25.
Assembly: Human genome (GRCh38)24
Supplementary files format and content: tab-delimited text file (raw_counts_All_Samples.txt) includes raw counts for all samples

source_name: clear cell renal cell carcinoma_PDX

extract_protocol:
Tissue xenografts extracted from the CAMs were homogenized using a mortar and pestle in liquid nitrogen. Total RNA was isolated using the RNeasy® Mini Kit (Qiagen, Mississauga, ON, Canada, cat#74106) in accordance with the manufacturer’s instructions. Each RNA-seq library was generated from 500 ng of total RNA free of genomic DNA.
RNA libraries were prepared using the NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Whitby, ON, Canada, cat#E7760S), following the manufacturer's protocol in combination with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, cat#E7490). The resulting libraries underwent a total of 11 amplification cycles and were purified using 0.9X Ampure XP beads (Beckman Boulter, Mississauga, ON, Canada, cat#A63881).

value: clear cell renal cell carcinoma_PDX


title: 22-64_Tumor

description:
Library name: Sample 5
Column name in raw_counts_All_Samples.txt: 22-64_Tumor

source_name: clear cell renal cell carcinoma_Tumor

value: clear cell renal cell carcinoma_Tumor


title: DL-1 PV bio rep 1


title: 22-64_PDX

description:
Library name: Sample 6
Column name in raw_counts_All_Samples.txt: 22-64_PDX


title: DN-192 PV


title: DL-3 PV


title: DN-209-LA


title: DL-8 PV biol rep 1


title: Primary human epidermal KCs (PCS-200-011, ATCC), acne, tapinarof (TAPI), rep1

first: Young In

last: Lee

state: Seoul

address: Yonsei-ro 50-1

department: Scar Laser and Plastic Surgery Center

institute: Yonsei Cancer Hospital

description:
Library name: TAPI1
Column in raw counts and fpkm files : TAPI1

data_processing:
Adapter & Quality Trimming : quality control of raw reads and preprocessing including trimming adaptor sequence, contaminant DNA, PCR duplicates using Trimmomatic
Genome Alignment : mapping read based on GRCh38 reference genome using HISAT2
Gene Expression Quantification : assembly gene/transcript based on reference gene model using String Tie
Gene Expression Profile : extract expression value ( Read count, FPKM, TPM ) using String Tie.
Differentially expressed gene analysis : DESeq2
Assembly: GRCh38
Supplementary files format and content: Binary alignment map (BAM) files containing reads mapped to the human reference genome
Supplementary files format and content: A cvs format file containing gene symbols - raw readcount values for each sample and a csv format file containg gene symbol - fpkm values for each samples.

source_name: Human skin (epidermis)

growth_protocol: Primary human epidermal KCs (PCS-200-011, ATCC) were maintained in KBM Gold medium (Lonza) supplemented with the KGM Gold SingleQuot kit (Lonza). C.acnes strian ATCC 6919 (ATCC, Manassas, VA,USA) - Reinforced Clostridial Medium under unaerobic conditions at 37°C  for 72 hours.Cell viability of KC was analyzed using the CCK-8 reagent (Dojindo, Japan). Cells were seeded into 96-well plates at 5 × 10⁴ cells per well and allowed to stabilize. After stabilization, C. acnes was added at a final concentration of 1 × 10⁷ CFU to induce acne-like inflammatory activation. For testing, cultures were treated with increasing concentrations

extract_protocol:
Total RNA was extracted using RNAiso Plus reagent (Takara Bio, Shiga, Japan)
total RNA was extracted from KCs treated under the same sequential protocol described above (C. acnes exposure for 24 h → medium replacement → metabolite treatment for 24 h). RNA integrity was confirmed before library preparation using a TruSeq RNA Library Prep Kit (Illumina, San Diego, CA, USA). Sequencing was conducted in paired-end 100 bp mode on the NextSeq 550 platform (Macrogen, Seoul, Korea).

treatment_protocol: C. acnes exposure for 24 h → medium replacement → metabolite treatment for 24 : ILA (0.25, 0.5, 1, 2, and 4 mM), IAA (0.25, 0.5, 1, 2, and 4 mM), IPA 282 (0.25, 0.5, 1, 2, and 4 mM), and TAPI (1.25, 2.5, 5, 10, and 20 μM)

value: Human skin (epidermis)

value: Primary human epidermal KCs


title: Primary human epidermal KCs (PCS-200-011, ATCC), acne, indole-3-propionic acid (IPA), rep3

description:
Library name: IPA3
Column in raw counts and fpkm files : IPA3


title: Primary human epidermal KCs (PCS-200-011, ATCC), acne, indole-3-lactic acid (ILA), rep2

description:
Library name: ILA2
Column in raw counts and fpkm files : ILA2


title: Primary human epidermal KCs (PCS-200-011, ATCC), acne, tapinarof (TAPI), rep2

description:
Library name: TAPI2
Column in raw counts and fpkm files : TAPI2


title: 18-08_PDX

description:
Library name: Sample 2
Column name in raw_counts_All_Samples.txt: 18-08_PDX


title: DN-209-PV


title: 18-16_Tumor

description:
Library name: Sample 3
Column name in raw_counts_All_Samples.txt: 18-16_Tumor


title: Primary human epidermal KCs (PCS-200-011, ATCC), acne, indole-3-propionic acid (IPA), rep1

description:
Library name: IPA1
Column in raw counts and fpkm files : IPA1


title: 18-08_Tumor

description:
Library name: Sample 1
Column name in raw_counts_All_Samples.txt: 18-08_Tumor

source_name: clear cell renal cell carcinoma_tumor

value: clear cell renal cell carcinoma_tumor


title: Primary human epidermal KCs (PCS-200-011, ATCC), acne, indole-3-lactic acid (ILA), rep1

description:
Library name: ILA1
Column in raw counts and fpkm files : ILA1


title: Primary human epidermal KCs (PCS-200-011, ATCC), control, rep 2

description:
Library name: CON2
Column in raw counts and fpkm files : CON2


title: Primary human epidermal KCs (PCS-200-011, ATCC), control, rep 1

description:
Library name: CON1
Column in raw counts and fpkm files : CON1


title: Primary human epidermal KCs (PCS-200-011, ATCC), acne, rep 3

description:
Library name: ACNE3
Column in raw counts and fpkm files : ACNE3


title: Primary human epidermal KCs (PCS-200-011, ATCC), acne, tapinarof (TAPI), rep3

description:
Library name: TAPI3
Column in raw counts and fpkm files : TAPI3


title: Primary human epidermal KCs (PCS-200-011, ATCC), acne, indole-3-acrylic acid (IAA), rep2

description:
Library name: IAA2
Column in raw counts and fpkm files : IAA2


title: MC38-ctrl

city: Houston

first: Ling

last: Yin

state: TX

address: 1515 Holcombe Boulevard

institute: MD Anderson Cancer Center

description:
Library name: sample4
Column name in raw_reads_All_sample.txt: MC38_T0

library_source: genomic

data_processing:
Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK)(31) and drug-Z(32) analysis were conducted to calculate the difference in gRNA enrichment between top 30% and bottom 30%.
Assembly: GRCm38
Supplementary files format and content: Processed data files are provided as tab-delimited text files containing sgRNA-level read counts for individual samples. Each entry includes the sgRNA identifier, the corresponding target gene name, and read counts for each sample using MAGeCK analysis.
Library strategy: CRISPR Screen

molecule: genomic DNA

extract_protocol:
Ccells were resuspended in PBS for flow cytometry selection (the top 30% with the highest signals and bottom 30% with the lowest signals cell populations, respectively). Cells were collected for genomic DNA extraction (Qiagen Kit). PCR reaction was performed to amplify gRNAs inserts via primers harboring Illumina TruSeq adapters with i5 and i7 barcodes. The resulting libraries were sequenced using an Illumina HiSeq 2500 system.
The Mouse Toronto KnockOut (mTKO) CRISPR Library contains 94,528 gRNAs targeting 19,463 protein-coding genes (4 gRNAs/ gene) and 418 EGFP-, LacZ-, and luciferase-targeted control gRNAs.

value: mouse cancer cell


title: MC38-low-CD47

description:
Library name: sample6
Column name in raw_reads_All_sample.txt: MC38_L


title: B16F10A-low-CD47

description:
Library name: sample3
Column name in raw_reads_All_sample.txt: B16_L


title: Primary human epidermal KCs (PCS-200-011, ATCC), acne, indole-3-lactic acid (ILA), rep3

description:
Library name: ILA3
Column in raw counts and fpkm files : ILA3


title: Primary human epidermal KCs (PCS-200-011, ATCC), acne, indole-3-propionic acid (IPA), rep2

description:
Library name: IPA2
Column in raw counts and fpkm files : IPA2


title: Primary human epidermal KCs (PCS-200-011, ATCC), acne, indole-3-acrylic acid (IAA), rep3

description:
Library name: IAA3
Column in raw counts and fpkm files : IAA3


title: mESC CTRL Rep 1

city: Irvine

first: Ivan

last: Marazzi

address: 839 Health Sciences Road

department: Department of Biological Chemistry

institute: University of California

description: Library name: CTRL-Mesc-2I-L-1

data_processing:
Quality- and adapter-trimmed raw sequences were aligned to the GRCm38 primary genome and deduplicated using bismark.
CpG methylation data extracted with the bismark_methylation_extractor function were modified to construct a bsseq object.
Only CpG sites covered at least 6 times in all four samples (two clones per genotype) (n= 19,027,274) were considered for the downstream analyses. There were 10.7x106 CpG sites in gene regions and 6.5x106 sites in the TE regions meeting this condition.
Assembly: GRCm38 primary genome
Supplementary files format and content: bigwig

source_name: mESC

extract_protocol:
Genomic DNA was isolated from two WT mESCs clones and two cKO clones using a Quick DNA kit (Zymo Research).
Bisulfite conversion and generation of sequencing libraries were performed by GENEWIZ (Azenta Life Sciences).

value: mESC

value: CTRL


title: Primary human epidermal KCs (PCS-200-011, ATCC), acne, indole-3-acrylic acid (IAA), rep1

description:
Library name: IAA1
Column in raw counts and fpkm files : IAA1


title: mESC CTRL Rep 2

description: Library name: CTRL-Mesc-2I-L-2


title: Primary human epidermal KCs (PCS-200-011, ATCC), control, rep 3

description:
Library name: CON3
Column in raw counts and fpkm files : CON3


title: EpiLC CTRL Rep 1

description: Library name: CTRL-EpiLC-1

source_name: EpiLC

value: EpiLC


title: Primary human epidermal KCs (PCS-200-011, ATCC), acne, rep 2

description:
Library name: ACNE2
Column in raw counts and fpkm files : ACNE2


title: EMT6-low-CD47

description:
Library name: sample9
Column name in raw_reads_All_sample.txt: EMT6_L


title: EpiLC Exosc3 cKO Rep 1

description: Library name: cKO-EpiLC-1

value: Exosc3 cKO


title: 507_SEB_only_D3

city: Redwood City

first: Amy

last: Jhatakia

address: 700 Bay Road

institute: Bristol Myers Squibb

description:
Library name: Sample 104
SEB_only

data_processing:
The TCRseq data were processed using Adaptive Biotechnology's immunoSEQ pipeline. Raw FASTQ files were not made available to customers. The TCR arrangement files included here represent the complete dataset.
For data analysis, GLIPH2 was utilized to analyze the local clustering of TCR sequences and to investigate the impact of SEB-specific TCRB motifs. All the TCR sequences from pretreatment samples were used as the reference panel, and sequences from day 3 and day 6 samples were utilized as the input panel. Additionally, all singleton and doubletons (TCR sequences with a count of one and two, respectively) were removed from both the reference and input panels. TurboGLIPH, an R implementation of GLIPH2, was configured and run with the following (default) parameters: sim_depth = 100, min_seq_length = 7, cluster_min_size = 2, and motif_length = (2, 3, 4). After clustering, the resulting cluster list was filtered so that only clusters with clones originating from at least two mice and a Fisher score >0.05 were kept.
Assembly: mm10
Supplementary files format and content: TSV file contains tab-delimited table mapping each TCR-seq sample
Library strategy: TCR-Seq

source_name: Whole Blood

extract_protocol:
genomic DNA per sample was extracted in 50 uL TE buffer. Sequencing libraries are generated following the instruction for Survey resolution of the immunoSEQ kit for mouse TCRB assay (Adaptive Biotechnologies).
OTHER

treatment_protocol: Mice (human CTLA-4 knock-in, C57BL/6NJ) received treatment of either anti-CTLA-4 (IPI), anti-CTLA-4 NF, anti-CTLA-4 Fc inert, isotype (KLH-NF) or no treatment with superantigen (SEB). Whole blood samples were collected (at pretreatment, day 3, and day 6) in Paxgene tubes

value: Whole Blood

value: human CTLA-4 KI, C57BL/6NJ

tag: time


title: EMT6-ctrl

description:
Library name: sample7
Column name in raw_reads_All_sample.txt: EMT6_T0


title: EMT6-high-CD47

description:
Library name: sample8
Column name in raw_reads_All_sample.txt: EMT6_H


title: B16F10A-high-CD47

description:
Library name: sample2
Column name in raw_reads_All_sample.txt: B16_H


title: MC38-high-CD47

description:
Library name: sample5
Column name in raw_reads_All_sample.txt: MC38_H


title: 202_SEB+IPI_D3

description:
Library name: Sample 101
SEB+IPI

value: SEB+IPI


title: 206_SEB+IPI_D3

description:
Library name: Sample 100
SEB+IPI


title: B10F10A-ctrl

description:
Library name: sample1
Column name in raw_reads_All_sample.txt: B16_T0


title: 304_SEB+anti-CTLA4_NF_D6

description:
Library name: Sample 98
SEB+anti-CTLA4_NF


title: EpiLC Exosc3 cKO Rep 2

description: Library name: cKO-EpiLC-2


title: 103_pre-tx

description:
Library name: Sample 96
pre-tx

value: pre-tx


title: Primary human epidermal KCs (PCS-200-011, ATCC), acne, rep 1

description:
Library name: ACNE1
Column in raw counts and fpkm files : ACNE1


title: EpiLC CTRL Rep 2

description: Library name: CTRL-EpiLC-2


title: mESC Exosc3 cKO Rep 2

description: Library name: cKO-Mesc-2I-L-2


title: 103_SEB+KLH-NF_D3

description:
Library name: Sample 93
SEB+KLH-NF

value: SEB+KLH-NF


title: 301_pre-tx

description:
Library name: Sample 94
pre-tx


title: 306_pre-tx

description:
Library name: Sample 92
pre-tx


title: 305_SEB+anti-CTLA4_NF_D3

description:
Library name: Sample 105
SEB+anti-CTLA4_NF


title: mESC Exosc3 cKO Rep 1

description: Library name: cKO-Mesc-2I-L-1


title: 303_SEB+anti-CTLA4_NF_D6

description:
Library name: Sample 91
SEB+anti-CTLA4_NF


title: 406_SEB+Fc_inert_D3

description:
Library name: Sample 90
SEB+Fc inert

value: SEB+Fc inert


title: 205_pre-tx

description:
Library name: Sample 87
pre-tx


title: 401_pre-tx

description:
Library name: Sample 84
pre-tx


title: 107_SEB+KLH-NF_D6

description:
Library name: Sample 102
SEB+KLH-NF


title: 404_SEB+Fc_inert_D6

description:
Library name: Sample 95
SEB+Fc inert


title: 403_SEB+Fc_inert_D6

description:
Library name: Sample 86
SEB+Fc inert


title: 404_pre-tx

description:
Library name: Sample 82
pre-tx


title: 502_SEB_only_D3

description:
Library name: Sample 103
SEB_only


title: 106_pre-tx

description:
Library name: Sample 75
pre-tx


title: 401_SEB+Fc_inert_D6

description:
Library name: Sample 99
SEB+Fc inert


title: 104_pre-tx

description:
Library name: Sample 72
pre-tx


title: 101_SEB+KLH-NF_D3

description:
Library name: Sample 89
SEB+KLH-NF


title: Pinus, TP, biol rep3

city: Chengdu

first: Xiaoping

last: Zhang

state: Sichuan

address: Huimin Road, Chengdu, 611130, China

department: College of Resources

institute: Sichuan Agricultural University

description: Library name: P_T4_TP3

data_processing:
Processed with Trimmomatic software to perform the quality control
Clean reads were assembled into expressed sequence tag clusters (contigs) and then de novo assembled into transcript by Trinity (version 2.4) using paired end method
CD-HIT software was used to cluster and remove redundancy to obtain a final set of unigenes.
Assembly: de novo assembled transcripts
Supplementary files format and content: xls files including FPKM values for samples of C. illinoinensis
Supplementary files format and content: xls files including FPKM values for samples of P. armandii

organism: Pinus armandii

source_name: Leaf

extract_protocol:
Total RNA  was extracted using TRIzol reagent according to the manufacturer’s protocol.
The libraries were generated using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (NR604-01, Vazyme, China) according to the manufacturer’s instructions.

value: Leaf

value: 30 months after inoculation

value: T. panzhihuanense inoculation


title: Pinus, TP, biol rep4

description: Library name: P_T4_TP4


title: 505_pre-tx

description:
Library name: Sample 79
pre-tx


title: 106_SEB+KLH-NF_D6

description:
Library name: Sample 83
SEB+KLH-NF


title: 201_SEB+IPI_D6

description:
Library name: Sample 74
SEB+IPI


title: 203_SEB+IPI_D6

description:
Library name: Sample 76
SEB+IPI


title: 505_SEB_only_D6

description:
Library name: Sample 97
SEB_only


title: 102_SEB+KLH-NF_D3

description:
Library name: Sample 80
SEB+KLH-NF


title: 304_pre-tx

description:
Library name: Sample 88
pre-tx


title: 405_SEB+Fc_inert_D3

description:
Library name: Sample 73
SEB+Fc inert


title: 504_SEB_only_D3

description:
Library name: Sample 85
SEB_only


title: 306_SEB+anti-CTLA4_NF_D3

description:
Library name: Sample 78
SEB+anti-CTLA4_NF


title: 501_SEB_only_D6

description:
Library name: Sample 81
SEB_only


title: 503_SEB_only_D6

description:
Library name: Sample 77
SEB_only


title: Pinus, Ti, biol rep3

description: Library name: P_T4_Ti3

value: T. indicum inoculation


title: Pinus, Ti, biol rep4

description: Library name: P_T4_Ti4


title: 504_SEB_only_D6

description:
Library name: Sample 69
SEB_only


title: Pinus, TP, biol rep2

description: Library name: P_T4_TP2


title: Pinus, TP, biol rep1

description: Library name: P_T4_TP1


title: 203_pre-tx

description:
Library name: Sample 71
pre-tx


title: 205_SEB+IPI_D3

description:
Library name: Sample 67
SEB+IPI


title: 207_SEB+IPI_D6

description:
Library name: Sample 70
SEB+IPI


title: Pinus, Ti, biol rep2

description: Library name: P_T4_Ti2


title: 201_SEB+IPI_D3

description:
Library name: Sample 66
SEB+IPI


title: Pinus, Ti, biol rep1

description: Library name: P_T4_Ti1


title: 204_SEB+IPI_D6

description:
Library name: Sample 68
SEB+IPI


title: 101_SEB+KLH-NF_D6

description:
Library name: Sample 65
SEB+KLH-NF


title: Pinus, CK, biol rep2

description: Library name: P_T4_CK2

value: control


title: 404_SEB+Fc_inert_D3

description:
Library name: Sample 62
SEB+Fc inert


title: 503_pre-tx

description:
Library name: Sample 64
pre-tx


title: Pinus, CK, biol rep4

description: Library name: P_T4_CK4


title: Pinus, CK, biol rep3

description: Library name: P_T4_CK3


title: Unmated,EcR RNAi, Myo1A,Replicate 2

description: Library name: 24047X14

source_name: gut

value: gut

value: Myo1A-Gal4/ EcR RNAi


title: 306_SEB+anti-CTLA4_NF_D6

description:
Library name: Sample 63
SEB+anti-CTLA4_NF


title: Unmated,EcR RNAi, Myo1A,Replicate 1

description: Library name: 24047X13


title: Unmated,EcR RNAi, Myo1A,Replicate 3

description: Library name: 24047X15


title: 406_SEB+Fc_inert_D6

description:
Library name: Sample 60
SEB+Fc inert


title: Pinus, CK, biol rep1

description: Library name: P_T4_CK1


title: 102_SEB+KLH-NF_D6

description:
Library name: Sample 56
SEB+KLH-NF


title: Mated, EcR RNAi, Myo1A, Replicate 3

description: Library name: 24047X11


title: Mated, EcR RNAi, Myo1A, Replicate 1

description: Library name: 24047X9


title: Unmated,EcR RNAi, Myo1A,Replicate 4

description: Library name: 24047X16


title: 402_SEB+Fc_inert_D6

description:
Library name: Sample 61
SEB+Fc inert


title: Unmated,Control, Myo1A,Replicate 4

description: Library name: 24047X8


title: Mated, EcR RNAi, Myo1A, Replicate 4

description: Library name: 24047X12


title: 502_SEB_only_D6

description:
Library name: Sample 57
SEB_only


title: Unmated,Control, Myo1A,Replicate 2

description: Library name: 24047X6


title: 305_pre-tx

description:
Library name: Sample 50
pre-tx


title: 307_pre-tx

description:
Library name: Sample 58
pre-tx


title: 407_SEB+Fc_inert_D3

description:
Library name: Sample 55
SEB+Fc inert


title: Mated, EcR RNAi, Myo1A, Replicate 2

description: Library name: 24047X10


title: Unmated,EcR RNAi, Actin,Replicate 3

description: Library name: 22551X15

value: Actin-Gal4/ EcR RNAi


title: Unmated,EcR RNAi, Actin,Replicate 2

description: Library name: 22551X14


title: 507_SEB_only_D6

description:
Library name: Sample 45
SEB_only


title: Mated, EcR RNAi, Actin, Replicate 4

description: Library name: 22551X12


title: 203_SEB+IPI_D3

description:
Library name: Sample 54
SEB+IPI


title: 305_SEB+anti-CTLA4_NF_D6

description:
Library name: Sample 42
SEB+anti-CTLA4_NF


title: 205_SEB+IPI_D6

description:
Library name: Sample 53
SEB+IPI


title: 506_SEB_only_D3

description:
Library name: Sample 52
SEB_only


title: 301_SEB+anti-CTLA4_NF_D3

description:
Library name: Sample 51
SEB+anti-CTLA4_NF


title: Unmated,Control, Myo1A,Replicate 1

description: Library name: 24047X5


title: 207_pre-tx

description:
Library name: Sample 59
pre-tx


title: Mated,Control, Myo1A, Replicate 4

description: Library name: 24047X4


title: 505_SEB_only_D3

description:
Library name: Sample 49
SEB_only


title: 204_pre-tx

description:
Library name: Sample 41
pre-tx


title: Mated,Control, Myo1A, Replicate 1

description: Library name: 24047X1


title: Mated,Control, Myo1A, Replicate 2

description: Library name: 24047X2


title: Mated, EcR RNAi, Actin, Replicate 1

description: Library name: 22551X9


title: 407_SEB+Fc_inert_D6

description:
Library name: Sample 48
SEB+Fc inert


title: 504_pre-tx

description:
Library name: Sample 39
pre-tx


title: 101_pre-tx

description:
Library name: Sample 47
pre-tx


title: Unmated,Control, Actin,Replicate 3

description: Library name: 22551X7


title: Unmated,EcR RNAi, Actin,Replicate 4

description: Library name: 22551X16


title: 104_SEB+KLH-NF_D6

description:
Library name: Sample 38
SEB+KLH-NF


title: Unmated,Control, Actin,Replicate 2

description: Library name: 22551X6


title: 107_pre-tx

description:
Library name: Sample 46
pre-tx


title: 303_pre-tx

description:
Library name: Sample 43
pre-tx


title: 304_SEB+anti-CTLA4_NF_D3

description:
Library name: Sample 36
SEB+anti-CTLA4_NF


title: 201_pre-tx

description:
Library name: Sample 44
pre-tx


title: Unmated,Control, Myo1A,Replicate 3

description: Library name: 24047X7


title: 206_SEB+IPI_D6

description:
Library name: Sample 35
SEB+IPI


title: Unmated,EcR RNAi, Actin,Replicate 1

description: Library name: 22551X13


title: Mated,Control, Actin, Replicate 4

description: Library name: 22551X4


title: Mated,Control, Actin, Replicate 3

description: Library name: 22551X3


title: Mated, EcR RNAi, Actin, Replicate 3

description: Library name: 22551X11


title: 206_pre-tx

description:
Library name: Sample 40
pre-tx


title: Mated, EcR RNAi, Actin, Replicate 2

description: Library name: 22551X10


title: Unmated,Control, Actin,Replicate 4

description: Library name: 22551X8


title: 405_pre-tx

description:
Library name: Sample 32
pre-tx


title: Mated,Control, Actin, Replicate 1

description: Library name: 22551X1


title: Mated,Control, Actin, Replicate 2

description: Library name: 22551X2


title: 102_pre-tx

description:
Library name: Sample 29
pre-tx


title: Unmated,Control, Actin,Replicate 1

description: Library name: 22551X5


title: 202_SEB+IPI_D6

description:
Library name: Sample 34
SEB+IPI


title: 307_SEB+anti-CTLA4_NF_D3

description:
Library name: Sample 33
SEB+anti-CTLA4_NF


title: 501_SEB_only_D3

description:
Library name: Sample 31
SEB_only


title: Donor 3 SA-ßGal-low,  siRUNX2--3 unstim

city: Piscataway

first: Ricardo

middle: Iván

last: Martínez Zamudio

state: New Jersey

address: 675 Hoes Lane West

department: Pharmacology

institute: Rutgers Biomedical and Health Sciences | Rutgers-Robert Wood Johnson Medical School

description: Library name: D3 low RUNX2-3 unstim

data_processing:
In-house pipeline
Adaptors were trimmed using cutadapt version 5.1.
Trimmed reads were mapped to GRCh38.d1.v1 using bowtie2 with the local option.
Alignments were analyzed for differential expression using DESeq2 and clustered using WGCNA.
Assembly: GRCh38.d1.v1
Supplementary files format and content: We include a tab-delimited text file that contains the RLD-transformed, normalized and debatched values of the compasiron 'SA-ßgal-low versus SA-ßgal-high' across all siRNA treatments for unstimulated cells. The DEGs in this file were matched to their nearest TF (JUN, KLF5, RUNX2) footprint, which is reported on the paper. The file contains the gene expression modules identified by WGCNA with their RLD values and annotated. We include a second file that contains the RLD transform values for the stimulation specific DEGs across all siRNA treatments in SA-ßGal-low and SA-ßGal-high CD8+ T cells.

source_name: Peripheral blood

growth_protocol: Cells were isolated from peripheral blood and immediately stained for SA-ßGal and isolated via FACS.

extract_protocol:
Macherey-Nagel RNA XS plus columns  from ~100,000 cells.
SMART-seq V4 as per the manufacturer's instructions.

treatment_protocol: Cells were electroporated with non-targeting and TF-targeting (2 siRNAs each JUN, KLF5 and RUNX2), left to rest for 24h and were subsequently collected or stimulated with anti-CD3/anti-CD28 antibodies for a further 16h and then collected. RNA was isolated for library construction using the SMART-seq-mRNA kit from Takara.

value: Peripheral blood

value: CD8+ T cell

value: untreated


title: 403_pre-tx

description:
Library name: Sample 26
pre-tx

value: Whole Blood


title: 303_SEB+anti-CTLA4_NF_D3

description:
Library name: Sample 30
SEB+anti-CTLA4_NF

value: human CTLA-4 KI, C57BL/6NJ


title: Donor 3 SA-ßGal-low,  scramble unstim

description: Library name: D3 low scramble unstim


title: 107_SEB+KLH-NF_D3

description:
Library name: Sample 28
SEB+KLH-NF


title: Donor 3 SA-ßGal-low,  siRUNX2--4 stim

description: Library name: D3 low RUNX2-4 stim

value: anti-CD3/anti-CD28, 16h


title: 307_SEB+anti-CTLA4_NF_D6

description:
Library name: Sample 25
SEB+anti-CTLA4_NF


title: 402_SEB+Fc_inert_D3

description:
Library name: Sample 27
SEB+Fc inert


title: Donor 3 SA-ßGal-low,  siRUNX2--4 unstim

description: Library name: D3 low RUNX2-4 unstim


title: 105_SEB+KLH-NF_D6

description:
Library name: Sample 24
SEB+KLH-NF


title: Donor 3 SA-ßGal-low,  siRUNX2--3 stim

description: Library name: D3 low RUNX2-3 stim


title: Donor 3 SA-ßGal-low,  siKLF5--3 stim

description: Library name: D3 low KLF5-3 stim


title: Donor 3 SA-ßGal-low,  scramble stim

description: Library name: D3 low scramble stim


title: Donor 3 SA-ßGal-low,  siKLF5--1 stim

description: Library name: D3 low KLF5-1 stim


title: Donor 3 SA-ßGal-low,  siKLF5--3 unstim

description: Library name: D3 low KLF5-3 unstim


title: 103_SEB+KLH-NF_D6

description:
Library name: Sample 20
SEB+KLH-NF


title: 302_pre-tx

description:
Library name: Sample 23
pre-tx

value: pre-tx


title: 302_SEB+anti-CTLA4_NF_D3

description:
Library name: Sample 37
SEB+anti-CTLA4_NF


title: 105_SEB+KLH-NF_D3

description:
Library name: Sample 21
SEB+KLH-NF

value: SEB+KLH-NF


title: Donor 3 SA-ßGal-low,  siJUN--2 stim

description: Library name: D3 low AP1-2 stim


title: 507_pre-tx

description:
Library name: Sample 18
pre-tx


title: 301_SEB+anti-CTLA4_NF_D6

description:
Library name: Sample 22
SEB+anti-CTLA4_NF


title: Donor 3 SA-ßGal-low,  siJUN--1 stim

description: Library name: D3 low AP1-1 stim


title: 501_pre-tx

description:
Library name: Sample 16
pre-tx


title: 105_pre-tx

description:
Library name: Sample 17
pre-tx


title: 202_pre-tx

description:
Library name: Sample 15
pre-tx


title: Donor 3 SA-ßGal-low,  siKLF5--1 unstim

description: Library name: D3 low KLF5-1 unstim


title: Donor 3 SA-ßGal-high,  scramble stim

description: Library name: D3 high scramble stim


title: Donor 3 SA-ßGal-low,  siJUN--1 unstim

description: Library name: D3 low AP1-1 unstim


title: Donor 3 SA-ßGal-high,  scramble unstim

description: Library name: D3 high scramble unstim


title: 406_pre-tx

description:
Library name: Sample 12
pre-tx


title: 407_pre-tx

description:
Library name: Sample 11
pre-tx


title: 401_SEB+Fc_inert_D3

description:
Library name: Sample 9
SEB+Fc inert

value: SEB+Fc inert


title: 506_SEB_only_D6

description:
Library name: Sample 8
SEB_only


title: Donor 3 SA-ßGal-high,  siKLF5--3 stim

description: Library name: D3 high KLF5-3 stim


title: Donor 3 SA-ßGal-high,  siRUNX2--4 stim

description: Library name: D3 high RUNX2-4 stim


title: Donor 3 SA-ßGal-high,  siKLF5--3 unstim

description: Library name: D3 high KLF5-3 unstim


title: Donor 3 SA-ßGal-high,  siRUNX2--4 unstim

description: Library name: D3 high RUNX2-4 unstim


title: 106_SEB+KLH-NF_D3

description:
Library name: Sample 14
SEB+KLH-NF


title: 402_pre-tx

description:
Library name: Sample 6
pre-tx


title: 104_SEB+KLH-NF_D3

description:
Library name: Sample 10
SEB+KLH-NF


title: Donor 3 SA-ßGal-high,  siRUNX2--3 stim

description: Library name: D3 high RUNX2-3 stim


title: 502_pre-tx

description:
Library name: Sample 13
pre-tx


title: Donor 3 SA-ßGal-high,  siJUN--1 unstim

description: Library name: D3 high AP1-1 unstim


title: Donor 3 SA-ßGal-high,  siRUNX2--3 unstim

description: Library name: D3 high RUNX2-3 unstim


title: Donor 3 SA-ßGal-high,  siKLF5--1 stim

description: Library name: D3 high KLF5-1 stim


title: Donor 3 SA-ßGal-high,  siJUN--2 unstim

description: Library name: D3 high AP1-2 unstim


title: 405_SEB+Fc_inert_D6

description:
Library name: Sample 3
SEB+Fc inert


title: 506_pre-tx

description:
Library name: Sample 5
pre-tx


title: 207_SEB+IPI_D3

description:
Library name: Sample 2
SEB+IPI

value: SEB+IPI


title: 503_SEB_only_D3

description:
Library name: Sample 19
SEB_only


title: Donor 3 SA-ßGal-high,  siJUN--1 stim

description: Library name: D3 high AP1-1 stim


title: 403_SEB+Fc_inert_D3

description:
Library name: Sample 1
SEB+Fc inert


title: Donor 2 SA-ßGal-low,  scramble stim

description: Library name: D2 low scramble stim


title: 302_SEB+anti-CTLA4_NF_D6

description:
Library name: Sample 4
SEB+anti-CTLA4_NF


title: Donor 2 SA-ßGal-low,  siRUNX2--4 stim

description: Library name: D2 low RUNX2-4 stim


title: 204_SEB+IPI_D3

description:
Library name: Sample 7
SEB+IPI


title: Donor 3 SA-ßGal-low,  siJUN--2 unstim

description: Library name: D3 low AP1-2 unstim


title: Donor 2 SA-ßGal-low,  siRUNX2--3 unstim

description: Library name: D2 low RUNX2-3 unstim


title: Donor 2 SA-ßGal-low,  siRUNX2--3 stim

description: Library name: D2 low RUNX2-3 stim


title: Donor 2 SA-ßGal-low,  siRUNX2--4 unstim

description: Library name: D2 low RUNX2-4 unstim


title: Donor 2 SA-ßGal-low,  siKLF5--1 unstim

description: Library name: D2 low KLF5-1 unstim


title: Donor 3 SA-ßGal-high,  siJUN--2 stim

description: Library name: D3 high AP1-2 stim


title: MV76_male_56day_VC_0

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada

description:
Library name: MV76_Male_VC_DMSO_Sept2024
Templated oligo sequencing (TempO-seq)

data_processing:
BCL files were converted to FASTQ format and demultiplexed using bcl2fastq (v2.20). Processing and quality control of the FASTQ files, differential expression analysis, and exploratory statistical analyses were performed using the Omics Data Analysis Frameworks for Regulatory application (R-ODAF) Health Canada pipeline (https://github.com/R-ODAF/R-ODAF_Health_Canada; accessed April 2025). The pipeline uses snakemake (v8.0) (Mölder et al., 2021) and scripts in R (v.4.3.2) to manage workflows. Fasta and GTF-formatted reference files were produced using the manifest provided by Biospyder. First, fastp (v0.23.2) was used for trimming, followed by STAR (v2.7.8a) (Dobin et al., 2013) to align raw reads to the reference sequence. Feature counts were extracted from the aligned reads (BAM files) using the qCount function of the QuasR R package (v1.30.0) (Gaidatzis et al., 2015) according to the features specified in a GTF file. A samples-by-probes count matrix was generated. Across experimental samples, the median number of mapped reads was 1,148,263.
Assembly: mm39
Supplementary files format and content: Tab-delimited table of absolute probe counts per sample.

source_name: liver

growth_protocol: All animal work has been approved by the Health Canada Animal Care Committee (HC-ACC) protocol: 2023-010. 6 to 9-week-old male and female C57BL/6-Elite (SOPF) mice (Charles River, cat#475C57BL/6-E) were acclimatized for two weeks and tail tattooed with the Somark Labstamp (green ultraviolet ink; Somark, cat#01-99032). Throughout the study, mice were housed individually (male) or in pairs (female) in the Tecniplast IVC cage system under negative pressure with a 12:12 light cycle. Mice were fed irradiated Teklad global 14% protein chow (Inotiv, cat#2914) ad libitum and provided autoclaved reverse osmosis water in Tecniplast bottles.

extract_protocol:
Snap-frozen livers were cut on dry ice using a cooled scalpel. 12-25 mg of livers were homogenized in PowerBead tubes (Qiagen, cat#13114-50) containing 2.8mm ceramic beads and 600 μL of RLT buffer (from the RNeasy Mini Kit; Qiagen, cat#74104) supplemented with β-mercaptoethanol (10 μL/mL of RLT; Sigma-Aldrich, cat#M3148-25ML). Homogenization was carried out in a Qiagen PowerLyzer 24 Homogenizer (two 45-second cycles at 3500 rpm with a 30-second pause in between). Following homogenization, the lysate was transferred to a new tube and centrifuged at 13,000xg for 2 minutes. The supernatant (lysate) was transferred to a new tube, and ribonucleic acid (RNA) was extracted with Qiagen RNeasy Mini Kit (Qiagen, cat#74104) according to the manufacturer’s instructions.
TempO-Seq mouse S1500+ surrogate gene panel (version 1.2; BioSpyder Technologies Inc.) was used to generate sequencing libraries to measure gene expression in total RNA purified from mouse liver tissues. Each RNA sample was first diluted to 100 ng/mL in water, then mixed with an equal volume of 2× TempO-Seq Lysis buffer, resulting in a final RNA concentration of 50 ng/µL. Two microliters of this diluted mixture (approximately 100 ng of RNA) were used as input for TempO-Seq library building. As per the manufacturer’s protocol, RNA was first hybridized with the detection oligos (DOs). Unbound DOs were digested with a nuclease, and the remaining bound DOs were ligated. These ligated oligos were then amplified by PCR using primers with sequencing tags to create the sequencing libraries. The resulting libraries were pooled together and quantified using qPCR with the KAPA SYBR FAST Universal kit, compatible with Illumina platforms (Roche, Wilmington, MA). The pooled libraries were sequenced using a 75-cycle flow cell on an Illumina NextSeq 500.

treatment_protocol: At 8 to 11 weeks of age, mice were exposed to 1.5 mg/kg/day of perfluorooctanoic acid (PFOA) or perfluorooctanesulfonic acid (PFOS) for 28 days or 0.166, 0.5, 1.0, or 1.5 mg/kg/day of PFOA or PFOS for 56 days by daily oral gavage (gavage volume: 7.5 mL/Kg). Gavage solutions were prepared as follows. In brief, Tween 20 (Sigma-Aldrich, cat#P1379) was diluted in optima water (Fisher, cat#W64) to obtain a 0.5% (v/v) Tween 20 solution. PFOA (Sigma-Aldrich, cat#171468) or PFOS (Sigma-Aldrich, cat#77283) was added to 0.5% Tween 20 to achieve a 1.5 mg/kg/day gavage solution. The 1.0, 0.5, and 0.166 mg/kg/day gavage solutions were obtained through serial dilution. The vehicle groups were gavaged with 0.5% Tween 20 in optima water (Fisher, cat#W64) while the naïve groups were not gavaged. Body weight was collected daily, and water consumption was measured weekly. Water consumption was calculated by multiplying the weight difference between the water bottle after one week of use and the full water bottle before use by the water density (1.3019 g/mL1). 24 hours following the last oral gavage, mice treated for 28 or 56 days were euthanized by exsanguination (cardiac puncture) under isoflurane.  The livers were collected and weighed followed, by flash freezing.

value: liver

value: male

value: Vehicle control; 0.5% Tween 20 in water

tag: treatment time_dose


title: MV17_male_28day_VC_0

description:
Library name: MV17_Male_VC_DMSO_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 2 SA-ßGal-low,  scramble unstim

description: Library name: D2 low scramble unstim


title: MV74_male_56day_VC_0

description:
Library name: MV74_Male_VC_DMSO_Sept2024
Templated oligo sequencing (TempO-seq)


title: MV75_male_56day_VC_0

description:
Library name: MV75_Male_VC_DMSO_Sept2024
Templated oligo sequencing (TempO-seq)


title: MS34_male_28day_PFOS_1.5

description:
Library name: MS34_Male_PFOS_D3_Oct2024
Templated oligo sequencing (TempO-seq)

value: Perfluorooctane sulfonic acid


title: Donor 2 SA-ßGal-low,  siKLF5--3 stim

description: Library name: D2 low KLF5-3 stim


title: MV77_male_56day_VC_0

description:
Library name: MV77_Male_VC_DMSO_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 2 SA-ßGal-high,  scramble stim

description: Library name: D2 high scramble stim


title: MV20_male_28day_VC_0

description:
Library name: MV20_Male_Vehicle_Oct2024
Templated oligo sequencing (TempO-seq)


title: MS33_male_28day_PFOS_1.5

description:
Library name: MS33_Male_PFOS_D3_Oct2024
Templated oligo sequencing (TempO-seq)


title: Donor 3 SA-ßGal-high,  siKLF5--1 unstim

description: Library name: D3 high KLF5-1 unstim


title: Donor 2 SA-ßGal-low,  siKLF5--1 stim

description: Library name: D2 low KLF5-1 stim


title: Donor 2 SA-ßGal-low,  siJUN--2 unstim

description: Library name: D2 low AP1-2 unstim


title: MS141_male_56day_PFOS_1.5

description:
Library name: MS141_Male_PFOS_D4_Sept2024
Templated oligo sequencing (TempO-seq)


title: MV24_male_28day_VC_0

description:
Library name: MV24_Male_Vehicle_Oct2024
Templated oligo sequencing (TempO-seq)


title: MV21_male_28day_VC_0

description:
Library name: MV21_Male_Vehicle_Oct2024
Templated oligo sequencing (TempO-seq)


title: MV73_male_56day_VC_0

description:
Library name: MV73_Male_VC_DMSO_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 2 SA-ßGal-high,  siRUNX2--3 unstim

description: Library name: D2 high RUNX2-3 unstim


title: MS35_male_28day_PFOS_1.5

description:
Library name: MS35_Male_PFOS_D3_Oct2024
Templated oligo sequencing (TempO-seq)


title: Donor 2 SA-ßGal-low,  siKLF5--3 unstim

description: Library name: D2 low KLF5-3 unstim


title: Donor 2 SA-ßGal-low,  siJUN--1 unstim

description: Library name: D2 low AP1-1 unstim


title: Donor 2 SA-ßGal-high,  scramble unstim

description: Library name: D2 high scramble unstim


title: MS36_male_28day_PFOS_1.5

description:
Library name: MS36_Male_PFOS_D3_Oct2024
Templated oligo sequencing (TempO-seq)


title: Donor 2 SA-ßGal-low,  siJUN--1 stim

description: Library name: D2 low AP1-1 stim


title: Donor 2 SA-ßGal-high,  siRUNX2--4 unstim

description: Library name: D2 high RUNX2-4 unstim


title: Donor 2 SA-ßGal-high,  siKLF5--3 stim

description: Library name: D2 high KLF5-3 stim


title: MS140_male_56day_PFOS_1.5

description:
Library name: MS140_Male_PFOS_D4_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 2 SA-ßGal-low,  siJUN--2 stim

description: Library name: D2 low AP1-2 stim


title: MV18_male_28day_VC_0

description:
Library name: MV18_Male_VC_DMSO_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 2 SA-ßGal-high,  siRUNX2--4 stim

description: Library name: D2 high RUNX2-4 stim


title: MS133_male_56day_PFOS_1

description:
Library name: MS133_Male_PFOS_D3_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 2 SA-ßGal-high,  siKLF5--3 unstim

description: Library name: D2 high KLF5-3 unstim


title: MS138_male_56day_PFOS_1.5

description:
Library name: MS138_Male_PFOS_D4_Sept2024
Templated oligo sequencing (TempO-seq)


title: MS139_male_56day_PFOS_1.5

description:
Library name: MS139_Male_PFOS_D4_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 2 SA-ßGal-high,  siRUNX2--3 stim

description: Library name: D2 high RUNX2-3 stim


title: MS137_male_56day_PFOS_1.5

description:
Library name: MS137_Male_PFOS_D4_Sept2024
Templated oligo sequencing (TempO-seq)


title: MS132_male_56day_PFOS_1

description:
Library name: MS132_Male_PFOS_D3_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 2 SA-ßGal-high,  siJUN--2 unstim

description: Library name: D2 high AP1-2 unstim


title: MS130_male_56day_PFOS_1

description:
Library name: MS130_Male_PFOS_D3_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 2 SA-ßGal-high,  siKLF5--1 unstim

description: Library name: D2 high KLF5-1 unstim


title: MS131_male_56day_PFOS_1

description:
Library name: MS131_Male_PFOS_D3_Sept2024
Templated oligo sequencing (TempO-seq)


title: MS129_male_56day_PFOS_1

description:
Library name: MS129_Male_PFOS_D3_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 2 SA-ßGal-high,  siKLF5--1 stim

description: Library name: D2 high KLF5-1 stim


title: Donor 2 SA-ßGal-high,  siJUN--1 unstim

description: Library name: D2 high AP1-1 unstim


title: MS125_male_56day_PFOS_0.5

description:
Library name: MS125_Male_PFOS_D2_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 2 SA-ßGal-high,  siJUN--2 stim

description: Library name: D2 high AP1-2 stim


title: Donor 1 SA-ßGal-low,  scramble unstim

description: Library name: D1 low scramble unstim


title: Donor 2 SA-ßGal-high,  siJUN--1 stim

description: Library name: D2 high AP1-1 stim


title: MS122_male_56day_PFOS_0.5

description:
Library name: MS122_Male_PFOS_D2_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 1 SA-ßGal-low,  siRUNX2--4 stim

description: Library name: D1 low RUNX2-4 stim


title: MS123_male_56day_PFOS_0.5

description:
Library name: MS123_Male_PFOS_D2_Sept2024
Templated oligo sequencing (TempO-seq)


title: MS121_male_56day_PFOS_0.5

description:
Library name: MS121_Male_PFOS_D2_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 1 SA-ßGal-low,  scramble stim

description: Library name: D1 low scramble stim


title: MS124_male_56day_PFOS_0.5

description:
Library name: MS124_Male_PFOS_D2_Sept2024
Templated oligo sequencing (TempO-seq)


title: MS115_male_56day_PFOS_0.166

description:
Library name: MS115_Male_PFOS_D1_Sept2024
Templated oligo sequencing (TempO-seq)


title: MS117_male_56day_PFOS_0.166

description:
Library name: MS117_Male_PFOS_D1_Sept2024
Templated oligo sequencing (TempO-seq)


title: MS114_male_56day_PFOS_0.166

description:
Library name: MS114_Male_PFOS_D1_Sept2024
Templated oligo sequencing (TempO-seq)


title: MA97_male_56day_PFOA_1

description:
Library name: MA97_Male_PFOA_D3_Sept2024
Templated oligo sequencing (TempO-seq)

value: Pefluorooctanoic acid


title: MS116_male_56day_PFOS_0.166

description:
Library name: MS116_Male_PFOS_D1_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 1 SA-ßGal-low,  siRUNX2--3 stim

description: Library name: D1 low RUNX2-3 stim


title: Donor 1 SA-ßGal-low,  siJUN--2 stim

description: Library name: D1 low AP1-2 stim


title: MA90_male_56day_PFOA_0.5

description:
Library name: MA90_Male_PFOA_D2_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 1 SA-ßGal-low,  siJUN--1 stim

description: Library name: D1 low AP1-1 stim


title: MA91_male_56day_PFOA_0.5

description:
Library name: MA91_Male_PFOA_D2_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 1 SA-ßGal-low,  siKLF5--3 unstim

description: Library name: D1 low KLF5-3 unstim


title: MS113_male_56day_PFOS_0.166

description:
Library name: MS113_Male_PFOS_D1_Sept2024
Templated oligo sequencing (TempO-seq)


title: MA98_male_56day_PFOA_1

description:
Library name: MA98_Male_PFOA_D3_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 1 SA-ßGal-low,  siKLF5--1 unstim

description: Library name: D1 low KLF5-1 unstim


title: Donor 1 SA-ßGal-high,  scramble stim

description: Library name: D1 high scramble stim


title: Donor 1 SA-ßGal-low,  siKLF5--3 stim

description: Library name: D1 low KLF5-3 stim


title: Donor 1 SA-ßGal-low,  siRUNX2--4 unstim

description: Library name: D1 low RUNX2-4 unstim


title: MA93_male_56day_PFOA_0.5

description:
Library name: MA93_Male_PFOA_D2_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 1 SA-ßGal-low,  siJUN--2 unstim

description: Library name: D1 low AP1-2 unstim


title: Donor 1 SA-ßGal-low,  siJUN--1 unstim

description: Library name: D1 low AP1-1 unstim


title: Donor 1 SA-ßGal-low,  siKLF5--1 stim

description: Library name: D1 low KLF5-1 stim


title: Donor 1 SA-ßGal-high,  scramble unstim

description: Library name: D1 high scramble unstim


title: MA81_male_56day_PFOA_0.166

description:
Library name: MA81_Male_PFOA_D1_Sept2024
Templated oligo sequencing (TempO-seq)


title: MA92_male_56day_PFOA_0.5

description:
Library name: MA92_Male_PFOA_D2_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 1 SA-ßGal-high,  siKLF5--1 stim

description: Library name: D1 high KLF5-1 stim


title: Donor 1 SA-ßGal-high,  siKLF5--3 stim

description: Library name: D1 high KLF5-3 stim


title: MA82_male_56day_PFOA_0.166

description:
Library name: MA82_Male_PFOA_D1_Sept2024
Templated oligo sequencing (TempO-seq)


title: MA84_male_56day_PFOA_0.166

description:
Library name: MA84_Male_PFOA_D1_Sept2024
Templated oligo sequencing (TempO-seq)


title: MA89_male_56day_PFOA_0.5

description:
Library name: MA89_Male_PFOA_D2_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 1 SA-ßGal-high,  siKLF5--3 unstim

description: Library name: D1 high KLF5-3 unstim


title: Donor 1 SA-ßGal-high,  siRUNX2--3 unstim

description: Library name: D1 high RUNX2-3 unstim


title: MA83_male_56day_PFOA_0.166

description:
Library name: MA83_Male_PFOA_D1_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 1 SA-ßGal-high,  siKLF5--1 unstim

description: Library name: D1 high KLF5-1 unstim


title: Donor 1 SA-ßGal-high,  siRUNX2--4 stim

description: Library name: D1 high RUNX2-4 stim


title: Donor 1 SA-ßGal-high,  siRUNX2--4 unstim

description: Library name: D1 high RUNX2-4 unstim


title: MA86_male_56day_PFOA_0.166

description:
Library name: MA86_Male_PFOA_D1_Sept2024
Templated oligo sequencing (TempO-seq)


title: MA51_male_28day_PFOA_1.5

description:
Library name: MA51_Male_PFOA_D3_Oct2024
Templated oligo sequencing (TempO-seq)


title: Donor 1 SA-ßGal-high,  siJUN--2 unstim

description: Library name: D1 high AP1-2 unstim


title: MA50_male_28day_PFOA_1.5

description:
Library name: MA50_Male_PFOA_D3_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 1 SA-ßGal-high,  siRUNX2--3 stim

description: Library name: D1 high RUNX2-3 stim


title: MA110_male_56day_PFOA_1.5

description:
Library name: MA110_Male_PFOA_D4_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 1 SA-ßGal-high,  siJUN--1 unstim

description: Library name: D1 high AP1-1 unstim


title: MA109_male_56day_PFOA_1.5

description:
Library name: MA109_Male_PFOA_D4_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 3, SA-ßGal-low, CADD522, RNA-seq

description: Library name: D3_Low_CADD522

data_processing:
In-house pipeline
Adaptors were trimmed using cutadapt version 5.1.
Trimmed reads were mapped to GRCh38.d1.v1 using bowtie2 with the local option.
Alignments were analyzed for differential expression using DESeq2 and clustered using WGCNA.
Assembly: GRCh38.d1.v1
Supplementary files format and content: We include a tab-delimited text file that contains the RLD-transformed, normalized and debatched values of the compasiron 'SA-ßgal-low versus SA-ßgal-high' across all inhibitor or DMSO treatments. The DEGs in this file were matched to their nearest TF (JUN, KLF5, RUNX2) footprint, which is reported on the paper. The file contains the gene expression modules identified by WGCNA with their RLD values and annotated.
Supplementary files format and content: BW

treatment_protocol: No treatment.

value: DMSO


title: MA106_male_56day_PFOA_1.5

description:
Library name: MA106_Male_PFOA_D4_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 1 SA-ßGal-high,  siJUN--1 stim

description: Library name: D1 high AP1-1 stim


title: Donor 3, SA-ßGal-high, T5224, RNA-seq

description: Library name: D3_High_T5224


title: Donor 3, SA-ßGal-low, DMSO, RNA-seq

description: Library name: D3_Low_DMSO


title: MA108_male_56day_PFOA_1.5

description:
Library name: MA108_Male_PFOA_D4_Sept2024
Templated oligo sequencing (TempO-seq)


title: FV158_female_56day_VC_0

description:
Library name: FV158_Female_VC__Sept2024
Templated oligo sequencing (TempO-seq)

value: female


title: MA52_male_28day_PFOA_1.5

description:
Library name: MA52_Male_PFOA_D3_Sept2024
Templated oligo sequencing (TempO-seq)


title: MA105_male_56day_PFOA_1.5

description:
Library name: MA105_Male_PFOA_D4_Sept2024
Templated oligo sequencing (TempO-seq)


title: MA100_male_56day_PFOA_1

description:
Library name: MA100_Male_PFOA_D3_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 2, SA-ßGal-low, CADD522, RNA-seq

description: Library name: D2_Low_CADD522

value: Peripheral blood


title: Donor 2, SA-ßGal-high, T5224, RNA-seq

description: Library name: D2_High_T5224

value: CD8+ T cell


title: MA101_male_56day_PFOA_1

description:
Library name: MA101_Male_PFOA_D3_Sept2024
Templated oligo sequencing (TempO-seq)


title: FV27_female_28day_VC_0

description:
Library name: FV27_Female_Vehicle_Oct2024
Templated oligo sequencing (TempO-seq)


title: Donor 3, SA-ßGal-low, T5224, RNA-seq

description: Library name: D3_Low_T5224


title: Donor 3, SA-ßGal-high, DMSO, RNA-seq

description: Library name: D3_High_DMSO


title: Donor 3, SA-ßGal-high, SR18662, RNA-seq

description: Library name: D3_High_SR18662


title: MA49_male_28day_PFOA_1.5

description:
Library name: MA49_Male_PFOA_D3_Oct2024
Templated oligo sequencing (TempO-seq)


title: Donor 3, SA-ßGal-low, SR18662, RNA-seq

description: Library name: D3_Low_SR18662


title: MA102_male_56day_PFOA_1

description:
Library name: MA102_Male_PFOA_D3_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 2, SA-ßGal-high, SR18662, RNA-seq

description: Library name: D2_High_SR18662


title: Donor 3, SA-ßGal-high, CADD522, RNA-seq

description: Library name: D3_High_CADD522


title: FV154_female_56day_VC_0

description:
Library name: FV154_Female_VC__Sept2024
Templated oligo sequencing (TempO-seq)


title: FV155_female_56day_VC_0

description:
Library name: FV155_Female_VC__Sept2024
Templated oligo sequencing (TempO-seq)


title: MA53_male_28day_PFOA_1.5

description:
Library name: MA53_Male_PFOA_D3_Oct2024
Templated oligo sequencing (TempO-seq)


title: Donor 2, SA-ßGal-low, T5224, RNA-seq

description: Library name: D2_Low_T5224


title: Donor 2, SA-ßGal-high, CADD522, RNA-seq

description: Library name: D2_High_CADD522


title: Donor 1 SA-ßGal-high,  siJUN--2 stim

description: Library name: D1 high AP1-2 stim


title: Donor 2, SA-ßGal-low, SR18662, RNA-seq

description: Library name: D2_Low_SR18662


title: Donor 1, SA-ßGal-low, T5224, RNA-seq

description: Library name: D1_Low_T5224


title: FV153_female_56day_VC_0

description:
Library name: FV153_Female_VC__Sept2024
Templated oligo sequencing (TempO-seq)


title: FV25_female_28day_VC_0

description:
Library name: FV25_Female_Vehicle_Oct2024
Templated oligo sequencing (TempO-seq)


title: FS43_female_28day_PFOS_1.5

description:
Library name: FS43_Female_PFOS_D3_Oct2024
Templated oligo sequencing (TempO-seq)


title: FV28_female_28day_VC_0

description:
Library name: FV28_Female_Vehicle_Oct2024
Templated oligo sequencing (TempO-seq)


title: Donor 1, SA-ßGal-high, DMSO, RNA-seq

description: Library name: D1_High_DMSO


title: FS42_female_28day_PFOS_1.5

description:
Library name: FS42_Female_PFOS_D3_Oct2024
Templated oligo sequencing (TempO-seq)


title: FS217_female_56day_PFOS_1.5

description:
Library name: FS217_Female_PFOS_D4_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 1, SA-ßGal-high, CADD522, RNA-seq

description: Library name: D1_High_CADD522


title: FS218_female_56day_PFOS_1.5

description:
Library name: FS218_Female_PFOS_D4_Sept2024
Templated oligo sequencing (TempO-seq)


title: FS219_female_56day_PFOS_1.5

description:
Library name: FS219_Female_PFOS_D4_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 1, SA-ßGal-low, DMSO, RNA-seq

description: Library name: D1_Low_DMSO


title: Donor 1, SA-ßGal-low, CADD522, RNA-seq

description: Library name: D1_Low_CADD522


title: FS211_female_56day_PFOS_1

description:
Library name: FS211_Female_PFOS_D3_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 1, SA-ßGal-low, SR18662, RNA-seq

description: Library name: D1_Low_SR18662


title: Donor 1, SA-ßGal-high, SR18662, RNA-seq

description: Library name: D1_High_SR18662


title: FV26_female_28day_VC_0

description:
Library name: FV26_Female_Vehicle_Oct2024
Templated oligo sequencing (TempO-seq)


title: Donor 2, SA-ßGal-low, DMSO, RNA-seq

description: Library name: D2_Low_DMSO


title: FS220_female_56day_PFOS_1.5

description:
Library name: FS220_Female_PFOS_D4_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 1, SA-ßGal-high, T5224, RNA-seq

description: Library name: D1_High_T5224


title: FS209_female_56day_PFOS_1

description:
Library name: FS209_Female_PFOS_D3_Sept2024
Templated oligo sequencing (TempO-seq)


title: FS44_female_28day_PFOS_1.5

description:
Library name: FS44_Female_PFOS_D3_Oct2024
Templated oligo sequencing (TempO-seq)


title: FS205_female_56day_PFOS_0.5

description:
Library name: FS205_Female_PFOS_D2_Sept2024
Templated oligo sequencing (TempO-seq)


title: FS213_female_56day_PFOS_1

description:
Library name: FS213_Female_PFOS_D3_Sept2024
Templated oligo sequencing (TempO-seq)


title: FS203_female_56day_PFOS_0.5

description:
Library name: FS203_Female_PFOS_D2_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 2, SA-ßGal-high, DMSO, RNA-seq

description: Library name: D2_High_DMSO


title: FV157_female_56day_VC_0

description:
Library name: FV157_Female_VC__Sept2024
Templated oligo sequencing (TempO-seq)


title: FS210_female_56day_PFOS_1

description:
Library name: FS210_Female_PFOS_D3_Sept2024
Templated oligo sequencing (TempO-seq)


title: FS202_female_56day_PFOS_0.5

description:
Library name: FS202_Female_PFOS_D2_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 3, SA-ßGal-high, SR18662

description: Library name: D3_High_SR18662_ATAC

data_processing:
In-house pipeline
Adaptors were trimmed using cutadapt version 5.1.
Trimmed reads were mapped to GRCh38.d1.v1 using bowtie2 with the following parameters: -no-mixed --no-discordant --maxins 2000
Alignments de-deduplicated using Picard and Samtools and subsequently blacklisted regions were removed using Bedtools.
Cleaned alignments were then used as input for peak calling using MACS2 with a relaxed threshold of q-value = 0.01 and a master peakset was constructed using bedops with individual sample peak sets as input. Differential accessibility was performed with DESeq2 and the differentially accessible regions (DARs) were used as input for TF footprinting using RGT-HINT.
Assembly: GRCh38.d1.v1
Supplementary files format and content: 1X normalized signal tracks per sample are provided. These were generated using deeptools normalized against the effective GRCh38 genome size.
Supplementary files format and content: BW

extract_protocol:
Nuclei were isolated and transposed as in Buenrostro et al, Nature Methods, 2013, from ~50,000 CD8+ T cells
Libraries were constructed by PCR amplification of tagmented DNA as in Buenrostro et al, Nature Methods, 2013.


title: Donor 3, SA-ßGal-low, CADD522

description: Library name: D3_Low_CADD522_ATAC


title: Donor 3, SA-ßGal-high, DMSO

description: Library name: D3_High_DMSO_ATAC


title: FS214_female_56day_PFOS_1

description:
Library name: FS214_Female_PFOS_D3_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 3, SA-ßGal-high, T5224

description: Library name: D3_High_T5224_ATAC


title: Donor 3, SA-ßGal-high, CADD522

description: Library name: D3_High_CADD522_ATAC


title: Donor 3, SA-ßGal-low, T5224

description: Library name: D3_Low_T5224_ATAC


title: FS221_female_56day_PFOS_1.5

description:
Library name: FS221_Female_PFOS_D4_Sept2024
Templated oligo sequencing (TempO-seq)


title: FS197_female_56day_PFOS_0.166

description:
Library name: FS197_Female_PFOS_D1_Sept2024
Templated oligo sequencing (TempO-seq)


title: FS41_female_28day_PFOS_1.5

description:
Library name: FS41_Female_PFOS_D3_Oct2024
Templated oligo sequencing (TempO-seq)


title: Donor 3, SA-ßGal-low, SR18662

description: Library name: D3_Low_SR18662_ATAC


title: FS196_female_56day_PFOS_0.166

description:
Library name: FS196_Female_PFOS_D1_Sept2024
Templated oligo sequencing (TempO-seq)


title: FS206_female_56day_PFOS_0.5

description:
Library name: FS206_Female_PFOS_D2_Sept2024
Templated oligo sequencing (TempO-seq)


title: FS198_female_56day_PFOS_0.166

description:
Library name: FS198_Female_PFOS_D1_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 2, SA-ßGal-low, T5224

description: Library name: D2_Low_T5224_ATAC


title: Donor 2, SA-ßGal-high, DMSO

description: Library name: D2_High_DMSO_ATAC


title: FS204_female_56day_PFOS_0.5

description:
Library name: FS204_Female_PFOS_D2_Sept2024
Templated oligo sequencing (TempO-seq)


title: FS193_female_56day_PFOS_0.166

description:
Library name: FS193_Female_PFOS_D1_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 2, SA-ßGal-low, CADD522

description: Library name: D2_Low_CADD522_ATAC


title: FA59_female_28day_PFOA_1.5

description:
Library name: FA59_Female_PFOA_D3_Oct2024
Templated oligo sequencing (TempO-seq)


title: FA189_female_56day_PFOA_1.5

description:
Library name: FA189_Female_PFOA_D4_Sept2024
Templated oligo sequencing (TempO-seq)


title: FA57_female_28day_PFOA_1.5

description:
Library name: FA57_Female_PFOA_D3_Oct2024
Templated oligo sequencing (TempO-seq)


title: Donor 1, SA-ßGal-high, T5224

description: Library name: D1_High_T5224_ATAC


title: Donor 1, SA-ßGal-high, SR18662

description: Library name: D1_High_SR18662_ATAC


title: FA187_female_56day_PFOA_1.5

description:
Library name: FA187_Female_PFOA_D4_Sept2024
Templated oligo sequencing (TempO-seq)


title: FA186_female_56day_PFOA_1.5

description:
Library name: FA186_Female_PFOA_D4_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 2, SA-ßGal-low, DMSO

description: Library name: D2_Low_DMSO_ATAC


title: FS195_female_56day_PFOS_0.166

description:
Library name: FS195_Female_PFOS_D1_Sept2024
Templated oligo sequencing (TempO-seq)


title: FA60_female_28day_PFOA_1.5

description:
Library name: FA60_Female_PFOA_D3_Oct2024
Templated oligo sequencing (TempO-seq)


title: Donor 2, SA-ßGal-high, T5224

description: Library name: D2_High_T5224_ATAC


title: FA188_female_56day_PFOA_1.5

description:
Library name: FA188_Female_PFOA_D4_Sept2024
Templated oligo sequencing (TempO-seq)


title: FA181_female_56day_PFOA_1

description:
Library name: FA181_Female_PFOA_D3_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 2, SA-ßGal-high, SR18662

description: Library name: D2_High_SR18662_ATAC


title: FA58_female_28day_PFOA_1.5

description:
Library name: FA58_Female_PFOA_D3_Oct2024
Templated oligo sequencing (TempO-seq)


title: FA185_female_56day_PFOA_1.5

description:
Library name: FA185_Female_PFOA_D4_Sept2024
Templated oligo sequencing (TempO-seq)


title: Donor 1, SA-ßGal-low, SR18662

description: Library name: D1_Low_SR18662_ATAC


title: Donor 1, SA-ßGal-low, T5224

description: Library name: D1_Low_T5224_ATAC


title: Donor 1, SA-ßGal-low, CADD522

description: Library name: D1_Low_CADD522_ATAC


title: Donor 2, SA-ßGal-high, CADD522

description: Library name: D2_High_CADD522_ATAC


title: Donor 2, SA-ßGal-low, SR18662

description: Library name: D2_Low_SR18662_ATAC


title: FA179_female_56day_PFOA_1

description:
Library name: FA179_Female_PFOA_D3_Sept2024
Templated oligo sequencing (TempO-seq)


title: H3K27ac, SAßGal-high, donor 1

description: Library name: H3K27ac_SAßGal-high_donor-1

data_processing:
In-house pipeline
Adaptors were trimmed using cutadapt version 5.1.
Trimmed reads were mapped to GRCh38.d1.v1 using bowtie2 with the following parameters: -no-mixed --no-discordant --maxins 2000
Alignments de-deduplicated using Picard and Samtools and subsequently blacklisted regions were removed using Bedtools.
Cleaned alignments were then used as input for peak calling using MACS2 with a relaxed threshold of q-value = 0.01 and a master peakset was constructed using bedops with individual sample peak sets as input. Differential chromatin states were identified using chromstaR as described in Martínez-Zamudio et al, Cell Genomics, 2023 except that the fold enrichment cut-off of >=1 was used.
Assembly: GRCh38.d1.v1
Supplementary files format and content: BW; 1X normalized signal tracks per sample are provided. These were generated using deeptools normalized against the effective GRCh38 genome size.

extract_protocol:
Nuclei were isolated and transposed as in Buenrostro et al, Nature Methods, 2013, from ~50,000 CD8+ T cells
Libraries were constructed as indicated in the Epycypher CuTANA Cut&Tag Kit.


title: FA180_female_56day_PFOA_1

description:
Library name: FA180_Female_PFOA_D3_Sept2024
Templated oligo sequencing (TempO-seq)


title: H3K27ac, SAßGal-high, donor 3

description: Library name: H3K27ac_SAßGal-high_donor-3


title: Donor 1, SA-ßGal-low, DMSO

description: Library name: D1_Low_DMSO_ATAC


title: Donor 1, SA-ßGal-high, CADD522

description: Library name: D1_High_CADD522_ATAC


title: Donor 1, SA-ßGal-high, DMSO

description: Library name: D1_High_DMSO_ATAC


title: H3K27me3, SAßGal-high, donor 2

description: Library name: H3K27me3_SAßGal-high_donor-2


title: H3K27ac, SAßGal-low, donor 3

description: Library name: H3K27ac_SAßGal-low_donor-3


title: FA173_female_56day_PFOA_0.5

description:
Library name: FA173_Female_PFOA_D2_Sept2024
Templated oligo sequencing (TempO-seq)


title: H3K27ac, SAßGal-high, donor 2

description: Library name: H3K27ac_SAßGal-high_donor-2


title: H3K27ac, SAßGal-low, donor 1

description: Library name: H3K27ac_SAßGal-low_donor-1


title: H3K27me3, SAßGal-high, donor 1

description: Library name: H3K27me3_SAßGal-high_donor-1


title: H3K27me3, SAßGal-low, donor 2

description: Library name: H3K27me3_SAßGal-low_donor-2


title: H3K4me1, SAßGal-high, donor 3

description: Library name: H3K4me1_SAßGal-high_donor-3


title: FA164_female_56day_PFOA_0.166

description:
Library name: FA164_Female_PFOA_D1_Sept2024
Templated oligo sequencing (TempO-seq)


title: FA178_female_56day_PFOA_1

description:
Library name: FA178_Female_PFOA_D3_Sept2024
Templated oligo sequencing (TempO-seq)


title: H3K4me1, SAßGal-high, donor 1

description: Library name: H3K4me1_SAßGal-high_donor-1


title: FA172_female_56day_PFOA_0.5

description:
Library name: FA172_Female_PFOA_D2_Sept2024
Templated oligo sequencing (TempO-seq)


title: H3K27me3, SAßGal-high, donor 3

description: Library name: H3K27me3_SAßGal-high_donor-3


title: H3K27me3, SAßGal-low, donor 1

description: Library name: H3K27me3_SAßGal-low_donor-1


title: H3K27ac, SAßGal-low, donor 2

description: Library name: H3K27ac_SAßGal-low_donor-2


title: Donor 3, SA-ßGal-low, DMSO

description: Library name: D3_Low_DMSO_ATAC


title: H3K27me3, SAßGal-low, donor 3

description: Library name: H3K27me3_SAßGal-low_donor-3


title: FA177_female_56day_PFOA_1

description:
Library name: FA177_Female_PFOA_D3_Sept2024
Templated oligo sequencing (TempO-seq)