title: Non-transmitter replicate 2

city: Birmingham

first: Steffanie

last: Sabbaj

address: 845 19th Street South

department: Medicine

institute: University of Alabama at Birmingham

description: 10X Genomics

data_processing:
The demultiplexing, barcode processing, gene counting were made using Cell Ranger software version 7.2.0
Assembly: GRCh38-202-A
Supplementary files format and content: Tab-separated values file and matrix files

source_name: Breast Milk

extract_protocol:
Cells isolated from breastmilk were adjusted to the correct density, mixed with 10X barcoded gel beads and oil (included in 10X Genomics Chromium Next GEM Single Cell 3' Kit v3.1 PN 1000268) and loaded onto 10X Chromium™ Single Cell Chips. The chips were placed in the 10X Chromium X Controller to generate Gel Bead-In-Emulsions (GEMs). cDNA from GEM/single cells was then synthesized, barcoded and purified.
Single cell cDNA libraries were constructed starting with cDNA fragmentation, end repair, A-tailing, size selection using SPRIselect beads (Beckman Coulter, PN B23318), adaptor ligation, sample index PCR amplification, and a final SPRIselect beads size exclusion step. The final constructed 3’-biased single cell libraries were then sequenced using an Illumina Novaseq 6000 instrument, targeting 50,000 read pairs/cell. The resulting sequencing FASTQ files were processed using the 10X Genomics Cell Ranger pipeline to map and count expressed transcripts.

value: Breast Milk

value: Leukocytes


title: Dox-inducible + WntloBMPhi, Day2, RNA rep2

status: Public on Apr 08 2025

type: SRA

city: Boston

first: Ramesh

middle: A

last: Shivdasani

state: MA

address: 450Brookline Ave.

department: Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

library_source: transcriptomic

data_processing:
sequence reads were mapped to hg19 using STAR aligner
Read count extraction were performed using STAR aligner v2.6.0c
Assembly: hg19
Supplementary files format and content: tab-delimited text files include STAR raw counts for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Ileum

growth_protocol: DMEM, 20% F12K, 20% FBS, 10% R-Spondin-2 conditioned medium, 10 mM nicotinamide, 100µg/ml Primocin, 1 μM A8301, 5 μg/ml  insulin, 10 μM Y-27632, 1 μM DMH1, 50 ng/ml EGF and 2 μM T3. Cells were cultured at 37C at 7.5% CO2.

extract_protocol:
RNA was harvested from FACs sorted viable (DAPI-) and EPCAM+ cells using Rneasy mini plus kit (Qiagen) and used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by Novogene Corporation Inc.

treatment_protocol: Secretory induction was done by treatment 4ug/ml Dox FOR 48 h. Cells were treated without Dox or with either Dox + WnthiBMPlo media or Dox+WntloBMPhi media for 48 h are harvested for RNA isolation.

tag: tissue

value: Ileum

tag: cell type

value: Intestine Epithelium

tag: genotype

value: TetO-ATOH1; PGK-rtTA-BlastR

tag: treatment

value: 4µg/ml Dox for 48 h


title: Transmitter replicate 2

state: AL

description: 10X Genomics

library_source: transcriptomic single cell


title: Dox-inducible + WntloBMPhi, Day2, RNA rep1


title: Transmitter replicate 1

description: 10X Genomics


title: Dox-inducible, Day2, RNA rep2


title: Non-transmitter replicate 1

description: 10X Genomics


title: Dox-inducible, Day0, RNA rep2

value: No treatment


title: pasmcs，Hypoxia+Ad-MrgD3

city: Jinan

first: hongyu

last: zhong

address: 07 Wenhua xi road, Jinan, Shandong

country: China

institute: Qilu hospital Shandong University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
Paired-end sequence files (fastq) were mapped to the reference genome GRCh38.108 using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression analysis for mRNA was performed using R package edgeR.
Assembly: GRCh38.108
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: human pulmonary artery smooth muscle cells

growth_protocol: HPASMCs were grown in Smooth Muscle Cell Medium (SMCM, ScienCell) at 37 °C and 5% CO2.

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After stimulating pulmonary artery smooth muscle cells with Ad-MrgD for 24 hours, HPASMCs were exposed to hypoxia (3% O2, 5% CO2, with N2 compensation) in a modular hypoxia chamber.

value: mrgd overexpression

value: Hypoxia+Ad-MrgD


title: pasmcs，Hypoxia+Ad-MrgD2

value: human pulmonary artery smooth muscle cells


title: Dox-inducible + WnthiBMPlo, Day2, RNA rep2


title: Dox-inducible, Day0, RNA rep1


title: A549 cells+DOX,IL-33-F 1

city: Changchun

first: Chen

last: Shao

state: Jilin

address: 126 Xinmin ST

institute: Jilin University

data_processing:
RNA-sequencing reads were first trimmed to remove poly(A) and unqualified reads with Cutadapt(v2.7). For CUT&Tag, the bam file generated from uniquely mapped reads was used as input for peak calling with macs2 software, applying a cutoff q-value < 0.05. The peaks were annotated using in-house scripts. Peak analysis involved counting the annotation results and plotting the distribution using R.
Assembly: hg38
Supplementary files format and content: xls, expression matrix
Supplementary files format and content: bw, IL-33_F, bw, IL-33_C

extract_protocol:
A549 Cells infected with the virus were seeded at a density of 2 × 106 cells per 10 cm dish and incubated overnight. After drug treatment, TRIzol reagent was used for cell lysis according to the manufacturer’s instructions. Three independent biological replicates were used for each experiment. For CUT&Tag, cells infected with the virus were seeded at a density of 2 × 107 cells per 10 cm dish and incubated overnight. The cells were sent to Jingjie PTM BioLab Co., Inc. (Hangzhou, China) for CUT&Tag analysis.
The lysates were sent to Personalbio (Shanghai, China) for cDNA library construction and sequencing by Illumina NovaSeq 6000. RNA-sequencing reads were first trimmed to remove poly(A) and unqualified reads with Cutadapt(v2.7).Briefly, the CUT&Tag assay was performed using the NovoNGS CUT&Tag 4.0 High-Sensitivity Kit ( Illumina), according to the manufacturer’s protocol. Library quality was assessed on the Agilent 5400 system (Agilent, USA) and quantified by qPCR. Raw data in fastq format were processed using the Trimmomatic (RRID:SCR_011848) software. All downstream analyses were based on high-quality clean data.

tag: cell line

value: lung cancer cells

value: IL-33-F overexpression

value: infected with lentivirus


title: Dox-inducible + WnthiBMPlo, Day2, RNA rep1


title: pasmcs，Hypoxia+Ad-MrgD1


title: pasmcs，Hypoxia+Ad-con1

value: wt

value: Hypoxia+Ad-con


title: A549 cells,IL-33-C 3

value: IL-33-C overexpression


title: pasmcs，Hypoxia+Ad-con2


title: Dox-inducible, Day2, RNA rep1


title: CS22

city: Pasadena

first: Magdalena

last: Zernicka Goetz

state: CALIFORNIA

address: CALIFORNIA INSTITUTE OF TECHNOLOGY

institute: California Institute of Technolog

data_processing:
Cell Ranger software from 10X Genomics was installed for data pre-processing. Raw sequencing data were organized, with the requirement that sequencing reads be demultiplexed into FASTQ format files for each sample. Using cellranger mkfastq to demultiplex raw base call (BCL) files generated by Illumina sequencers into FASTQ files. Reads were mapped to the human hg38 genome and counted with GRCh38-3.0.0 annotation using cellranger count. The data pre-processing workflow was streamlined and standardized to maintain consistency across samples.
Assembly: hg38,GRCh38-3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: amnion

extract_protocol:
All tissues for sequencing and spatial work were collected in HypoThermosol FRS preservation solution (H4416-100ML Merck) and stored at 4 °C until processing. Tissue dissociation was conducted within 24 h of tissue retrieval.Tissues were cut into <1 mm3 segments before being digested with Trypsin/EDTA 0.25% phenol red (25200072 Thermo Fisher Scientific) for 10-15 min at 37 °C with intermittent shaking. Digested tissue was passed through a 100 µm filter and cells collected by centrifugation (500g for 5 min at 4 °C). Cells were washed with PBS and then resuspended in PBS 0.04% BSA before cell counting.
cells were loaded according to the manufacturer’s protocol for the Chromium Next GEM Single Cell 5 v2 (Dual index) kit for CS17 amnion and Chromium Next GEM Single Cell 3 v3.1 (Dual index) kit for CS19 and CS22 amnion from 10X Genomics to attain 7,000 cells per reaction. Library preparation was carried out according to the manufacturer’s protocol. Libraries were sequenced, aiming at a minimum coverage of 20,000 raw reads per cell, on the Illumina HiSeq4000 or Novaseq 6000 systems using the sequencing format: read 1, 26 cycles; i7 index, 8 cycles, i5 index, 0 cycles; read 2, 98 cycles.

value: amnion

value: amnion cells


title: CS19


title: HA239-T2

city: Detroit

first: Roger

last: Pique-Regi

state: Michigan

address: 540 E Canfield (Scott Hall 3309)

institute: Wayne State University

data_processing:
We aligned the RNA-seq reads with HISAT232 to the human genome version ‘grch38_snp_tran’, which considers splicing and common genetic variants.
Aligned and cleaned (deduplicated) reads were counted using HTSeq and Homo_sapiens.GRCh38.103 transcriptome assembly genes.
Assembly: Homo_sapiens.GRCh38.103
Supplementary files format and content: tab-delimited text files

source_name: Whole Blood

extract_protocol:
Cells were thawed and transferred into RPMI1640 (Gibco Cat# 11835030) medium containing 10% FBS (Gibco Cat# 10082147). Cells were then collected by centrifugation at 1200 RPM for 7 min and washed twice using ice-cold PBS (Gibco Cat# 10010002). Collected pellets were lysed using Lysis/Binding Buffer (Invitrogen Cat# 61012), and frozen at −80°C. Polyadenylated mRNAs were subsequently isolated from thawed lysates using the Dynabeads mRNA Direct Kit (Invitrogen), following the manufacturer’s instructions.
RNA-seq libraries were prepared using a protocol modified from the NEBNext Ultradirectional (Illumina® - NEB Cat# E7760L) library preparation protocol. RNA was fragmented at 94°C for 5 minutes to obtain 200–1500 bp fragments in size. SPRISelect beads (Beckman Coulter) were used in all purification steps and size selection. Barcodes from PerkinElmer were added by ligation.

value: Whole Blood

value: PBMC

tag: Sex

value: Female

tag: poverty status

value: Above

tag: race

value: AfrAm


title: HA239-T1


title: pasmcs，Hypoxia+Ad-con3


title: HA238-T2

value: Below


title: HA238-T1


title: HA236-T1

value: White


title: HA235-T2

value: Male


title: HA235-T1


title: HA234-T2


title: HA236-T2


title: HA233-T1


title: HA232-T2


title: HA234-T1


title: HA233-T2


title: HA229-T1


title: HA229-T2


title: HA230-T2


title: HA228-T2


title: HA230-T1


title: HA227-T1


title: HA232-T1


title: HA231-T2


title: HA228-T1


title: HA225-T2


title: HA231-T1


title: HA227-T2


title: HA225-T1


title: HA224-T2


title: HA223-T2


title: HA226-T2


title: HA221-T2


title: HA221-T1


title: HA223-T1


title: HA220-T1


title: HA218-T2


title: HA219-T1


title: HA218-T1


title: HA217-T1


title: HA216-T2


title: HA226-T1


title: HA214-T2


title: HA215-T1


title: HA215-T2


title: HA213-T2


title: HA224-T1


title: HA216-T1


title: HA214-T1


title: HA210-T1


title: HA210-T2


title: HA212-T1


title: HA213-T1


title: HA217-T2


title: HA212-T2


title: HA208-T1


title: HA209-T2


title: HA209-T1


title: HA207-T1


title: HA219-T2


title: HA207-T2


title: HA205-T2


title: HA206-T1


title: HA206-T2


title: HA201-T2


title: HA202-T2


title: HA201-T1


title: HA202-T1


title: HA199-T2


title: HA200-T2


title: HA200-T1


title: HA198-T2


title: HA197-T2


title: HA208-T2


title: HA197-T1


title: HA195-T2


title: HA199-T1


title: HA196-T2


title: HA196-T1


title: HA198-T1


title: HA194-T2


title: HA194-T1


title: HA195-T1


title: HA193-T2


title: HA192-T2


title: HA205-T1


title: HA190-T2


title: HA193-T1


title: HA192-T1


title: HA190-T1


title: HA189-T2


title: HA188-T2


title: HA189-T1


title: HA188-T1


title: HA187-T2


title: HA187-T1


title: HA186-T2


title: HA220-T2


title: HA186-T1


title: HA185-T1


title: HA184-T1


title: HA183-T2


title: HA183-T1


title: HA180-T2


title: HA180-T1


title: HA182-T2


title: HA185-T2


title: HA178-T2


title: HA179-T1


title: HA181-T1


title: HA178-T1


title: HA176-T2


title: HA175-T2


title: HA176-T1


title: HA182-T1


title: HA177-T2


title: HA177-T1


title: HA175-T1


title: HA174-T2


title: HA179-T2


title: HA174-T1


title: HA173-T1


title: HA173-T2


title: HA172-T2


title: HA184-T2


title: HA172-T1


title: HA170-T2


title: HA181-T2


title: HA169-T1


title: HA169-T2


title: HA168-T2


title: HA168-T1


title: HA167-T2


title: HA166-T2


title: HA164-T2


title: HA166-T1


title: HA163-T2


title: HA162-T2


title: HA161-T1


title: HA160-T2


title: HA162-T1


title: HA161-T2


title: HA163-T1


title: HA160-T1


title: HA159-T2


title: HA159-T1


title: HA158-T2


title: HA157-T2


title: HA158-T1


title: HA156-T2


title: HA156-T1


title: HA170-T1


title: HA153-T2


title: HA154-T1


title: HA152-T1


title: HA152-T2


title: HA151-T2


title: HA167-T1


title: HA151-T1


title: HA150-T2


title: HA164-T1


title: HA148-T2


title: HA147-T1


title: HA149-T1


title: HA148-T1


title: HA146-T1


title: HA145-T2


title: HA147-T2


title: HA144-T2


title: HA157-T1


title: HA143-T2


title: HA154-T2


title: HA142-T2


title: HA142-T1


title: HA141-T2


title: HA144-T1


title: HA140-T2


title: HA141-T1


title: HA143-T1


title: HA153-T1


title: HA140-T1


title: HA150-T1


title: HA139-T2


title: HA137-T2


title: HA137-T1


title: HA149-T2


title: HA146-T2


title: HA136-T1


title: HA145-T1


title: HA134-T2


title: HA134-T1


title: HA133-T2


title: HA132-T2


title: HA133-T1


title: HA131-T1


title: HA130-T2


title: HA131-T2


title: HA132-T1


title: HA130-T1


title: HA128-T2


title: HA128-T1


title: HA126-T1


title: HA127-T1


title: HA129-T2


title: HA139-T1


title: HA127-T2


title: HA126-T2


title: HA125-T2


title: HA125-T1


title: HA124-T1


title: HA136-T2


title: HA123-T2


title: HA124-T2


title: HA123-T1


title: HA122-T2


title: HA122-T1


title: HA121-T2


title: HA120-T2


title: HA121-T1


title: HA120-T1


title: HA118-T2


title: HA118-T1


title: HA117-T1


title: HA129-T1


title: HA116-T2


title: HA113-T2


title: HA117-T2


title: HA115-T2


title: HA111-T1


title: HA115-T1


title: HA113-T1


title: HA110-T2


title: HA111-T2


title: HA108-T2


title: HA110-T1


title: HA108-T1


title: HA106-T1


title: HA109-T1


title: HA106-T2


title: HA105-T2


title: HA109-T2


title: HA104-T2


title: HA105-T1


title: HA119-T1


title: HA119-T2


title: HA104-T1


title: HA103-T2


title: HA103-T1


title: HA116-T1


title: HA102-T2


title: HA102-T1


title: HA100-T1


title: HA099-T2


title: HA098-T2


title: HA097-T2


title: HA096-T2


title: HA095-T1


title: HA099-T1


title: HA098-T1


title: HA097-T1


title: HA096-T1


title: HA093-T2


title: HA094-T1


title: HA092-T1


title: HA094-T2


title: HA090-T2


title: HA090-T1


title: HA093-T1


title: HA092-T2


title: HA091-T1


title: HA088-T2


title: HA089-T1


title: HA087-T2


title: HA089-T2


title: HA091-T2


title: HA087-T1


title: HA100-T2


title: HA085-T2


title: HA084-T2


title: HA095-T2


title: HA084-T1


title: HA083-T1


title: HA082-T1


title: HA081-T2


title: HA082-T2


title: HA080-T2


title: HA080-T1


title: HA076-T2


title: HA075-T2


title: HA081-T1


title: HA076-T1


title: HA074-T2


title: HA074-T1


title: HA073-T2


title: HA073-T1


title: HA072-T2


title: HA071-T2


title: HA071-T1


title: HA072-T1


title: HA088-T1


title: HA085-T1


title: HA070-T1


title: HA069-T2


title: HA069-T1


title: HA083-T2


title: HA068-T1


title: HA067-T1


title: HA067-T2


title: HA066-T2


title: HA066-T1


title: HA065-T2


title: HA075-T1


title: HA065-T1


title: HA062-T2


title: HA064-T2


title: HA060-T2


title: HA060-T1


title: HA059-T2


title: HA064-T1


title: HA057-T1


title: HA059-T1


title: HA056-T2


title: HA055-T2


title: HA068-T2


title: HA057-T2


title: HA056-T1


title: HA070-T2


title: HA051-T1


title: HA053-T1


title: HA055-T1


title: HA052-T1


title: HA053-T2


title: HA054-T1


title: HA062-T1


title: HA051-T2


title: HA048-T1


title: HA052-T2


title: HA048-T2


title: HA047-T1


title: HA047-T2


title: HA045-T1


title: HA046-T1


title: HA045-T2


title: HA046-T2


title: HA044-T1


title: HA043-T2


title: HA041-T2


title: HA044-T2


title: HA039-T2


title: HA039-T1


title: HA037-T1


title: HA041-T1


title: HA037-T2


title: HA038-T2


title: HA038-T1


title: HA035-T2


title: HA031-T1


title: HA035-T1


title: HA033-T1


title: HA033-T2


title: HA032-T1


title: HA031-T2


title: HA043-T1


title: MT954_ChIP_seq_INPUT_SV20_WT_D5_rep1

city: London

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

country: United Kingdom

institute: Imperial College London

description:
Library name: MT954_ChIP_seq_INPUT_SV20_WT_D5_rep1
ChIP-Seq

library_source: genomic

data_processing:
Adaptors were removed using TrimGalore! RNA-seq reads were mapped and quantified using Kallisto and differential gene expression was analysed using DESeq2.
ChIP-seq data were aligned to hg19 using BWA-mem. MACS2 was used to call peaks using default parameters and FDR <5%
Cut&run data were aligned to hg19 using BWA-mem. HOMER was used to call peaks using default parameters and FDR <5%
ATAC-seq data were aligned to hg19 using BWA-mem. MACS2 was used to call peaks using default parameters and FDR <5%
Assembly: hg19 (homo sapiens)
Supplementary files format and content: kallisto quantified abundance files for RNA-seq data
Supplementary files format and content: bigwig files for ChIP-seq, CUT&RUN, and ATAC-seq

molecule: genomic DNA

source_name: SV20 WT

growth_protocol: Human iPSCs were plated on Geltrex LDEV-Free hESC-qualified Reduced Growth Factoer Basement Membrane Matrix and maintained in feeder-free, serum-free mTeSR plus medium in small clusters

extract_protocol:
RNA was extracted using the Monarch Total RNA Miniprep Kit (New England Biolabs, T2010).
RNA libraries were constructed using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, E7760). 1 μg of total RNA input was used for each library. Libraries were sequenced on Illumina NextSeq 2000, producing 60bp paired-end reads.
Barcoded CUT&RUN libraries were made with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L) using NEBNext Multiplex Oligos Dual Index Primers for Illumina (NEB, E7600S), and sequenced on Illumina NextSeq2000, producing 50 bp paired-end reads
Barcoded CHIP-seq libraries were made with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L) using NEBNext Multiplex Oligos Dual Index Primers for Illumina (NEB, E7600S), and sequenced on Illumina NextSeq2000, producing 50 bp paired-end reads
ATAC-seq was performed using 50,000 cells per sample. Libraries were prepared using the ATAC-seq Kit (Active Motif, 53150) and sequenced on either Illumina NextSeq2000, producing 60 bp paired-end reads or 150 bp paired-end reads.

treatment_protocol: iPSCs were cultured with CNCC specification media: 1:1 Neurobasal medium/D-MEM F-12 medium, 1X penicillin-streptomycin solution, 1x Glutamax supplement, 0.5x B-27 supplement with Vitamin A, 0.5x N-2 supplement, 5 μg/ml bovine insulin, 20 ng/ml EGF, and 20 ng/ml hFGF for 6 days. At day ~7 when early migratory CNCCs first appeared, the cells were transitioned to CNCC early maintenance media: 1:1 Neurobasal medium/D-MEM F-12 medium, 1X penicillin-streptomycin solution, 1x Glutamax supplement, 0.5x B-27 supplement with Vitamin A, 0.5x N-2 supplement, 1 mg/ml bovine serum albumin, serum replacement grade, 20 ng/ml EGF, and 20 ng/ml hFGF for 7 days.

tag: chip antibody

value: Anti-BRG1 antibody [EPNCIR111A]

value: SV20 WT

value: day 5 cranial neural crest cell

value: cranial neural crest cell specification


title: HA028-T2


title: HA028-T1


title: HA026-T2


title: HA030-T2


description:
Library name: MT952_ChIP_seq_BRG1_SV20_SALL4_KO_D5_rep1
ChIP-Seq

source_name: SV20 SALL4-KO clone F1 (SALL4-het-KO)

value: SV20 SALL4-KO clone F1 (SALL4-het-KO)


title: HA029-T1


title: HA029-T2


title: MT950_ChIP_seq_BRG1_SV20_WT_D5_rep1

description:
Library name: MT950_ChIP_seq_BRG1_SV20_WT_D5_rep1
ChIP-Seq


title: HA032-T2


title: HA023-T2


title: HA025-T1


title: HA023-T1


title: PAD24_125nm

city: Schwerzenbach

first: Guillermo

last: Turiel

address: Schorenstrasse 16

department: D-HEST

country: Switzerland

institute: ETH Zurich

description: Library name: PAD24_125um_2

data_processing:
Sequencing reads were processed using Kallisto and the human genome assembly GENCODE GRCh38.p13 Annotation release 42 to generate a count file matrix for each individual sample. Samples were pooled together into a single matrix and analyzed following DESeq2 pipeline
Assembly: Human genome assembly GENCODE GRCh38.p13 Annotation release 42
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Skeletal muscle

growth_protocol: We isolated muscle ECs from 3 PAD patients using an established protocol: https://doi.org/10.3389/fbioe.2022.964705

extract_protocol:
RNeasy Plus Micro Kit (74034, Qiagen)
TruSeq Stranded mRNA Library Kit (Illumina)

treatment_protocol: Confluent EC cultures were treated for 24h with vehicle (DMSO, A994.1, Carl Roth) or celastrol (C0869, Sigma-Aldrich) (125 or 250 nM). Celastrol powder was dissolved in DMSO at 2 mg/mL (stock concentration) and later diluted to experimental doses (125 or 250 nM) directly into EGM-2 media (CC-3202, Lonza) right before use. Control samples (Vehicle) were given the same amount of DMSO as used to dilute celastrol in the 250 nM condition. After 24h incubation, RNA was extracted for bulk RNA sequencing.

value: Skeletal muscle

value: Primary ECs

tag: patient

value: Patient 24

tag: sequencing plate

tag: disease

value: Peripheral artery disease

value: Celastrol 125 nM

value: male


title: HA026-T1

value: Whole Blood

value: PBMC

value: Female


title: PAD24_250nm

description: Library name: PAD24_250um_2

value: Celastrol 250 nM


title: HA030-T1

value: Below

value: AfrAm


title: PAD23_250nm

description: Library name: PAD23_250um_2

value: Patient 23


title: HA022-T2


title: PAD23_vehicle

description: Library name: PAD23_vehicle_2

value: Vehicle (DMSO)


title: PAD23_125nm

description: Library name: PAD23_125um_2


title: HA020-T2

value: Male


title: PAD22_vehicle

description: Library name: PAD22_vehicle_2

value: Patient 22


title: PAD24_vehicle_2

description: Library name: PAD24_vehicle_2


title: HA020-T1


title: PAD22_250nm

description: Library name: PAD22_250um_2


title: HA054-T2

value: Above


title: HA019-T2


title: HA017-T1


title: HA017-T2


title: HA019-T1


title: A549 cells,IL-33-F

data_processing:
RNA-sequencing reads were first trimmed to remove poly(A) and unqualified reads with Cutadapt(v2.7). For CUT&Tag, the bam file generated from uniquely mapped reads was used as input for peak calling with macs2 software, applying a cutoff q-value < 0.05. The peaks were annotated using in-house scripts. Peak analysis involved counting the annotation results and plotting the distribution using R.
Assembly: hg38
Supplementary files format and content: xls, expression matrix
Supplementary files format and content: bw, IL-33_F, bw, IL-33_C
Library strategy: CUT&Tag

value: lung cancer cells

value: IL-33-F overexpression

value: infected with lentivirus


title: HA025-T2


title: A549 cells,IL-33-C

value: IL-33-C overexpression


title: PAD22_125nm

description: Library name: PAD22_125um_2

value: Skeletal muscle

value: Primary ECs

value: Peripheral artery disease

value: Celastrol 125 nM


title: HA016-T2

value: Whole Blood

value: PBMC


title: HA016-T1

value: Below


title: HA014-T1

value: Female

value: AfrAm


title: HA014-T2


title: HA012-T2

value: White


title: HA022-T1


title: HA011-T2


title: HA011-T1


title: HA012-T1

value: Male


title: HA010-T2


title: HA010-T1


title: HepG2 mixture25 4h biological rep6

type: RNA

city: Chapel Hill

first: Julia

last: Rager

state: NC

address: 135 Dauer Drive, CB 7431

institute: UNC

hyb_protocol: Fragmented and labeled cDNA was used to prepare a hybridization cocktail with the Thermo Fisher GeneTitan Hybridization Wash and Stain Kit for WT Arrays.

scan_protocol: Affymtrix peg plate arrays was carried out using the Affymetrin GeneTitan MC Instrument.

data_processing:
Raw expression values were normalized across the entire dataset to reduce background signal and improve fold change using Signal Space Transformation — Robust Multi-chip Analysis (SST — RMA) via Affymetrix Transcriptome Analysis Console
SST-RMA via Transcriptome Analysis Console from Thermo

label: biotin

source_name: HepG2 immortalized liver cell line

label_protocol: Total RNA (250 ng) was used to synthesize fragmented and labeled sense-strand cDNA and hybridized onto the Affymetrix Clariom S HT Human peg plate.  Following synthesis of sense-strand cDNA, the cDNA was fragmented and labeled with the kit.

growth_protocol: Cells were procured from the American Type Culture Collection and cultured in Gibco Minimum Essential Media, supplemented with 10% Fetal Bovine Serum under at 5% CO2 and 37.5˚C

extract_protocol: HepG2 cell lysates were added to a Qiagen QIAshredder spin column and centrifuged at 16,000 x g for two minutes. RNA was isolated from resulting cell lysates using the Qiagen RNeasy Mini Kit according to manufacturer’s protocol.

treatment_protocol: To create stock solutions, PFAS compounds (PFOS, PFOA, and/or PFHxA) were dissolved in 100% biology-grade methanol. PFAS stocks were diluted in MEM media + 10% exosome-depleted FBS. These diluted stocks were then applied individually or as an equimolar mixture in concentration-response to cells, with individual PFAS concentrations of 2.5 µM, 10 µM, 25 µM or 35 µM.

value: immortalized liver cell

tag: compound

value: Equimolar PFOS, PFOA, PFHxA

tag: concentration

value: 25 µM each

tag: time

value: 4 hour


title: HA009-T2


title: HA008-T1


title: HepG2 mixture25 4h biological rep5


title: HepG2 mixture25 4h biological rep2


title: HepG2 mixture25 4h biological rep3


title: HepG2 PFHxA35 biological rep4

value: PFHxA

value: 35 µM

value: 24 hour


title: HepG2 PFHxA35 biological rep5


title: HepG2 mixture25 4h biological rep4


title: HepG2 mixture25 4h biological rep1


title: HepG2 PFHxA35 biological rep1


title: HA006-T2

value: Above


title: HA008-T2


title: HA007-T2


title: HepG2 PFHxA35 biological rep3


title: HepG2 PFHxA35 biological rep2


title: HA007-T1


title: HA006-T1


title: HA005-T2


title: HepG2 PFHxA25 biological rep3

value: 25 µM


title: HA005-T1


title: HA009-T1


title: HepG2 PFHxA25 biological rep4


title: HA004-T2


title: HepG2 PFHxA25 biological rep5


title: HepG2 PFHxA10 biological rep4

value: 10 µM


title: HepG2 PFHxA25 biological rep1


title: HA003-T2

value: Whole Blood


title: HA004-T1

value: PBMC


title: HepG2 PFHxA10 biological rep2


title: HA001-T2


title: HA003-T1


title: HepG2 PFHxA10 biological rep1


title: HepG2 PFHxA25 biological rep2


title: HepG2 PFHxA10 biological rep3


title: 18_TB0093_scVDJ

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

description: scVDJ library

data_processing:
RNA DEMULTIPLEXING - bcltofastq-2.19.0
RNA CLEANING - fastp 0.20.0, --in1 ../${SAMPLE}_R1.fastq.gz --out1 clt_${SAMPLE}_R1.fastq.gz --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y -r -j ${SAMPLE}_fastp.json
RNA MAPPING - STAR_2.7.0f, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
RNA COUNTING - subread-1.6.4, featurecounts, -s 2 -t exon -g gene_name
RNA DIFFERENTIAL EXPRESSION - DESeq2_1.22.1
scRNA and scVDJ DEMULTIPLEXING - cellRanger 5.0.0 mkfastq --run=. --samplesheet=cellRanger.csv --output-dir ./cellRanger
scRNA COUNTING - cellRanger 5.0.0 count fastqs=./fastq_path --jobmode=slurm --maxjobs=100 --transcriptome=${REF} --project=${PROJECT} --id=Sample_${SAMPLEPREFIX} --sample=${SAMPLEPREFIX}
scVDJ COUNTING - cellRanger 5.0.0 vdj --fastqs=./fastq_path --jobmode=local --nopreflight --reference=${REF} --id=Sample_${SAMPLEPREFIX} --sample=${SAMPLEPREFIX} --localcores=20 --localmem=100
VDJ AMPLICON PROCESSING - Defining dominant L1 clones  L1 clones were defined by a common Jh identity and 6 identical upstream D-Jh junctional nucleotides (termed “6NJx”) comprising ≥5% of all IgH reads according to defined methods6. In their 2012 NGS analysis of IgH heterogeneity, Gawad et al. compared the extent of shared, consecutive intermediary non-Jh or Vh nucleotides (“NDN”) upstream of a common Jh among B-ALL clones to chronic lymphocytic leukemia (CLL), a malignancy of mature B cell lineage which would not be expected to demonstrate evolution by RAG-mediated Vh recombination6. They observed that only 0.03% of CLL clones with a common Jh shared >6 NDN bases with the index clone; they thus defined a threshold of 6 shared NDN nucleotides with a common Jh – or “6NJx” – as a marker of shared clonal lineage.   Because the 5% read threshold for defining clonality is arbitrarily defined, we assessed 2 end of induction (EOI) minimal residual disease (MRD)-negative samples as controls to ensure specificity. We observed that the presence of a 6NJx cluster at ≥5% read frequency was exclusively a feature of active disease specimens; 6NJx sequence clusters between this arbitrary 5% threshold and 1% were observed in some leukemia specimens, but not in MRD-negative control specimens7.  Defining L2 subclones  L2 subclones were defined as all sequences with an identical NDN sequence. NDN sequences include non-templated sequences on both sides of the D gene that arise during RAG-mediated recombination, including bases immediately downstream of the Vh alignment to the beginning of the Jh gene alignment, as determined by IgBlast8. Each novel NDN sequence was interpreted as an L2 subclone within its L1 grouping. For cases in which both the bone marrow (BM) and peripheral blood (PB) were analyzed, the greater L2 subclone proportion observed in either site was reported. To limit overcalling of L2 subclones due to sequencing errors, we allowed for 1 base difference in either length or sequence within NDN grouping.       L3 single nucleotide variation (SNV) analysis  SNV analysis with ultradeep NGS data is challenged by the high load of processing errors. Multiple steps were taken to minimize the effects of false base calls, including the merging of paired reads and replacement of base discrepancies with the base call of highest quality, and removal of all primers to eliminate base changes arising in primer preparation. Additional steps to minimize false SNVs are detailed below.   Defining L3 subclones  We defined a trimmed Vh sequence as the error-corrected and IgBlast-mapped DNA sequence beginning at the Vh gene start through 20 bp upstream of the Vh end. The number of L3 subclones was defined as the number of distinct, trimmed Vh sequences. Pairwise, global alignments were performed on each trimmed Vh and distance matrices were used to assess phylogenic relationships between L3 subclones. We compared the number of L3 subclones per L2 subclone between patients using Poisson mixed regression models, with random intercept for Patient ID, fixed and random effect for the number of L2 reads, and fixed effect for tissue site (PB vs. BM). Our software is available at github.com/amcdavid/igh-leukemia.  eUCR-based noise reduction  As an internal control, we incorporated a targeted amplicon of eUCR41 into each sample for use as a measure of processing and sequencing noise. Ultra-conserved regions have extremely low rates of biological mutations, thereby allowing these regions to be used as a measure of systematic error in the NGS pipeline (ranging from gDNA quality to initial PCR through final read sequencing)9. This error correction is used after mapping analysis by LoFreq10 to determine which SNV calls in amplicons of interest occur above the threshold for probable false calls.  Each biologically valid mutation call represents a mixture of true signal and false calls due to process errors. We use observed mutation calls and read depth in eUCR to generate a probable upper frequency boundary for false positives for each of the possible 12 transitions and transversions. Using the Clopper-Pearson confidence interval for binomial distribution11, we place upper bounds on the probability of a false positive observation based on eUCR SNV frequency, even for SNVs with 0 observations. Conversely, we likewise set lower bounds for each observed transition and transversion SNV for IgH amplicons, factoring in the read depth. From these data, we establish the set of SNV calls that occur above the false positive threshold, at p<0.0001, for each IgH of interest.   To collect the set of reads to evaluate for point mutations in L2 subclones, a multi-step process was used: Reads were mapped (SHRiMP212) and analyzed with LoFreq10 to establish an eUCR-based threshold for true SNVs.  Reads were then remapped and individually evaluated for putative SNV calls based on eUCR threshold, with SNV reverted to reference base at failure. Reads with more than 3 putative SNVs outside the eUCR determined set of true positive calls were eliminated from further analysis. To insure clonality via this mapping result, only reads with a CDR3 sequence identical to the reference of interest were taken to L3 analysis.   An important consideration involved the selection of IgH reference sequences for mapping, as the highly repetitive nature of IgH gene usages challenges mapping programs. To limit mapping errors, the following rules were applied to generate the mix of IgH reference sequences: 1. all single IgH sequences occurring at ≥1% total IgH; 2. The shortest representative of the L2s of interest, up to the top 3 if available; 3. Any other L1 IgH sequence that occurred at ≥10% of total reads in that L1 subset, up to a maximum of 15 sequences.
Assembly: GRCh38.p13 + Gencode-31 Annotation, 10X Genomics published transcriptome GRCh38-2020-A, 10X Genomics published VDJ reference refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0
Supplementary files format and content: deSeq2_counts.txt contains the combined counts for all samples for use within DeSeq2 as well as the results of differential expression across the condition groups. RNA and VDJ files are output formats of 10X cellRanger workflow.

source_name: Peripheral blood

extract_protocol: IgH AMPLICON SEQUENCING - Genomic DNA was isolated from frozen cell pellets and unsorted viably frozen samples (Wizard® Genomic DNA Purification; Promega™). DNA was quantified by absorbance at 260 nm (NanoDrop™, Thermo Fisher Scientific) and dsDNA binding of fluorescent dyes (Qubit™, Thermo Fisher Scientific). PCR amplification was performed using Q5 High Fidelity Polymerase (New England Biolabs, Inc., Ipswich, MA) using 500 ng genomic DNA as template divided across 4 amplicon reactions, representing approximately 80,000 mononuclear cells per specimen. Recombined IgH primers were specific to each joining (Jh) gene (J1-6) and family specific Framework 2 (FR2) variable (Vh) gene of the IgH locus (Supplemental Table 1). An ultraconserved region (eUCR41) found on Chr 11 was also amplified for use as an internal control for gDNA preparation damage, PCR, and NGS errors2. All amplicons were of similar size of approximately 250-300 nucleotides. Gene-specific primers were modified by the addition of NexteraXT sequences (Illumina Inc., San Diego, CA) at the 5’ primer end. Amplicons were size-selected and purified (SPRIselect; Beckman Coulter®) to maximize selection of 300 nt amplicons for NGS. Specimens were sequenced on an Illumina MiSeq System using 2x300 bp sequencing chemistry. BULK RNA SEQUENCING - Using viably frozen BM and/or PB, RNA was purified and total RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE). RNA quality was assessed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA). The TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer protocol. mRNA was purified from 200ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis using dUTP incorporation for strand marking. End repair and 3’ adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by AMPURE XP bead cleanup and amplified with PCR primers specific to the adaptor sequences to generate cDNA amplicons of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the NovaSeq6000 DNA sequencer (Illumina, San Diego, CA). Single end reads of 100nt were generated for each sample. SINGLE CELL PREPARATION - Cellular suspensions were loaded on a Chromium Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell Gel Bead-in-Emulsions (GEMs). Single-cell RNA-Seq libraries were prepared using the Chromium Single-Cell 5′ Library & Gel BeadKit (10x Genomics). The beads were dissolved and cells were lysed per manufacturer’s recommendations.GEM reverse transcription (GEM-RT) was performed to produce a barcoded, full-length cDNA from poly-adenylated mRNA.After incubation, GEMs were broken and the pooled post-GEM-RT reaction mixtures were recovered and cDNA was purified with silane magnetic beads (DynaBeads MyOne Silane Beads, ThermoFisher Scientific).The entire purified post GEM-RT product was amplified by PCR. This amplification reactiongenerated sufficient material to construct a B cell-enriched library and a 5’ gene expression library.The barcoded, full-length V(D)J segments were enriched by PCR with primers specific to the BCR constant regions using the Chromium Single Cell V(D)J Enrichment Kit, Human B cell (10x Genomics).For both B-cell enriched library and 5’ gene expression library, enzymatic fragmentation and size selection was used to optimize the cDNA amplicon size and indexed sequencing libraries were constructed by End Repair, A-tailing, Adaptor Ligation, and PCR. Final libraries contain the P5 and P7 priming sites used in Illumina bridge amplification.  The 5’ gene expression and B-cell libraries were sequenced following 10X Genomics read length guidelines on the NovaSeq6000 sequencer (Illumina). The sequencing run was demultiplexed and counted using 10x Genomics Cell Ranger 5.0.0 mkfastq and count, using the 10x Genomics provided human reference (refdata-gex-GRCh38-2020-A).Cellular suspensions were loaded on a Chromium Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell Gel Bead-in-Emulsions (GEMs). Single-cell RNA-Seq libraries were prepared using the Chromium Single-Cell 5′ Library & Gel BeadKit (10x Genomics). The beads were dissolved and cells were lysed per manufacturer’s recommendations.GEM reverse transcription (GEM-RT) was performed to produce a barcoded, full-length cDNA from poly-adenylated mRNA.After incubation, GEMs were broken and the pooled post-GEM-RT reaction mixtures were recovered and cDNA was purified with silane magnetic beads (DynaBeads MyOne Silane Beads, ThermoFisher Scientific).The entire purified post GEM-RT product was amplified by PCR. This amplification reactiongenerated sufficient material to construct a B cell-enriched library and a 5’ gene expression library.The barcoded, full-length V(D)J segments were enriched by PCR with primers specific to the BCR constant regions using the Chromium Single Cell V(D)J Enrichment Kit, Human B cell (10x Genomics).For both B-cell enriched library and 5’ gene expression library, enzymatic fragmentation and size selection was used to optimize the cDNA amplicon size and indexed sequencing libraries were constructed by End Repair, A-tailing, Adaptor Ligation, and PCR. Final libraries contain the P5 and P7 priming sites used in Illumina bridge amplification.  The 5’ gene expression and B-cell libraries were sequenced following 10X Genomics read length guidelines on the NovaSeq6000 sequencer (Illumina). The sequencing run was demultiplexed and counted using 10x Genomics Cell Ranger 5.0.0 mkfastq and count, using the 10x Genomics provided human reference (refdata-gex-GRCh38-2020-A).

tag: patient id

tag: disease state

value: B cell acute lymphoblastic leukemia

value: Peripheral blood


title: HepG2 PFHxA2.5 biological rep5


title: HA001-T1

tag: tissue


title: HepG2 PFHxA2.5 biological rep4

tag: cell type


title: 11-TB0594_scVDJ

description: scVDJ library


title: 18_TB0093_scRNA

description: scRNA library


title: HepG2 PFHxA10 biological rep5


title: 18-TB0350_scVDJ

description: scVDJ library

source_name: Bone marrow

value: Bone marrow


title: 11-TB0594_scRNA

description: scRNA library


title: 18-TB0350_scRNA

description: scRNA library


title: 18-TB0350_bulkRNA

description:
bulkRNA library
deSeq2_counts.txt


title: 18-TB0294

description:
bulkRNA library
deSeq2_counts.txt


title: 18-TB0238

description:
bulkRNA library
deSeq2_counts.txt


title: 18-TB0130

description:
bulkRNA library
deSeq2_counts.txt


title: HepG2 PFOA35 biological rep4

value: PFOA


title: HepG2 PFHxA2.5 biological rep3


title: HepG2 PFHxA2.5 biological rep2


title: HepG2 PFHxA2.5 biological rep1


title: 18-TB0013

description:
bulkRNA library
deSeq2_counts.txt


title: 17-TB0278_scVDJ

description:
bulkRNA library
deSeq2_counts.txt


title: 17-TB0278_bulkRNA

description: scRNA library


title: HepG2 PFOA35 biological rep5


title: HepG2 PFOA35 biological rep3


title: 17-TB0094

description:
bulkRNA library
deSeq2_counts.txt


title: HepG2 PFOA25 biological rep4


title: 17-TB0095

description:
bulkRNA library
deSeq2_counts.txt


title: 17-TB0225

description:
bulkRNA library
deSeq2_counts.txt


title: HepG2 PFOA25 biological rep5


title: HepG2 PFOA35 biological rep2


title: 17-TB0278_scRNA

description: scVDJ library


title: 13-TB0143

description:
bulkRNA library
deSeq2_counts.txt


title: HepG2 PFOA25 biological rep2


title: 12-TB0624

description:
bulkRNA library
deSeq2_counts.txt


title: HepG2 PFOA25 biological rep1


title: HepG2 PFOA25 biological rep3


title: HepG2 PFOA10 biological rep4


title: HepG2 PFOA10 biological rep1


title: HepG2 PFOA35 biological rep1


title: HepG2 PFOA10 biological rep3


title: HepG2 PFOA10 biological rep2


title: HepG2 PFOA2.5 biological rep5


title: HepG2 PFOA2.5 biological rep4


title: HepG2 PFOA2.5 biological rep3


title: 12-TB0366

description:
bulkRNA library
deSeq2_counts.txt


title: 13-TB0388

description:
bulkRNA library
deSeq2_counts.txt


title: 11-TB0603_scRNA

description: scRNA library


title: HepG2 PFOA10 biological rep5


title: HepG2 PFOA2.5 biological rep1


title: 13-TB0148

description:
bulkRNA library
deSeq2_counts.txt


title: 07-TBM0075_scVDJ

description: scVDJ library


title: 07-TBM0075_scRNA

description: scRNA library


title: HepG2 PFOS35 biological rep3

value: PFOS


title: 07-TBL0074_scVDJ

description: scVDJ library


title: 07-TBM0075_bulkRNA

description:
bulkRNA library
deSeq2_counts.txt


title: HepG2 PFOS35 biological rep5

value: immortalized liver cell


title: 07-TBL0074_scRNA

description: scRNA library


title: 07-TBL0074_bulkRNA

description:
bulkRNA library
deSeq2_counts.txt


title: 11-TB0603_scVDJ

description: scVDJ library


title: HepG2 PFOS35 biological rep1


title: 11-TB0603_bulkRNA

description:
bulkRNA library
deSeq2_counts.txt


title: PBMCs from Healthy4 hashed (Vehicle/Albumin) - Post discovery cohort (HTO scRNA-seq)

city: Barcelona

first: Ferran

last: Aguilar

state: Barcelona

address: Travessera de Gràcia, 11

country: Spain

institute: EF-CLIF

description: single-cell RNA-seq

data_processing:
Cell Ranger v3.1.0 [alignment, filtering, barcode counting, and UMI counting]
Genome_build: human: GRCh38-3.0.0
Supplementary_files_format_and_content: barcodes.tsv: cell barcodes
Supplementary_files_format_and_content: features.tsv: gene names
Supplementary_files_format_and_content: matrix.mtx: count matrix

source_name: Peripheral blood mononuclear cells (PBMCs)

extract_protocol:
As described in the v3.0 single-cell 3’ mRNA kit (10x Genomics) protocol (CGO00183 Rev C), after GEMs generation and reverse transcription, the cDNA was extracted by Dynabeads MyOne SILANE clean up following manufacturer’s instructions. The obtained cDNA was then used for amplification.
The amplified cDNA was subjected to enzymatic fragmentation, end repair and A-tailing. Size selected fragments subsequently underwent R2 adaptor ligation and Index PCR for the insertion of sample index for library demultiplexing, P5 and P7 Illumina adapters. Libraries were purified by SPRI selected beads clean up. Fragments size distribution and concentration were verified on an Agilent Bioanalyzer High Sensitivity Chip (Agilent Technologies). Libraries were sequenced on a NovaSeq6000 (Illumina) to obtain approximately 25000 reads per cell.

tag: group

value: Healthy

tag: hashing

value: Hashed (Vehicle:HD4-control / Albumin:HD4-HSA)

tag: protocol

value: 10X Chromium 3' RNA-seq


title: HepG2 PFOS25 biological rep5

tag: cell line


title: HepG2 PFOA2.5 biological rep2


title: HepG2 PFOS25 biological rep4


title: HepG2 PFOS35 biological rep4


title: HepG2 PFOS35 biological rep2


title: PBMCs from Healthy3 hashed (Vehicle/Albumin) - Post discovery cohort (HTO scRNA-seq)

description: single-cell RNA-seq

value: Peripheral blood mononuclear cells (PBMCs)

value: Hashed (Vehicle:3b-3Veh-HD-3HD / Albumin:3b-3Veh-HD-3HD-HSA)


title: HepG2 PFOS25 biological rep1

value: 24 hour


title: HepG2 PFOS10 biological rep5


title: PBMCs from Healthy2_Albumin non-hashed - Post discovery cohort (scRNA-seq)

description: single-cell RNA-seq

value: Non-hashed


title: HepG2 PFOS10 biological rep3


title: PBMCs from Healthy2_Vehicle non-hashed - Post discovery cohort (scRNA-seq)

description: single-cell RNA-seq


title: PBMCs from Healthy1_Vehicle non-hashed - Post discovery cohort (scRNA-seq)

description: single-cell RNA-seq


title: HepG2 PFOS25 biological rep2

value: 25 µM


title: PBMCs from Healthy1_Albumin non-hashed - Post discovery cohort (scRNA-seq)

description: single-cell RNA-seq


title: HepG2 PFOS10 biological rep2

value: 10 µM


title: PBMCs from Patient9_Vehicle non-hashed - Post discovery cohort (scRNA-seq)

description: single-cell RNA-seq

value: Acutely Decompensated Cirrhosis Patient


title: PBMCs from Patient9_Albumin non-hashed - Post discovery cohort (scRNA-seq)

description: single-cell RNA-seq


title: HepG2 PFOS25 biological rep3


title: PBMCs from Patient7 hashed (Vehicle/Albumin) - Post discovery cohort (HTO scRNA-seq)

description: single-cell RNA-seq

value: Hashed (Vehicle:ACLF8-control / Albumin:ACLF8-HSA)


title: HepG2 PFOS10 biological rep1


title: HepG2 PFOS2.5 biological rep5


title: PBMCs from Patient5 hashed (Vehicle/Albumin) - Post discovery cohort (HTO scRNA-seq)

description: single-cell RNA-seq

value: Hashed (Vehicle:1c-1Veh-AD2-2AD2 / Albumin:1c-1Veh-AD2-2AD2-HSA)


title: PBMCs from Patient8 hashed (Vehicle/Albumin) - Post discovery cohort (HTO scRNA-seq)

description: single-cell RNA-seq

value: Hashed (Vehicle:AD4-control /  Albumin:AD4-HSA)


title: PBMCs from Patient6 hashed (Vehicle/Albumin) - Post discovery cohort (HTO scRNA-seq)

description: single-cell RNA-seq

value: Hashed (Vehicle:AD3-control / Albumin:AD3-HSA)


title: PBMCs from Patient4 hashed (Vehicle/Albumin) - Post discovery cohort (HTO scRNA-seq)

description: single-cell RNA-seq

value: Hashed (Vehicle:2b-2Veh-CFL5-2ACFL5 / Albumin:2b-2Veh-CFL5-2ACFL5-HSA)


title: PBMCs from Patient2 hashed (Vehicle/Albumin) - Post discovery cohort (HTO scRNA-seq)

description: single-cell RNA-seq

value: Hashed (Vehicle:2-2ACFL-2H-ACFL / Albumin:2-2ACFL-2H-ACFL-HSA)


title: PBMCs from Patient1 hashed (Vehicle/Albumin) - Post discovery cohort (HTO scRNA-seq)

description: single-cell RNA-seq

value: Hashed (Vehicle:1-1AD-1H-AD / Albumin:1-1AD-1H-AD-HSA)


title: HepG2 PFOS2.5 biological rep2

value: immortalized liver cell

value: PFOS


title: HepG2 PFOS2.5 biological rep3


title: P5 Retina Cx3cr1-GFP+ nuclei

city: Durham

first: Jeremy

last: Kay

institute: Duke University

description:
Library name: P5N
10x Genomics 3' assay v3

data_processing:
10x Genomics CellRanger software (v5.0.1) was used to map reads to the genome and to generate cell x gene matrices.
Ambient RNA correction was performed with SoupX R package (v1.6.2). Raw and filtered feature-barcode matrices generated by CellRanger were used as input to SoupX, which estmates ambient RNA contamination and generates a corrected feature-barcode matrix based on these estimates. The corrected count matrix was saved in CellRanger format using the DropletUtils R package.
Assembly: Mouse mm10
Supplementary files format and content: SoupX-corrected feature-barcode matrices in CellRanger format.

organism: Mus musculus

source_name: Retina

extract_protocol:
For scRNA-seq, eyes from Cx3cr-CreER-ires-YFP mice were enucleated into ice cold oxygenated AMES media. Tissues and cells were kept on ice throughout the procedure except as noted, and centrifugation was carried out at 4˚C. To isolate the retina, the anterior portion of the eye was removed and the retina was dissected free of the eyecup. The retinal pigment epithelium typically remained partially attached upon removal from the eyecup. All YFP-positive mice in each litter were used, and retinas were pooled for subsequent steps. Retinal tissue was dissociated in a solution of activated papain (Worthington, 16 U/mL) at 37˚C for 25 to 30 min, then triturated in an ovomucoid solution (Worthington, 15 mg/mL) to prepare a single cell suspension. The suspension was passed through a 30 μm cell strainer and pelleted at 400 g for 7 min. The cells were resuspended in AMES solution and incubated in LIVE/DEAD Fixable Aqua Dead Cell Stain (Thermo, 1:1000) for 30 min at 4˚C. Cells were washed twice, centrifuged at 400 g for 2 min, and resuspended in 0.4% BSA in 1X PBS. The YFP+ live population was collected via flow cytometry (MoFlo Astrios or BD Diva cytometers) and sorted into 0.4% BSA in 1X PBS. Post-sorting, samples were pelleted and resuspended in PBS + 0.04% BSA. For snRNA-seq, animals of genotype Cx3cr1CreER; Rosa26-loxStoplox-Sun1GFP were injected with tamoxifen at P0-1 and collected at P5 or P10. An entire litter of mice labeled in this manner were used at each timepoint. Retinas were isolated in ice-cold oxygenated AMES media, flash-frozen in liquid nitrogen, and stored at -80 degrees C until processing. On the day of sorting, nuclei were isolated as follows: Retinas were thawed for 5 min on ice; incubated for 5 min on ice in lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl; 3 mM MgCl2; 10% Nonidet-P40 substitute; 40U/µL RNAse inhibitor); triturated 20 times with a wide-bore pipette tip; incubated on ice an additional 10 min; and homogenized with 20 strokes of a disposable microcentrifuge tube dounce homogenizer. The preparation was then suspended in 0.5 mL AMES + 2% BSA containing 40U/µL RNAse inhibitor; passed through at 30 µm cell strainer; and pelleted at 500 g for 5 min at 4˚C before resuspending in AMES + 2% BSA. GFP+ nuclei were isolated by flow cytometry and resuspended in PBS + 0.04% BSA.
Samples were processed for 10x Genomics droplet encapsulation and library construction by the Duke Molecular Genomics Core. The 10x Genomics 3' single cell assay v3 kits were used, according to the manufacturer's instructions.

value: Retina

tag: developmental stage

value: microglia, macrophages, monocytes

tag: genotype

value: Cx3cr1-CreER-ires-YFP; LSL-Sun1GFP

tag: treatment

value: nuclei


title: P10 Retina Cx3cr1-GFP+ nuclei

description:
Library name: P10N
10x Genomics 3' assay v3


title: Whole-blood RNA-seq from preACLF (S66)

description:
S66
Whole-blood RNA-seq from preACLF (S66).
mRNAseq

data_processing:
Mapping of the reads were obtained using the STAR program against human genome (hg38) and the quantification of genes and transcripts were done with the RSEM program using GENCODE v26.
We use TMM method and limma-voom transformation from rounded expected counts to normalize the non biological variability.
Genome_build: Human genome (hg38)
Supplementary_files_format_and_content: *.tsv: RSEM expected counts.

source_name: Whole blood

extract_protocol:
RNA was isolated from blood stored in Tempus tubes using the Tempus™ Spin RNA Isolation Kit (reference 4380204, Applied Biosystems). RNA quality was assessed using Agilent RNA 6000 Nano and Pico Chips (Agilent Technologies, Cat.# 5067-1511 and Cat.# 5067-151, respectively) and concentration via Qubit RNA HS Assay Kit (Thermo Fisher Scientific, Cat.# Q32855).
Sequencing libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Globin kit (Illumina Inc., Cat.# 20020612) and TruSeq RNA CD Index Plate (Illumina Inc., Cat.# 20019792) following TruSeq Stranded Total RNA Sample Prep-guide (Part # 15031048 Rev. E). Briefly, starting from 500 ng of total RNA, rRNA and globin mRNA were depleted and remaining RNA was purified, fragmented and primed for cDNA synthesis. cDNA first strand was synthesized with SuperScript-II Reverse Transcriptase (Thermo Fisher Scientific, Cat.#18064-014) for 10 min at 25°C, 15 min at 42°C, 15 min at 70°C and pause at 4°C. cDNA second strand was synthesized with Illumina reagents at 16°C for 1 hour. Then, A-tailing and adaptor ligation were performed. Finally, enrichment of libraries was achieved by PCR (30 sec at 98°C; 15 cycles of 10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C; 5min at 72°C and pause at 4°C). Afterwards, libraries were visualized on an Agilent 2100 Bioanalyzer using Agilent High Sensitivity DNA kit (Agilent Technologies, Cat. # 5067-4626), quantified using Qubit dsDNA HS DNA Kit (Thermo Fisher Scientific, Cat. # Q32854) and sequenced in a NovaSeq-6000 (Illumina Inc.) by at least 40 million paired-end 100nt reads.

value: preACLF

value: Whole blood


title: HepG2 PFOS10 biological rep4

value: 10 µM

value: 24 hour


title: Whole-blood RNA-seq from preACLF (S65)

description:
S65
Whole-blood RNA-seq from preACLF (S65).
mRNAseq


title: HepG2 mixture35 biological rep6

value: Equimolar PFOS, PFOA, PFHxA

value: 35 µM each


title: PBMCs from Patient3 hashed (Vehicle/Albumin) - Post discovery cohort (HTO scRNA-seq)

description: single-cell RNA-seq

value: Peripheral blood mononuclear cells (PBMCs)

value: Acutely Decompensated Cirrhosis Patient

value: Hashed (Vehicle:1b-1VehACFL4-1ACFL4 / Albumin:1b-1VehACFL4-1ACFL4-HSA)

value: 10X Chromium 3' RNA-seq


title: HepG2 PFOS2.5 biological rep1


title: Whole-blood RNA-seq from preACLF (S72)

description:
S72
Whole-blood RNA-seq from preACLF (S72).
mRNAseq


title: P17 Retina Cx3cr1-YFP+ cells, sample2

description:
Library name: P17C2
10x Genomics 3' assay v3

value: cells-no inhibitors


title: HepG2 mixture35 biological rep5

value: immortalized liver cell


title: HepG2 mixture35 biological rep1


title: HepG2 PFOS2.5 biological rep4

value: PFOS


title: HepG2 mixture25 biological rep2

value: 25 µM each


title: HepG2 mixture25 biological rep4


title: P17 Retina Cx3cr1-YFP+ cells, sample1

description:
Library name: P17C1
10x Genomics 3' assay v3

value: Retina

value: microglia, macrophages, monocytes


title: HepG2 mixture35 biological rep4


title: HepG2 mixture35 biological rep2


title: HepG2 mixture25 biological rep6


title: HepG2 mixture35 biological rep3


title: HepG2 mixture25 biological rep5


title: Whole-blood RNA-seq from preACLF (pS07)

description:
pS07
Whole-blood RNA-seq from preACLF (pS07).
mRNAseq


title: HepG2 mixture25 biological rep3


title: P10 Retina Cx3cr1-YFP+ cells, sample2, with inhibitors

description:
Library name: P10C2
10x Genomics 3' assay v3

value: cells-with inhibitors


title: HepG2 mixture25 biological rep1


title: HepG2 mixture10 biological rep6

value: 10 µM each


title: HepG2 mixture10 biological rep5


title: Whole-blood RNA-seq from preACLF (S88)

description:
S88
Whole-blood RNA-seq from preACLF (S88).
mRNAseq

value: preACLF

value: Whole blood


title: P5 Retina Cx3cr1-YFP+ cells, sample1

description:
Library name: P5C1
10x Genomics 3' assay v3


title: HepG2 mixture10 biological rep2

value: 24 hour


title: HepG2 mixture10 biological rep4

value: Equimolar PFOS, PFOA, PFHxA


title: Whole-blood RNA-seq from preACLF (S68)

description:
S68
Whole-blood RNA-seq from preACLF (S68).
mRNAseq


title: HepG2 mixture10 biological rep3


title: Whole-blood RNA-seq from preACLF (S28)

description:
S28
Whole-blood RNA-seq from preACLF (S28).
mRNAseq


title: Whole-blood RNA-seq from preACLF (S07)

description:
S07
Whole-blood RNA-seq from preACLF (S07).
mRNAseq


title: HepG2 mixture10 biological rep1


title: Whole-blood RNA-seq from preACLF (S59)

description:
S59
Whole-blood RNA-seq from preACLF (S59).
mRNAseq


title: BPRNF SI Tum, replicate 4

city: Glasgow

first: Kathryn

last: Gilroy

address: Switchback Road

institute: Cancer Research UK Scotland Institute

description:
Library name: BPRNF SI Tum 4
10x Genomics

data_processing:
Demultiplexing, barcode processing and gene counting were performed using Cell Ranger software v6.1.2
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Small Intestine

extract_protocol:
Samples were homogenised and digested using a McIlwain Tissue CHopper and the GentleMACS Octo Dissociator in combination with the Mouse tumor dissociation kit (Miltenyi Biotec). Debris was removed, and then cells were sorted using a FACSAria sorter (BD Biosciences) and DAPI to remove dead cells.
Cells were loaded into a Chromium Chip G using a 10x Chromium Single-Cell 3’ v3 Gel Bead kit and Library (10x Genomics), then libraries were analysed using the Bioanalyzer High Sensitivity DNA kit (Agilent technologies). Sequencing was performed on an Illumina NovaSeq 6000 with paired-end 150-base reads.

treatment_protocol: Recombination of floxed genes was induced with 2mg tamoxifen, administered via intraperitoneal injection. Mice were culled at clinical endpoint, and tumors harvested.

value: Small Intestine

value: whole tumor

value: VilCreER BrafV600E/+ P53fl/fl Rnf43fl/fl

tag: Sex

value: Male


title: BPRNF SI Tum, replicate 5

description:
Library name: BPRNF SI Tum 5
10x Genomics


title: BPRNF SI Tum, replicate 3

description:
Library name: BPRNF SI Tum 3
10x Genomics


title: BPRNF SI Tum, replicate 2

description:
Library name: BPRNF SI Tum 2
10x Genomics

value: Female


title: Whole-blood RNA-seq from preACLF (S55)

description:
S55
Whole-blood RNA-seq from preACLF (S55).
mRNAseq


title: BPRNF SI Tum, replicate 1

description:
Library name: BPRNF SI Tum 1
10x Genomics


title: Whole-blood RNA-seq from preACLF (S42)

description:
S42
Whole-blood RNA-seq from preACLF (S42).
mRNAseq


title: BP SI Tum, replicate 3

description:
Library name: BP SI Tum 3
10x Genomics

value: VilCreER BrafV600E/+ P53fl/fl


title: Whole-blood RNA-seq from preACLF (S22)

description:
S22
Whole-blood RNA-seq from preACLF (S22).
mRNAseq


title: P10 Retina Cx3cr1-YFP+ cells, sample1, without inhibitors

description:
Library name: P10C1
10x Genomics 3' assay v3

value: cells-no inhibitors


title: BP SI Tum, replicate 2

description:
Library name: BP SI Tum 2
10x Genomics


title: Whole-blood RNA-seq from preACLF (S86)

description:
S86
Whole-blood RNA-seq from preACLF (S86).
mRNAseq


title: Liver, 6hrs, unstim

city: Toronto

first: Zoe

middle: Alixandra

last: Clarke

state: Ontario

address: 27 King's College Cir

department: Molecular Genetics

country: Canada

institute: University of Toronto

description: integrated_3391_stimulation_pmaio_unstim_downsampled_cca_kanchor5_scClustViz.RData

data_processing:
Cell Ranger (v.6.1.2)  followed by standard Seurat protocol using SCTransform normalisation.
Assembly: Custom woodchuck genome and annotation. Available at https://doi.org/10.5281/zenodo.10855128.
Supplementary files format and content: Filtered data matrices from CellRanger outputs: gene expression matrices, feature lists, and barcode lists.
Supplementary files format and content: .RDS and .Rdata files of integrated Seurat objects

molecule: nuclear RNA

organism: Marmota monax

source_name: Liver

growth_protocol: Biopsies of 3-mm diameter were obtained from woodchuck livers using biopsy punches (Integra Miltex). Biopsy embedding: 5% low-temperature agarose gel was prepared by dissolving 1 g of agarose (Sigma-Aldrich- A0701) in 10 mL of MilliQ water followed by the addition of 10 mL of pre-warmed Williams E Media. Biopsies were placed in peelable base molds and overlaid by the liquid agarose gel without displacing the tissue. After solidification, base molds were peeled to free the agarose blocks. Excess agarose on the sides of the block was trimmed and tissue was glued onto the cutting platform with surgical glue (3M Vetbond, 1469Sb). Generated slices of 250-μM thickness were collected in a petri dish containing ice-cold HTK solution until all biopsies were sectioned. Upon completion of the slicing procedure, one slice per well was  plated in 24-well plates containing 500 μL of culture medium and organotypic cell inserts (Sigma Aldrich PICM01250).

extract_protocol:
Nuclei were extracted from 4 slices per condition using a CHAPS with salts and Tris (CST) protocol, as previously reported.  2X stock solution of salt-Tris solution (ST buffer) was made with 292 mM NaCl (Sigma-Aldrich), 2 mM CaCl2 (Sigma-Aldrich), 42 mM MgCl2 (Sigma-Aldrich), and 20 mM Tris-HCl, pH 7.5 (Thermo Fisher Scientific) in ultrapure water (Thermofisher). 1X ST buffer was prepared via an additional 1:1 dilution with Ultrapure water. The CST detergent buffer containing 50% 2X ST stock solution, 0.0049% CHAPS (Sigma-Aldrich), 0.0001% BSA (New England BioLabs) was used for isolation. Each sample was diced by spring scissors for 10 minutes in the CST buffer. The solution was washed with 1X ST through a 40-μM mesh filter (Falcon), and spun down at 500 x g. The resulting nuclei were resuspended, stained with a 1XST solution containing DAPI, and fluorescence-activated cell sorted (FACS) using an ARIA II FACS sorter.
Samples were sequenced with 10X Genomics SingleCell 3' v3 chemistry according to manufacturer's instructions.

treatment_protocol: Plates were left to incubate on a rotator at 18 rpm overnight prior to stimulation with phorbol myristate acetate (PMA) (100 ng/mL) /ionomycin (1 μg/mL) or without stimulation as a control. Slices were collected after 6 hours of stimulation and snRNA-seq was performed on 4 slices per condition.

value: Liver

tag: woodchuck type

value: Outbred

value: Liver cells

tag: sorting

value: Unsorted

value: Unstimulated control


title: Liver, 6hrs, PMAIO

value: Stimulated with PMAIO


title: HepG2 mixture2.5 biological rep6

value: immortalized liver cell

tag: compound

value: 2.5 µM each


title: PBMC, healthy, rep 7

description: integrated_PBMC_cca_kanchor5_scClustViz.RData

data_processing:
Cell Ranger (v.5.0.0) followed by standard Seurat protocol using SCTransform normalisation and DropletQC filtering.
Assembly: Custom woodchuck genome and annotation. Available at https://doi.org/10.5281/zenodo.10855128.
Supplementary files format and content: Filtered data matrices from CellRanger outputs: gene expression matrices, feature lists, and barcode lists.
Supplementary files format and content: .RDS and .Rdata files of integrated Seurat objects

source_name: PBMC

growth_protocol: Healthy scRNA-seq was from freshly isolated liver cells and PBMCs, never cultured.

extract_protocol:
Woodchuck livers were dissociated according to a previously described 2-step collagenase perfusion protocol https://doi.org/10.1038/s41467-018-06318-7. For PBMCs, whole blood was collected in EDTA tubes. Plasma was collected from these tubes via 1000 x g spin for 10 minutes. Remaining blood was diluted using a 1:1 ratio of 1X PBS. This mixture was carefully layered on a Ficoll density gradient. Tubes containing layered blood were centrifuged at 400 x g for 20 minutes without brakes. The buffy coat layer was isolated using a Pasteur pipette and washed with 1X PBS.
Single-cell samples were sequenced with 10X Genomics SingleCell 3' v2 chemistry according to manufacturer's instructions.

value: PBMC

value: PBMCs


title: HepG2 mixture2.5 biological rep4

value: Equimolar PFOS, PFOA, PFHxA

tag: concentration

value: 24 hour


title: BP SI Tum, replicate 1

description:
Library name: BP SI Tum 1
10x Genomics

value: Small Intestine

value: whole tumor


title: PBMC, healthy, rep 6


title: Whole-blood RNA-seq from preACLF (S38)

description:
S38
Whole-blood RNA-seq from preACLF (S38).
mRNAseq

value: preACLF

value: Whole blood


title: HepG2 mixture2.5 biological rep3

tag: time


title: HepG2 mixture2.5 biological rep5


title: PBMC, healthy, rep 5


title: PBMC, healthy, rep 4


title: OVA-T-3_R1

city: Shenzhen

first: Xuefei

last: Li

address: 1068 Xueyuan Avenue, Shenzhen University Town, Nanshan

institute: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences

description: Library name: Sample 12

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-houseperl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-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.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.6.0 was used to count the reads numbers mapped to each gene.
Assembly: GRCm39 (GCA_000001635.9)
Supplementary files format and content: text files (.txt) containing raw, unnormalized read counts per gene (rows) across samples (columns), with gene identifiers (e.g., Ensembl IDs).

source_name: Tumor (from B16-F10-OVA melanoma model)

extract_protocol:
Total RNA was extracted from tissue samples using standard methods. RNA quality assessment was performed using three approaches: Nanodrop spectrophotometer was used for preliminary concentration and purity assessment. Qubit fluorometer was used for precise RNA quantification. RNA integrity (RIN value) was assessed using the RNA Nano 6000 Assay Kit on the Agilent Bioanalyzer 2100 system.
A total of 1 µg of RNA per sample was used as input for RNA library preparation. Sequencing libraries were generated using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations. Index codes were added to attribute sequences to each sample.  Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First-strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H-), followed by second-strand cDNA synthesis using DNA Polymerase I and RNase H. Overhangs were converted into blunt ends via exonuclease/polymerase activities, and 3' ends of DNA fragments were adenylated.  NEBNext Adaptor with a hairpin loop structure was ligated to prepare for hybridization. cDNA fragments of 250–300 bp were size-selected using the AMPure XP system (Beckman Coulter, USA). Then, 3 µl of USER Enzyme (NEB, USA) was used at 37°C for 15 min, followed by 5 min at 95°C before PCR amplification. PCR was performed using Phusion High-Fidelity DNA Polymerase, Universal PCR primers, and Index (X) Primer. Finally, PCR products were purified using the AMPure XP system, and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Tumor (from B16-F10-OVA melanoma model)

value: CD8+ T lymphocytes

value: B16-F10-OVA tumor-bearing mice treated with OT-1 CD8+ T cells; isolated from the suspension using Dynabeads positive selection with a CD8+ antibody


title: HepG2 mixture2.5 biological rep2


title: PBMC, healthy, rep 3

value: Outbred


title: Whole-blood RNA-seq from preACLF (S37)

description:
S37
Whole-blood RNA-seq from preACLF (S37).
mRNAseq


title: HepG2 control biological rep6

value: methanol control


title: Liver, healthy, biopsy, rep 6

description: allIntegrated_cca_kanchor5_noBiopsyHeps_dropletQCFiltered.RDS

value: Liver

value: Liver cells

value: Unsorted


title: HepG2 control biological rep2

value: immortalized liver cell


title: HepG2 control biological rep5


title: OVA-T-1_R1

description: Library name: Sample 10


title: Liver, healthy, biopsy, rep 4


title: Whole-blood RNA-seq from preACLF (S99)

description:
S99
Whole-blood RNA-seq from preACLF (S99).
mRNAseq


title: HepG2 mixture2.5 biological rep1

value: 2.5 µM each


title: B16-T-3_R1

description: Library name: Sample 9

source_name: Tumor (from B16-F10 melanoma model)

value: Tumor (from B16-F10 melanoma model)

value: B16-F10 tumor-bearing mice treated with OT-1 CD8+ T cells; isolated from the suspension using Dynabeads positive selection with a CD8+ antibody


title: HepG2 control biological rep1

value: 24 hour


title: Liver, healthy, biopsy, rep 2


title: Whole-blood RNA-seq from preACLF (S94)

description:
S94
Whole-blood RNA-seq from preACLF (S94).
mRNAseq


title: HepG2 control biological rep4


title: B16-T-2_R1

description: Library name: Sample 8


title: Liver, healthy, biopsy, rep 1


description:
pS04
Whole-blood RNA-seq from ACLF not treated (pS04).
mRNAseq

value: ACLF not treated


title: MT830_CUT_RUN_SALL4_SV20_WT_D5_rep2

description:
Library name: MT830_CUT_RUN_SALL4_SV20_WT_D5_rep2
CUT&Run

data_processing:
Adaptors were removed using TrimGalore! RNA-seq reads were mapped and quantified using Kallisto and differential gene expression was analysed using DESeq2.
ChIP-seq data were aligned to hg19 using BWA-mem. MACS2 was used to call peaks using default parameters and FDR <5%
Cut&run data were aligned to hg19 using BWA-mem. HOMER was used to call peaks using default parameters and FDR <5%
ATAC-seq data were aligned to hg19 using BWA-mem. MACS2 was used to call peaks using default parameters and FDR <5%
Assembly: hg19 (homo sapiens)
Supplementary files format and content: kallisto quantified abundance files for RNA-seq data
Supplementary files format and content: bigwig files for ChIP-seq, CUT&RUN, and ATAC-seq
Library strategy: CUT&Run

tag: chip antibody

value: Sall4 (D16H12) Rabbit mAb #86590

value: SV20 WT

value: day 5 cranial neural crest cell

value: cranial neural crest cell specification


description:
S12
Whole-blood RNA-seq from ACLF not treated (S12).
mRNAseq

value: Whole blood


title: B16-T-1_R1

description: Library name: Sample 7

value: CD8+ T lymphocytes


title: OVA-T-2_R1

description: Library name: Sample 11

value: Tumor (from B16-F10-OVA melanoma model)

value: B16-F10-OVA tumor-bearing mice treated with OT-1 CD8+ T cells; isolated from the suspension using Dynabeads positive selection with a CD8+ antibody


title: MT777_CUT_RUN_SALL4_SV20_WT_D0_rep1

description:
Library name: MT777_CUT_RUN_SALL4_SV20_WT_D0_rep1
CUT&Run

value: induced pluripotent stem cell


title: Whole-blood RNA-seq from preACLF (S102)

description:
S102
Whole-blood RNA-seq from preACLF (S102).
mRNAseq

value: preACLF


title: MT842_ATAC_seq_SV20_WT_D5_rep2

description:
Library name: MT842_ATAC_seq_SV20_WT_D5_rep2
ATAC-seq


title: Liver, healthy, biopsy, rep 5

value: Liver

value: Outbred

value: Liver cells

value: Unsorted


title: MT674_ATAC_seq_SV20_SALL4_KO_D5_rep1

description:
Library name: MT674_ATAC_seq_SV20_SALL4_KO_D5_rep1
ATAC-seq

value: SV20 SALL4-KO clone F1 (SALL4-het-KO)


title: MT844_ATAC_seq_SV20_SALL4_KO_D5_rep2

description:
Library name: MT844_ATAC_seq_SV20_SALL4_KO_D5_rep2
ATAC-seq


description:
S105
Whole-blood RNA-seq from ACLF not treated (S105).
mRNAseq


title: B16-OVA-3

description: Library name: Sample 6

value: melanoma

value: B16-F10-OVA tumor-bearing mice treated with OT-1 CD8+ T cells; isolated by FACS based on GCaMP6s expression


title: MT673_ATAC_seq_SV20_WT_D5_rep1

description:
Library name: MT673_ATAC_seq_SV20_WT_D5_rep1
ATAC-seq


description:
pS55
Whole-blood RNA-seq from ACLF not treated (pS55).
mRNAseq

value: ACLF not treated


title: MT748_ATAC_seq_SV20_WT_D0_rep2

description:
Library name: MT748_ATAC_seq_SV20_WT_D0_rep2
ATAC-seq

value: SV20 WT


title: HepG2 control biological rep3

value: immortalized liver cell

value: methanol control

value: 24 hour


title: B16-OVA-1

description: Library name: Sample 4


description:
S41
Whole-blood RNA-seq from ACLF not treated (S41).
mRNAseq

value: Whole blood


title: MT859_RNA_seq_SV20_SALL4_KO_D14_rep2

description:
Library name: MT859_RNA_seq_SV20_SALL4_KO_D14_rep2
RNA-Seq

value: day 14 cranial neural crest cell

value: cranial neural crest cell specification


title: MT857_RNA_seq_SV20_SALL4_KO_D14_rep1

description:
Library name: MT857_RNA_seq_SV20_SALL4_KO_D14_rep1
RNA-Seq


title: Liver healthy, biopsy, rep 3

description: allIntegrated_cca_kanchor5_noBiopsyHeps_dropletQCFiltered.RDS


description:
pS71
Whole-blood RNA-seq from ACLF not treated (pS71).
mRNAseq


title: B16-OVA-2

description: Library name: Sample 5

value: Tumor (from B16-F10-OVA melanoma model)


title: MT829_CUT_RUN_SALL4_SV20_WT_D5_rep1

description:
Library name: MT829_CUT_RUN_SALL4_SV20_WT_D5_rep1
CUT&Run

value: Sall4 (D16H12) Rabbit mAb #86590

value: day 5 cranial neural crest cell


title: B16-F10-2

description: Library name: Sample 2

value: Tumor (from B16-F10 melanoma model)

value: B16-F10; pLV[Exp]-Puro-EF1A>GCaMP6s

value: B16-F10 tumor-bearing mice treated with OT-1 CD8+ T cells; isolated by FACS based on GCaMP6s expression


title: MT855_RNA_seq_SV20_SALL4_KO_D5_rep3

description:
Library name: MT855_RNA_seq_SV20_SALL4_KO_D5_rep3
RNA-Seq

value: SV20 SALL4-KO clone F1 (SALL4-het-KO)


description:
pS37
Whole-blood RNA-seq from ACLF not treated (pS37).
mRNAseq


title: B16-F10-1

description: Library name: Sample 1

value: melanoma


title: MT858_RNA_seq_SV20_WT_D14_rep2

description:
Library name: MT858_RNA_seq_SV20_WT_D14_rep2
RNA-Seq


title: MT854_RNA_seq_SV20_WT_D5_rep3

description:
Library name: MT854_RNA_seq_SV20_WT_D5_rep3
RNA-Seq


description:
pS19
Whole-blood RNA-seq from ACLF not treated (pS19).
mRNAseq


title: B16-ova-IFN-r-3

description: Library name: Sample 10

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-houseperl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-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.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.6.0 was used to count the reads numbers mapped to each gene.
Assembly: GRCm39 (GCA_000001635.9)
Supplementary files format and content: xls file containing read counts per gene (rows) across samples (columns), with gene identifiers (e.g., Ensembl IDs).

value: B16-F10; pLV[Exp]-Neo-EF1A>{ovalbumin}

value: B16-OVA, treated with IFN-γ (50 ng/mL) for 24 hours


title: MT853_RNA_seq_SV20_SALL4_KO_D5_rep2

description:
Library name: MT853_RNA_seq_SV20_SALL4_KO_D5_rep2
RNA-Seq


title: MT852_RNA_seq_SV20_WT_D5_rep2

description:
Library name: MT852_RNA_seq_SV20_WT_D5_rep2
RNA-Seq

value: SV20 WT


description:
S32
Whole-blood RNA-seq from ACLF not treated (S32).
mRNAseq

value: ACLF not treated


title: MT851_RNA_seq_SV20_SALL4_KO_D5_rep1

description:
Library name: MT851_RNA_seq_SV20_SALL4_KO_D5_rep1
RNA-Seq


title: B16-ova-IFN-r-1

description: Library name: Sample 8


title: MT669_ATAC_seq_SV20_WT_D0_rep1

description:
Library name: MT669_ATAC_seq_SV20_WT_D0_rep1
ATAC-seq

value: induced pluripotent stem cell


title: MT850_RNA_seq_SV20_WT_D5_rep1

description:
Library name: MT850_RNA_seq_SV20_WT_D5_rep1
RNA-Seq


title: B16-ova-IFN-r-2

description: Library name: Sample 9


title: MT773_RNA_seq_SV20_SALL4_KO_D0_rep2

description:
Library name: MT773_RNA_seq_SV20_SALL4_KO_D0_rep2
RNA-Seq


description:
S10
Whole-blood RNA-seq from ACLF not treated (S10).
mRNAseq


title: U2OS IgG C207 treatment Rep3a

first: Austin

middle: J

last: Hepperla

address: 7018B Mary Ellen Jones Building

department: Genetics

institute: University of North Carolina at Chapel Hill

data_processing:
The CUT&RUN data was processed using the Nextflow (v23.04.2) nf-core/cutandrun pipeline (v3.2.2). Briefly, the nf-core/cutandrun pipeline performed the following steps: sequencing adapters were removed using Trim Galore (v0.6.6). A custom hg-38-AAV genome was made by combining hg38 chromosomes 1-22, X, Y, and M with the AAV SRW039 vector generated above. Using Bowtie 2 (v2.4.4), reads were aligned to both the custom hg38-AAV and E. coli (R64-1-1) genome. Reads were quality filtered, sorted, and indexed using samtools (v1.17), followed by duplicate read removal in both the hg38-AAV and E. coli genomes using Picard MarkDuplicates (v3.1.0). Spike-in normalized bigwig files were generated by converting the bam to a bedGraph using bedtools genomecov (v2.31.0) followed by running bedGraphToBigWig. Peaks were called on individual samples using MACS2 (v2.1.2). Peak windows were created by taking the peak summits and adding 500 base pairs in both directions to create equal-sized regions for even comparisons in subsequent analyses.
To create a union set of peaks across CUT&RUN replicates, we used a “score per million” (SPM) method first described by Corces et al. In brief, this method is more robust to peak and significance score increases that are driven by increased sample read depth. SPM creates relative peak (or region) score for each sample that can more directly be compared. Within each sample we calculated the per-region SPM by taking the individual peak score (−log10 × adjusted p-value) and dividing by the sum of all peak scores divided by 1 million. For each CUT&RUN target protein, every region in every sample was collected to make a cumulative union region set. A greedy algorithm stepped through each peak in the genome, keeping only the peak with the highest SPM value when peaks overlapped. deepTools (v3.5.4) was then used to calculate mean signal per peak. BRD4 signal scatterplots comparing treatments with and without C207 were generated in Python3 (v3.10.9), using the Pandas (v2.1.4) and Seaborn (v0.13.2) libraries by plotting the average, per-peak signal across replicates. deepTools multiBigwigSummary BED-file was used to calculate the per-replicate spike-in normalized, mean signal across the AAV genome, which was plotted using Python3 and Seaborn.
Assembly: hg38-AAV/SRW039
Supplementary files format and content: BigWig files contain the genome-wide, spike-in normalized signal.
Supplementary files format and content: The BRD4 union peaks txt file contains the 1000 bp peak region and the mean spike-in normalized signal from all four replicates. It also contains the log2 fold-change between -C207 and +C207 treatment (log2 -C207/+C207). Note: chrM peaks were removed to avoid artifacts in our analyses.
Supplementary files format and content: The hg38-AAV fasta file contains the custom hg38-AAV genome sequence, separated by chromosome. Only the standard chromosomes are included, and are labeled as chr1, chr2, … chr22, chrX, chrY, chrM, and chrAAV.
Supplementary files format and content: The hg38-AAV gtf file contains the custom hg38-AAV gene information, and combines the hg38 gene information with the AAV gene information as generated in this project.
Library strategy: CUT&RUN

source_name: cell line

growth_protocol: U2OS (ATCC) lines were cultured in McCoy’s 5A (Corning 10-050-CV) supplemented with 10% FBS (Atlantic Biologicals S11550) and 1% Penicillin-Streptomycin (Gibco 15140-122). All cells were maintained at 20%-90% confluency in a humidified incubator at 37C and 5% CO2. AAV transduction occurred 24h after cell seeding unless otherwise indicated.

extract_protocol:
The procedure for the isolation of nuclei and subsequent CUT&RUN of AAV genomes was adapted from the Epicypher CUTANA protocol (https://www.epicypher.com/resources/protocols/cutana-cut-and-run-protocol; see especially Appendex I: Isolation of Nuclei) using BioMag Plus Concanavalin A beads (Polysciences 86057), pAG-MNase (Cell Signaling Technologies 40366), and primary antibodies for BRD4 (Abcam ab128874, 1:50) or IgG (Jackson ImmunoResearch 009-000-003, 1:50). Approximately 500k U2OS nuclei were used for each CUT&RUN reaction. U2OS cells were permeabilized in the presence of 0.01% digitonin. Primary antibody incubation occurred on a nutating mixer (Corning 10-320-100) at 4C overnight. To improve the signal-to-noise ratio, an additional step of secondary antibody incubation (Guinea Pig Anti-IgG, ABIN101961, 1:100) on a nutating mixer for 1h at 4C was included. Per reaction, 50 ng of S. cerevisiae genomic spike-in DNA (Provided with Cell Signaling Technologies 40366) was added with the addition of stop buffer. Released DNA fragments were purified using the DNA Clean & Concentrator-25 Kit (Zymo D4033) and double eluted in 28 uL of warm elution buffer.
CUT&RUN-enriched DNA was barcoded and amplified using the NEBNext Ultra II DNA Library Prep with Sample Purification Beads kit (New England Biolabs E7103L) and NEBNext Multiplex Oligos for Illumina (E6440L). Bead based size selection was conducted by a 28 uL first bead addition and a 13 uL second bead addition. Library concentrations were determined using the Qubit 1X dsDNA High Sensitivity (HS) Assay Kit (Invitrogen Q33230) and a Qubit 4 Fluorometer (Thermo Fischer). The average fragment size of each library (~350-450 bp) was determined using High Sensitivity D1000 Reagents (Agilent 5067-5585) and ScreenTape (Agilent 5067-5584) on a 2100 Bioanalyzer (Agilent). Libraries were pooled and sequenced to a depth of > 11M reads per sample (2 x 150 bp paired-end reads) with NextSeq1000/2000 P2 Reagents 300 cycles (Illumina 20050264).

treatment_protocol: U2OS cells were seeded into 10 cm plates at a density of 875k cells/plate. After 24h, cell media was replenished with fresh media containing 10k vg/cell of ssAAV2-Jet-T2a-Luc. 24h later, C207 or an equivalent volume of DMSO was diluted in media and added in biological quadruplicate. Following 24h of chemical incubation, cells were harvested with 0.05% Trypsin-EDTA, pelleted, and washed twice with PBS.

value: cell line

tag: antibody

value: IgG

value: AAV-transduced


title: MT856_RNA_seq_SV20_WT_D14_rep1

description:
Library name: MT856_RNA_seq_SV20_WT_D14_rep1
RNA-Seq

value: day 14 cranial neural crest cell

value: cranial neural crest cell specification


description:
S08
Whole-blood RNA-seq from ACLF not treated (S08).
mRNAseq

tag: tissue

value: Whole blood


title: MT771_RNA_seq_SV20_SALL4_KO_D0_rep1

description:
Library name: MT771_RNA_seq_SV20_SALL4_KO_D0_rep1
RNA-Seq

tag: cell type


title: B16-ova-2

description: Library name: Sample 7

value: Untreated control


title: B16-ova-1

description: Library name: Sample 6


title: U2OS IgG C207 treatment Rep2


title: MT770_RNA_seq_SV20_WT_D0_rep1

description:
Library name: MT770_RNA_seq_SV20_WT_D0_rep1
RNA-Seq


title: U2OS IgG C207 treatment Rep1


description:
S62
Whole-blood RNA-seq from ACLF not treated (S62).
mRNAseq

tag: group


description:
pS30
Whole-blood RNA-seq from ACLF not treated (pS30).
mRNAseq


title: B16-IFN-r-2

description: Library name: Sample 4

value: B16-F10, treated with IFN-γ (50 ng/mL) for 24 hours


title: U2OS IgG no treatment Rep2


description:
pS58
Whole-blood RNA-seq from ACLF not treated (pS58).
mRNAseq


title: U2OS IgG no treatment Rep3


title: U2OS IgG no treatment Rep1


title: B16-IFN-r-3

description: Library name: Sample 5


description:
S47
Whole-blood RNA-seq from ACLF not treated (S47).
mRNAseq


title: U2OS H3K27ac C207 treatment Rep4


title: B16-IFN-r-1

description: Library name: Sample 3


title: B16-2

description: Library name: Sample 2


description:
pS68
Whole-blood RNA-seq from ACLF not treated (pS68).
mRNAseq


title: U2OS H3K27ac C207 treatment Rep2


title: U2OS H3K27ac C207 treatment Rep1


title: U2OS H3K27ac no treatment Rep1


title: U2OS H3K27ac C207 treatment Rep3


description:
S84
Whole-blood RNA-seq from ACLF not treated (S84).
mRNAseq


title: U2OS H3K27ac no treatment Rep3


title: B16-1

description: Library name: Sample 1


title: MT772_RNA_seq_SV20_WT_D0_rep2

description:
Library name: MT772_RNA_seq_SV20_WT_D0_rep2
RNA-Seq


title: Tiki2-ko kidneys after ischemia-reperfusion on day 7, rep3

city: Wuhan

first: Cui

last: Yang

state: hubei

address: Luoyu Road 1037

department: College of Life Science and Technology

institute: Huazhong University of Science and Technology

description:
Library name: A814_Cre_3
RNA-Seq of Mus musculus: Sample-6

data_processing:
Software fastp 0.23.0 was used to process the raw data and filter low-quality sequences.
The transcriptome sequencing Reads were compared to the reference genome using the software HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts, 2.1.0).
Reads Count was calculated using HTSeq,
Normalization of Reads Count by using DESeq2 (1.18.1) software, and the data were used for difference analysis |log2(FoldChange)|＞1 & padj＜0.05.
Software ClusterProfier (3.6.0) was used for functional enrichment analysis.
Assembly: mm10
Supplementary files format and content: csv files include TPM values for each Sample

source_name: kidney

extract_protocol:
The total RNA was extracted by RNA-easy Isolation Reagent (Vazyme, R701),  2ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Oligo (DT) beads, (1) The mRNA with polyA structure was captured by magnetic beads with Oligo (DT);  (2) The first strand of cDNA was synthesized in M-MuLV reverse transcriptase system using fragmented mRNA as template and random oligonucleotides as primers; (3) The RNA strand was degraded by RNaseH and the second cDNA strand was synthesized by dNTPs in the DNA polymerase I system; (4) The double-stranded cDNA was purified, and the end was repaired, the A-tail was added and the sequencing joint was connected; (5) cDNA about 200bp was screened with AMPure XP beads, amplified by PCR, purified by AMPure XP beads again, and finally sequencing library was obtained.

treatment_protocol: Control and Tiki2PTKO mice were suffered unilateral ischemia-reperfusion injury for 30 min at 37±0.2℃, the injured kidneys were harvested on day 7 after reperfusion.

value: kidney

value: Tiki2 conditional knockout

value: ischemia reperfusion injury


title: U2OS H3K27ac no treatment Rep2


description:
pS70
Whole-blood RNA-seq from ACLF not treated (pS70).
mRNAseq


description:
pS41
Whole-blood RNA-seq from ACLF not treated (pS41).
mRNAseq


title: U2OS H3K27ac no treatment Rep4


title: Tiki2-ko kidneys after ischemia-reperfusion on day 7, rep2

description:
Library name: A811_Cre_2
RNA-Seq of Mus musculus: Sample-5


title: U2OS H3K9ac C207 treatment Rep2


title: U2OS H3K9ac C207 treatment Rep3


description:
S67
Whole-blood RNA-seq from ACLF treated (S67).
mRNAseq

value: ACLF treated


title: Tiki2-ko kidneys after ischemia-reperfusion on day 7, rep1

description:
Library name: A808_Cre_1
RNA-Seq of Mus musculus: Sample-4


title: U2OS H3K9ac no treatment Rep4


title: kidneys after ischemia-reperfusion on day 7, rep3

description:
Library name: A825_Con_3
RNA-Seq of Mus musculus: Sample-3

value: WT


title: U2OS H3K9ac C207 treatment Rep1


title: U2OS H3K9ac no treatment Rep3


description:
S71
Whole-blood RNA-seq from ACLF treated (S71).
mRNAseq


title: U2OS H3K9ac no treatment Rep1


title: kidneys after ischemia-reperfusion on day 7, rep1

description:
Library name: A802_Con_1
RNA-Seq of Mus musculus: Sample-1


description:
pS10
Whole-blood RNA-seq from ACLF treated (pS10).
mRNAseq


title: U2OS H3K9ac no treatment Rep2


title: kidneys after ischemia-reperfusion on day 7, rep2

description:
Library name: A805_Con_2
RNA-Seq of Mus musculus: Sample-2


title: U2OS H3K9ac C207 treatment Rep4


title: U2OS BRD4 C207 treatment Rep4


title: U2OS BRD4 C207 treatment Rep2


title: PHx_7d_2

city: jinan

first: Jiabei

last: Lian

state: Shandong

address: No.44, Wenhauxi Road, Lixia District, Jinan, China

department: College of Basic Medical Sciences

institute: Shandong University

description:
Library name: PHx_7d_2
7 d after 70% partial hepatectomy

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes FPKM values for each sample, which have been adjusted for batch effects across the two sample submissions to ensure data consistency and comparability.

source_name: liver

growth_protocol: Hepatocytes were freshly isolated from different time points (6 h,12 h,24 h,48 h,72 h,7 d,14 d,21 d) of the liver regeneration after PHx in mice for RNA extraction.

extract_protocol:
Total mRNA was isolated by TRIzol (Takara) or FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme) following the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

value: liver

value: partial hepatectomy


title: PHx_21d_2

description:
Library name: PHx_21d_2
21 d after 70% partial hepatectomy


description:
S87
Whole-blood RNA-seq from ACLF treated (S87).
mRNAseq


description:
S89
Whole-blood RNA-seq from ACLF treated (S89).
mRNAseq


title: PHx_14d_2

description:
Library name: PHx_14d_2
14 d after 70% partial hepatectomy


description:
S27
Whole-blood RNA-seq from ACLF treated (S27).
mRNAseq


title: U2OS BRD4 C207 treatment Rep1


title: U2OS BRD4 no treatment Rep3


title: U2OS BRD4 no treatment Rep4


title: U2OS BRD4 no treatment Rep1


description:
S64
Whole-blood RNA-seq from ACLF treated (S64).
mRNAseq


description:
S09
Whole-blood RNA-seq from ACLF treated (S09).
mRNAseq


title: SV20 HEP, TF input

city: Vancouver

first: Tabea

middle: L

last: Stephan

state: BC

address: 2329 West Mall

institute: University of British Columbia

data_processing:
aligned to hg19/GRCH37 using STAR (v2.5.0)
Bam files filtered using encode_task_filter.py from the ENCODE chip-seq-pipeline2, dublicate reads mapped using Picard (v2.1.1.1), unmapped, unpaired, low quality (MAPQ<5), non-primary alignment reads removed using SAM flag filter '-F 1804' using SAMtools (v1.3)
peaks were called using MACS2
Bigwig files were generated using MACS2 and deeptools
Assembly: hg19
Supplementary files format and content: bigwig

source_name: Hepatoblast stage

growth_protocol: SV20 iPSCs were differentiated as previously described (Si-Tayeb et al., 2010 and Teng Ang et al., 2018). Briefly, cells were grown on Geltrex-coated plates to 100% confluency and subsequently differentiated into mesendodermal progenitors using RPMI media supplemented with 1x B27 minus insulin, Activin A (100ng/ml), FGF2 (20ng/ml) and BMP4 (10ng/ml) for 48h. Definitive endodermal cells were further differentiated with Activin A (100 ng/ml) and 1x B27 minus insulin only for additional 48h. Alternatively, definitive endodermal cells were generated using STEMdiff definitive Endoderm Kit (Stemcell Technologies). Subsequently, cells were specified to hepatic endodermal cells for 96h in RPMI supplemented with 1x B27 with insulin, BMP4 (20ng/ml) and FGF2 (10ng/ml) at 4% O2 or for 24h in IMDM/F12 supplemented with A8301 (1uM), BMP4 (30ng/ml), FGF2 (10ng/ml) and TTNPB (75nM) for 24h followed by Activin A (10ng/ml), BMP4 (30ng/ml), 8-bromo-cAMP (1mM) and C-59 (1µM, first 24h)/CHIR99201(1µM, next 48h) for 96h in atmospheric O2. Hepatoblasts were generated with BMP4 (10ng/ml), OSM (10ng/ml), Dexamethasone (10µM), RO4929097 (2µM), Forskolin (10µM), insulin (10µg/ml), transferrin (15µg/ml), AAP (200µg/ml) and SB505124 (1µM, just first 48h) in full IMDM/F12 media for 6 days in atmospheric O2 or by incubation at 4% O2 and in RPMI supplemented with 1x B27 with insulin and HGF (20ng/ml) only.

extract_protocol:
1 million (histone modification ChIP-seq) to 10 million (transcription factor ChIP-seq) cells were cross-linked with 1 % fresh methanol-free formaldehyde for 10 min at room temperature (RT). The cross-linking was stopped with the addition of fresh glycine to a final concentration of 0.125M and incubation for 5 min at RT. Cells were subsequently washed twice with cold PBS, pelleted and resuspended in cold ChIP lysis buffer and lysed for 15 min on ice while dounce homogenizing 20x during the incubation. After re-pelleting, nuclei were resuspended in ChIP nuclear lysis buffer for 30-60 min on ice. Chromatin was sheared by sonication for 20 cycles at 60 hz for 30 sec on/30 sec off. Cellular debris was removed by centrifugation. Chromatin was pre-cleared by rotating at 4 °C for 1h with Protein A/G Ultralink beads (Thermo Fisher Scientific, Pierce) in ChIP dilution buffer. Chromatin was incubated with primary antibodies overnight at 4°C while rotating. Protein A/G Ultralink beads (Thermo Fisher Scientific, Pierce) were added to the immunoprecipitation (chromatin + antibody) mix and incubated at 4°C for further 4 hours. Unbound fraction of the IgG chromatin solution was kept as input DNA. Beads were subsequently washed for 5 min at 4°C once each in low salt buffer, high salt buffer, lithium chloride buffer, followed by two washes in TE buffer, before eluting the DNA by incubating the beads in 125µl-250µl fresh elution buffer for 15 min at RT while vortexing/rotating. To reverse the cross-linking, samples were incubated overnight at 65°C in 0.192M NaCl, 40mM Tris-Cl, pH6.5, 10mM EDTA, 0.08mg/ml Proteinase K and 0.1 mg/ml RNaseA. DNA was subsequently extracted and purified by phenol-chloroform extraction and precipitated in Ethanol at -80°C before being resuspended in 50µl of H2O.
samples were library prepped using the NEBNext Ultra II DNA library Prep Kit for Illumina following manufacturer’s recommendations

value: Hepatoblast stage

value: differentiated iPSC


title: PHx_72h_2

description:
Library name: PHx_72h_2
72 h after 70% partial hepatectomy


title: U2OS BRD4 no treatment Rep2

value: cell line


title: SV20 HE, TF input

source_name: Hepatic endodderm stage

value: Hepatic endodderm stage


description:
S60
Whole-blood RNA-seq from ACLF treated (S60).
mRNAseq


title: SV20 GT, input

source_name: Gut tube stage

value: Gut tube stage


title: PHx_48h_2

description:
Library name: PHx_48h_2
48 h after 70% partial hepatectomy


title: U2OS BRD4 C207 treatment Rep3

value: AAV-transduced


title: SV20 HEP,HNF4A, ChIP

value: clone K9218, abcam


description:
S57
Whole-blood RNA-seq from ACLF treated (S57).
mRNAseq

value: Whole blood


title: SV20 HE, TBX3, ChIP

value: 22HCLC, Thermo Fisher Scientific


title: SV20 GT, HNF4A, ChIP


title: PHx_24h_2

description:
Library name: PHx_24h_2
24 h after 70% partial hepatectomy


title: SV20 HEP, TBX3, ChIP


description:
S45
Whole-blood RNA-seq from ACLF treated (S45).
mRNAseq


description:
S23
Whole-blood RNA-seq from ACLF treated (S23).
mRNAseq


description:
S83
Whole-blood RNA-seq from ACLF treated (S83).
mRNAseq


title: PHx_6h_2

description:
Library name: PHx_6h_2
6 h after 70% partial hepatectomy


title: WT CRE 3

city: Nanjing

first: Yuzhuo

last: Xu

address: 12 Xue-fu Road, Pukou District

institute: Nanjing University

description: Library name: Sample6

data_processing:
FastQc were used for data quality control.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SeqPrep and Sickle.
Paired-end clean reads were aligned to the reference genome using the HISAT2 2.1.0; RSEM was used to calculate FPKM.
Differential expression analysis was performed using the DESeq v1.26.0.
Assembly: GRCm39
Supplementary files format and content: xls files include counts and tpm values for each sample

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA sample prep kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: mouse embryonic stem cell


title: WT CRE 2

description: Library name: Sample5