title: P1_7dpr,mouse heart,visium

city: Shanghai

first: Qi

last: Tang

address: 320 Yue Yang Road

institute: CAS Center for Excellence in Molecular Cell Science

data_processing:
Raw sequencing data were processed using 10x Genomics Space Ranger pipeline to generate FASTQ files. Sequencing data  were aligned to mm10 genenome to gene expressing counts using default seting of Space Ranger.
Assembly: mm10
Supplementary files format and content: zip
Library strategy: Spatial Transcriptomics

source_name: heart

extract_protocol:
the post-injury hearts were harvested after the blood was washed with PBS (DEPC). Harvested hearts were immersed in pre-cooled OCT and maintained at -80°C until section. 10μm sections were taken from the largest cross-section of the heart and attached to the 10x Visim gene expression chip.
library preparation was performed according to the manufacturer’s instructions.

value: heart

value: apex resection

value: neonatal mouse heart

value: 7day post injury at P1


title: HUVECs transduced with FOXA3, HNF1A and HNF6, Day16, Lot.2-2

status: Public on Nov 24 2025

type: SRA

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

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

department: Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

library_source: genomic

data_processing:
The raw sequences were initially trimmed using Trim Galore (v0.6.5). Subsequently, the trimmed sequences were aligned to the reference genome with bowtie2 (v2.3.5.1). Mitochondrial genome-derived reads and PCR duplicates were removed using samtools (v1.14) and Picard (v2.21.4), respectively. Finally, bigWig files were generated by calculating coverage with deepTools (v3.5.1).
Assembly: GRCh38
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Homo sapiens

source_name: Umbilical Vein

growth_protocol: hiHepPCs were cultured in DMEM/F12 and Fibrolife mixture medium with 4% FBS, 1 µg/ml insulin, 10^-7 M dexamethasone, 10 mM nicotinamide, 2 mM L-glutamine, 50 µM 2-mercaptoethanol, and penicillin/streptomycin, containing 20 ng/ml HGF, 1 µM A83-01, 2 µM SB431542, and 5 µM Y27632.

extract_protocol:
The cultured cells were collected at specified time points by trypsinization. Using 50,000 cells per reaction, the experiment was conducted following the publicly available standard Omni ATAC-seq protocol (PMID: 28846090).
The collected genomic DNA fragments were purified using a PCR purification kit (QIAGEN), and indexing and amplification were performed with the NEBNext High-Fidelity 2X PCR Master Mix (NEB). The amplified library was then purified and size-selected using AMPure XP (BECKMAN COULTER).

treatment_protocol: Induction of hiHepPCs was carried out with or without 3 µM CHIR99021.

tag: tissue

value: Umbilical Vein

tag: cell line

value: Primay Cells

tag: cell type

value: Endothelial Cells

tag: genotype

value: Forced expression of FOXA3, HNF1A and HNF6

tag: treatment

tag: time

value: Day 16


title: P1_3dpr,mouse heart,visium

country: China

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

value: WT

value: 3day post injury at P1


title: P1_1dpr,mouse heart,visium

value: 1day post injury at P1


title: Apex1 KO 14 days post fracture rep 3

city: Pamplona

first: Asier

last: Ullate-Agote

state: Navarra

address: Av. de Pío XII, 55

department: Hemato-Oncology

country: Spain

institute: CIMA

data_processing:
bcl2fastq v2.20 was used to demultiplex and FASTQ files were aligned to the mouse genome (mm39) using STAR (v2.7.0d). Gene expression quantification was performed using the featureCounts function implemented in the R package Rsubread (v2.4.3) counting uniquely mapped paired-end reads with reverse strandness. The Ensembl v104 gene annotation was considered as the reference.
Normalization, processing and differential expression analyses were performed using DEseq2 (v1.32.0)
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Fracture callus

extract_protocol:
RNA was extracted using Trizol reagent after homogenizing the fracture callus with liquid nitrogen and a mortar
RNA-seq libraries were prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus according to the manufacturer’s instructions

value: Fracture callus

tag: Sex

value: Female

value: Apex1 KO

value: 14 days post fracture


title: Cyp2c29 KO mouse liver 3

city: Durham

first: Brian

last: Bennett

address: 111 T.W. Alexander Drive

country: USA

institute: NIEHS

description: Library name: Sample 10

data_processing:
Counts generated with Salmon and GENCODE vM36
Assembly: mm39
Supplementary files format and content: tab-delimited text: column 1 = gene, column 2 = counts

source_name: Liver

extract_protocol:
Qiagen Midiprep
Total RNA-seq libraries were generated in the NIEHS Epigenomics Core using Ribo-Zero Gold and sequenced on the Illumina NovaSeq 6000 to over 140 million reads per biological replicate.

value: Liver

value: Cyp2c29 KO

value: CDAA diet


title: P1,mouse heart,visium

value: heart

value: no injury

value: neonatal mouse heart

value: P1 without injury


title: HUVECs transduced with FOXA3, HNF1A and HNF6, Day44, Lot.2-1

value: Umbilical Vein

value: Primay Cells

value: Endothelial Cells

value: Day 44


title: AAV-Clu,mouse heart,singlecell

description: AAV-Clu

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counitng and aggregation were made using the Cell Ranger software v2.1.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: mm10
Supplementary files format and content: zip

extract_protocol:
The mouse heart was delicately placed within a 1.5ml EP tube and precisely sectioned into uniform 1mM^3 pieces, using chilled scissors to maintain a low temperature throughout the process. Subsequently, the tissue fragments underwent digestion in a solution consisting of 0.125% trypsin and 0.026g of collagenase II per 10 ml of DMEM medium. The resulting mixture was transferred to a digestion flask and incubated at 37°C for 15 min. After incubation, the supernatant was gently transferred into PBS (0.04% BSA). To ensure thorough cell dissociation, an additional 5ml of the digestion solution was introduced to the residual tissue precipitate, undergoing an additional 15 min of digestion. The subsequent supernatant was combined with the previously collected supernatant, and the resulting solution underwent centrifugation at 300g for 5 min at 4°C. The cellular precipitate was then treated with red blood cell lysis buffer (BD, 555899) for 5 min, followed by resuspension of the cells in PBS (0.04% BSA). The dead cell removal kit (Miltenyi, 130-090-101) was meticulously employed to remove non-viable cells per the manufacturer's instructions. Following removal, the cells underwent centrifugation and were ultimately resuspended in PBS, with cell concentration adjusted following the guidelines provided by the 10x Genomics sequencing instructions. For the scRNA-seq analysis of CD45+ cells, cells were obtained using flow cytometry. Cells were then resuspended in PBS (containing 0.04% BSA) and centrifuged for 5 min at 500g at 4°C. The resulting cell pellet was resuspended in 500 μl of FACs buffer, to which an anti-CD45 antibody was added. The mixture underwent a 40-minute incubation period. Following incubation, cells were sorted to isolate F4/80+ cells selectively for subsequent construction of the scRNA-seq library.
The generation of single-cell RNA-seq libraries followed a meticulously executed protocol utilizing the Single Cell 3′ Reagent Kits v3.1 (10x Genomics). In a concise overview of the process, reagents (10x Genomics, PN-120237), gel beads (10x Genomics, 220104), and partitioning oil (10x Genomics, 220088) were accurately loaded alongside the sorted cells into the Chromium Single Cell A Chip (10x Genomics, 2000019). This procedure aimed to target approximately 8000 cells per channel. Following the careful loading of the chip, it was placed within the Chromium Controller (10x Genomics) to initiate the generation of Gel Bead-In-Emulsions (GEMs). After GEM generation, the preparation of single-cell RNA-Seq libraries was executed with the Chromium Single Cell 3’ Gel Bead and Library Kit. Sequencing was performed employing the Illumina Nextseq 150 PE system, utilizing two paired-end kits.

value: overexpressed Clu by AAV9

value: CD45+ cells

value: WT

value: 3day post injury at P8


title: Cyp2c29 KO mouse liver 4

description: Library name: Sample 11


title: P1_7dpr,mouse heart,singlecell

value: apex resection

value: 7day post injury at P1


title: AAV-GFP,mouse heart,singlecell

description: AAV-GFP

value: overexpressed GFP as control by AAV9


title: HUVECs transduced with FOXA3, HNF1A and HNF6, Day9, Lot.2-1

value: Forced expression of FOXA3, HNF1A and HNF6

value: Day 9


title: P1_3dpr,mouse heart,singlecell

value: heart

value: 3day post injury at P1


title: Apex1 KO 14 days post fracture rep 1

value: Fracture callus

value: Female

value: Apex1 KO

value: 14 days post fracture


title: HUVECs transduced with FOXA3, HNF1A and HNF6, Day16, Lot.2-1

value: Umbilical Vein

value: Primay Cells

value: Endothelial Cells

value: Day 16


title: HUVECs transduced with FOXA3, HNF1A and HNF6, with CHIR99021, Day9, Lot.1-2


title: Cyp2c29 KO mouse liver 2

description: Library name: Sample 9

value: Liver

value: Cyp2c29 KO

value: CDAA diet


title: Cyp2c29 KO mouse liver 5

description: Library name: Sample 12


title: P1,mouse heart,singlecell

value: no injury

value: neonatal mouse heart

value: WT

value: P1 without injury


title: P1_1dpr,mouse heart,singlecell

value: heart

value: apex resection

value: 1day post injury at P1


title: WT mouse liver 6

description: Library name: Sample 6


title: HUVECs transduced with FOXA3, HNF1A and HNF6, with CHIR99021, Day9, Lot.1-1

value: Forced expression of FOXA3, HNF1A and HNF6

value: Day 9


title: Ctrl_3.

first: Wei

last: Zuo

state: Shanghai

address: No. 500 Zhennan Road, Putuo District, Shanghai

institute: University

description:
Library name: Sample 3
Column name in Count_FPKM_Matrix: Ctrl_3_count and Ctrl_3_fpkm

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PECluster Kit v3-cBot-HS (Illumia) according to the manufacturer's instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: 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. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM,expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Supplementary files format and content: csv file include Count and FPKM values for each sample

source_name: Lung

growth_protocol: Human airway BCs were plated onto irradiated 3T3 fibroblast feeder cells from ATCC and cultured in Dulbecco's Modified Eagle Medium (DMEM)/Nutrient Mixture F-12 (Gibco, NY, USA), including 10% FBS (ExCell Bio, Shanghai, China), Pen/Strep (Gibco), L-glutamine (Gibco), and growth factor cocktail for BC-selective growth and expansion.

extract_protocol:
Total RNA was extracted from Human basal cells using Trizol (15596018CN, Invitrogen), and RNA extraction was performed according to the manufacturer’s instructions. Subsequently, the extracted RNA was treated with Dnase I (Invitrogen, Life Technologies, USA) to remove any contaminating DNA. RNA integrity was assessed using theRNA Nano 6000 Assay Kit of the Bioanalyzer2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. 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 First StrandSynthesisReaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLVReverse Transcriptase(RNaseH-). Second strand cDNA synthesis was subsequently performed usingDNAPolymeraseI and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNAfragments of preferentially370~420 bp in length, the library fragments were purified with AMPure XP system(Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XPsystem) and library quality was assessed on the Agilent Bioanalyzer2100 system.

treatment_protocol: Human BCs were stimulated with control or bleomycin BALF in culture for 24hours.

value: Lung

value: P63+ airway basal stem cells

value: airway basal stem cells

value: stimulated by BALF from mouse normal lungs


title: Ctrl_2.

description:
Library name: Sample 2
Column name in Count_FPKM_Matrix: Ctrl_2_count and Ctrl_2_fpkm


title: BLM_1

description:
Library name: Sample 4
Column name in Count_FPKM_Matrix: BLM_1_count and BLM_1_fpkm

value: stimulated by BALF from mouse fibrotic lungs


title: WT mouse liver 5

description: Library name: Sample 5

value: Liver


title: Ctrl_1.

description:
Library name: Sample 1
Column name in Count_FPKM_Matrix: Ctrl_1_count and Ctrl_1_fpkm


title: PROTAC_3

description:
Library name: Sample 6
Column name in TGF-β_Count_FPKM_Matrix: PROTAC_3_count and PROTAC_3_fpkm

growth_protocol: WT BCs and PROTAC BCs were plated onto irradiated 3T3 fibroblast feeder cells from ATCC and cultured in Dulbecco's Modified Eagle Medium (DMEM)/Nutrient Mixture F-12 (Gibco, NY, USA), including 10% FBS (ExCell Bio, Shanghai, China), Pen/Strep (Gibco), L-glutamine (Gibco), and growth factor cocktail for BC-selective growth and expansion.

extract_protocol:
Total RNA was extracted from Ctrl BCs and PROTAC BCs using Trizol (15596018CN, Invitrogen), and RNA extraction was performed according to the manufacturer’s instructions. Subsequently, the extracted RNA was treated with Dnase I (Invitrogen, Life Technologies, USA) to remove any contaminating DNA. RNA integrity was assessed using theRNA Nano 6000 Assay Kit of the Bioanalyzer2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. 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 First StrandSynthesisReaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLVReverse Transcriptase(RNaseH-). Second strand cDNA synthesis was subsequently performed usingDNAPolymeraseI and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNAfragments of preferentially370~420 bp in length, the library fragments were purified with AMPure XP system(Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XPsystem) and library quality was assessed on the Agilent Bioanalyzer2100 system.

treatment_protocol: WT BCs and PROTAC BCs were stimulated with 10ng/ml recombinant TGF-β1 in culture for 24hours

value: PROTAC

value: 10ng/ml recombinant TGF-β1


title: PROTAC_2

description:
Library name: Sample 5
Column name in TGF-β_Count_FPKM_Matrix: PROTAC_2_count and PROTAC_2_fpkm


title: WT mouse liver 4

description: Library name: Sample 4

value: CDAA diet


title: Cyp2c29 KO mouse liver 1

description: Library name: Sample 8

value: Cyp2c29 KO


title: WT mouse liver 3

description: Library name: Sample 3

value: WT


title: HUVECs transduced with FOXA3, HNF1A and HNF6, with CHIR99021, Day16, Lot.1-1

value: Umbilical Vein

value: Primay Cells

value: Endothelial Cells

value: Day 16


title: WT mouse liver 7

description: Library name: Sample 7


title: Ctrl_3

description:
Library name: Sample 3
Column name in TGF-β_Count_FPKM_Matrix: Ctrl_3_count and Ctrl_3_fpkm


title: HUVECs transduced with FOXA3, HNF1A and HNF6, with CHIR99021, Day16, Lot.1-2

value: Forced expression of FOXA3, HNF1A and HNF6


title: HUVECs transduced with FOXA3, HNF1A and HNF6, Day44, Lot.1-2

value: Day 44


title: BLM_2

description:
Library name: Sample 5
Column name in Count_FPKM_Matrix: BLM_1_count and BLM_1_fpkm

value: Lung


title: WT mouse liver 2

description: Library name: Sample 2


title: Ctrl_2

description:
Library name: Sample 2
Column name in TGF-β_Count_FPKM_Matrix: Ctrl_2_count and Ctrl_2_fpkm

value: P63+ airway basal stem cells


title: BLM_3

description:
Library name: Sample 6
Column name in Count_FPKM_Matrix: BLM_1_count and BLM_1_fpkm

value: airway basal stem cells


title: WT mouse liver 1

description: Library name: Sample 1


title: HUVECs transduced with FOXA3, HNF1A and HNF6, Day16, Lot.1-2


title: HUVECs transduced with FOXA3, HNF1A and HNF6, Day9, Lot.1-2

value: Day 9


title: Ctrl_1

description:
Library name: Sample 1
Column name in TGF-β_Count_FPKM_Matrix: Ctrl_1_count and Ctrl_1_fpkm


title: Patient3, CDK9

city: Ann Arbor

first: Chenguang

last: Wang

state: Michigan

address: 1500E Medical Center Dr, Room 4411

department: Department of Internal Medicine

institute: University of Michigan

description: Library name: Pt3_CDK9

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (v2.3)
Trimmed sequence reads were mapped to GRCh38/hg38 using bwa (v0.7.15), all uniquely matched reads were retained
Mapped reads were sorted and multimapping reads were filtered using samtools (v0.1.19). PCR duplicates were marked using Picard Markduplicate.
Peak calling was performed by MACS2 (v2.1.2) to generate bed files with following parameters: --nomodel --extsize 50 -f BAM --keep-dup auto -g hs -p 0.01 -B
Bigwig(bw) files were generated by Deeptools (v2.0)
Assembly: hg38
Supplementary files format and content: bw file showing binding density across genome

source_name: lymph node

growth_protocol: All cell lines were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was digested using a Micrococcal Nuclease (CST). Chromatin DNA was purified using QIAquick PCR purification kit. 500ng DNA were used for library preparation.
ChIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit following manufacturer's protocol.

value: lymph node

value: FFPE sections

value: PTCL, NOS


title: Patient3, input

description: Library name: Pt3_input


title: Patient3, cyclin T1

description: Library name: Pt3_CCNT1


title: HUVECs transduced with FOXA3, HNF1A and HNF6, Day9, Lot.1-1


title: HUVECs transduced with FOXA3, HNF1A and HNF6, Day16, Lot.1-1


title: Patient2, input

description: Library name: Pt2_input


title: PROTAC_1

description:
Library name: Sample 4
Column name in TGF-β_Count_FPKM_Matrix: PROTAC_1_count and PROTAC_1_fpkm

value: PROTAC

value: 10ng/ml recombinant TGF-β1


title: T cells, SspA/HDM-treated skin

city: Charlestown

first: Jin Mo

last: Park

state: MA

address: 149 Thirteenth Street

department: Cutaneous Biology Research Center

institute: Massachusetts General Hospital

description:
Library name: Sample library
10X Genomics

data_processing:
Sequencing reads were processed for single-cell gene expression analysis using Cell Ranger (v7.1.0).
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Skin

extract_protocol:
Single-cell suspensions were prepared from mouse dorsal skin. T cells in the single-cell suspensions were enriched using the EasySep Mouse T Cell Isolation Kit (STEMCELL Technologies) and further purified by soring with FACSAria (BD Biosciences).
Sorted live T cells were loaded onto a Chromium chip for encapsulation and barcoding. Libraries were constructed using the Single Cell 5’ Kit (10X Genomics). The resulting libraries were sequenced using NovaSeq 6000 (Illumina).

treatment_protocol: Shaved and depilated mouse dorsal skin was treated with epicutaneous SspA and HDM.

tag: strain

value: Wild-type

value: Skin

value: T cell

value: SspA and HDM combination

tag: batch


title: Patient2, cyclin T1

description: Library name: Pt2_CCNT1


title: Patient2, CDK9

description: Library name: Pt2_CDK9


title: LbT2b_activin_rep_2

city: Los Angeles

first: Michel

middle: A

last: Zamojski

state: California

address: 8700 Beverly Boulevard

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

description: Library name: act_Veh_2_S13

data_processing:
The nf-core/atacseq (v2.1.2) pipeline was used to process ATAC-seq data. Preprocessed reads were aligned to GRCm38 reference genome using bowtie2; the rest of the pipeline was run using default settings.
Assembly: GRCm38/mm10
Supplementary files format and content: Normalized coverage tracks of open chromatin: BigWig format.
Supplementary files format and content: MACS2 called peaks in BED-like broadPeak format.
Supplementary files format and content: HOMER peak annotations: tab-delimited text file.
Supplementary files format and content: ATAQV QC report in JSON format.

growth_protocol: LβT2b cells were seeded in 12-well plates at 350,000 cells/well in Dulbecco's Modified Eagle Medium (DMEM)/10% fetal bovine serum (FBS).

extract_protocol:
Cells  were trypsinized, counted, and 50,000 cells were placed per tube. Briefly, cells were washed with cold PBS at 4°C and lysed for 10 min at 4°C, before proceeding with the ATAC protocol.
Cell pellets were resuspended in the transposase reaction mix [5 µl 2× TD buffer, 0.5 µl transposase (Illumina) and 4.5 µl nuclease-free water] and incubated at 37°C for 30 min. DNA from the transposase reaction was purified with a DNA Clean & Concentrator-5 Kit (Zymo Research). PCR amplification was performed using Nextera PCR primers. The optimal number of cycles was determined via quantitative real-time PCR (qPCR) to stop the amplification before saturation. Libraries were purified with AMPure beads. Dual-side purification of the libraries was performed, and the libraries were resuspended in 20 μl of H2O. All libraries were QCed using Bioanalyzer and Qubit. Libraries were sequenced on a Novaseq sequencer at the New York Genome Center.

treatment_protocol: Cells were switched to serum-free DMEM overnight, and treated for 6 hours the next day with either vehicle or 1 nM activin A.

value: gonadotrope

value: Activin A


title: HUVECs, Lot.3-2

value: Umbilical Vein

value: Primay Cells

value: Endothelial Cells

value: WT

value: Day 0


title: H9 cells, WT GATA3 transduced, phosphorylated RPB1

description: Library name: GFP-GATA3_pS2

value: T cell lymphoma cells

value: CTCL


title: H9 cells, WT GATA3 transduced, RPB1

description: Library name: GFP-GATA3_RPB1


title: HUVECs, Lot.2-2


title: H9 cells, WT GATA3 transduced, input

description: Library name: GFP-GATA3_input


title: H9 cells, WT GATA3 transduced, GATA3

description: Library name: GFP-GATA3_GATA3


title: HUVECs, Lot.1-2


title: LbT2b_vehicle_rep_1

description: Library name: veh_veh_1_S10

value: Vehicle


title: H9 cells, GFP control transduced, phosphorylated RPB1

description: Library name: GFP_pS2


title: LbT2b_vehicle_rep_2

description: Library name: veh_veh_2_S11


title: HUVECs, Lot.2-1


title: H9 cells, GFP control transduced, RPB1

description: Library name: GFP_RPB1


title: CM-treated fibroblasts, mdx aldosterone sample 3, biol rep 3

city: Columbus

first: Jill

last: Rafael-Fortney

state: OH

address: 460 W. 12th Ave

department: Physiology & Cell Biology

institute: The Ohio State University

description: Library name: M3FA

data_processing:
The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina Novaseq6000, according to effective library concentration and data amount.
Reads mapped to genes were counted using featureCounts v1.5.0-p3. Differential expression analysis was performed using the DESeq2RPackage (1.20.0). P-values were adjusted using the Benjamini-Hochberg method. p ≤ 0.1 and |log2 fold change| ≥ 0.6 were used to determine significance.
Assembly: mm39
Supplementary files format and content: gene count (.txt file), fpkm (.csv file), and differentially expressed genes (.xlsx files).

source_name: skeletal muscle

growth_protocol: Myoblasts isolated from less than 5-day-old C57BL/10 and (mdx) C57BL/10-Dmdmdx  were expanded in growth media containing F10 ham, 15% horse serum, 1% Pen/Strep, 1.2mM CaCl2, and 1mM L-glutamine supplemented with 6 ng/mL bFGF for the first week and 2 ng/mL bFGF for after that until differentiation. For differentiation, the myoblats were serum-restricted using  F10 ham, 5% horse serum, 1% Pen/Strep, 1.2mM CaCl2, and 1mM L-glutamine (no bFGF). The differentiated myotubes were maintained in F10 ham, 10% horse serum, 1% Pen/Strep, 1.2mM CaCl2, and 1mM L-glutamine (no bFGF) until treatment. Fibroblasts were maintained in media containing DMEM, 10% fetal bovine serum and 1% Pen/Strep. For aldosterone and conditioned media treatment, media containing charcoal stripped horse serum was used.

extract_protocol:
The myotubes (following the collection of CM) and fibroblasts (following 24 hours CM treatment) were directly lysed by adding 100 μL TRIzol (15596026, Invitrogen) for each cm2 of surface area of the culture plate. RNA was isolated using the DirectzolTM RNA miniprep kit (R2060, Zymo Research) following the manufacturer’s protocol. 200ng of total RNA from each sample were sent to Novogene Co., Ltd. (Davis, CA) for sequencing.  RNA integrity was assessed using a Bioanalyzer 2100 system (Agilent Technologies).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP for non-directional library. The non-directional library, was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Myotubes were treated with either aldosterone (1 µM) or vehicle (DMSO 0.001% v/v ) for 48 hrs in media containing charcoal stripped horse serum to eliminate steroids. Media was replaced with fresh media (with charcoal stripped horse serum) to eliminate aldosterone transfer,and myotubes were incubated for 15 hrs until collection of this conditioned media (CM) for treating the fibroblaststs. Fibroblasts were treated with CM for 24 hrs.

value: skeletal muscle

value: conditioned media (from myotubes)-treated primary neonatal hindlimb skeletal muscle fibroblasts

value: conditioned media from aldosterone-treated mdx myotubes


title: CM-treated fibroblasts, mdx aldosterone sample 2, biol rep 2

description: Library name: M2FA


title: H9 cells, GFP control transduced, GATA3

description: Library name: GFP_GATA3


title: H9 cells, GATA3 KO, input

description: Library name: sgGATA3_input


title: LbT2b_activin_rep_1

description: Library name: act_Veh_1_S12


title: CM-treated fibroblasts, mdx aldosterone sample 1, biol rep 1

description: Library name: M1FA


title: Patient3, GATA3

description: Library name: Pt3_GATA3

value: lymph node

value: FFPE sections

value: PTCL, NOS


title: Patient2, GATA3

description: Library name: Pt2_GATA3


title: HUVECs, Lot.3-1


title: HUVECs, Lot.3

data_processing:
By using the celseq2 pipeline (https://github.com/yanailab/celseq2), demultiplexing of the raw data was performed, and also UMI counts were calculated.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include UMI count values of all samples.

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen)
Detailed protocol is described in "CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq (PMID: 27121950)".


title: H9 cells, GFP control transduced, input

description: Library name: GFP_input


title: H9 cells, GATA3 KO, phosphorylated RPB1

description: Library name: sgGATA3_pS2


title: H9 cells, GATA3 KO, RPB1

description: Library name: sgGATA3_RPB1


title: CM-treated fibroblasts, mdx vehicle sample 3, biol rep 3

description: Library name: M3FV

value: conditioned media from vehicle-treated mdx myotubes


title: H9 cells, GATA3 KO, GATA3

description: Library name: sgGATA3_GATA3


title: HUVECs, Lot.2


title: H9 cells, control, input

description: Library name: sgCtrl_input


title: H9 cells, control, RPB1

description: Library name: sgCtrl_RPB1


title: H9 cells, control, phosphorylated RPB1

description: Library name: sgCtrl_pS2


title: CM-treated fibroblasts, mdx vehicle sample 2, biol rep 2

description: Library name: M2FV


title: HUVECs transduced with FOXA3, HNF1A and HNF6, with CHIR99021, Day44, Lot.3

value: Forced expression of FOXA3, HNF1A and HNF6

value: Day 44


title: CM-treated fibroblasts, mdx vehicle sample 1, biol rep 1

description: Library name: M1FV


title: H9 cells, control, GATA3

description: Library name: sgCtrl_GATA3


title: CM-treated fibroblasts, C57 aldosterone sample 3, biol rep 3

description: Library name: C3FA

value: conditioned media from aldosterone-treated C57 myotubes


title: Patient1, AZD4573, 4h, input

description: Library name: Pt1_AZD4573_input

source_name: PBMC

value: PBMC


title: HUVECs transduced with FOXA3, HNF1A and HNF6, with CHIR99021, Day16, Lot.3

value: Umbilical Vein

value: Primay Cells

value: Endothelial Cells

value: Day 16


title: HUVECs, Lot.1

value: WT

value: Day 0


title: CM-treated fibroblasts, C57 aldosterone sample 2, biol rep 2

description: Library name: C2FA

value: skeletal muscle


title: H9 cells, AZD4573, 4h, input

description: Library name: H9_AZD4573_input

value: T cell lymphoma cells

value: CTCL


title: Patient1, DMSO, input

description: Library name: Pt1_DMSO_input


title: HUVECs transduced with FOXA3, HNF1A and HNF6, with CHIR99021, Day9, Lot.3

value: Day 9


title: Patient1, AZD4573, 4h, RPB1

description: Library name: Pt1_AZD4573_RPB1


title: HUVECs transduced with FOXA3, HNF1A and HNF6, Day44, Lot.3


title: H9 cells, AZD4573, 4h, RPB1

description: Library name: H9_AZD4573_RPB1


title: H9 cells, DMSO, CDK9

description: Library name: H9_DMSO_CDK9


title: CM-treated fibroblasts, C57 vehicle sample 3, biol rep 3

description: Library name: C3FV

value: conditioned media (from myotubes)-treated primary neonatal hindlimb skeletal muscle fibroblasts

value: conditioned media from vehicle-treated C57 myotubes


title: H9 cells, DMSO, input

description: Library name: H9_DMSO_input


title: HUVECs transduced with FOXA3, HNF1A and HNF6, Day16, Lot.3


title: H9 cells, DMSO, RPB1

description: Library name: H9_DMSO_RPB1


title: CM-treated fibroblasts, C57 vehicle sample 2, biol rep 2

description: Library name: C2FV


title: H9, AZD4573, 4h, replicate3

description: Library name: 7787-CW-6

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (v2.3)
Trimmed sequence reads were mapped to GRCh38/hg38 using STAR (v2.7.8a)
Read count extraction and normalization were performed using RSEM (v1.3.3)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene counts for each sample

molecule: polyA RNA

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 50 ng of total RNA was used for the construction of sequencing libraries. For ChIP-seq, cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was digested using a Micrococcal Nuclease (CST). 10ug were used for library preparation.
RNA libraries for RNA-seq were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module and xGen Broad-range RNA Library Prep following manufacturer's protocols. ChIP-seq libraries were prepared using NEBNext Ultra II FS DNA Library Prep Kit following manufacturer's protocol.


title: H9, AZD4573, 4h, replicate2

description: Library name: 7787-CW-5


title: CM-treated fibroblasts, C57 vehicle sample 1, biol rep 1

description: Library name: C1FV


title: myotubes, mdx aldosterone sample 3, biol rep 3

description: Library name: M3MA

value: cultured myotubes differentiated from isolated primary neonatal hindlimb skeletal muscle myoblasts

value: aldosterone


title: HUVECs transduced with FOXA3, HNF1A and HNF6, with CHIR99021, Day44, Lot.2

value: Forced expression of FOXA3, HNF1A and HNF6

value: Day 44


title: H9, DMSO, replicate3

description: Library name: 7787-CW-3

value: DMSO


title: H9, AZD4573, 4h, replicate1

description: Library name: 7787-CW-4


title: HUVECs transduced with FOXA3, HNF1A and HNF6, Day9, Lot.3

value: Umbilical Vein


title: HUVECs transduced with FOXA3, HNF1A and HNF6, with CHIR99021, Day16, Lot.2

value: Primay Cells


title: H9, DMSO, replicate2

description: Library name: 7787-CW-2


title: Patient1, DMSO, RPB1

description: Library name: Pt1_DMSO_RPB1

value: PBMC

value: PTCL, NOS


title: myotubes, mdx aldosterone sample 2, biol rep 2

description: Library name: M2MA


title: CM-treated fibroblasts, C57 aldosterone sample 1, biol rep 1

description: Library name: C1FA

value: conditioned media from aldosterone-treated C57 myotubes


title: H9, DMSO, replicate1

description: Library name: 7787-CW-1

value: WT


title: myotubes, mdx aldosterone sample 1, biol rep 1

description: Library name: M1MA

value: skeletal muscle


title: HUVECs transduced with FOXA3, HNF1A and HNF6, Day44, Lot.2

value: Endothelial Cells


title: HUVECs transduced with FOXA3, HNF1A and HNF6, Day16, Lot.2

value: Day 16


title: myotubes, mdx vehicle sample 3, biol rep 3

description: Library name: M3MV

value: vehicle (DMSO)


title: RMS_S1102Rx107

type: RNA

city: Seattle, WA

first: Leonid

middle: M

last: Yermakov

state: WA

address: 1959 NE Pacific St, Box 357470

institute: University of Washington

hyb_protocol: Target molecules hybridize in solution with a matched Reporter Probe and a biotinylated Capture Probe, forming a complex that is later immobilized, washed, and digitally counted.

scan_protocol: A Charge-Coupled Device (CCD) camera captures fluorescent barcode images, and software decodes and counts them to determine target molecule numbers.

data_processing: Stringent normalization of miRNA data was performed by eliminating low digital counts and counts with high variability. Positive control and codeset normalization were then performed using the geometric mean algorithm to create a normalization factor. The expression of 827 human miRNAs was assessed.

source_name: rhabdomyosarcoma

label_protocol: There is no separate labeling of the sample; the fluorescent “labels” are pre‑encoded within the Reporter Probes provided by NanoString.

extract_protocol: RNA was retrieved from de-identified FFPE tumor tissue scrolls from pediatric hospital patients (n=108) using the Qiagen miRNeasy FFPE kit. Extracted RNA had RIN values of 1.1-2.7 and was deemed of sufficient quantity and quality to be processed for the NanoString multiplex platform (nCounter Human v3 miRNA Expression Assay kit), according to previously described methods (PMID: 27581030). An input of 100 ng of RNA was loaded into the assay.

tag: ethnicity

value: Hispanic

tag: pnc

tag: high or low

value: low

tag: relapsed

tag: alive/dead

tag: molecule subtype

value: miRNA


title: myotubes, mdx vehicle sample 2, biol rep 2

description: Library name: M2MV

value: cultured myotubes differentiated from isolated primary neonatal hindlimb skeletal muscle myoblasts


title: RMS_S1102Rx108

value: high


title: RMS_S1102Rx106


title: RMS_S1102Rx103


title: RMS_S1102Rx105


title: HUVECs transduced with FOXA3, HNF1A and HNF6, Day9, Lot.2

value: Forced expression of FOXA3, HNF1A and HNF6

value: Day 9


title: myotubes, C57 aldosterone sample 3, biol rep 3

description: Library name: C3MA

value: aldosterone


title: RMS_S1102Rx102


title: HUVECs transduced with FOXA3, HNF1A and HNF6, with CHIR99021, Day16, Lot.1

value: Umbilical Vein

value: Primay Cells


title: RMS_S1102Rx101


title: RMS_S1102Rx104


title: HUVECs transduced with FOXA3, HNF1A and HNF6, with CHIR99021, Day44, Lot.1

value: Day 44


title: RMS_S1102Rx98


title: RMS_S1102Rx100


title: RMS_S1102Rx99


title: HUVECs transduced with FOXA3, HNF1A and HNF6, with CHIR99021, Day9, Lot.1


title: HUVECs transduced with FOXA3, HNF1A and HNF6, with CHIR99021, Day9, Lot.2


title: myotubes, C57 aldosterone sample 2, biol rep 2

description: Library name: C2MA


title: myotubes, C57 aldosterone sample 1, biol rep 1

description: Library name: C1MA


title: RMS_S1102Rx97


title: RMS_S1102Rx94


title: RMS_S1102Rx96


title: RMS_S1102Rx95


title: HUVECs transduced with FOXA3, HNF1A and HNF6, Day44, Lot.1


title: myotubes, C57 vehicle sample 3, biol rep 3

description: Library name: C3MV


title: HUVECs transduced with FOXA3, HNF1A and HNF6, Day16, Lot.1


title: myotubes, mdx vehicle sample 1, biol rep 1

description: Library name: M1MV


title: myotubes, C57 vehicle sample 2, biol rep 2

description: Library name: C2MV


title: RMS_S1102Rx93


title: RMS_S1102Rx91


title: RMS_S1102Rx92


title: myotubes, C57 vehicle sample 1, biol rep 1

description: Library name: C1MV


title: HUVECs transduced with FOXA3, HNF1A and HNF6, Day9, Lot.1


title: WT

city: shanghai

first: yunxue

last: yin

address: 825 Zhangheng Road

institute: Fudan unversity

description:
Library name: sample2
BD Rhapsody

data_processing:
We applied  STARsolo with default parameter to analyze single-cell
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

extract_protocol:
Sorted tumor-derived total CD8+ T cells from three Tfe3fl/fl and three Cd4-Cre+Tfe3fl/fl mice were multiplexed using sample tags to facilitate simultaneous processing.
BD Rhapsody system  were used to capture the single cells and construct the scRNA-Seq libraries

value: Tumor

value: CD8 T cell

value: T cell

tag: strain background


title: RMS_S1102Rx89


title: RMS_S1102Rx90


title: 12h_DMSO4

city: Lausanne

first: Dalu

last: CHANG

state: Not US or Canada

address: EPFL SB ISIC LEAGO, CH A2 397,Station 6

country: Switzerland

institute: EPFL,

data_processing:
The polyA selection step was replaced by an rRNA depletion step with the QIAseq FastSelect - rRNA HMR kit (Qiagen).
Library preparation was performed on a Sciclone liquid handling robot (PerkinElmer; Waltham, Massachusetts, USA) with a PerkinElmer-developed automated script
Assembly: Sequencing data were demultiplexed using the bcl2fastq2 Conversion Software (version 2.20, Illumina)
Supplementary files format and content: text files have all information for each example

extract_protocol:
RNA was extracted with trizol, concenrtation was mearsured by nanodrop
RNA-seq libraries were prepared from 250 ng of total RNA with the Illumina TruSeq Stranded mRNA reagents (Illumina).

value: epithelial-like cell

value: WT

value: 12h post control DMSO, repeat4


title: RMS_S1102Rx86

value: Hispanic


title: RMS_S1102Rx88


title: Cre

description:
Library name: sample1
BD Rhapsody

value: Cre


title: RMS_S1102Rx85

value: miRNA


title: RMS_S1102Rx87

value: low


title: 12h_DMSO2

value: 12h post control DMSO, repeat2


title: RMS_S1102Rx83

value: high


title: RMS_S1102Rx84


title: VOM_1m_3_mix27

data_processing:
Base-calling was performed with bcl2fastq program (v2.20).
By using the celseq2 pipeline (https://github.com/yanailab/celseq2), demultiplexing of the raw data was performed, and also UMI counts were calculated.
Using binomial statistics, the number of UMI was converted to transcript counts. The mathematical formula is described in "Validation of noise models for single-cell transcriptomics (PMID: 24747814)". In this calculation method, if the UMI is the maximum value of 4096, the transcriptome count diverges to infinity and cannot be converted, so 9genes (Fga, Mt-Rnr2, Mt-Nd4, Mt-Cytb, Mup14, Mup20, Mup8, Mup13, Mup15) with a UMI count of 4096 in at least one sample genes were excluded from the analysis.
Lowly expressed genes were filtered out, and batch correction of transcript counts was performed using Combat-Seq(PMID: 33015620). The numbers following the string “mix” at the end of each sample name are the same for the same batch, and this information was used for batch correction.
Assembly: GRCh38
Supplementary files format and content: Comma Separated Values files include Batch correlated transcript counts of all samples

growth_protocol: We bred wild-type C57BL/6 mice to ages of 11-14 weeks (young), 60 weeks (old), and 100 weeks (very old), and used them in the experiment.

extract_protocol:
Total RNA was extracted from mouse hepatocytes isolated from mouse livers using ISOGEN II (Nippongene), and purified using the RNeasy MinElute Cleanup Kit (Qiagen). The quality and concentration of the total RNA was evaluated using a NanoDrop 2000 (Thermo Fisher Scientific), and only RNA with an A260/A280 ratio of 2 or higher was used.
Detailed protocol is described in "CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq (PMID: 27121950)".
OTHER: CEL-Seq2 (an RNA-seq protocol)

treatment_protocol: Detailed protocol of PH is described in "Partial hepatectomy in mice(PMID: 25835741)". The Sham surgery is performed under inhalation anesthesia with an abdominal median incision and suture closure. Hepatic cells were isolated from mouse livers by performing two-step collagenase digestion. Detailed protocol of hepatocyte isolation is described in "Hepatocyte suspensions and cultures as tools in experimental carcinogenesis (PMID: 224209)".

value: Liver

value: Primary Cells

value: Hepatocyte

value: PH


title: OM_1m_3_mix27


title: RMS_S1102Rx82


title: 12h_Pre4

value: 12h post control Pre, repeat4


title: TIE2-TGF-191

city: Utrecht

first: Frank

last: Riemers

address: Uppsalalaan 8

country: Netherlands

institute: Utrecht University

data_processing:
Quality control on the sequence reads from the raw FASTQ files was done with FastQC (v0.11.9).
TrimGalore (v0.6.7) as used to trim reads based on quality and adapter presence after which FastQC was again used to check the resulting quality.
rRNA reads were filtered out using SortMeRNA (v4.3.6) after which the resulting reads were aligned to the reference genome fasta (GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna) using the STAR (v2.7.10b) aligner.
Followup QC on the mapped (bam) files was done using Sambamba (v0.8.2), RSeQC (v5.0.1) and PreSeq (v3.2.0).
Readcounts were then generated using the Subread FeatureCounts module (v2.0.3) with the Homo_sapiens.GRCh38.106.ncbi.gtf gtf file as annotation.
Assembly: GRCh38
Supplementary files format and content: tab delimited counts
Supplementary files format and content: tab delimited meta data

source_name: Nucleus pulposus-derived

growth_protocol: The iPSC line were expanded in mTESR1 medium until the start of the experiment.

extract_protocol:
Cell pellets were crushed with a pestle after snap freezing in liquid nitrogen. RNA was extracted using the RNeasy® Micro kit (74004, Qiagen) according to the manufacturer’s instructions.
Trueseq RNA stranded polyA

treatment_protocol: The iPSC lines were differentiated into mesendoderm progenitor cells (MEPCs) according to the publish protocol by Warin et al. (2024) (https://doi.org/10.1016/j.isci.2024.109018).  At this timepoint the cells were transfected with NOTO mRNA and simulteneously plated into low-adherent culture plates to obtain 3D cell pellets of 35,000 cells in NP-genic medium (hgDMEM  (11965, Thermo Fisher) supplemented with 1% ITS+, 40 µg/ml L-proline (P5607, Sigma-Aldrich), 1% NEAA, 50 µg/mL Ascorbic acid-2-Phosphate (ASAP; A8960, Sigma-Aldrich), and 10 ng/mL TGF-β1 (240-B-010, R&D Systems, Minneapolis, USA)). On day 7, half of the samples were switched to NP-genic medium in which the TGF-β1 was replaced by decellularized notochordal cell-derived matrix, the other half was continued in TGF-β1.

value: Nucleus pulposus-derived

value: iPSCs

value: TGF-β1 10ng/mL


title: 12h_DMSO1

value: epithelial-like cell

value: 12h post control DMSO, repeat1


title: YM_1m_3_mix27

value: WT


title: RMS_S1102Rx81

value: Hispanic


title: RMS_S1102Rx80


title: 12h_DMSO3

value: 12h post control DMSO, repeat3


title: 12h_Pre3

value: 12h post control Pre, repeat3


title: YM_Ctrl_5_mix27


title: RMS_S1102Rx79

value: low

value: miRNA


title: RMS_S1102Rx76

value: Caucasian


title: RMS_S1102Rx77


title: RMS_S1102Rx78


title: 12h_Pre2

value: 12h post control Pre, repeat2


title: VOM_44h_3_mix26

value: Liver

value: Primary Cells


title: 12h_Pre1

value: 12h post control Pre, repeat1


title: RMS_S1102Rx75

value: high


title: 12h_UV4

value: 12h post control UV, repeat4


title: OM_44h_3_mix26

value: Hepatocyte

value: PH


title: RMS_S1102Rx74


title: RMS_S1102Rx73

value: African american


title: 12h_UV3

value: epithelial-like cell

value: 12h post control UV, repeat3


title: YM_44h_3_mix26

value: WT


title: HUVECs, Lot.1-1

extract_protocol:
The cultured cells were collected at specified time points by trypsinization. Using 50,000 cells per reaction, the experiment was conducted following the publicly available standard Omni ATAC-seq protocol (PMID: 28846090).
The collected genomic DNA fragments were purified using a PCR purification kit (QIAGEN), and indexing and amplification were performed with the NEBNext High-Fidelity 2X PCR Master Mix (NEB). The amplified library was then purified and size-selected using AMPure XP (BECKMAN COULTER).

value: Umbilical Vein

value: Primay Cells

value: Endothelial Cells

value: Day 0


title: RMS_S1102Rx71

value: Hispanic

value: low

value: miRNA


title: YM_Ctrl_4_mix26

value: Liver

value: Primary Cells


title: 12h_UV2

value: 12h post control UV, repeat2


title: 12h_UV1

value: 12h post control UV, repeat1


title: RMS_S1102Rx70


title: RMS_S1102Rx66

value: high


title: RMS_S1102Rx68


title: RMS_S1102Rx67


title: 12h_T4

value: 12h post reaction, repeat4


title: RMS_S1102Rx65


title: 12h_T3

value: 12h post reaction, repeat3


title: OM_1m_2_mix25

value: Hepatocyte

value: PH


title: OM_1m_1_mix25

value: WT


title: RMS_S1102Rx64


title: 12h_T2

value: epithelial-like cell

value: 12h post reaction, repeat2


title: YM_1m_2_mix25


title: RMS_S1102Rx72


title: RMS_S1102Rx62


title: RMS_S1102Rx63


title: RMS_S1102Rx61


title: VOM_1m_2_mix25


title: 12h_T1

value: 12h post reaction, repeat1


title: RMS_S1102Rx69


title: YM_1m_1_mix25


title: RMS_S1102Rx60

value: Caucasian


title: 6h_DMSO4

value: 6h post control DMSO, repeat4


title: EWS_S1102Rx58

source_name: Ewing Sarcoma

value: Hispanic

value: low


title: RMS_S1102Rx59

value: miRNA


title: EWS_S1102Rx57


title: EWS_S1102Rx56


title: EWS_S1102Rx55


title: VOM_1m_1_mix25

value: Liver

value: Primary Cells


title: EWS_S1102Rx54


title: VOM_44h_2_mix24


title: EWS_S1102Rx53


title: EWS_S1102Rx52


title: 6h_DMSO3

value: 6h post control DMSO, repeat3


title: VOM_44h_1_mix24


title: OM_44h_1_mix24


title: 6h_DMSO2

value: 6h post control DMSO, repeat2


title: 6h_DMSO1

value: 6h post control DMSO, repeat1


title: EWS_S1102Rx50

value: high


title: 6h_Pre2

value: 6h post control Pre, repeat2


title: EWS_S1102Rx51


title: EWS_S1102Rx47


title: EWS_S1102Rx48


title: YM_44h_2_mix24

value: Hepatocyte

value: PH


title: 6h_Pre3

value: epithelial-like cell

value: WT

value: 6h post control Pre, repeat3


title: 6h_Pre4

value: 6h post control Pre, repeat4


title: EWS_S1102Rx44


title: 6h_Pre1

value: 6h post control Pre, repeat1


title: OM_44h_2_mix24


title: Foxp3+iTreg_PGE2_2

city: Kyoto

first: Ryuma

last: Matsuura

address: 53 Kawara-cho, Shogoin, Sakyo-ku, Kyoto City,

institute: Kyoto University

data_processing:
Low quality bases and adapter sequences were removed from raw Fastq read sequences by Trim Galore.
Trimmed reads were aligned to mm10 using HISAT2.
The expression level of each gene was calculated from mapped read counts using Strintie and prepDE.py.
Assembly: mm10
Supplementary files format and content: tab-delimited text files of raw count

source_name: splenocyte

extract_protocol:
RNA was extracted from sorted cells using QIAGEN RNeasy plus micro kit.
cDNA was synthesized from isolated RNA, and RNA-seq libraries were constructed using the Illumina TruSeq Stranded mRNA kit, following the manufacturer's protocol.

treatment_protocol: Splenic CD4+ T cells isolated from Foxp3-DTR/EGFP mice were cultured under iTreg-skewing conditions with plate-bound anti-CD3 mAb, soluble anti-CD28 mAb, and TGF-β for 2 days. After this incubation period, cells were collected and treated with either vehicle or 100 nM PGE2 for 6 hours. Subsequently, Foxp3+ iTregs were FACS-sorted based on GFP fluorescence and subjected to RNA sequencing.

value: splenocyte

value: primary cell

value: PGE2 100nM


title: 6h_UV4

value: 6h post control UV, repeat4


title: Foxp3+iTreg_PGE2_1


title: EWS_S1102Rx45

value: Hispanic

value: miRNA


title: YM_44h_1_mix24

value: Liver

value: Primary Cells


title: EWS_S1102Rx49

value: high


title: EWS_S1102Rx46


title: Foxp3+iTreg_PGE2_3


title: Foxp3+iTreg_Vehicle_3

value: Vehicle (DMSO)


title: EWS_S1102Rx43


title: EWS_S1102Rx40


title: EWS_S1102Rx42


title: EWS_S1102Rx41

value: low


title: EWS_S1102Rx37


title: 6h_UV3

value: 6h post control UV, repeat3


title: EWS_S1102Rx38


title: 6h_T4

value: epithelial-like cell

value: 6h post reaction, repeat4


title: Foxp3+iTreg_Vehicle_1


title: 6h_UV1

value: WT

value: 6h post control UV, repeat1


title: 6h_UV2

value: 6h post control UV, repeat2


title: OS_S1102Rx29

source_name: osteosarcoma


title: 6h_T2

value: 6h post reaction, repeat2


title: 6h_T3

value: 6h post reaction, repeat3


title: nTreg_EP4ago_3

treatment_protocol: Splenic nTregs isolated from Foxp3-DTR/EGFP mice were activated  with plate-bound anti-CD3 mAb, soluble anti-CD28 mAb, and IL-2 for 2 days. After this incubation period, cells were collected and treated with either vehicle or 100 nM EP4 agonist for 6 hours. Subsequently, nTregs were FACS-sorted based on GFP fluorescence and subjected to RNA sequencing.

value: splenocyte

value: primary cell

value: nTreg

value: EP4 agonist 100nM


title: nTreg_EP4ago_2


title: EWS_S1102Rx35

value: Hispanic

value: miRNA


title: EWS_S1102Rx39

value: high


title: EWS_S1102Rx33

value: Asian


title: OS_S1102Rx30


title: OS_S1102Rx32

value: low


title: EWS_S1102Rx36

value: Caucasian


title: OS_S1102Rx31


title: Foxp3+iTreg_Vehicle_2

value: Vehicle (DMSO)


title: nTreg_EP4ago_1


title: 3h_DMSO3

value: epithelial-like cell

value: 3h post control DMSO, repeat3


title: OS_S1102Rx27


title: OS_S1102Rx28


title: OS_S1102Rx26


title: OS_S1102Rx24


title: OS_S1102Rx25


title: OS_S1102Rx21


title: nTreg_Vehicle_3


title: nTreg_Vehicle_1


title: 3h_DMSO2

value: WT

value: 3h post control DMSO, repeat2


title: EWS_S1102Rx34


title: 6h_T1

value: 6h post reaction, repeat1


title: 3h_DMSO4

value: 3h post control DMSO, repeat4


title: OS_S1102Rx22


title: OS_S1102Rx23


title: OS_S1102Rx18


title: OS_S1102Rx17


title: Wild-type mouse derived macrophages, Lot2

first: Keiichi

last: Ishihara

state: Kyoto

address: 5 Misasagi Nakauchi-cho, Yanashina-ku

institute: Kyoto Pharmaceutical University

data_processing:
Quality check: FastQC ver. 0.11.7
Trimming: Trimmomatic ver. 0.38, Low quality (<20) bases and adaptor sequences were trimmed.
Mapping: HISAT2 ver.2.1.0
Caliculation of read count and TPM: featureCounts ver. 1.6.3
Statistic analysis: stats ver. 3.6.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes TPM value for each sample

source_name: ESCs derived cells

growth_protocol: Mouse ESCs were maintained in KnockOut DMEM contained 20% KnockOut serumn replacement and LIF in humodified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Nucleospin RNA, XS kit (Macherey-Nagel). 450 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-seq HT Plus kit following manufacturer's protocols.

treatment_protocol: Primitive macrophages were induced by addtion of FGF2, BMP-4, activin A, VEGF, SCF, IL-3, and M-CSF for 12 days (Takata et al., Immunity 2017, 47:183-198. doi: 10.1016/j.immuni.2017.06.017)

value: ESCs derived cells

value: Estublishesd from wild-type mouse

value: Differentiation into primitive macrophages


title: 3h_DMSO1

value: 3h post control DMSO, repeat1


title: Wild-type mouse derived macrophages, Lot3


title: Ts1Cje mouse derived macrophages, Lot3

value: Estublishesd from Ts1Cje mouse


title: OS_S1102Rx20

value: Hispanic

value: miRNA


title: 3h_Pre4

value: 3h post control Pre, repeat4


title: nTreg_Vehicle_2

value: splenocyte

value: primary cell

value: nTreg


title: Wild-type mouse derived macrophages, Lot1


title: OS_S1102Rx16

value: high


title: OS_S1102Rx12

value: low


title: 3h_Pre1

value: epithelial-like cell

value: WT

value: 3h post control Pre, repeat1


title: 3h_Pre2

value: 3h post control Pre, repeat2


title: 3h_Pre3

value: 3h post control Pre, repeat3


title: OS_S1102Rx11

value: Caucasian


title: 3h_UV4

value: 3h post control UV, repeat4


title: Ts1Cje mouse derived macrophages, Lot2

value: ESCs derived cells

value: Differentiation into primitive macrophages


title: OS_S1102Rx10


title: OS_S1102Rx14

value: Hispanic


title: OS_S1102Rx19

value: miRNA


title: Ts1Cje mouse derived macrophages, Lot1

value: Estublishesd from Ts1Cje mouse


title: OS_S1102Rx08


title: 3h_UV3

value: 3h post control UV, repeat3


title: 3h_UV2

value: 3h post control UV, repeat2


title: OS_S1102Rx06


title: OS_S1102Rx07


title: OS_S1102Rx15


title: OS_S1102Rx13


title: Wild-type mouse derived cells, Lot #2

extract_protocol:
RNA was harvested using Nucleospin RNA, mini kit (Macherey-Nagel). 1.3 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Primitive macrophage progenitors were induced by addtion of FGF2, BMP-4, activin A, and VEGF for 4 days (Takata et al., Immunity 2017, 47:183-198. doi: 10.1016/j.immuni.2017.06.017)

value: Estublishesd from wild-type mouse

value: Differentiation into primitive macrophage progenitors


title: Wild-type mouse derived cells, Lot #1


title: OS_S1102Rx05

value: African american

value: low


title: 3h_UV1

value: epithelial-like cell

value: WT

value: 3h post control UV, repeat1


title: Ts1Cje mouse derived cells, Lot #3


title: OS_S1102Rx04


title: Ts1Cje mouse derived cells, Lot #2


title: OS_S1102Rx09


title: OS_S1102Rx03

value: high


title: foregut mesoderm+endoderm explant rfx6-MO NF15-25  rep3

city: Cincinnati

first: Aaron

last: Zorn

address: 240 Albert Sabin Way, Bld S

department: Developmental Biology

institute: Cincinnati Children's Hospital and Medical Center

description:
Library name: laevis_NF25_fg_mesendo_explant_Rfx6_LOF_rep3
laevis_NF25_fg_mesendo_explant_Rfx6_LOF_rep3

data_processing:
Quality of reads was asessed with factqc
Quality trimmed reads in fastq format were mapped and quantified using RSEM (v1.3.0) with bowtie2
Assembly: Xenopus Laevis v10
Supplementary files format and content: Raw counts and TPM files in .txt format

organism: Xenopus laevis

source_name: embryo

growth_protocol: Foregut explants containing mesoderm+endoderm were dissected at NF15 and cultured at 15 degrees C for 16 hours to NF25, or for an additional 16 hours to NF33, to NF38 (+12 hours)

extract_protocol:
RNA was extracted  using Macherey-Nagel Nucleospin RNA isolation kit (Cat. No. 740955) according to manufacturer's instructions.
Library prep was performed using Illumina’s TruSeq stranded mRNA library preparation kit according to manufacturer's instructions.

treatment_protocol: For Rfx6 loss of function, Rfx6 translation blocking morpholino oligo (2.5ng) or control 5bp mismatch oligo (2.5ng) was injected at 2-cell stage (1.25 ng per cell).   For RA loss of function, explants were treated with 250nM BMS493 immediately after dissection at NF15.

value: embryo

value: wild type embryo

value: foregut mesoderm+endoderm

value: NF15 to NF25


title: foregut mesoderm+endoderm explant rfx6-MO NF15-25  rep2

description:
Library name: laevis_NF25_fg_mesendo_explant_Rfx6_LOF_rep2
laevis_NF25_fg_mesendo_explant_Rfx6_LOF_rep2


title: 3h_T3

value: 3h post reaction, repeat3


title: Ts1Cje mouse derived cells, Lot #1

value: ESCs derived cells


title: RnaSeq paired end CHX i14G1-12 rep2

city: Petah Tikva

first: Rom

last: Barzilay

address: Harav Unterman 10

department: Biomolecular Sciences

country: Israel

institute: Weizmann Institute of Science, Israel

description:
Library name: Sample 12
RNA_CHX_D12_2

data_processing:
Trimming first base, removing adapter sequence and read length selection using Cutadapt. Removal of reads mapping to non-coding RNA (ncRNA) using the Bowtie algorithm. Unique alignment of pre-processed reads to P. falciparum reference 3D7 (PlasmoDB version 68) using the STAR algorithm with a value of 500 for the --alignIntronMax parameter. Quality control using FastQC and multiQC tools.
read counting per gene using summarizeOverlaps in R GenomicAlignments package.
Assembly: Plasmodium falciparum 3D7 (version 68) as provided in the PlasmoDB website.
Supplementary files format and content: Tab-delimited text files include raw count values for each sample

organism: Plasmodium falciparum

source_name: Trophozoite stage, 3D7 strain

growth_protocol: Parasite line 3D7. P. falciparum was grown in pooled donor red blood cells (RBCs) provided by the Israeli blood bank (Magen David Adom blood donations in Israel) at 4% hematocrit and incubated at 37 °C in a gas mixture of 1% O2, 5% CO2 in N2.

extract_protocol:
RNA was extracted by hot acid phenol extraction
Ingolia et al, 2012
Ribosome profiling and RNA-seq

treatment_protocol: DMSO or 20 µM i14G1-12 for 1 hour at 37 C degrees

value: Trophozoite stage, 3D7 strain


title: RnaSeq paired end CHX i14G1-12 rep1

description:
Library name: Sample 11
RNA_CHX_D12_1


title: foregut mesoderm+endoderm explant rfx6-MO NF15-25  rep1

description:
Library name: laevis_NF25_fg_mesendo_explant_Rfx6_LOF_rep1
laevis_NF25_fg_mesendo_explant_Rfx6_LOF_rep1


title: OS_S1102Rx01

value: Caucasian

value: miRNA


title: 3h_T2

value: 3h post reaction, repeat2


title: Wild-type mouse derived cells, Lot #3

value: Estublishesd from wild-type mouse

value: Differentiation into primitive macrophage progenitors


title: foregut mesoderm+endoderm explant rfx6-MO NF15-38  rep3

description:
Library name: laevis_NF38_fg_mesendo_explant_Rfx6_LOF_rep3
laevis_NF38_fg_mesendo_explant_Rfx6_LOF_rep3

value: NF15 to NF38


title: Mouse TTFs KO 8

city: Zurich

first: Jess

middle: Gerrit

last: Snedeker

address: Lengghalde 5

department: D-HEST

institute: ETH Zurich

data_processing:
RNA-seq reads were counted with Kallisto using the genome build GENCODE Mus musculus GRCm39 M26
Gene expression values were computed with the function featureCounts from the R package Rsubread.
Assembly: GENCODE Mus musculus GRCm39 M26
Supplementary files format and content: tab-delimited .txt files include 2 columns: ensemble feature identifier and count number.

source_name: Tendon tail fascicles

extract_protocol:
Mice were euthanized and tail tendon fascicles were immediately dissected, placed in 2mL Eppendorf Lock tubes, snap frozen in liquid nitrogen and stored at -80C. On the day of isolation, tubes were placed immediately in dry ice. Samples were transferred to supercooled Spex microvial cylinder (6757C3, SPEX™ SamplePrep) containing 150µl of GENEzol™ reagent (GZR200, Geneaid). Samples were cryogrinded in a bath of liquid nitrogen using FreezerMill (6870, SPEX™ SamplePrep) until fascicles were completely disrupted. Pulverized samples were collected in a 1.5 ml tube by rinsing the tubes with 900µl GENEzol™ and kept on ice. To purify RNA, tissue homogenate was mixed well with 200µl of Chloroform (102445, Merck) at a mixing ratio of 1:5. Samples were then spun down for 15min (at 15,000g, 4°C). The upper RNA-containing aqueous phase was transferred to a clean 1.5 ml tube and mixed with one part of 70% ethanol. RNA cleanup was subsequently performed using RNeasy Plus Micro Kit (74034, Qiagen), including a step to remove genomic DNA (Qiagen gDNA Eliminator spin columns). Cleaned RNA concentration and quality were determined by spectrophotometric determination of A260/A280 ratio. Samples were stored at -80 °C, and only samples with A260/A280 ratio of 1.8-2 were used.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Tendon tail fascicles

value: All tissue cells

value: KO


title: RnaSeq paired end CHX DMSO rep2

description:
Library name: Sample 10
RNA_CHX_DMSO_2

value: WT

value: DMSO 1hr


title: OS_S1102Rx02

value: African american

value: low


title: 3h_T4

value: epithelial-like cell

value: 3h post reaction, repeat4


title: Mouse TTFs KO 7


title: foregut mesoderm+endoderm explant rfx6-MO NF15-38  rep1

description:
Library name: laevis_NF38_fg_mesendo_explant_Rfx6_LOF_rep1
laevis_NF38_fg_mesendo_explant_Rfx6_LOF_rep1

value: embryo

value: wild type embryo

value: foregut mesoderm+endoderm


title: 3h_T1

value: 3h post reaction, repeat1


title: RnaSeq single end CHX DMSO rep1

description:
Library name: Sample 9
RNA_CHX_DMSO_1

value: Trophozoite stage, 3D7 strain


title: Mouse TTFs KO 6


title: RiboSeq HAR i14G1-12 rep2

description:
Library name: Sample 8
RIBO_HAR_D12_2

data_processing:
Trimming first base, removing adapter sequence and read length selection using Cutadapt. Removal of reads mapping to non-coding RNA (ncRNA) using the Bowtie algorithm. Unique alignment of pre-processed reads to P. falciparum reference 3D7 (PlasmoDB version 68) using the STAR algorithm with a value of 500 for the --alignIntronMax parameter. Quality control using FastQC and multiQC tools.
read counting per gene using summarizeOverlaps in R GenomicAlignments package.
Assembly: Plasmodium falciparum 3D7 (version 68) as provided in the PlasmoDB website.
Supplementary files format and content: Tab-delimited text files include raw count values for each sample
Library strategy: Ribo-seq


title: HCT116_shARID1A_SETDB1

first: Nestor

last: Zhang

address: Dongchuan Road

institute: Shanghai Jiao Tong University

data_processing:
Raw data of fastq format was processed using FastQC 0.11.9 software.
Clean reads were aligned to the reference genome GRCh38 using Bowtie2 v2.2.5 to generate bam files.
After removing PCR duplicates with Sambamba 0.8.2 software, MACS2 2.2.7.1 was used to identify regions of IP enrichment over background.
Deeptools 3.5.1 was used to transfer deduplicated bam file to BigWig format and to generate heatmaps and density plot figures.
ChIPseeker package and ChIPpeakAnno package were used for peak annotation and visualization.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

growth_protocol: HCT116 cells were maintained in RPMI1640 medium (Gibco, C11875500BT). Media were supplemented with 10% FBS with glutamine, penicillin, and streptomycin. Cells were incubated at 37 °C in a humidified incubator with 5% CO2.

extract_protocol:
HCT116 cells per sample were cross-linked with 1% formaldehyde for 15 min, quenched with glycine, and subjected to two-step cell and nuclear lysis in the presence of protease inhibitors. Shearing of samples was optimized such that the final DNA length was approximately 500 bp using a Bioruptor sonifier (Diagenode, ucd-200), and was followed by incubation with H3K9me3 polyclonal antibody (Abcam, ab8898) or ARID1A monoclonal antibody (CST, 12354) or TIF1β monoclonal antibody (CST,4124T) or SETDB1 monoclonal antibody (ABclonal, A6145) overnight at 4 °C. Immunoprecipitation was performed with 50:50 mixes of Pierce™ Protein A/G Magnetic Beads (ThermoFisher Scientific, #26162). Following elution and reverse cross-linking, purification (TIANGEN, DP203).
10–20 ng DNA were used to make the ChIP-seq library as per instructions from Illumina’s ChIP-Seq Sample Prep kit (Illumina, IP-102-1001).

value: coloncancercellline

tag: chip antibody

value: SETDB1 (Abclonal A6145)


title: HCT116_shARID1A_TRIM28


title: foregut mesoderm+endoderm explant rfx6-MO NF15-33  rep3

description:
Library name: laevis_NF33_fg_mesendo_explant_Rfx6_LOF_rep3
laevis_NF33_fg_mesendo_explant_Rfx6_LOF_rep1

tag: tissue

value: NF15 to NF33


title: foregut mesoderm+endoderm explant rfx6-MO NF15-33  rep2

description:
Library name: laevis_NF33_fg_mesendo_explant_Rfx6_LOF_rep2
laevis_NF33_fg_mesendo_explant_Rfx6_LOF_rep1

tag: cell line


title: RiboSeq HAR i14G1-12 rep1

description:
Library name: Sample 7
RIBO_HAR_D12_1


title: HCT116_shARID1A_IgG

tag: cell type

value: normal rabbit IgG (CST #2729)


title: Mouse TTFs KO 5

value: Tendon tail fascicles

value: All tissue cells

tag: genotype


title: foregut mesoderm+endoderm explant rfx6-MO NF15-33  rep1

description:
Library name: laevis_NF33_fg_mesendo_explant_Rfx6_LOF_rep1
laevis_NF33_fg_mesendo_explant_Rfx6_LOF_rep1

tag: treatment


title: HCT116_shARID1A_H3K9m3

value: H3K9me3 (Abclonal A2360)


title: RiboSeq HAR DMSO rep2

description:
Library name: Sample 6
RIBO_HAR_DMSO_2

value: WT

value: DMSO 1hr


title: Mouse TTFs WT 7


title: Mouse TTFs KO 4

value: KO


title: HCT116_CTR_SETDB1


title: foregut mesoderm+endoderm explant rfx6-MO NF15-38  rep2

description:
Library name: laevis_NF38_fg_mesendo_explant_Rfx6_LOF_rep2
laevis_NF38_fg_mesendo_explant_Rfx6_LOF_rep2

value: NF15 to NF38


title: RiboSeq CHX i14G1-12 rep2

description:
Library name: Sample 4
RIBO_CHX_D12_2


title: RiboSeq HAR DMSO rep1

description:
Library name: Sample 5
RIBO_HAR_DMSO_1


title: foregut mesoderm+endoderm explant BMS493 treated NF15-25 rep2

description:
Library name: laevis_NF25_fg_mesendo_explant_RA_LOF_rep2
laevis_NF25_fg_mesendo_explant_RA_LOF_rep2

value: NF15 to NF25


title: Mouse TTFs WT 6


title: HCT116_shARID1A_input

value: Cell lysate supernatant


title: HCT116_CTR_TRIM28


title: foregut mesoderm+endoderm explant BMS493 treated NF15-33 rep3

description:
Library name: laevis_NF33_fg_mesendo_explant_RA_LOF_rep3
laevis_NF33_fg_mesendo_explant_RA_LOF_rep3

value: embryo

value: wild type embryo


title: Mouse TTFs WT 8


title: foregut mesoderm+endoderm explant BMS493 treated NF15-25 rep1

description:
Library name: laevis_NF25_fg_mesendo_explant_RA_LOF_rep1
laevis_NF25_fg_mesendo_explant_RA_LOF_rep1

value: foregut mesoderm+endoderm


title: HCT116_CTR_H3K9m3


title: Mouse TTFs WT 4


title: foregut mesoderm+endoderm explant BMS493 treated NF15-33 rep2

description:
Library name: laevis_NF33_fg_mesendo_explant_RA_LOF_rep2
laevis_NF33_fg_mesendo_explant_RA_LOF_rep2


title: RiboSeq CHX DMSO rep2

description:
Library name: Sample 2
RIBO_CHX_DMSO_2

value: Trophozoite stage, 3D7 strain


title: HCT116_CTR_ARID1A

value: coloncancercellline


title: Mouse TTFs WT 3


title: RiboSeq CHX DMSO rep1

description:
Library name: Sample 1
RIBO_CHX_DMSO_1


title: WT A455D PMPs and CAGG WT PMPs co-transplanted, DSAD-tau treated, replication 2

city: Piscataway

first: Ziyuan

last: Ma

state: NJ

address: 604 Allison Rd

department: Cell Biology and Neuroscience

institute: Rutgers University

description:
10x Genomics 3' Gex v3.1
Human (Homo sapiens) cell engrafted chimeric mouse (Mus musculus) brain.

data_processing:
The demuiltiplexing, barcoded processing, gene counting were made using the Cell Ranger (version v7.1.0) using the Human (GRCh38) and mouse (mm10) reference - 2020-A (10x Genomics) with EGFP gene built in.
Assembly: Human (GRCh38) and mouse (mm10) reference - 2020-A
Supplementary files format and content: Filtered cell-associated barcodes in MEX format (feature-barcode matrices).

organism:
Homo sapiens
Mus musculus

source_name: Brain

growth_protocol: PMPs were generated from the three pairs of Cont and DS hiPSC cell lines using a previously established protocol. The yolk sac embryoid bodies (YS-EBs) were generated by treating the YS-EBs with mTeSR 1 media (STEMCELL Technologies) supplemented with bone morphogenetic protein 4 (BMP4, 50 ng/ml), vascular endothelial growth factor (VEGF, 50 ng/ml), and stem cell factor (SCF, 20 ng/ml) for 6 days. To stimulate myeloid differentiation, the YS-EBs were plated on dishes with X-VIVO 15 medium (Lonza) supplemented with interleukin-3 (IL-3, 25 ng/ml) and macrophage colony-stimulating factor (M-CSF, 100 ng/ml). At 4-6 weeks after plating, human PMPs emerged into the supernatant and were continuously produced for more than 3 months. PMPs were collected from the supernatant and suspended at a concentration of 100,000 cells/µl in PBS. Cells were then injected into the brains of P0 Rag2−/−hCSF1 immunodeficient mice (C;129S4-Rag2tm1.1FlvCsf1tm1(CSF1)FlvIl2rgtm1.1Flv/J, The Jackson Laboratory) as previously described. The transplantation sites were bilateral from the midline = ±1.0 mm, posterior from bregma = −2.0 mm, and dorsoventral depths = −1.5 and −1.2 mm 43. All pups were placed in ice for 4-5 mins to anesthetize. The pups were then injected with 0.5 μl of cells into each site (four sites total), using a digital stereotaxic device (David KOPF Instruments) that was equipped with a neonatal mouse adapter (Stoelting). The pups were weaned at three weeks and kept for further experimentation at different time points.

extract_protocol:
Chimeric mice were anesthetized and perfused with cold DPBS (1x). Brains were dissected and dissociated using Adult Brain Dissociation Kit (Miltenyi) according to the manufacturer’s instructions. Human cells were isolated by mouse cell depletion kit (Miltenyi) following the manufacturer’s protocols. Isolated cell suspension then loaded to the Chromium controller for mRNA barcoding and reverse transcription using Chromium Next GEM Single Cell 3' Kit v3.1.
scRNA-seq libraries were constructed using Chromium Next GEM Single Cell 3' Kit v3.1 and Dual Index Kit TT Set A, following the manufacturer’s protocols. Quality control of the scRNA-seq libraries were performed by Agilent 2100 Bioanalyzer, and libraries were sequenced in Novaseq 6000 S4 flow cells.

treatment_protocol: Soluble S1 fractions from human samples (provided by the University of California Alzheimer's Disease Research Center (UCI-ADRC) and the Institute for Memory Impairments and Neurological Disorders) were prepared as described before. The human tissues were homogenized in TBS (20 mM Tris-HCl, 140 mM NaCl, pH 7.5) containing protease and phosphatase inhibitors (Roche). Homogenates were ultracentrifuged (4 °C for 60 min) at 100,000×g (Optima MAX Preparative Ultracentrifuge, Beckman Coulter). Supernatants, S1 fractions, were aliquoted and stored at −80 °C. The total amount of soluble tau in S1 fractions was determined by using an ELISA kit (human Tau, Invitrogen), according to the manufacturer’s protocol. The ELISA experiments were repeated in three independent experiments using triplicate replicas. All adult brain injections were performed using a Kopf stereotaxic apparatus (David Kopf, Tujunga, CA). Stereotaxic surgery was performed on two months old transplanted Rag2−/−hCSF1 immunodeficient mice. The mice were aseptically injected with human brain extracts (Cont tau or DSAD tau) in the dorsal hippocampus and the overlying cortex (bregma: −2.5 mm; lateral: +2 mm; depth: −2.4 mm and −1.8 mm from the skull). A dose of tau at 3.2 µg, which was previously shown to be able to induce tau pathology in tau transgenic mice, was injected into each human microglial chimeric mouse. Concentrations of tau per injection site were 0.8 μg/µl each site for both DSAD- Tau and Cont-Tau. The mice were injected with 1 μl of Cont or DSAD tau into each site (four sites total). After the injection, the mice were kept for further experiments.

value: Brain

value: WT A455D iPSC- and CAGG WT ESC-differentiated PMP

value: Human microglia

value: CSF2RB A455D mutation and WT

value: DSAD tau


title: foregut mesoderm+endoderm explant BMS493 treated NF15-25 rep3

description:
Library name: laevis_NF25_fg_mesendo_explant_RA_LOF_rep3
laevis_NF25_fg_mesendo_explant_RA_LOF_rep3


title: Mouse TTFs KO 3

value: Tendon tail fascicles

value: All tissue cells


title: foregut mesoderm+endoderm explant BMS493 treated NF15-33 rep1

description:
Library name: laevis_NF33_fg_mesendo_explant_RA_LOF_rep1
laevis_NF33_fg_mesendo_explant_RA_LOF_rep1

value: NF15 to NF33


title: foregut mesoderm+endoderm explant control DMSO treated NF15-25 rep3

description:
Library name: laevis_NF25_fg_mesendo_explant_control_rep3
laevis_NF25_fg_mesendo_explant_control_rep3

value: mismatch MO + DMSO (0.1%)


title: HCT116_CTR_IgG

city: Shanghai

value: normal rabbit IgG (CST #2729)


title: WT A455D PMPs and CAGG WT PMPs co-transplanted, DSAD-tau treated, replication 1


title: HCT116_CTR_input


title: WT A455D PMPs and CAGG WT PMPs co-transplanted, Cont-tau treated

value: Control tau


title: RiboSeq CHX i14G1-12 rep1

description:
Library name: Sample 3
RIBO_CHX_D12_1

value: WT


title: Mouse TTFs WT 1


title: foregut mesoderm+endoderm explant control DMSO treated NF15-25 rep2

description:
Library name: laevis_NF25_fg_mesendo_explant_control_rep2
laevis_NF25_fg_mesendo_explant_control_rep2

value: embryo

value: NF15 to NF25


title: Mouse TTFs WT 2


title: DS A455D PMPs transplanted, DSAD-tau treated

value: DS A455D iPSC-differentiated PMP

value: CSF2RB A455D mutation


title: foregut mesoderm+endoderm explant control DMSO treated NF15-25 rep1

description:
Library name: laevis_NF25_fg_mesendo_explant_control_rep1
laevis_NF25_fg_mesendo_explant_control_rep1

value: wild type embryo

value: foregut mesoderm+endoderm


title: HCT116_TRIM28

value: coloncancercellline


title: HCT116_ARID1A


title: Mouse TTFs KO 2

value: KO


title: Mouse TTFs WT 5


title: DS A455D PMPs transplanted, Cont-tau treated

value: Brain

value: Human microglia


title: foregut mesoderm+endoderm explant control DMSO treated NF15-38 rep3

description:
Library name: laevis_NF38_fg_mesendo_explant_control_rep3
laevis_NF38_fg_mesendo_explant_control_rep3

value: NF15 to NF38


title: Mouse TTFs KO 1

value: Tendon tail fascicles

value: All tissue cells


title: OCEAN-C, HL-60, RA 4d 1

city: Beijing

first: Cheng

last: Li

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

department: School of Life Sciences

institute: Peking University

data_processing:
HiC-Pro (version 3.0.0 ) was utilized to process Hi-C data.The allValidPairs of replicates were merged together and then transform to .hic file use the tool hicpro2juicebox.sh provided by HiC-Pro.
Assembly: hg19
Supplementary files format and content: .hic

growth_protocol: HL-60 cell was cultured in a 5% CO2 incubator at 37 °C . The complete medium consist of ATCCformulated Iscove's Modified Dulbecco's Medium with 20% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
Cells were fixed with 1% formaldehyde first and then suspended with lysis buffer. DNA was then digested with MboI enzyme,  and the ends of restriction fragments were filling-in with biotin- labeled dATP followed by re-ligation by the T4 ligase. Then the nucleus were subject to sonication in 2 ml lysis buffer (10 mM Tris-HCl [pH 8.0], 2% Triton X-100, 1% SDS, 100 mM NaCl, and 1 mM EDTA) to get an average DNA fragment size of 300–400 ,bp. The supernatant was then used to get the open chromatin using the zymo DNA extraction kit. To reverse the cross-linking, 1 μl DNase-free RNase A was added to the DNA solution and incubate at 37 °C for 30min. Then 1 μl of proteinase K was added and incubated at 55 °C for 1 h and then followed by incubation at 65 °C overnight. Myone Streptavidin T1 beads (65602) was used to pull down biotinylated DNA.
The library construction was then performed on beads following in situ Hi-C protocol.
OCEAN-C

treatment_protocol: 1 μM all-trans-Retinoic acid (ATRA ) was applied to induce neutrophil differentiation


title: foregut mesoderm+endoderm explant control DMSO treated NF15-38 rep2

description:
Library name: laevis_NF38_fg_mesendo_explant_control_rep2
laevis_NF38_fg_mesendo_explant_control_rep2

value: mismatch MO + DMSO (0.1%)


title: OCEAN-C, HL-60, RA 4d 2


title: HCT116_Input

value: Cell lysate supernatant


title: HCT116_H3K9m3

value: H3K9me3 (Abclonal A2360)


title: OCEAN-C, HL-60, RA 2d 2


title: KO CD4 T cells

city: Baltimore

first: Drew

last: Pardoll

state: Maryland

address: 1650 Orlean St.

department: Oncology

institute: Johns Hopkins Medical Institute

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using Cell Ranger v7.0.0.
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

source_name: CD4 T cells

extract_protocol:
Spinal cords were removed from WT and KO mice post-euthanasia and placed in 0.5% FBS 2mM EDTA containing 1X PBS. Spinal cords were homogenized through a 100um filter to single cell suspension. Immune cells were enriched with a Percoll gradient protocol. Cells were stained with aqua live/dead stain and antibodies against CD4. Live CD4 cells were sorted by FACS and resuspended in 10% FBS RPMI.
Following FACS, cells were concentrated for a targeted cell recovery of 20,000 cells using the 10X Next GEM Single Cell 3’ HT Reagents (10X Genomics; v3.1). Gene expression libraries were prepared according to manufacturer's instructions. Libraries were sequenced on the Illumina NovaSeq 6000 using v1.5 kits, targeting 50K reads/cell, at read lengths of 28 (R1), 8 (i7), 91 (R2). Demultiplexing and FASTQ generation is completed using Illumina’s BaseSpace software.Cell Ranger v7.0.0was used to demultiplex the FASTQ reads, align them to the mm10 mouse transcriptome, and extract their cell and unique molecular identifier (UMI) barcodes.

value: CD4 T cells


title: WT CD4 T cells

description: 10X Genomics

value: WT


title: G123KO iTreg D3_4

data_processing:
raw fastq files QC, FastQC v0.11.8
trim low quality bases, Trimmomatic (version 0.38)
reads mapping, STAR Aligner version 2.7.1a
mapping QC, Picard (version 2.20.4)
gene feature count, FeatureCounts version 1.6.0
Assembly: calculate normalized gene counts, StringTie version 2.0.4
Supplementary files format and content: tab-delimited text files iread count values for each Sample

source_name: CD4 iTreg cells

extract_protocol:
RNA easy mini kit
NEBNext® Ultra™ II Non-Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Massachusetts, USA).

value: CD4 iTreg cells

value: iTreg day 3 differentiated


title: HCT116_IgG

value: normal rabbit IgG (CST #2729)


title: OCEAN-C, HL-60, RA 2d 1


title: foregut mesoderm+endoderm explant control DMSO treated NF15-33 rep2

description:
Library name: laevis_NF33_fg_mesendo_explant_control_rep2
laevis_NF33_fg_mesendo_explant_control_rep2

value: embryo

value: wild type embryo

value: NF15 to NF33


title: OCEAN-C, HL-60, RA 4h 2


title: WT iTreg D3_2


title: G123KO iTreg D3_3


title: foregut mesoderm+endoderm explant control DMSO treated NF15-33 rep1

description:
Library name: laevis_NF33_fg_mesendo_explant_control_rep1
laevis_NF33_fg_mesendo_explant_control_rep1

value: foregut mesoderm+endoderm


title: OCEAN-C, HL-60, RA 4h 1


title: ΔrsbX rep 2

city: Berlin

first: Dmitriy

last: Ignatov

address: Charitéplatz 1

country: Germany

institute: Max Planck Unit for the Science of Pathogens

description:
Library name: rsbx_2
Column name in raw_counts.xlsx: rsbx_2

data_processing:
The sequencing reads were aligned to L. monocytogenes EGD-e genome (NC_003210) with Bowtie 2 (v. 2.5.4) in the "local" alignment mode. The counts of reads overalpping L. monocytogenes genes in each sample were calculated using GeneOverlap package (v. 1.46.0) for R programming language.
Assembly: NC_003210.1
Supplementary files format and content: XLSX file containing raw counts for each sample

organism: Listeria monocytogenes

source_name: Listeria monocytogenes EGD-e rsbX deletion

growth_protocol: WT and ∆rsbX bacterial strains of Listeria monocytogenes EGD-e were grown in BHI at 23°C at normal laboratory light conditions until OD = 0.85.

extract_protocol:
Bacterial cultures were mixed 5:1 with Stop solution (5% phenol in ethanol) and collected by centrifugation. The pellets were resuspended in Disruption solution (10% glucose, 12.5 mM Tris-HCl pH 7.6, and 5 mM EDTA) and bacteria were disrupted with 0.1 mm glass beads using a mini bead beater (BioSpec Products). RNA was isolated by mixing the lysates with TRI Reagent Solution (ThermoFisher) and chloroform, followed by centrifugation. The aqueous samples were thereafter subjected to two additional chloroform extractions. RNA was precipitated with isopropanol, the pellets were washed with 80% ethanol and dissolved in RNase-free water.
RNA was treated with DNase I (Roche) and purified on RNeasy MinElute columns (Qiagen). The cDNA libraries were prepared using TruSeq Stranded mRNA kit (Illumina) following manufacturer's protocol.

value: EGD-e

value: rsbX deletion


title: WT rep 3

description:
Library name: wt_3
Column name in raw_counts.xlsx: wt_3

source_name: Listeria monocytogenes EGD-e wild type

value: Listeria monocytogenes EGD-e wild type


title: ΔrsbX rep 1

description:
Library name: rsbx_1
Column name in raw_counts.xlsx: rsbx_1

value: Listeria monocytogenes EGD-e rsbX deletion


title: ΔrsbX rep 3

description:
Library name: rsbx_3
Column name in raw_counts.xlsx: rsbx_3


title: OCEAN-C, HL-60, RA 0h 2


title: 2AG_24hrs_4

city: Bonn

first: Susanne

middle: Viktoria

last: Schmidt

address: Venusberg Campus 1

institute: Institute of Clinical Chemistry and Clinical Pharmacology

description: Library name: DE91NGSUKBR114159_S153

data_processing:
50bp single-end reads, 10mio reads deep per sample, HiSeq 2400 V4
Alignment and quantification with STAR against the HG19 reference genome
DEseq2 normalization
n.a.
n.a.
Assembly: HG19
Supplementary files format and content: tab-delimited csv file inlcudes raw counts for each sample
Supplementary files format and content: tab-delimited csv file inlcudes normalised gene counts for each sample

source_name: Blood

growth_protocol: Please find the detailed protocol in the manuscript.

extract_protocol:
RNA was isolated via Qiagen RNeasy micro kit
QuantSeq 3´-mRNA Library Prep / Lexogen (for details contact the NGS Core Facility of the University Hospital Bonn)

treatment_protocol: Monocytes were cultured in the presence or absence of 2-AG for 4 or 24hrs.

value: Blood

value: primary Monocytes


title: WT iTreg D3_1


title: Ctrl_4hrs_3

description: Library name: DE87NGSUKBR114134_S128

value: Ctrl


title: foregut mesoderm+endoderm explant control DMSO treated NF15-38 rep1

description:
Library name: laevis_NF38_fg_mesendo_explant_control_rep1
laevis_NF38_fg_mesendo_explant_control_rep1

value: mismatch MO + DMSO (0.1%)

value: NF15 to NF38


title: WT rep 1

description:
Library name: wt_1
Column name in raw_counts.xlsx: wt_1

value: WT


title: OCEAN-C, HL-60, RA 0h 1


title: cko wound edge, biol rep 2

first: Yifan

address: No.639, Zhizaoju Road

department: Department of Plastic and Reconstructive Surgery

institute: Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

description:
EX2_2
sample from K14cre;Hdac5fl/fl mice skin wounded edge

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: skin

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: skin

value: K14cre;Hdac5fl/fl mice


title: ATAC-seq, HL-60, RA 4d 2

data_processing:
The sequencing quality of ATAC-seq libraries was assessed by FastQC (v0.11.8)(https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
ATAC-seq reads were trimmed using Trim Galore (0.6.7) (-q 20 --phred33 --stringency 3 --fastqc --length 30 -e 0.1) to trim low quality sequences and remove adapters.
Bowtie2 v2.3.4.1 was used to align the sequencing reads to the hg19 human genome, and only uniquely mapped reads were retained with PCR duplicates removal using MarkDuplicate from Picard(picard-2.25.5-0)
MACS2( V2.1.1.20160309) as used for calling ATAC peaks, with FDR < 0.05
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
Cells were treated with Tn5 transposase to generate tagged DNA fragments.
Tn5-tagged DNA fragements were purified with Qiagen MinElute PCR Purification Kit , PCR amplified with barcoded Nextera primers to build ATAC-seq libraries


title: cko wound edge, biol rep 1

description:
EX2_1
sample from K14cre;Hdac5fl/fl mice skin wounded edge


title: d15_vCM_ATAC_ZNF436kd_r3

first: Evarist

last: Planet

state: Vaud

address: Route Cantonale

institute: EPFL

description: Library name: d15_vCM_ATAC_ZNF436kd_r3

data_processing:
Libraries were quantified and sequenced using 75-bp paired-end sequencing on an AVITI sequencer (Element Biosciences). Raw reads were aligned to the human genome (hg19) using Bowtie2 v2.4.5 in sensitive local mode. Bam files were filtered to remove low-quality reads (MAPQ < 10). Bigwig coverage tracks were generated using bedtools v2.30.0.
Assembly: hg19
Supplementary files format and content: bigwig coverage files

source_name: H9 ESC

growth_protocol: Human embryonic stem cell (hESC) line H9 was grown at 37ºC in 95% air, 5% CO2 in mTeSR plus media (STEMCELL Technologies, 100-0276) on plates previously coated with Matrigel (Corning, 354277). Cells were differentiated into cardiomyocytes using a ventricular cardiomyocyte differentiation kit (STEMCELL Technologies, 05010) following the manufacturer’s protocol. At day 15 of differentiation, ventricular-like cardiomyocytes (vCMs) were dissociated using 0.25% trypsin (Thermo Fisher Scientific, 25300054) for 5 min at 37ºC, which was quenched using cardiomyocyte support media (STEMCELL Technologies, 05027).

extract_protocol:
ATAC-seq was done by the protocol described in Grandi, et al. 2017. Cells were detached as single cells, and each condition was processed in triplicates, as independent differentiations, with 50,000 cells per replicate lysed in ATAC-seq lysis buffer (10% NP40, 10% Tween-20 and 1% digitonin in ATAC-RSD) to isolate the nuclei. After the washing, chromatin was incubated with Tn5 transposition mix (in TDE1 enzyme, 10% Tween-20, 1% digitonin in TD buffer and PBS). DNA fragments were then purified on Zymo columns (Zymo, D4014), and used as input for PCR for library amplification using custom index (Buenrostro, et al. 2013).
ATAC-seq

value: H9 ESC

value: cardiomyocyte differentiation


title: foregut mesoderm+endoderm explant control DMSO treated NF15-33 rep3

description:
Library name: laevis_NF33_fg_mesendo_explant_control_rep3
laevis_NF33_fg_mesendo_explant_control_rep3

value: embryo

value: wild type embryo


title: 2AG_24hrs_2

description: Library name: DE82NGSUKBR114127_S121


title: Ctrl_4hrs_1

description: Library name: DE78NGSUKBR114102_S96


title: wounded edge, biol rep 2

description:
CTRL2_2
sample from Hdac5fl/fl mice skin wounded edge

value: Hdac5fl/fl mice


title: Ctrl_24hrs_3

description: Library name: DE65NGSUKBR114142_S136


title: ATAC-seq, HL-60, RA 4d 1


title: d15_vCM_ATAC_ZNF436kd_r2

description: Library name: d15_vCM_ATAC_ZNF436kd_r2


title: ATAC-seq, HL-60, RA 2d 2


title: wounded edge, biol rep 1

description:
CTRL2_1
sample from Hdac5fl/fl mice skin wounded edge


title: 2AG_4hrs_1

description: Library name: DE56NGSUKBR114110_S104


title: WT rep 2

description:
Library name: wt_2
Column name in raw_counts.xlsx: wt_2

value: EGD-e


title: unwounded skin, biol rep 2

description:
CTRL1_2
sample from Hdac5fl/fl mice skin


title: d15_vCM_ATAC_ZNF436kd_r1

description: Library name: d15_vCM_ATAC_ZNF436kd_r1


title: d15_vCM_ATAC_ctrl_r3

description: Library name: d15_vCM_ATAC_ctrl_r3


title: Ctrl_24hrs_1

description: Library name: DE51NGSUKBR114103_S97


title: ATAC-seq, HL-60, RA 4h 2


title: unwounded skin, biol rep 1

description:
CTRL1_1
sample from Hdac5fl/fl mice skin


title: Hdac5cko-wound-edge-2

data_processing:
Raw reads were filtered to obtain high-quality clean reads by removing sequencing adapters, short reads (length <35 bp) and low-quality reads using trim-galore (v0.6.4)
Then FastQC (v0.11.9) and Multiqc (v1.8) is used to ensure high reads quality
The clean reads were mapped to the human genome (assembly human genome hg38) using the Burrow-Wheeler Aligner (BWA v0.7.17) software
Peak detection was performed using the MACS2 (v2.2.6) peak finding algorithm with 0.05 set as the q-value cutoff
Annotation of peak sites to gene features was performed using the homer annotatePeaks.pl (v4.10)
Assembly: mm10
Supplementary files format and content: bigwig

source_name: K14cre;Hdac5fl/fl mice skin epidermis

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes and quenched with 125 mM glycine.
The DNA libraries were amplified for 15 cycles and sequenced using Illumina NovaSeq 6000 with paired-end 150 as the sequencing mode

value: skin epidermis

tag: tissue region

value: wound-edge


title: 2AG_24hrs_3

description: Library name: DE37NGSUKBR114161_S155


title: d15_vCM_ATAC_ctrl_r2

description: Library name: d15_vCM_ATAC_ctrl_r2


title: ATAC-seq, HL-60, RA 4h 1


title: d15_vCM_ATAC_ctrl_r1

description: Library name: d15_vCM_ATAC_ctrl_r1


title: Ctrl_4hrs_2

description: Library name: DE33NGSUKBR114136_S130


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo TetOn-SAF-A(RBD del)-SNAP, dox, 24hr, 5-Ph-IAA, 12hr, Hi-C_rep2

city: Daejeon

first: Wonki

last: Cho

address: 291 Daehak-ro Yuseong-gu

country: South Korea

institute: KAIST

description: Library name: Hi-C_RBD_del_IAA_12hr_dox_rep2

data_processing:
In situ Hi-C sequencing data were analyzed using HiC-Pro. FASTQ files were aligned to the human reference genome (hg38), and low-quality and duplicate reads were removed. Valid paired-end reads were used to construct contact matrices, which were subsequently normalized using the Iterative Correction and Eigenvector decomposition (ICE) method.
Assembly: GRCh38
Supplementary files format and content: bedGraph files of eigenvalue

extract_protocol:
After cross-link reversal, 1μl of RNase A was added to each sample, followed by incubation at 37 ℃ for 30 min. DNA was purified using phenol:chloroform:isoamyl alcohol (25:24:1, v/v/v), followed by ethanol precipitation. The pellet was resuspended in 90 μl of TLE buffer (10 mM Tris-HCl pH 8.0, 0.1mM EDTA). Biotin removal was performed in a 100μl reaction containing 1x NEBuffer 2.1, 25μM each of dATP and dGTP, and 30 units of T5 DNA polymerase. The reaction was incubated at 20 ℃ for 4 h, then heat-inactivated at 75 ℃ for 20 min. DNA was fragmented using a Covaris S220 sonicator to an average fragment size of ~400 bp (peak power: 140W; duty factor: 10%; cycles per burst: 200; duration: 55 s). Fragment size selection was performed using a dual-sided AMPure XP bead cleanup: 0.6x bead volume for initial selection and 0.25x for secondary purification. Biotinylated fragments were captured using 10μl of MyOne C1 streptavidin beads per sample. The beads were washed with Tween wash buffer (5 mM Tris-HCl pH 8.0, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20) and resuspended in 400μl of 2x binding buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 2 M NaCl). DNA diluted in TLE (400μl) was added to beads and incubated for 15 min at RT on a nutator. The beads were sequentially washed with 400μl of 1x binding buffer and 100 μl of 0.1x TE buffer (10mM Tris-HCl pH 8.0, 1mM EDTA), resuspended in 50μl of 0.1x TE, and transferred to 0.2 ml PCR tubes.
Library preparation was conducted using the NEBNext Ultra II DNA library Prep Kit (NEB, #E7645L), with slight modifications to the standard protocol. Following adaptor ligation, the beads were transferred to DNA LoBind tubes and washed twice with 400μl of Tween wash buffer for 5 min at RT on a nutator, then with 200μl of 1x binding buffer and 200μl of 0.1x TE. Final elution was performed in 15μl of 0.1x TE by heating at 98 ℃ for 10 min. Supernatants were collected and subjected to PCR amplification for 10 cycles. Amplified libraries were purified using 0.9x AMPure XP beads and sequenced on an Illumina Novaseq X platform (150bp paired-end reads).


title: Hdac5cko-wound-edge-1


title: ATAC-seq, HL-60, RA 0h 2


title: ATAC-seq, HL-60, RA 0h 1


title: Hdac5fl/fl-wound-edge-2

source_name: Hdac5fl/fl mice skin epidermis


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo TetOn-SAF-A(RBD del)-SNAP, dox, 24hr, 5-Ph-IAA, 12hr, Hi-C_rep1

description: Library name: Hi-C_RBD_del_IAA_12hr_dox_rep1


title: 2AG_24hrs_1

description: Library name: DE28NGSUKBR114129_S123


title: Ctrl_24hrs_4

description: Library name: DE21NGSUKBR114158_S152


title: Hdac5fl/fl-wound-edge-1


title: RA4d_3

data_processing:
libraries were assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
low-quality bases and adapters were removed through Trim Galore (v0.6.7)
The reads were mapped to human genome hg19 using hisat2(v2.1.0).
Mapped reads were then processed by htseq-count (v1.99.2) to calculate the read count of all genes.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw count value for each gene

source_name: RNA-seq, HL-60, RA 4d

extract_protocol: RNA-Seq protocol

value: RA 4d


title: 2AG_4hrs_4

description: Library name: DE16NGSUKBR114151_S145

value: Blood


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo TetOn-SAF-A(RBD del)-SNAP, 5-Ph-IAA, 12hr, Hi-C_rep2

description: Library name: Hi-C_RBD_del_IAA_12hr_rep2


title: Hdac5fl/fl-normal-skin-2

value: normal-skin


title: ATAC-seq, HL-60, RA 2d 1


title: RA4d_2


title: Ctrl_24hrs_2

description: Library name: DE12NGSUKBR114126_S120

value: primary Monocytes

value: Ctrl


title: Hdac5fl/fl-normal-skin-1


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo TetOn-SAF-A(RBD del)-SNAP, 5-Ph-IAA, 12hr, Hi-C_rep1

description: Library name: Hi-C_RBD_del_IAA_12hr_rep1


title: 2AG_4hrs_2

description: Library name: DE07NGSUKBR114119_S113


title: RA4d_1


title: RA2d_3

source_name: RNA-seq, HL-60, RA 2d

value: RA 2d


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo TetOn-SAF-A(RBD del)-SNAP, dox, 24hr, 5-Ph-IAA, 3hr, Hi-C_rep1

description: Library name: Hi-C_RBD_del_IAA_3hr_dox_rep1


title: MEP_8F5042_34+_F_21

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

country: Canada

institute: University Health Network

data_processing:
Aligned to hg38 using BWA with default parameters
Duplicates removed using PICARD. All ENCODE hg38 blacklist regions removed, as well as reads from outside autosomes/sex chromosomes.
MACS2 used to call peaks, and Bedtools used to compute maximum signal over background from MACS2 data over catalogue of all called peaks, which was then subjected to quantile normalizartion.
Assembly: hg38
Supplementary files format and content: bed files of called narrowPeaks from MACS2
Supplementary files format and content: tsv file of max signal over background from MACS2 data over catalogue of called peaks (quantile normalized)

source_name: Bone Marrow

growth_protocol: Cells were freshly sorted from bone marrow samples and resuspended in lysis buffer. They were stored at -20C until processing.

extract_protocol:
DNA purification following Buenrostro et al. 2013 protocol
Nextera DNA Sample Preparation kit (Illumina) following Buenrostro et al. 2013 protocol
4 libraries were sequenced/lane on a HiSeq 2500 following manufacturer’s protocol generating paired-end reads of 125-bp in length

value: Bone Marrow

value: Primary

value: MEP

tag: Sex

value: female

tag: age