title: Cerebellum, Input, rep1

data_processing:
Fastp was used to trim adapter off of sequences
Bowtie2 was used to align files to the mm10 genome
Sambamba was used to filter out multimappers and deduplicate reads
MACS3 was used to perform peak calling with -g 1.87e9 and -q 0.05
Bedtools was used to merge overlapping peaks across biological replicates
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each sample

extract_protocol:
Cerebella from two non-pooled P21 B6J.Tg(PCP2-V7-3V5) mice were frozen in liquid nitrogen. Tissue was minced in 1% formaldehyde-PBS and incubated 10 minutes, rotating, at room temperature. Glycine was added at a final concentration of 0.125M to terminate crosslinking and samples were incubated an additional 10 minutes and then washed three times in PBS. After the final wash, tissue was resuspended in 600µL ChIP lysis buffer (50mM Tris-HCl pH 7.5, 0.150M NaCl, 1mM EDTA, 1% Igepal CA-630(Sigma, I8896), 0.25% Sodium deoxycholate, 0.10% SDS, protease inhibitor cocktail (Roche, 11836170001)), homogenized with a plastic pestle and incubated on ice 10 minutes.  Chromatin immunoprecipitation was performed as previously described (Texari et al. 2021). Briefly, lysate was sonicated for 10 seconds on, 30 seconds off, for 12 cycles at 20% amplitude with 2 minutes rest on ice, then 10 cycles at 30% amplitude with 2 minutes rest on ice, followed by 12 cycles at 30% amplitude. A microliter of each sample was run on the Tape Station using high sensitivity D1000 screen tape (Agilent, 5067- 5584) to test sonication efficacy. A 5µL aliquot of each sample was set aside as input and 50µL of V5 antibody conjugated to magnetic beads (MBL International, M167-11) was added to the remaining lysate and incubated overnight at 4˚C. After 3 washes with 200µL wash buffer I (20mM Tris-HCl pH 7.5, 150mM NaCl, 0.10% SDS, 1% Triton X-100, 2mM EDTA, 1x protease inhibitors) and 3 washes with 200µL wash buffer II (250mM LiCl, 1% Triton-X 100, 0.70% sodium deoxycholate, 10mM Tris-HCl pH 7.5, 1mM EDTA, 1x protease inhibitors), and 2 washes in 180µL TET buffer (10mM Tris-HCl pH 7.5, 1mM EDTA, 0.20% Tween 20, 1x protease inhibitors), bead-bound samples were resuspended in 80µL elution buffer (10mM Tris pH 8.0, 0.50% SDS, 5mM EDTA, 280mM NaCl) and reverse crosslinked with 1µL proteinase K (20mg/mL) for 1 hr at 55˚C followed by 1 hr at 65˚C.
Library preparation was performed on beads as previously described (Texari et al., 2021) using the NEB DNA Ultra II Kit (NEB, E7645S). Adapters used were from KAPA (KAPA, KR1317).


title: CA19_2_Enz

status: Public on Jan 01 2024

type: SRA

city: Rochester

first: Liewei

last: Wang

state: MN

address: 200 2st Str SW

department: Neurology

country: USA

institute: Mayo Clinic

description:
CA19_2
AR_PGxeQTL_rawcount.txt

library_source: transcriptomic

data_processing:
Raw RNA sequencing reads were aligned to the human genome GRCh37 (hg19) using STAR[24], and gene counts were performed using HTSEQ
Assembly: GRCh37
Supplementary files format and content: tab deliminated text file of gene counts per sample

molecule: polyA RNA

organism: Homo sapiens

source_name: Blood

growth_protocol: LCLs were cultured in RPMI 1640 supplemented with 15% FBS and 1% penicillin/streptomycin, under 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted with the RNeasy RNA extraction kit per manufacturer's instruction (Qiagen). RNA integrity was examined by Agilent Bioanalyzer
polyA enrichment; RNA-seq libraries were prepared with the TruSeq2 RNA Library Prep Kit v2 (Illumina).

treatment_protocol: Prior to DHT/Enz treatment, all cells were grown in 5% charcoal-stripped media for 24 h, then either DHT in Ethanol (final concentration 10nM) or Enz in DMSO (final concentration 100nM), combination of both drugs, or pure vehicle of 0.1%DMSO/0.1%Ethanol was added to the culture and incubated for 8 hours before harvesting by centrifugation and snap frozen in trizol lysis buffer.

tag: tissue

value: Blood

tag: cell line

tag: cell type

value: B lymphoblastoid cell line

tag: treatment

value: Enz


title: CA19_1_Veh

description:
CA19_1
AR_PGxeQTL_rawcount.txt

value: Veh


title: HEK293T

city: Shanghai City

first: Peisong

last: Zhai

address: Zhizaoju Rd. No.639

country: China

institute: Shanghai Jiao Tong universisy medical school affiliated Shanghai ninth people's hospital

library_source: genomic

data_processing:
The quality control for sequencing data used Trimmomatic, blastn and NT databases. Bowtie2 was used to align the reads to the human genome. Strand cross-correlation (SCC) was used to assess the ChIRP pull-down quality. MACS2 was used to call the peaks.
Gene symbols and other information were annotated onto the peaks by chipseeker (v1.12.1). MEME-ChIP was used to analyse motifs in the peaks, and Tomtom was used to compare the motifs and to annotate them.
Manorm (v 1.18.0) was used to analyse differences in peak reads between groups (p value<0.01 and log2(M value)>1).
Statistical significance was analysed by the R package DiffBind
Assembly: mm10
Supplementary files format and content: Excel spreadsheet with peak name -log10(pvalue), peak location, length, fold enrichment -log10(qvalue), ect..
Library strategy: ChIRP-seq

molecule: genomic DNA

growth_protocol: CAL27 and HEK-293T cells were cultured in high-glucose Dulbecco’s modified Eagle’s medium containing 10% foetal bovine serum and treated with 300μg/mL cetuximab in a humidified 37°C incubator with a 5% CO2 atmosphere.

extract_protocol:
ChIRP was carried out based on a standard ChIP assay using a SimpleChIP® Enzymatic Chromatin IP Kit (Cell Signaling Technology, USA). Briefly, cells were first transfected with biotinylated miRNA (RiboBio, China). Within 24 h, cells were prepared by crosslinking with formaldehyde. Chromatin was segmented using micrococcal nuclease, and cell lysis was carried out via sonication to break the nuclear membrane. Total DNA template (20 µL) was collected after centrifugation and sample dilution. The remaining segmented chromatin was then incubated with streptavidin magnetic beads (Merck, Germany) overnight at 4°C. The samples were collected with a magnetic stand and washed several times before elution. The eluted samples were reverse crosslinked and subjected to DNA purification. Finally, each sample DNA was eluted in a total volume of 30 µL twice and stored with templates at -20°C before sequencing.
A total of 20 ng of DNA templates was used to build libraries for ChIRP-seq.

treatment_protocol: CAL27 and HEK293T cells were treated with 300μg/mL cetuximab. Cells were transfected with biotin labelled miR-451a probes before ChIRP according to the manufacturer's instruction.

value: Tongue carconoma cells

tag: chirp probe


title: Cerebellum, RREB1-3V5 ChIP, rep2

city: La Jolla

first: Susan

last: Ackerman

state: CA

address: 9500 Gilman Drive

department: CMM

institute: UCSD

organism: Mus musculus

source_name: cerebellum

value: cerebellum

tag: genotype

tag: age

value: 3 weeks

tag: Sex

value: Male

tag: antibody for_ip

value: V5 (MBL International, #M167-11)


title: CAL27_input


title: 4FH_D4_Actin_replicate_2

city: New Haven

first: Shangqin

last: Guo

state: CT

address: 10 Amistad ST

department: Cell Biology

institute: Yale University

data_processing:
After quality control, the clean reads were mapped to mouse genome (mm10) using Cufflinks.
Genes expression level were quantitated with HTSeq.
Differentially expressed genes (DEGs) were identified with DESeq2. An absolute log2 fold change >1 and the adjusted p-value (FDR) significance score <0.05 were used as thresholds to identify DEGs.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read counts for each Sample

source_name: MEF

growth_protocol: We performed bulk RNA-seq of control (EV), Actin overexpressed (Actin)  and NLS-actin OE (NLA-Actin) in mouse MEF and day 4 reporgramming cells. We also performed bulk RNA-seq of green positive or red positive reporogramming cells with or witiour NLS-actin under day 10 and day 14.

extract_protocol:
Total RNA with polyA+ selection was extracted from cells for RNA-seq using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.), from three replicates of each group.
RNA-seq was performed at Illumina Hiseq 2500 platform that included quality control, library preparation, fragmentation and PCR enrichment of target RNA according to standardized procedures.
150 bp paired-end raw reads were initially processed to obtain clean reads by removing adaptor sequences, low quality sequences, empty reads.

treatment_protocol: Total RNA was extracted from cells for RNA-seq using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.), from two or three replicates of each group.

value: MEF

value: reprogramming

value: Actin OE


title: CA18_4_EnzDHT

description:
CA18_4
AR_PGxeQTL_rawcount.txt

value: EnzDHT


title: 4FH_D4_Actin_replicate_1


title: Cerebellum, RREB1-3V5 ChIP, rep1

value: Female


title: CAL27


title: CA18_3_DHT

description:
CA18_3
AR_PGxeQTL_rawcount.txt

value: DHT


title: CA19_3_DHT

description:
CA19_3
AR_PGxeQTL_rawcount.txt


title: CA28_2_Enz

description:
CA28_2
AR_PGxeQTL_rawcount.txt


title: 4FH_D4_EV_replicate_2

value: WT


title: scRNA-seq_Spleen recipient 3

city: Regensburg

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

country: Germany

institute: University Hospital Regensburg

library_source: transcriptomic single cell

data_processing:
ScRNA:Sequencing reads were demultiplexed using cellranger mkfastq (version 4.0.0),scTCR:Fastq files were processed using cellranger (version 5.0.0)
ScRNA:The reads were subsequently mapped to the mouse genome using cellranger count (version 4.0.0).
ScRNA: Quality control and analysis was performed with the Seurat package (v4.0.0) in R.
scTCR:Fastq files were processed using cellranger (version 5.0.0)
ScTCR:The reads were subsequently mapped to the mouse genome using cellranger count (version 5.0.0).
ScTCR: Quality control and analysis was performed with the Seurat package (v5.0.0) in R
Assembly: ScRNA: Mouse reference, mm10 (GENCODE vM23/Ensembl98),scTCR: mm10 reference genome (refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0
Supplementary files format and content: cellranger output, rds (R.4.1.1), loom (python 3.8.13), H5ad (python 3.8.13)

molecule: total RNA

source_name: Donor allo reisolated from Recipient 3

growth_protocol: Donor Treg Expansion: Splenocytes from transgenic FoxP3EGFP mice (B6; CD45.2; H-2b) were stained with anti-CD25-PE and anti-PE UltraPure MicroBeads and enriched for CD25+ cells by MACS® (Miltenyi Biotec). The CD25+ fraction was further stained for CD4, CD8 and CD62L and Treg were sorted on a FACSAriaTM IIu or FACSAriaTM Fusion (Becton Dickinson) as CD4+CD25highCD62L+ cells; purity of sorted cells was >98%. For allospecific in vitro expansion, sorted Treg were seeded at 5x104/well in cDMEM together with 2,5x104/well (d0) or 1x104/well (restimulation on d7) anti-CD11c MicroBead-enriched (Miltenyi Biotec) and irradiated (30 Gy) CD11c+ DC from BALB/c mice. Cells received fresh medium on d4 and d10 and were harvested on d12.

extract_protocol:
For re-isolation of donor Treg on day 7 after transplantation, single cell suspensions from spleen, liver and colon were prepared, stained for H-2Kb, CD45.1, CD45.2, TCRβ and CD4 and sorted on a FACSAria IIuTM or a FACSAriaTM Fusion.
ScRNA-seq libraries were constructed using 13-16 cycles of PCR. Products were purified using Ampure XP beads and quality was controlled using Agilent Tapestation.  ScTCR-seq libraries were generated from the same cDNAs using the Single Cell V(D)J Enrichment Kit, Mouse T Cell (10x Genomics).
ScRNA-libraries were sequenced using single-read sequencing (S1 flow cell, 100 bp) on the Illumina NovaSeq™. scTCR-libraries were sequenced on the Illumina NextSeq 550 with 150 cycles single-read sequencing.

treatment_protocol: Prophylactic treatment of GvHD: Single cell suspensions from BM (femora and tibiae of both hind legs) and spleen were prepared. T cells were depleted from BM (T cell depleted bone marrow; TCDBM) by using anti-CD90.2 MicroBeads with the MidiMACS® system (Miltenyi Biotec). CD4+CD25- conventional T cells (Tconv) were isolated from splenocytes by depletion of CD25+ cells using anti-CD25-PE and anti-PE UltraPure MicroBeads (Miltenyi Biotec), followed by enrichment of CD4+ cells from the CD25- fraction through labeling with anti-CD4 MicroBeads (Miltenyi Biotec) using the MidiMACS® system. For short-term (d7) FACS and RNA-seq experiments BALB/c recipients were lethally irradiated (8 Gy) on the day of BMT and transplanted i.v. with 2.5 x106 TCDBM cells and 1x106 Tconv from B6-CD45.1 mice with or without in vitro expanded alloTreg from Foxp3gfp mice at a 1:1 ratio.

tag: phenotype

value: female

value: Donor Treg allo reisolated from Spleen recipient 3

tag: cell markers


title: TE5SPNS1Si(SPNS1SiRNA)

city: taiyuan

first: xin

last: yang

state: shanxi

address: 56 Xinjian South Road, Yingze District, Taiyuan City, Shanxi Province

institute: shanxi medical university

description:
parent cell transferred SPNS1 SiRNA by Invitrogen™ Lipofectamine™ 2000, and protein level and RNA level verified the knockdown efficiency.
TE5S2

data_processing:
The Illumina platform converts sequencing image signals into text signals via CASAVA Base Calling and stores them in fastq.gz format as raw data. The data of each sample are distinguished according to the index sequence for subsequent analysis. In the fastq.gz file, each sequence consists of 4 lines of data, the first line and the third line are read segment identifiers (the first line starts with "@", the third line starts with "+"), the second line is the base sequence, and the fourth line is the sequencing quality value corresponding to each base of the second line sequence.
Sequencing-related quality assessment was performed on the original sequencing data of each sample, including: ① base error rate distribution statistics; ② Base content distribution statistics.Using software: fastp
Due to the fact that the original sequencing data will contain sequencing connector sequences, low-quality read segments, high N-rate sequences (N indicates uncertain base information), and excessively short sequences, the quality of subsequent analysis will be seriously affected. Therefore, quality control will be performed on the original sequencing data before analysis, so as to obtain high-quality clean data to ensure the accuracy of subsequent analysis results. Using software: fastp, the specific steps and sequence are as follows: 1) Remove the joint sequence in reads, and remove the reads without inserted fragments due to the joint self-connection and other reasons; 2) The bases at the first end of the sequence (5 ends) with low quality (mass value less than 20: the average mass value is calculated according to the slide window size of 4) are pruned away, and the bases at the end of the sequence (3 ends) with low quality (mass value less than 3) are pruned away; 3) reads containing N (fuzzy bases) were removed: reads with more than 5 N were discarded; 4) Discard sequences whose length is less than 30 bp after adapter removal and quality pruning. After data quality control is completed, statistics and quality assessment of the data after quality control are carried out again, including: base error rate distribution statistics and base content distribution statistics. The connector sequence is (default) : 5: AGATCGGAAGAGCACACGTC 3: AGATCGGAAGAGCGTCGTGT
Assembly: HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml), use the default HISAT2 HISAT2  is the second generation sequencing sequence alignment software, can use whole genome, transcriptome and exon group data and compare the reference genome, Using the improved BWT algorithm, the sequencing Reads can be compared to the reference genome efficiently. HISAT will first build a graph FM index (GFM) of the whole genome, and also segment the genome to build a large number of small local indexes.
Supplementary files format and content: processed data.csv

extract_protocol:
extract total RNA, Oligo dT enriched mRNA, Fragmented mRNA, Reverse synthesis of cDNA, Connection adaptor, illumina sequencing
Illumina TruseqTM RNA sample prep Kit was used to construct the library

value: ESCC cell lines

tag: sirna


title: 4FH_D4_EV_replicate_1


title: scRNA-seq_Liver recipient 3

value: transgenic FoxP3EGFP mice (B6; CD45.2; H-2b)

value: Donor Treg allo reisolated from Liver recipient 3


title: CA18_2_Enz

description:
CA18_2
AR_PGxeQTL_rawcount.txt

value: Blood

value: B lymphoblastoid cell line

value: Enz


title: TE5NC(negative control)

description:
parent cell transferred negative control by Invitrogen™ Lipofectamine™ 2000
TE5NC

value: negative control


title: 19994X19 superficial BCC

city: Salt Lake City

first: Doug

last: Grossman

state: Utah

address: Huntsman Cancer Institute, 2000 Circle of Hope

department: Dermatology

institute: Huntsman Cancer Institute

data_processing:
The mouse GRCm39 genome and gene annotation files were downloaded from Ensembl release 106 and a reference database was created using STAR version 2.7.9a
A custom Perl script (smallRNA_pe_umi_extractor.pl) from https://github.com/HuntsmanCancerInstitute/UMIScripts was used to trim adapters and extract the Unique Molecular Index (UMI)
The trimmed reads were aligned to the reference database using STAR options optimized for shorter miRNA reads
A second Perl script (bam_umi_dedup.pl) removed PCR duplicates from the aligned BAM file
Mapped reads were assigned to miRNAs in miRbase release 22.1 using featureCounts version 1.6.3
Differentially expressed miRNA in miRbase were identified using a 5% false discovery rate with DESeq2 version 1.36.0
Assembly: GRCm39
Supplementary files format and content: FeatureCount ouput files combined into a single tab-delimited count matrix

source_name: skin

extract_protocol:
Whole RNA was isolated using a RecoverAll kit (Thermo Fisher Scientific, AM1975), quantitated by ScreenTape Assay (Agilent), converted to cDNA  for sequencing.
Small RNA sequencing libraries were prepared from 10-100 ng of total RNA using the Qiagen QIAseq miRNA Library Kit

value: superficial BCC


title: 4FH_D4_NLS-Actin_replicate_1

value: MEF

value: NLS-Actin OE


title: CA18_1_Veh

description:
CA18_1
AR_PGxeQTL_rawcount.txt

value: Veh


title: CA15_4_EnzDHT

description:
CA15_4
AR_PGxeQTL_rawcount.txt

value: EnzDHT


title: scRNA-seq_Colon recipient 3

value: Donor Treg allo reisolated from Colon recipient 3


title: MEF_NLS-Actin_replicate_2


title: TE5(Parent cell)

description:
parent cell, ESCC cell line
TE5


title: scRNA-seq_Spleen recipient 2

source_name: Donor allo reisolated from Recipient 2

value: Donor Treg allo reisolated from Spleen recipient 2


title: K150SPNS1Si(SPNS1SiRNA)

description:
parent cell transferred SPNS1 SiRNA by Invitrogen™ Lipofectamine™ 2000, and protein level and RNA level verified the knockdown efficiency.
K150S2


title: scRNA-seq_Liver recipient 2

value: Donor Treg allo reisolated from Liver recipient 2


title: MEF_Actin_replicate_2

value: Actin OE


title: CA15_3_DHT

description:
CA15_3
AR_PGxeQTL_rawcount.txt

value: DHT


title: CA15_2_Enz

description:
CA15_2
AR_PGxeQTL_rawcount.txt


title: KYSE150NC(negative control)

description:
parent cell transferred negative control by Invitrogen™ Lipofectamine™ 2000
K150NC

value: ESCC cell lines


title: scRNA-seq_Colon recipient 2

value: transgenic FoxP3EGFP mice (B6; CD45.2; H-2b)

value: female

value: Donor Treg allo reisolated from Colon recipient 2


title: KYSE150(Parent cell)

description:
parent cell, ESCC cell line
K150


title: scRNA-seq_Donor allo

source_name: Donor allo

value: Donor Treg allo


title: CA15_1_Veh

description:
CA15_1
AR_PGxeQTL_rawcount.txt

value: Blood

value: B lymphoblastoid cell line


title: MEF_EV_replicate_2

value: WT


title: PT164

city: Saint Louis

first: Fan

last: He

state: MO

address: Room 8834, 320 S. Euclid Ave, CSRB building

institute: Washington University School of Medicine in St. Louis

description: 10x Genomics

data_processing:
Cellranger (10x Genomics, version 3.0.1) was used for transcript alignment, counting, and inter-library normalization of single cell samples. Seurat(version 4.0.0) was used for cluster analysis.
Assembly: GRCh38
Supplementary files format and content: barcodes, features, and matrix files

source_name: PBMC

extract_protocol: Following the 10x genomics protocol, oligonucleotide labeled cells were subjected to droplet bead capture, followed by cell lysis, reverse transcription, and amplification following protocol.

value: PBMC

tag: disease state

value: essential Thrombocythemia


title: scRNA-seq_Spleen recipient 1

source_name: Donor allo reisolated from Recipient 1

value: Donor Treg allo reisolated from Spleen recipient 1


title: PT158

description: 10x Genomics


title: scRNA-seq_Liver recipient 1

value: Donor Treg allo reisolated from Liver recipient 1


title: 5STIM5

city: Lausanne

first: Chris

last: Donnelly

address: Quartier UNIL Centre

department: Institute of Sport Sciences

country: Switzerland

institute: University of Lausanne

data_processing:
Quality check of RNA sequencing reads was performed with FastQC v0.11.7.
Reads were aligned to the reference mouse model GRCm38 using STAR v2.5.4b.
Expression levels were quantified using RSEM v1.3.0 with default parameters.
Assembly: m38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: C2C12 cells, 5STIM, Day5

growth_protocol: C2C12 myoblasts were differentiated to myotubes under 5% O2.

extract_protocol:
RNA extraction was performed using an RNAeasy kit (Qiagen).
Libraries were prepared from 500 ng of total RNA with the TruSeq Stranded MRNA regents (Illumina).

treatment_protocol: Myotubes were then electrically stimulated after acute exposure (2 hours) to 1% or 5% O2. Non-stimulated cells were used as controls.

value: Skeletal Muscle

value: myotubes

value: 2 hours 5% O2 + electrical stimulation


title: MEF_NLS-Actin_replicate_1

value: MEF

value: NLS-Actin OE


title: CA14_3_DHT

description:
CA14_3
AR_PGxeQTL_rawcount.txt

value: DHT


title: 5STIM6


title: PT139

description: 10x Genomics


title: PT153

description: 10x Genomics


title: CA14_2_Enz

description:
CA14_2
AR_PGxeQTL_rawcount.txt

value: Enz


title: CA14_1_Veh

description:
CA14_1
AR_PGxeQTL_rawcount.txt

value: Veh


title: PT130

description: 10x Genomics


title: 5STIM4


title: mouse_adult_mTEC_Insm1-mutant_rep3

city: Guangzhou

first: Shiqi

last: Jia

address: Huangpu Avenue West 613

institute: Jinan University

description:
mouse_adult_RNAseq_gene_read_count.tsv.gz
mouse_adult_RNAseq_gene_FPKM.tsv.gz

data_processing:
All RNAseq fastq files were aligned to mouse genome (mm10) using STAR with parameter --outFilterMismatchNmax 2.
Bam files were sorted by read ID using samtools, and read number were counted using HTSeq-count with parameter -s reverse and annotation Mus_musculus.GRCm38.79.
Fragments per kilobase of exon model per million mapped reads (FPKM) were calculated according to its definition. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript was counted and normalized by the length of the meta-transcript and by the total number of mapped reads. Only protein-coding and lincRNA genes were considered.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene read counts and RPKM values for all samples

source_name: medullary thymic epithelial cells

extract_protocol:
For E18.5 embryoes, six to nine thymi of each genotype (wildtype and Insm1 mutant) were collected and mTECs were isolated from the pool of two to three thymi with the same genotype using UEA1 coupled Dynabeads. Total RNAs were isolated using TRIZOL reagents. For adult mice, mTEC was isolated from each of the thymus using UEA1 coupled Dynabeads.
According to NEBNextRUltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA).
Three sequencing libraries for each genotype were generated

value: medullary thymic epithelial cells

tag: strain

tag: developmental stage

value: adult


title: 5STIM3


title: CA14_4_EnzDHT

description:
CA14_4
AR_PGxeQTL_rawcount.txt

value: Blood

value: EnzDHT


title: mouse_adult_mTEC_Insm1-mutant_rep1


title: HI111

description: 10x Genomics

value: healthy


title: 5STIM2

value: WT


title: HI108

description: 10x Genomics

value: PBMC


title: mouse_adult_mTEC_widetype_rep3

value: wt


title: scRNA-seq_Colon recipient 1

value: transgenic FoxP3EGFP mice (B6; CD45.2; H-2b)

value: female

value: Donor Treg allo reisolated from Colon recipient 1


title: 5STIM1

value: Skeletal Muscle

value: myotubes

value: 2 hours 5% O2 + electrical stimulation


title: CA06_2_Enz

description:
CA06_2
AR_PGxeQTL_rawcount.txt

value: B lymphoblastoid cell line


title: CA06_1_Veh

description:
CA06_1
AR_PGxeQTL_rawcount.txt


title: mouse_adult_mTEC_widetype_rep2


title: MEF_Actin_replicate_1

value: MEF

value: Actin OE


title: PT179_DMSO

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software.
Assembly: GrCh38
Supplementary files format and content: Tab-separated values of raw counts.

source_name: CD14+ MPN monocyte

extract_protocol:
Total RNA was extracted with RNeasy Mini Kit (Qiagen, Hilden, Germany) with DNAse treatment following the manufacturer's protocol.
Samples were then indexed, pooled, and sequenced by Illumina NovaSeq 6000 following standard Illumina protocol.

value: CD14+ MPN monocyte

value: DMSO


title: HI105

description: 10x Genomics


title: CA24_4_EnzDHT

description:
CA24_4
AR_PGxeQTL_rawcount.txt

value: Blood


title: CA06_4_EnzDHT

description:
CA06_4
AR_PGxeQTL_rawcount.txt

value: EnzDHT


title: 5CTRL6

source_name: C2C12 cells, 5CTRL, Day5

value: 2 hours 5% O2


title: CA03_4_EnzDHT

description:
CA03_4
AR_PGxeQTL_rawcount.txt


title: mouse_adult_mTEC_Insm1-mutant_rep2

value: medullary thymic epithelial cells

value: adult


title: mouse_E18.5_mTEC_Insm1-mutant_rep3

description:
mouse_E18.5_mTEC_RNAseq_gene_read_count.tsv.gz
mouse_E18.5_mTEC_RNAseq_gene_FPKM.tsv.gz

value: E18.5 embryo


title: mouse_adult_mTEC_widetype_rep1

value: wt


title: 5CTRL4

value: WT


title: 5CTRL5


title: CA03_3_DHT

description:
CA03_3
AR_PGxeQTL_rawcount.txt

value: DHT


title: CA06_3_DHT

description:
CA06_3
AR_PGxeQTL_rawcount.txt


title: 5CTRL3

value: Skeletal Muscle


title: PT139_DMSO


title: mouse_E18.5_mTEC_Insm1-mutant_rep2


title: CA03_2_Enz

description:
CA03_2
AR_PGxeQTL_rawcount.txt

value: Enz


title: mouse_E18.5_mTEC_Insm1-mutant_rep1


title: 5CTRL2

value: myotubes


title: PT137_DMSO


title: mouse_E18.5_mTEC_widetype_rep2


title: 5CTRL1


title: HI4_DMSO

source_name: CD14+ healthy monocyte

value: CD14+ healthy monocyte


title: HI4_akg

value: α-KG


title: 1STIM5

source_name: C2C12 cells, 1STIM, Day5

value: 2 hours 1% O2 + electrical stimulation


title: mouse_E18.5_mTEC_widetype_rep1


title: N_10_G-R+_replicate_1

tag: time

value: 10 days

value: MEF

value: reprogramming

value: NLS-Actin OE

tag: group

value: G-R+


title: CUTandTag_IgG_mouse_adult_mTEC_rep2

data_processing:
library strategy: Cut&Tag
Raw CUT&Tag sequencing data was trimmed adopters using fastp and aligned to mouse genome (mm10) using Bowtie2 with the parameters “--local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -X 700”.
BigWig files were generated using deepTools bamCoverage under default parameters.
Assembly: mm10
Supplementary files format and content: BigWig

extract_protocol:
mTECs were isolated using UEA1 coupled Dynabeads from wildtype 6-8weeks old mice. 0.5ul of Insm1 or 2ul of  IgG (DIA.AN, Q6008) antibody was incubated with 5x104 mTEC cells in a volume of 100ul first antibody buffer for overnight at 4°C. Then, the Donkey anti-guinea pig antibody (Jackson ImmunoResearch,706-005-148) was used and incubated with the mTEC for 45 minutes in 100ul secondary antibody buffer at room temperature. After washing away the unbound antibodies, the ChiTag transposon was incubated with mTECs for one hour at room temperature. The fragmentation, DNA purification and library construction were performed according to the product protocol.
The fragmentation, DNA purification and library construction were performed according to the instruction of the manufactory (Novoprotein, N259-YH01)
Nextera index-kit adapter primers were used for library construction, 16x cycles were used for PCR amplification

tag: target

value: IgG

tag: developmenta stage

value: medullary thymic epithelial cells


title: HI3_DMSO

tag: cell type

value: DMSO


title: 1STIM4

tag: tissue

tag: cell line

tag: treatment


title: 19994X4 control skin

value: control skin


title: 1STIM3

tag: genotype

value: WT


title: PT139_akg

value: CD14+ MPN monocyte


title: CUTandTag_IgG_mouse_adult_mTEC_rep1

value: wt

value: adult


title: HI3_akg


title: CA03_1_Veh

description:
CA03_1
AR_PGxeQTL_rawcount.txt

value: Blood

value: B lymphoblastoid cell line

value: Veh


title: CUTandTag_Insm1_mouse_adult_mTEC_rep2


title: 1STIM2

value: Skeletal Muscle

value: myotubes

value: 2 hours 1% O2 + electrical stimulation


title: mouse_E18.5_mTEC_widetype_rep3

value: E18.5 embryo


title: 1STIM1


title: donor 3, replicate 2, XY018

city: Saarbrücken

first: Julia

middle: Maria

last: Schulze-Hentrich

address: Campus, Building A2.4

department: Genetics and Epigenetics

institute: Saarland University

data_processing:
Read preprocessing was performed with the Lexogen pipeline that uses bbduk of the BBTools suite (https://sourceforge.net/projects/bbmap/) for quality trimming.
Cleaned reads were aligned with STAR to the reference genome GRCh38.104
Assembly: Ensembl GRCh38.104
Supplementary files format and content: tab-separated raw read counts

source_name: cord blood-derived CD34+ cells

growth_protocol: t(4;11) cells were maintained in StemMACS™ HSC Expansion Media (Miltenyi) supplemented with 10% FCS, 1% Penicillin/Streptomycin, human cytokines (IL-3, IL-6, SCF, FLT3L, SCF, G-CSF, 50 ng/ml each), SR-1 and UM-729 (0.75 µM each).

extract_protocol:
Total RNA was isolated using NucleoSpin RNA Kit (Macherey-Nagel) according to the manufacturer’s instructions. All samples were examined for quality assessment using Nanodrop One (Thermo Fisher Scientific) and Bioanalyzer (Agilent, Santa Clara, CA, USA). Only samples with an RNA integrity number (RIN) of 7 and higher were used for sequencing library preparation.
Libraries for 3′ RNA-seq were prepared using the 3′ method by Lexogen as used in the NGS Competence Center Tübingen (NCCT) where both library preparation and sequencing in randomized batches was performed. First strand synthesis of polyA-tailed RNA from total RNA using oligo dT primers was followed by degradation of the RNA template, second strand synthesis with random primers containing 5′ Illumina-compatible linker sequences and amplification using random primers that add barcodes and cluster generation sequences.
The libraries were sequenced on the NCCT Nova sequencing platform at a depth of about 10 million reads with 100 bp in length.

treatment_protocol: t(4;11) cells were seeded in 48- or 96-well plates at a density of 7.5x105/ml in appropriate media and cultured for a maximum of seven days. XY018 (Tocris Bioscience) was prepared in stock solutions with DMSO and added to the cells in serial dilution on day 0. Cells were reseeded in the origin density and retreated with inhibitors after 48 hours and 72 hours.

value: cord blood-derived CD34+ cells


title: 1STIM6


title: donor 3, replicate 2, DMSO


title: CUTandTag_IgG_mouse_E18.5_mTEC_rep3


title: CUTandTag_Insm1_mouse_adult_mTEC_rep1


title: donor 3, replicate 1, XY018


title: 1CTRL5

source_name: C2C12 cells, 1CTRL, Day5

value: 2 hours 1% O2


title: CUTandTag_IgG_mouse_E18.5_mTEC_rep2

value: IgG


title: 1CTRL4


title: CUTandTag_IgG_mouse_E18.5_mTEC_rep1

value: medullary thymic epithelial cells


title: 1CTRL6


title: donor 2, replicate 2, XY018


title: 1CTRL3


title: donor 2, replicate 2, DMSO

value: DMSO


title: CUTandTag_Insm1_mouse_E18.5_mTEC_rep3


title: 1CTRL2


title: CUTandTag_Insm1_mouse_E18.5_mTEC_rep2


title: CUTandTag_Insm1_mouse_E18.5_mTEC_rep1


title: donor 2, replicate 1, XY018


title: MEF_EV_replicate_1

value: MEF


title: 1CTRL1

value: WT


title: donor 2, replicate 1, DMSO


title: Mice-6-Tregs

city: Paris

first: Wilfrid

last: Richer

address: 26 rue d'Ulm

country: France

institute: Institut Curie

data_processing:
Sequence were trimmed using Atropos (parameters: --auto --overlap 3 --times 3 --minimum-length 10)
Trimmed sequence reads were mapped to GrCM38/mm10 using bowtie-1.2 (parameters: -v 2 -a -m 1 --best --strata --nomaqround -y) and STAR-2.5.3a (parameters: --outSAMtype BAM SortedByCoordinate --runMode alignReads --quantMode GeneCounts --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --outSAMprimaryFlag OneBestScore --outMultimapperOrder Random --outSAMattributes All).
Read count extraction and normalization were performed using STAR.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count values for each Sample
Supplementary files format and content: tab-delimited text files include tpm values for each Sample

source_name: Tumor

extract_protocol:
RNA was isolated using a Single Cell RNA purification kit (Norgen), including RNase-Free DNase Set (Qiagen) treatment. The RNA integrity numbers were evaluated with an Agilent RNA 6000 pico kit. All samples were assessed according to the manufacturer's instructions.
Reverse transcription and barcoded Illumina compatible libraries were generated from <10ng of DNA of each sample SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian (Takara) . Libraries were sequenced on an Illumina HiSeq - Rapid Run  using 100bp paired-end mode, 40 million reads per sample.

treatment_protocol: Tumors were shaped into 3 pools and purified CD4+ T cells were obtained by positive selection with the "EasySep Mouse CD4 Positive Selection II" kit (StemCell Technologies). Then, cells were stained with CD45-AF700, TCR?-APC-Cy7, CD8-APC, CD4-PE-TexasRed, CD39-PE, CD11b-PE-Cy7, CD19-PE-Cy7, NK1.1-PE-Cy7, F4/80-PE-Cy7 and then with 4',6-diamidino-2-phenylindole (DAPI) LIVE/DEAD stain. Among the live CD4+ T cells (DAPI- CD11b- CD19- NK1.1- F4/80- CD8- CD45+ TCR+ CD4+), equal number of Treg, CD39 positive Tconv, and CD39 negative Tconv were sorted with a purity of 98-99% using BD FACS ARIA II cell sorter (GFP+, GFP- CD39+, GFP- CD39-, respectively). Cells were collected and lysed with TCL buffer (Qiagen) with 1% of ß-mercaptoethanol and stored at -80 until subsequent analysis.

value: Tumor

value: B16F10-OVA tumors

value: CD4+ Treg cells

value: DTR-GFP mice


title: Isogenic 1 (3rd differentiation)

city: Leuven

first: Yingli

last: Zhu

address: ON4 Herestraat 49

country: Belgium

institute: KULeuven

description:
OD@RR@GE3@S30@CTGCTTCC@GATAGATC
RNAseqCounts-RH-RR.xlsx

data_processing:
RNA was extracted and quality control was performed as mentioned above. Library preparation was performed with the LexoGen Quant Seq. Kit. Libraries were sequenced on an Illumina HiSeq4000 sequencing system. Single-end reads were generated, with an average of 4 million reads obtained per sample. Alignment was performed with Hisat2. Raw counts were log2 transformed before performing downstream analyses. Principal component analysis (PCA) was done using the ggplot2 package in R, written in Jupyter Notebook. Differentially expressed genes were calculated with the DESeq2 package in R among different pairwise comparisons. The threshold criteria of p-value and false discovery rate were ≤ 0.05 and for fold change ≥ 2 in gene expression to identify differentially expressed genes. Further enrichment analyses for biological processes or pathways were performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment.
Supplementary files format and content: counts_results.csv
Supplementary files format and content: RNAseqCounts-RH-RR.xlsx

source_name: oligodendrocyte progenitor cells

growth_protocol: Briefly, Single cell suspensions of iSOX10-iPSCs were plated at a density of 25 000 cells/cm2 on matrigel-coated plates in mTeSRTM1 medium supplemented with 1X Revitacell. 48 hours later, medium was changed to basal medium supplemented with 1 µM LDN-193189, 10 µM SB431542 and 100 nM RA with daily medium changes for 7 days. Basal medium consisted of DMEMF12 GlutamaxTM  supplemented with 1X N2 supplement, 1X B27 supplement without vitamin A , 25 μg/ml human insulin solution, 5 μM 2-Mercaptoethanol, 1X MEM NEAA and 100 U/ml Penicillin-streptomycin. For the next 4 days, basal medium supplemented with 100 nM RA and 1 µM SAG was added to the cells and changed daily. Next, DIV12 NPCs were detached using accutase and single cell suspensions were plated on matrigel-coated plates at 20,000 cells/cm2 in basal medium supplemented with 100 nM RA, 1 µM SAG and 1X Revitacell. The following day, medium was changed every other day.

extract_protocol:
We performed RTqPCR, using progeny from 1 well of 6-well-plate for RNA extraction using the Quick-RNA Microprep Kit (Zymo research) according to the manufacturer’s instructions with addition of DNAseI from the On-Column DNase I Digestion kit (Sigma-Aldrich).
Library preparation was performed with the LexoGen Quant Seq. Kit. Libraries were sequenced on an Illumina HiSeq4000 sequencing system.

value: oligodendrocyte progenitor cells

value: Isogenic 1 iPSC

value: cryopreserved oligodendrocyte progenitor cells

tag: gender

value: female

tag: age

value: 71 years old


title: LIVER-input

city: NANJING

first: ZILONG

last: LI

state: JIANGSU

address: 639 Longmian Avenue

institute: China Pharmaceutical University

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 mouse genome (assembly mouse genome GRCm38) 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: bw

source_name: liver

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 single-end 150 as the sequencing mode

value: liver


title: Mice-6-CD39pos

value: CD4+ Tconv CD39pos cells


title: donor 3, replicate 1, DMSO

value: cord blood-derived CD34+ cells


title: LIVER-CON_MKL1

value: Sham operation


title: donor 1, replicate 2, DMSO


title: donor 1, replicate 2, XY018


title: LIVER-PHX_MKL1

value: Two-thirds hepatectomy


title: Isogenic 1  (1st differentiation)

description:
OD@RR@GE1@S28@AACTGTAG@ACGCCGCA
RNAseqCounts-RH-RR.xlsx


title: Mice-4-Tregs


title: Mice-6-CD39neg

value: CD4+ Tconv CD39neg cells


title: Isogenic 1 (2nd differentiation)

description:
OD@RR@GE2@S29@GGTCACGA@GTATTATG
RNAseqCounts-RH-RR.xlsx


title: FUSR521H Mutant (3rd differentiation)

description:
OD@RH@GE3@S27@ACGCACCT@GGTGAAGG
RNAseqCounts-RH-RR.xlsx

value: FUSR521H Mutant iPSC


title: Mitral valve, control, 25 weeks

city: Minneapolis

first: Bryce

middle: A

last: Binstadt

state: Minnesota

address: 2-200 WMBB Bench 8

department: Pediatrics

institute: University of Minnesota

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0.
Assembly: mm10-3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Mitral valve

extract_protocol:
Mitral valves were isolated from B.g7 and K/B.g7 hearts and digested using Collagenase 2 and DNAse. Following digestion, cells were washed and filtered, then red blood cells lysed using AKC buffer. Cells were stained with a viability dye and live, single cells were sorted using fluorescence-activated cell sorting (FACS).
Library was performed according to the manufacter’s instructions (single cell 3’ protocol, v2, 10x Genomics).

value: Mitral valve

value: 25 weeks


title: Mitral valve, control, 8 weeks

value: 8 weeks


title: HNRNPD_KO_nascent_SW839_rep2

city: Hefei

first: Yucong

state: Anhui

address: 443 Huangshan Road

institute: USTC

description:
nascent RNA
KO_SW839_nascent_circ.tsv

data_processing:
The Hisat2 and feature counts software were used to map clean reads to reference genome (hg19) and calculate the gene expression level which was normalized to FPKM.
the CIRI2 software (v 2.0.6) was utilized to predict the junction of circRNAs.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include reads of RNAs for each sample

growth_protocol: SW839 cells were maintained in DMEM medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in a humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was extracted with Trizol.
The rRNA was removed by Illumina Ribo-Zero Gold kit and surplus RNA was purified for end repair and 50-adaptor ligation. Then, reverse transcription was performed with random primers containing 3’ adaptor sequences. Finally, the cDNAs were purified and amplified with PCR reaction. The products with 300-500 length were purified and quantified. These libraries were utilized to 150 nt paired-end sequencing with an Illumina Nova seq 6000 system (Novogene, China).

value: Renal clear cell carcinoma cells

value: HNRNPD KO


title: FUSR521H Mutant (2nd differentiation)

description:
OD@RH@GE2@S26@GTATGTTC@AACAGGAA
RNAseqCounts-RH-RR.xlsx

value: oligodendrocyte progenitor cells


title: Mitral valve, control, 3 weeks

value: 3 weeks


title: Mice-1-Tregs

value: Tumor

value: B16F10-OVA tumors

value: CD4+ Treg cells

value: DTR-GFP mice


title: FUSR521H Mutant (1st differentiation)

description:
OD@RH@GE1@S25@CGCTATGT@TCCGACAC
RNAseqCounts-RH-RR.xlsx

value: cryopreserved oligodendrocyte progenitor cells

value: female

value: 71 years old


title: HNRNPD_KO_nascent_SW839_rep1

description:
nascent RNA
KO_SW839_nascent_circ.tsv


title: HNRNPD_KO_input_SW839_rep2

description:
nascent RNA
KO_SW839_nascent_circ.tsv


title: Cerebellum, Input, rep2

data_processing:
Fastp was used to trim adapter off of sequences
Bowtie2 was used to align files to the mm10 genome
Sambamba was used to filter out multimappers and deduplicate reads
MACS3 was used to perform peak calling with -g 1.87e9 and -q 0.05
Bedtools was used to merge overlapping peaks across biological replicates
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: cerebellum

extract_protocol:
Cerebella from two non-pooled P21 B6J.Tg(PCP2-V7-3V5) mice were frozen in liquid nitrogen. Tissue was minced in 1% formaldehyde-PBS and incubated 10 minutes, rotating, at room temperature. Glycine was added at a final concentration of 0.125M to terminate crosslinking and samples were incubated an additional 10 minutes and then washed three times in PBS. After the final wash, tissue was resuspended in 600µL ChIP lysis buffer (50mM Tris-HCl pH 7.5, 0.150M NaCl, 1mM EDTA, 1% Igepal CA-630(Sigma, I8896), 0.25% Sodium deoxycholate, 0.10% SDS, protease inhibitor cocktail (Roche, 11836170001)), homogenized with a plastic pestle and incubated on ice 10 minutes.  Chromatin immunoprecipitation was performed as previously described (Texari et al. 2021). Briefly, lysate was sonicated for 10 seconds on, 30 seconds off, for 12 cycles at 20% amplitude with 2 minutes rest on ice, then 10 cycles at 30% amplitude with 2 minutes rest on ice, followed by 12 cycles at 30% amplitude. A microliter of each sample was run on the Tape Station using high sensitivity D1000 screen tape (Agilent, 5067- 5584) to test sonication efficacy. A 5µL aliquot of each sample was set aside as input and 50µL of V5 antibody conjugated to magnetic beads (MBL International, M167-11) was added to the remaining lysate and incubated overnight at 4˚C. After 3 washes with 200µL wash buffer I (20mM Tris-HCl pH 7.5, 150mM NaCl, 0.10% SDS, 1% Triton X-100, 2mM EDTA, 1x protease inhibitors) and 3 washes with 200µL wash buffer II (250mM LiCl, 1% Triton-X 100, 0.70% sodium deoxycholate, 10mM Tris-HCl pH 7.5, 1mM EDTA, 1x protease inhibitors), and 2 washes in 180µL TET buffer (10mM Tris-HCl pH 7.5, 1mM EDTA, 0.20% Tween 20, 1x protease inhibitors), bead-bound samples were resuspended in 80µL elution buffer (10mM Tris pH 8.0, 0.50% SDS, 5mM EDTA, 280mM NaCl) and reverse crosslinked with 1µL proteinase K (20mg/mL) for 1 hr at 55˚C followed by 1 hr at 65˚C.
Library preparation was performed on beads as previously described (Texari et al., 2021) using the NEB DNA Ultra II Kit (NEB, E7645S). Adapters used were from KAPA (KAPA, KR1317).

value: cerebellum

tag: Sex

value: Male

tag: antibody for_ip


title: donor 1, replicate 1, XY018

value: cord blood-derived CD34+ cells


title: FUSP525L Mutant (5th differentiation)

description:
GC119557
counts_results.csv

value: SIGi001-A iPSC (Sigma)

value: 20-24 years old


title: Mice-1-CD39pos

value: CD4+ Tconv CD3pos cells


title: Mitral valve, inflamed, 8 weeks

value: Mitral valve

value: 8 weeks


title: donor 1, replicate 1, DMSO

value: DMSO


title: FUSP525L Mutant (4th differentiation)

description:
GC119556
counts_results.csv

value: oligodendrocyte progenitor cells


title: Mice-1-CD39neg

value: Tumor

value: CD4+ Tconv CD39neg cells


title: HNRNPD_KO_input_SW839_rep1

description:
nascent RNA
KO_SW839_nascent_circ.tsv

value: Renal clear cell carcinoma cells

value: HNRNPD KO


title: Mitral valve, inflamed, 3 weeks

value: 3 weeks


title: HNRNPD_WT_nascent_SW839_rep2

description:
nascent RNA
WT_SW839_nascent_circ.tsv

value: WT


title: FUSP525L Mutant (3rd differentiation)

description:
GC119555
counts_results.csv

value: cryopreserved oligodendrocyte progenitor cells

value: female


title: PT179_akg

value: CD14+ MPN monocyte

value: α-KG


title: Mice-4-CD39pos

value: B16F10-OVA tumors

value: CD4+ Tconv CD39pos cells

value: DTR-GFP mice


title: Isogenic 2 (4th differentiation)

description:
GC119554
counts_results.csv

value: SIGi001-A iPSC (Sigma)

value: 20-24 years old


title: GL261-Nes-high-2

city: Orsay

first: Giorgio

last: Seano

address: Bâtiment 110, Rue Henri Becquerel

department: INSERM U1021 - CNRS UMR3347

description:
GL261_tpm.csv
D651T063

data_processing:
The reads obtained were processed using the Curie Institute Nextflow RNA-seq analysis pipeline
reads quality was assessed using FastQC and mapped to the reference genome (hg19/GRCh37 or mm10/GRCm38 for GL261) using STAR software
raw reads count tables were generated using STAR
Software versions and full pipelines are available at https://github.com/bioinfo-pf-curie/RNA-seq/
Assembly: hg19, mm10
Supplementary files format and content: Matrix table with TPM gene counts for every gene and every sample (.csv)

source_name: brain

growth_protocol: cells were maintained in neurospheres using NeuroCult basal medium with NeuroCult proliferation supplement (STEMCELL technologies, #05751), 20ng/ml EGF, 20ng/ml bFGF, 5ug/ml heparin (STEMCELL Technologies, #07980) and gentamycin (Sigma) (NC complete media) in low attachment flasks (Corning, #3814)

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (Qiagen)
RNA-seq libraries were constructed using 100ng to 1ug of RNA using Illumina library structure (Stranded mRNA Library preparation, Illumina), according to the manufacturer’s instructions. For MGG4-BV samples only, SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian protocol was used. Samples were sequenced as 100bp paired-end runs on the Novaseq 6000 (Illumina).

treatment_protocol: In-vitro MGG4 cells were treated with 25uM of temozolomide for 3 days before RNA extraction. For in-vivo MGG4 samples, mouse were irradiated with 10 Gy using a X-ray irradiator, or treated with 10mg/kg of temozolomide. Tissue was harvested 7 days after treatment. MGG4-Nes, MGG18-Nes and GL261-Nes samples were FACS-sorted based on reporter expression before RNA extraction with no additional treatment. For co-culture experiment, MGG4 cells were co-cultured 3 days with brain blood vessels before isolation of tumor cells for RNA extraction.

value: brain

value: chemically-induced murine glioblastoma cell line

value: Nes-high


title: metastastic tumor tissue 2

city: sichuan

first: Qunli

last: Xiong

state: State...

address: sichuan

institute: sichuan university

description: liver

library_source: other

data_processing:
Sequencing quality are examined by FastQC  and trimmed reads (pass Illumina quality filter, trimmed 5',3'-adaptor bases by cutadapt ) are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software .
Assembly: hg38
Supplementary files format and content: fa.gz files including Compressed rrimmed data counts

molecule: other

source_name: tumor

extract_protocol:
RNA was extracted using trizol.Agarose electrophoresis was used to check the integrality of total RNA samples, and then the samples were quantified on the NanoDrop ND-1000 instrument. Total RNA samples were first pretreated as following to remove some RNA modifications
1) 3'-adapter ligation; 2) 5'-adapter ligation; 3) cDNA synthesis; 4) PCR amplification; 5) size selection of  134-160bp PCR amplified fragments (corresponding to  14-40nt small RNAs).
tRF & tiRNA Sequencing

value: tumor


title: HNRNPD_WT_nascent_SW839_rep1

last: Wang

description:
nascent RNA
WT_SW839_nascent_circ.tsv

value: Renal clear cell carcinoma cells


title: GL261-Nes-low-1

description:
GL261_tpm.csv
D651T062

value: Nes-low


title: HNRNPD_WT_input_SW839_rep2

description:
nascent RNA
WT_SW839_nascent_circ.tsv


title: Mice-4-CD39neg

value: Tumor

value: CD4+ Tconv CD39neg cells


title: Mitral valve, inflamed, 25 weeks

value: Mitral valve

value: 25 weeks


title: GL261-Nes-low-2

description:
GL261_tpm.csv
D651T064


title: HNRNPD_WT_input_SW839_rep1

description:
nascent RNA
WT_SW839_nascent_circ.tsv

value: WT


title: FUSP525L Mutant (2nd differentiation)

description:
GC118030
counts_results.csv

value: oligodendrocyte progenitor cells

value: cryopreserved oligodendrocyte progenitor cells

value: female


title: metastastic tumor tissue 1

description: liver


title: GL261-Nes-high-3

description:
GL261_tpm.csv
D651T065


title: FUSP525L Mutant (1st differentiation)

description:
GC118029
counts_results.csv


title: HNRNPD_circ_KO_SW839_rep2

value: HNRNPD KO


title: GL261-Nes-high-1

description:
GL261_tpm.csv
D651T061


title: primary tumor tissue 2

description: pancreas


title: HNRNPD_circ_KO_SW839_rep1


title: Isogenic 2 (2nd differentiation)

description:
GC118027
counts_results.csv

value: SIGi001-A iPSC (Sigma)


title: metastastic tumor tissue 3

description: liver


title: GL261-Nes-low-3

description:
GL261_tpm.csv
D651T066


title: HNRNPD_circ_WT_SW839_rep2


title: RNA Seq OVCAR5NTX301_100nM-3

city: Chicago

first: Daniela

last: Matei

address: 420 E. Superior St.

institute: Northwestern University Feinberg School of Medicine

data_processing: none provided

growth_protocol: OVCAR5 were maintained in RPMI-1640 with L-glutamine (Corning, Cat# 10-040-CV) plus 10% FBS, 1% GlutaMAX, and 1% penicillin-streptomycin.

extract_protocol:
For HumanMethylation 450 Epic Array, genomic DNA were extracted using QIAmp DNA Mini Kit.
For RNA sequencing, total RNA was extracted with TRI Reagent (Sigma, Cat# T9424). DNA was removed by using a RNeasy MinElute Cleanup Kit (QIAGEN) with RNase-Free DNase Set (QIAGEN).
Libraries were prepared with a NEBNext Ultra II RNA library prep kit from Illumina (New England Biolabs Inc., Ipswich, MA) as described in the manufacturer’s protocol.

treatment_protocol: OVCAR5 cells were treated with DMSO, NTX301 (10nM, 100nM) for 3 days.


title: primary tumor tissue 1

description: pancreas


title: HNRNPD_circ_WT_SW839_rep1


title: Isogenic 2 (1st differentiation)

description:
GC118026
counts_results.csv

value: 20-24 years old


title: no028

city: Jena

first: Emanuel

last: Barth

address: Leutragraben 1

department: Bioinformatics Core Facility FSU Jena

institute: Friedrich Schiller University Jena

data_processing:
Reads were trimmed (including adapter removal) and filtered using fastp (version 0.23.2). Bases with a quality lower than 30 were trimmed from both ends of each read. Reads with a mean quality lower than 30, shorter than 15 bases or reads containing more than 2 N bases were removed.
Mapping was performed using HIST2 (version 2.2.1) using standard parameters onto the Mus musculus reference genome GRCm39 (Ensembl release 107).
For read counting featureCounts (version 2.0.1) was employed using the paramters -M and -O.
Assembly: GRCm39.107
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

extract_protocol:
Total RNA from cells was extracted and purified using the TRIzol reagent following the manufacturer's protocol.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA rRNA- Library Prep Kit following the manufacturer's protocol.

value: mammary epithalial cells

value: cancer

value: DOX


title: DF human keratinocytes, PIAS1 ChIP rep1

city: Evanston

first: Xiaomin

last: Bao

state: IL

address: 633 Clark Street

department: Molecular Biosciences

institute: Northwestern University

data_processing:
For RNA-seq, adaptor trimming and quality control was performed using Trim Galore and FastQC, respectively. Alignment was performed using STAR and transcript quantification was performed using Salmon. Differential expression analysis was performed using DESeq2.
ChIP-seq adaptor trimming and quality control was performed using Trim Galore and FastQC, respectively. Alignment was performed using BWA-MEM. Bigwig files were generated using BEDTools and normalized based on counts per million reads. Differential analysis was performed using EdgeR via Diffbind.
Assembly: hg38
Supplementary files format and content: Processed RNA-seq data is presented as the DESeq2 output information, featuring the normalized counts for each gene.
Supplementary files format and content: Processed ChIP-seq data is presented as a bigWig file and/or MACS2 broadPeak file.

source_name: Foreskin

growth_protocol: Keratinocytes were cultured from a mixture of multiple unidentified donors using a 1:1 mixture of Keratinocyte-SFM and 50% Medium 154. To induce differentiation, keratinocytes were seeded at 100% confluency and treated with 1.2 mM CaCl2 over 4 days.

extract_protocol:
RNA was extracted using Quick-RNA MiniPrep (Zymo Research) with DNase I treatment following the manufacturer protocol.
NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit were used to prepare RNA-seq libraries. NEBNext Ultra II DNA Library Prep Kit was used to prepare ChIP-seq and CUT&RUN libraries.

treatment_protocol: For the shRNA-mediated knockdown, shRNA lentivirus was added to the keratinocytes in addition to polybrene (20 ug/mL) and centrifuged at 1,250 rpm for 1 hour at 32oC. The keratinocytes were then selected with puromycin (2 ug/mL) for 48 hours.

value: Foreskin

value: primary human neonatal keratinocytes

value: DF

value: PIAS1 (Santa Cruz, #sc-365127)


title: no027


title: no026


title: RNA Seq OVCAR5NTX301_100nM-1


title: UD human keratinocytes, PIAS1 ChIP rep2

value: UD


title: HEK293 cells, ZNF687 P937R replicate 1

city: Portland

first: Andrew

last: Adey

state: OR

address: 3181 S.W. Sam Jackson Park Rd, RHH, L103

department: MMG

institute: Oregon Health & Science University

data_processing:
Fastq files were generated from the resulting base call files using bcl2fastq (Illumina).
The paired-end reads were aligned to hg38 (NCBI build 39) and aligned reads were analyzed using the Rsubread Package.
Differential expression analysis was performed using the deSeq2 package by FPKM (fragments of kilo- base per exon per million fragments mapped) on the human RefSeq transcript database.
iDEP platform was used for K-means clustering and generation of heat-maps.
Assembly: hg38 (NCBI build 39)
Supplementary files format and content: csv file includes cpm for each sample

source_name: Human embryonic kidney

growth_protocol: HEK293 cells were obtained from American Type Culture Collection (Manassas, VA) and cultured in DMEM medium supplemented with 10% FBS, (Atlanta Biologicals), penicillin/streptomycin (Invitrogen), and fungizone at 37°C in 5% CO2.

extract_protocol:
RNA was purified using the QIAGEN RNeasy Mini Kit.
Total RNA integrity was evaluated using the Bioanalyzer (Agilent). RNA-seq libraries were prepared from total RNA using the Illumina Stranded mRNA kit (Illumina). Libraries were then profiled on a TapeStation D1000 tape (Agilent) and quantified using an NGS Library Quantification Kit (Roche/Kapa) on a StepOnePlus Real Time PCR Workstation (Thermo/ABI).

treatment_protocol: Six-well plates were seeded with 3e5 HEK293 cells overnight. The cells were transfected with ZNF687 WT, frameshift, missense variant containing plasmids and pMIG empty using Fugene6 (Promega) according to the manufacturer’s protocol. Cells were cultured and harvested for protein lysate extraction following the observation of GFP fluorescence 72h after transfection

value: Human embryonic kidney

value: Overexpressing ZNF687 P937R

value: transient transfection


title: HEK293 cells, ZNF687 P937R replicate 2


title: Isogenic 2 (3rd differentiation)

description:
GC119553
counts_results.csv

value: oligodendrocyte progenitor cells


title: primary tumor tissue 3

description: pancreas

value: tumor


title: HEK293 cells, ZNF687 R939Pfs*Ter36 replicate 2

value: Overexpressing ZNF687 R939Pfs*Ter36


title: no025


title: RNA Seq OVCAR5DMSO-3

value: DMSO


title: no024


title: RNA Seq OVCAR5DMSO-2


title: DF human keratinocytes, PBRM1 ChIP rep2


title: HEK293 cells, ZNF687 R939Pfs*Ter36 replicate 1


title: no023


title: HEK293 cells, ZNF687 WT replicate 2

value: Overexpressing ZNF687 WT


title: RNA Seq OVCAR5NTX301_100nM-2


title: HEK293 cells, ZNF687 WT replicate 1


title: no021


title: no022


title: RNA Seq OVCAR5DMSO-1


title: DF human keratinocytes, PBRM1 ChIP rep1

value: PBRM1 (Bethyl, #A700-019T)


title: PC3-NRP2-low-2

city: Worcester

first: Rui

last: Li

state: Massachusetts

address: 364 Plantation Street, LRB

department: MCCB

institute: University of Massachusetts Medical School

data_processing:
Paired- end reads were aligned to human primary genome hg38, with star_2.5.3a
annotated with GENCODE GRCh38.p12 annotation release 29
Aligned exon fragments with mapping quality higher than 20 were counted toward gene expression with featureCounts_1.5.2
Differential expression (DE) analysis was performed with DESeq2_1.20.0
Assembly: hg38
Supplementary files format and content: TPM table

source_name: PC3 cells with low NRP2 expression

growth_protocol: All cell were maintained at 37°C with 5% CO2 atmosphere and maintained in complete growth medium indicated by ATCC.

extract_protocol:
RNA was extracted from the indicated cells using a Qiagen RNeasy Micro Kit (74004) and sent to Quick Biology for quantification, sequencing, and analysis. Each sample had a sequencing depth of 20-30 million.
The conpany Quick Biology constructed library.

treatment_protocol: Cells were stained with NRP2 antibody and sorted based on NRP2 expression by flow cytometry. Cells were cultured for up to 2 weeks and RNAs at different passages were extracted for analysis.


title: HEK293 cells, Empty Vector replicate 2

value: Empty vector


title: PC3-NRP2-low-3


title: UD human keratinocytes, PBRM1 ChIP rep2


title: no020

value: mammary epithalial cells

value: untransformed

value: DOX + DIP


title: UD human keratinocytes, PBRM1 ChIP rep1

value: Foreskin

value: primary human neonatal keratinocytes


title: PC3-NRP2-low-1


title: DF human keratinocytes, PIAS1 ChIP rep2

value: DF

value: PIAS1 (Santa Cruz, #sc-365127)


title: DF human keratinocytes, PBRM1 sh3

value: DF PBRM1 knockdown


title: HEK293 cells, Empty Vector replicate 1

value: Human embryonic kidney


title: UD human keratinocytes, PIAS1 ChIP rep1

value: UD


title: no019


title: DF human keratinocytes, PBRM1 sh2


title: no018

value: DOX


title: PC3-NRP2-high-2

source_name: PC3 cells with high NRP2 expression


title: PC3-NRP2-high-3


title: IgG control of CUT&Tag in HCT116

city: Changsha

first: Ke-wei

last: Zheng

address: Lushan Road (S), Yuelu District

department: School of Medical Sciences

institute: Hunan University

data_processing:
CUT&Tag reads were aligned with bowtie2 (Galaxy Version 2.5.0+galaxy0) using default parameters. Normalized (RPKM, reads per kilobase per million) coverage tracks were generated using deepTools bamcoverage (Galaxy Version 3.5.1.0.0) with parameters -binSize 50 –ignoreDuplicates.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: colon cancer tissue

growth_protocol: HCT116 cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin (P/S)

extract_protocol:
CUT&Tag was constructed as described (Kaya-Okur et al., 2019) with some modifications. 10^5 cells were washed twice with 100 μL wash buffer (20 mM HEPES-KOH at pH 7.5, 150 mM KCl, 0.5 mM spermidine, 1× protease inhibitors), and then resuspended with 100 μL wash buffer. 10 μL pre-activated concanavalin A coated magnetic beads (Novoprotein, Shanghai) were added to the cells and incubated on a rotator for 10 minutes at room temperature. The supernatant was removed and bead-bound cells were resuspended in 100 μL dig-wash buffer (0.05% digitonin, 0.1% BSA, 20 mM HEPES-KOH at pH 7.5, 150 mM KCl, 0.5 mM spermidine, 2 mM EDTA, 1× protease inhibitors) containing 9 µg/mL recombinant anti-DNA:RNA hybrid antibody (S9.6, Abcam) or 1 µg/mL recombinant anti-Topoisomerase I antibody (ab109374, Abcam). After one-hour rotation at room temperature, the cells were washed twice with 100 μL of dig-wash buffer and resuspended with 100 μL dig-wash buffer containing 1 μL Goat anti-mouse IgG, incubated for another one hour at room temperature in the dark, and washed three times with dig-wash buffer. A 1:250 dilution of pA-Tn5 adapter complex (~0.2 μM) was prepared in 100 μL dig-wash buffer and added to the cells followed by one-hour rotation at room temperature. After five washes with dig-wash buffer, the bead-bound cells were resuspended with 50 μL of tagmentation buffer (20 mM HEPES-KOH at pH 7.5, 150 mM KCl, 10 mM MgCl2, 0.5 mM spermidine, 1× protease inhibitors) and incubated at 37°C for one hour. To terminate the tagmentation reaction, 2.5 μL of 0.5 M EDTA, 2.5 μL of 10% SDS and 1 μL of 20 mg/mL proteinase K were added and incubated at 55°C for 30 min and then for 15 minutes at 65°C. The DNA was extracted with 122 µL Ampure XP beads for library preparation. DNA was eluted in 40 µL of 5 mM Tris-HCl (pH 8.0).
To amplify libraries, 21 μL DNA was mixed with a universal i5 and a uniquely barcoded i7 primer, and amplified with NEB Q5 high-fidelity 2× master mix. The libraries were purified with 1.2× volume of Ampure XP beads (Beckman Counter), and libraries were eluted in 30 µL 10 mM Tris-HCl (pH 8.0).

value: colon cancer tissue

value: untreated

value: control group

value: None (IgG)

tag: methodology

value: CUT&Tag

tag: replicate

value: not provided


title: DF human keratinocytes, PBRM1 sh1


title: Replicate 2 of R-loop CUT&Tag in HCT116, add ZnTTAPc

value: add ZnTTAPc

value: experiment group

value: R-loop (S9.6)


title: PC3-NRP2-high-1


title: Replicate 1 of R-loop CUT&Tag in HCT116, add ZnTTAPc


title: no017

value: mammary epithalial cells

value: untransformed


title: DF human keratinocytes, Control shB for PBRM1 KD (GFP)

value: Foreskin

value: primary human neonatal keratinocytes

value: DF control


title: no016

value: DOX + DIP


title: Esophageal Tissue, TOC, T554

city: London

first: Keat-Eng

last: Ng

state: England

address: William Harvey Heart Centre

country: United Kingdom

institute: Queen Mary University of London

description: In processed data file, sample is found on column 17

data_processing:
Paired-end FASTQ files were uploaded to the RaNA-seq server
Salmon was used to align files to the GRCh38 human genome to produce gene-level expression estimates.
Assembly: GRCh38 Human Genome
Supplementary files format and content: Tab-delimited text files contain normalised TPM gene-level expression estimates

source_name: Esophageal Tissue

extract_protocol:
RNA was extracted and processed by Queen Mary University of London’s Genome Centre using TRIZOL reagent
Polyadenylated mRNAs were captured using NEBNext® Poly(A) mRNA Magnetic Isolation Module, and the NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina® was used to create cDNA libraries

value: Esophageal Tissue


title: no015


title: Esophageal Tissue, TOC, T553

description: In processed data file, sample is found on column 16


title: DF human keratinocytes, Control shA for PBRM1 KD (non-targeting)


title: Replicate 2 of R-loop CUT&Tag in HCT116, untreated


title: Replicate 1 of R-loop CUT&Tag in HCT116, untreated


title: UD human keratinocytes, PIAS1 shB

value: UD PIAS1 knockdown


title: no014

value: DOX


title: Replicate 2 of Top1 CUT&Tag in HCT116, add ZnTTAPc

value: colon cancer tissue


title: Esophageal Tissue, TOC, T550

description: In processed data file, sample is found on column 15


title: no013


title: Esophageal Tissue, TOC, T549

description: In processed data file, sample is found on column 14


title: UD human keratinocytes, PIAS1 shA


title: Esophageal Tissue, TOC, T547

description: In processed data file, sample is found on column 13


title: Replicate 1 of Top1 CUT&Tag in HCT116, add ZnTTAPc


title: no011


title: Esophageal Tissue, TOC, T544

description: In processed data file, sample is found on column 12


title: UD human keratinocytes, Control shA for PIAS1 KD (non-targeting)

value: UD control


title: Replicate 1 of Top1 CUT&Tag in HCT116, untreated

value: untreated


title: Replicate 2 of Top1 CUT&Tag in HCT116, untreated

value: CUT&Tag


title: no012


title: UD human keratinocytes, PBRM1 sh3

value: UD PBRM1 knockdown


title: no009


title: Esophageal Tissue, TOC, T538

description: In processed data file, sample is found on column 11


title: Related Low Risk sibling sample1 on Monocyte

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.2.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: peripheral blood

extract_protocol:
Cryopreserved PBMC samples of 8 age-matched subjects (2 well-controlled ROT1D patients, 2 HRS, 2 LRS, 2 uHC) were thawed and incubated with the fixable Live/Dead Violet dye (Life Technologies, Grand Island, NY, USA) for 30 minutes on ice.  The cells were subsequently stained with antibodies targeting CD14 (clone M5E2; BD Biosciences, Franklin Lakes, NJ, USA), CD16 (clone 3G8; BD Biosciences), HLA-DR (clone G46-6; BD Biosciences) for 30 minutes on ice and then washed and passed through a 30µM filter.  PBMCs were sorted with a FACS Aria III cell sorter (BD Biosciences), with specific forward and side scatter settings to exclude doublets.  Using a hemocytometer and trypan blue staining, the recovered HLA-DRhi, CD14+, CD16+, and HLA-DRlow, CD14-, and CD16- cells were determined to possess >40,000 cells/sample and viability exceeding than 90%.  These two populations were mixed in a 1:1 ratio to generate a monocyte-enriched, single cell, PBMC population.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics)

value: peripheral blood

value: Monocyte

value: LowRisk HLA

value: LRS

tag: disease state

value: control


title: Esophageal Tissue, TOC, T534

description: In processed data file, sample is found on column 10


title: UD human keratinocytes, PBRM1 sh2

value: Foreskin


title: PT137_akg

city: Saint Louis

first: Fan

last: He

address: Room 8834, 320 S. Euclid Ave, CSRB building

institute: Washington University School of Medicine in St. Louis

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software.
Assembly: GrCh38
Supplementary files format and content: Tab-separated values of raw counts.

source_name: CD14+ MPN monocyte

extract_protocol:
Total RNA was extracted with RNeasy Mini Kit (Qiagen, Hilden, Germany) with DNAse treatment following the manufacturer's protocol.
Samples were then indexed, pooled, and sequenced by Illumina NovaSeq 6000 following standard Illumina protocol.

value: CD14+ MPN monocyte

value: α-KG


title: UD human keratinocytes, PBRM1 sh1

value: primary human neonatal keratinocytes


title: Related High Risk sibling sample1 on Monocyte

description: 10x Genomics

value: HighRisk HLA

value: HRS


title: no008

value: mammary epithalial cells

value: untransformed

value: DOX + DIP


title: Esophageal Tissue, TOC, T530

description: In processed data file, sample is found on column 9

value: Esophageal Tissue


title: UD human keratinocytes, Control shB for PBRM1 KD (GFP)

value: UD control


title: UD human keratinocytes, Control shB for PIAS1 KD (GFP)


title: UD human keratinocytes, Control shA for PBRM1 KD (non-targeting)


title: Recent Onset sample1 on Monocyte

description: 10x Genomics

value: RO


title: Esophageal Tissue, TOC, T527

description: In processed data file, sample is found on column 8


title: Unrelated Healthy Control sample1 on Monocyte

description: 10x Genomics

value: peripheral blood

value: uHC


title: no006

value: DOX


title: no007


title: RNA-seq, A549-shNAT10-3

city: Shanghai

first: Jianxiu

last: Yu

address: Room 202, Building 7, 280 South Chongqing Road

department: Department of Biochemistry and Molecular Cell Biology

institute: Shanghai Jiao Tong University school of medicine

description: experiment: RNA-seq

data_processing:
ac4C-RIP-seq and NAT10-RIP-seq RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit. Constructed libraries were controlled for quality by Q30 and quantified using the BioAnalyzer 2100 system , and the libraries sequencing were performed on an illumina Hiseq 4000 sequencer with 150 bp paired-end reads. After 3`-adaptor-trimming and removing low quality reads using cutadapt software, the high quality clean of trimmed reads were aligned to the human reference genome (UCSC hg19) by Hisat2 software. Acetylated sites on RNAs and NAT10 bound RNAs were identified by MACS2 software. High-confidence regions of ac4C modification and binding to NAT10 and were identified by stringent cutoff threshold, and then annotated with the latest UCSC RefSeq database to connect the peak information with the gene annotation.
RNA-seq libraries were constructed by using TruSeq Stranded Total RNA Library Prep Kit, then controlled for quality and quantified using the BioAnalyzer 2100 system , and the libraries sequencing were performed on an illumina Hiseq instrument with 150 bp paired-end reads. High-quality clean reads were aligned to the reference genome (UCSC hg19) with hisat2 software. Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene-level FPKM as the expression profiles of mRNA
miRNA sequencing library consctruction include 3′-adaptor ligation, 5′-adaptor ligation, cDNA synthesis and PCR amplification, approximately 150 bp PCR amplicons (corresponding to ~22 nt miRNAs) size of products were selected
Assembly: hg19 for RIP-Seq and RNA-Seq, miRBase for miRNA-Seq

growth_protocol: A549 (Cat#TCHu150) stable cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Corning) containing 10% fetal calf serum (FBS, GIBCO) with 1% penicillin-streptomycin (Invitrogen) at 37 °C with 5% CO2.

extract_protocol:
The rRNAs were removed from the ac4C modified RNA, NAT10 bound RNA and total RNAs (as an input) by using RNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA). The rRNA-depleted RNAs were constructed RNA sequencing libraries by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts, USA) according to the manufacturer’s instructions
RIP-seq, RNA and miRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Total RNA extracted  from A549 cell was randomly fragmented and then conducted by RIP (RNA-immunoprecipitation) with ac4C antibody for ac4C-RIP-seq; A549 cell was measured with RIP with anti-NAT10 antibody for NAT10-RIP-seq; A549-shNAT10 stable cell lines were treated with RNA-seq and miRNA-seq, respectively.

value: lung cancer cell


title: no010


title: no005


title: RNA-seq, A549-shNAT10-2

description: experiment: RNA-seq


title: Esophageal Tissue, Control, CTRL5

description: In processed data file, sample is found on column 6

value: Wildtype


title: Esophageal Tissue, Control, CTRL4

description: In processed data file, sample is found on column 5


title: no004


title: no003


title: SKOV3 cells, YTHDC1_IP

city: nanjing

first: xiaogang

last: wang

address: Hankou road 22

institute: nanjing university

data_processing:
illumina Novaseq™ 6000 software used for basecalling.
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing.
The de-duplicated consensus sequences were used for protein binding site analysis. They were mapped to the reference genome using STAR software (version 2.5.3a) with default parameters. The RSeQC（version 2.6）was used for reads distribution analysis
The exomePeak（Version 3.8）software was used for peak calling. Peaks were annotated using bedtools（Version 2.25.0）
The deepTools（version 2.4.1）was used for peak distribution analysis. The differentially binding peaks were identified by a python script，using fisher test. Sequence motifs enriched in peak regions were identified using Homer（version 4.10）.
Assembly: hg19
Supplementary files format and content: processed data-binding_protein_gene_expr_with_anno.txt

extract_protocol:
SKOV3 cells were washed twice with PBS and then lysed with RIP lysis buffer containing protease and RNase inhibitor. The RNA of input and IP was extracted using TRIzol reagent.
The stranded RNA sequencing library was constructed by using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction

value: Ovarian cancer

tag: rip antibody


title: RNA-seq, A549-pLKO.1

description: experiment: RNA-seq


title: Esophageal Tissue, Control, CTRL3

description: In processed data file, sample is found on column 4


title: no002


title: miRNA-seq, A549-shNAT10-3

description: experiment: miRNA-seq


title: Esophageal Tissue, Control, CTRL2

description: In processed data file, sample is found on column 3


title: miRNA-seq, A549-shNAT10-2

description: experiment: miRNA-seq


title: miRNA-seq, A549-pLKO.1

description: experiment: miRNA-seq


title: no001


title: S24_20h untreated, S24

city: Lund

first: Petter

last: Storm

state: Select...

address: Sölvegatan 19, BMC A11

country: Sweden

institute: Lund University

data_processing:
Transcriptomic data was aligned to the GRCm38 genome using gencode version 25 as the gene model using STAR (2.7.6a).
Gene quantification was done using featureCounts
Pre-processing including transformation of count data to log2-counts per million (logCPM) was done using the voom-function (limma version 3.46).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: lung

extract_protocol:
Total RNA was extracted from murine lungs in RLT buffer with 1% β-Mercaptoethanol after disruption in a tissue homogenizer (TissueLyser LT, Qiagen) using Ceramic Beads 1.4 mm (Qiagen) with the RNeasy Mini Kit (Qiagen).
Library was prepared with 500 ng of RNA using TruSeq® Stranded mRNA Library Prep Kit (20020594, Illumina).

tag: strain background

value: lung

value: untreated

tag: time


title: Esophageal Tissue, Control, CTRL6

description: In processed data file, sample is found on column 7


title: S23_20h untreated, S23


title: SHED, scRNAseq

city: Beijing

first: Xueying

last: Wu

state: Beijing

address: No. 10, Tieyi Road, Yangfangdian, Haidian District

department: Beijing Shijitan Hospital

institute: Capital Medical University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.5 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38-3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: exfoliated deciduous teeth

extract_protocol:
We collected naturally exfoliated deciduous incisors from an 8-year-old child. The dental pulp tissue was gently isolated from the crown and minced into small pieces. Then the mixed solution, which was 3mg/ml collagenase type I and 4 mg/ml dispase in phosphate-buffered saline (PBS) buffer, was used to digest the pieces in 37°C for 1h. The single-cell solution of SHED was seeded into six-well plates and incubated in a 37°C 5%CO2 incubator. The culture medium was -MEM (Gibco) supplemented with 15% fetal bovine serum (Gibco), 1% glutamine (Gibco) and 1% penicillin/streptomycin (Gibco) and renewed every third day. The third-generation cells were digested with 0.25% trypsin and the single-cell suspensions obtained were applied for scRNA-seq.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: exfoliated deciduous teeth

value: mesenchymal stem cell


title: SUM149PT COMBO REP C

city: Boston

first: Amy

middle: E

last: Schade

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham and Women's Hospital

description: WT

data_processing:
FASTQ files were aligned using STAR. BAM files were sorted using samtools. Sorted BAM files were then converted into Count files using HTSeq to the HG19 genome.
Assembly: hg19
Supplementary files format and content: *.count.txt: Count files are generated from htseq of aligned and sorted BAM files.
Supplementary files format and content: DESeqSUM149PT.txt: DESeq2 normalized counts are uploaded and processed using DESeq2 with count files as input.

growth_protocol: On day -5, SUM149PT cells were seeded at 40% confluency and treated with 5uM tazemetostat or DMSO. On day -3, cells were passaged again at 40% confluency and maintained in DMSO or tazemetostat. On day -1, cells were seeded into 6cm plates at 250,000 cells per plate and maintained in DMSO or tazemetostat. On day 0, cells were treated in media containing 2% FBS with AKTi (ipatasertib) and/or EZH2i (tazemetostat). Cells were collected at 24 hours, RNA was isolated and then sequenced using NGS.

extract_protocol:
RNA was extracted using Qiagen RNeasy Plus kit.
Kapa Hyper Prep

treatment_protocol: Tazemetostat was dosed at 5 uM. Ipatasertib was dosed at 5 uM.

value: breast cancer

value: Tazemetostat + Ipatasertib


title: NAT10-RIP-seq, rep1

description: experiment: NAT10-RIP-seq

value: WT


title: S22_20h untreated, S22


title: ac4C-RIP-seq, rep2

description: experiment: ac4C-RIP-seq


title: S21_20h untreated, S21


title: SUM149PT COMBO REP B

description: WT


title: S12_20h LPS+50, S12


title: SUM149PT TAZEMETOSTAT REP C

description: WT

value: Tazemetostat


title: S11_20h LPS+50, S11


title: RIP-seq, input, rep2

description:
experiment: Input
The Inputs were used for ac4C-RIP-seq and NAT10-RIP-seq at the same time.


title: SUM149PT TAZEMETOSTAT REP B

description: WT


title: RIP-seq, input, rep1


title: S10_20h LPS+50, S10


title: SUM149PT TAZEMETOSTAT REP A

description: WT


title: S9_20h LPS+50, S9


title: Esophageal Tissue, Control, CTRL1

description: In processed data file, sample is found on column 2

value: Esophageal Tissue


title: NAT10-RIP-seq, rep2

description: experiment: NAT10-RIP-seq


title: S8_20h 50ugsHVF18, S8


title: eosinophil, asthma, sample 39

city: Warszawa

first: Katarzyna

last: Mycroft

address: ul. Banacha 1a

department: Department of Internal Medicine, Pulmonary Diseases and Allergy

country: Poland

institute: Medical Univesity of Warsaw

data_processing:
Genes receiving less than 10 reads on an average across the compared groups were removed.
The abundance counts of each gene were then used to perform differential gene expression (DGE).
DGE was performed using R/Bioconductor DESeq2 package, which essentially normalizes the abundance counts to account for observed variance (due to differences in sequencing depths, sample groups and replicates) generating normalized gene counts.
Assembly: hg38
Supplementary files format and content: tab delimited text file including raw counts for each sample

source_name: blood

extract_protocol:
The RNA was isolated from eosinophils using column-based method with NucleoSpin RNA (Machery&Nagel) using the protocol including DNA digestion.
RNA was prepared and sequenced using an NGSelect RNA (NGS Built For You (eurofinsgenomics.eu)) product. This included purification of mRNA, fragmentation, strand-specific cDNA synthesis, end-repair, ligation of sequencing adapters, amplification, and purification.

value: blood

value: eosinophil

value: asthma


title: ac4C-RIP-seq, rep1

description: experiment: ac4C-RIP-seq


title: S6_20h 50ugsHVF18, S6


title: SKOV3 cells, YTHDC1_Input


title: eosinophil, COPD, sample 31

value: COPD


title: SUM149PT COMBO REP A

description: WT


title: SUM149PT IPATASERTIB REP B

description: WT

value: Ipatasertib


title: SUM149PT IPATASERTIB REP C

description: WT


title: eosinophil, asthma, sample 34


title: S7_20h 50ugsHVF18, S7


title: S5_20h 50ugsHVF18, S5


title: SUM149PT IPATASERTIB REP A

description: WT


title: SUM149PT DMSO REP B

description: WT

value: DMSO


title: eosinophil, COPD, sample 29


title: S4_20h LPS, S4

value: LPS


title: SUM149PT DMSO REP A

description: WT


title: eosinophil, COPD, sample 27


title: S3_20h LPS, S3


title: eosinophil, asthma, sample 26


title: MDA-MB-468 COMBO C

description: WT

data_processing:
FASTQ files were aligned using STAR. BAM files were sorted using samtools. Sorted BAM files were then converted into Count files using HTSeq to the HG19 genome.
Assembly: hg19
Supplementary files format and content: *.count.txt: Count files are generated from htseq of aligned and sorted BAM files.
Supplementary files format and content: DEseqMM468.txt: DESeq2 normalized counts are uploaded and processed using DESeq2 with count files as input.

growth_protocol: On day -5, MDA-MB-468 cells were seeded at 40% confluency and treated with 5uM tazemetostat or DMSO. On day -3, cells were passaged again at 40% confluency and maintained in DMSO or tazemetostat. On day -1, cells were seeded into 6cm plates at 250,000 cells per plate and maintained in DMSO or tazemetostat. On day 0, cells were treated in media containing 2% FBS with AKTi (ipatasertib) and/or EZH2i (tazemetostat). Cells were collected at 24 hours, RNA was isolated and then sequenced using NGS.


title: SUM149PT DMSO REP C

description: WT


title: CAL27

type: RNA

city: Shanghai City

first: Peisong

last: Zhai

address: Zhizaoju Rd. No.639

institute: Shanghai Jiao Tong universisy medical school affiliated Shanghai ninth people's hospital

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Feature Extraction software was used to analyze array images to get raw data. Next, the raw data was normalized with the quantile algorithm. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test.

source_name: cell lysates, CAL27 cells, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were cultured in DMEM medium with 10% fetal bovine serum. CAL27_CTX and CAL27_451A cells were cultured with 300μg/mL cetuximab.

extract_protocol: Total RNA was extracted using mirVanaTM RNA Isolation Kit, AM1561 following the manufacturer's instructions. And quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: CAL27_451A and CAL27_CTX cells were treated with cetuximab for 48h before collected for RNA extraction.

value: control for cetuximab resistance


title: CAL27_NC

description: negative control for overexpression

source_name: cell lysates, negative control of overexpression, replicate1

value: NC


title: MDA-MB-468 COMBO B

description: WT


title: eosinophil, COPD, sample 25


title: S2_20h LPS, S2

value: lung


title: MDA-MB-468 COMBO A

description: WT


title: S24_8h untreated, S24

value: untreated


title: eosinophil, asthma, sample 23


title: S1_20h LPS, S1


title: CAL27_CTX

description: cetuximab treatment for 48h

source_name: cell lysates, CAL27 cetuximab resistant cells, treated with cetuximab for 48h, replicate1

value: cetuximab resistant


title: eosinophil, asthma, sample 21


title: S23_8h untreated, S23


title: CAL27_451A

description: miR-451a overexpression, cetuximab treatment for 48h

source_name: cell lysates, miR-451a overexpression treated with cetuximab for 48h, replicate1

value: miR-451a overexpression


title: MDA-MB-468 TAZEMETOSTAT REP B

description: WT

value: breast cancer


title: MDA-MB-468 TAZEMETOSTAT REP A

description: WT


title: TDN06

city: Tsukiji, Chuo-ku

first: Chihiro

last: Takeuchi

state: Tokyo

department: Division of Epigenomics

country: Japan

institute: National Cancer Center Research Institute

hyb_protocol: Samples were hybridized according to the Agilent One-Colour Microarray-based Gene Expression Analysis Protocol.

scan_protocol: Arrays were scanned using the Agilent Technologies G2600D SG12494263.

data_processing: Raw data were extracted using the software provided by Agilent Feature Extraction Software(v11.0.1.1).

source_name: Gastric mucosa

label_protocol: Amplified double-stranded cDNA was labelled with Cy3 using the Agilent’s Quick Amp Labeling Kit.

extract_protocol: Total RNA was extracted (miRNeasy Mini kit, Qiagen) from tissue samples, and its integrity was verified by Nanodrop 1000 spectrometer.

value: Normal gastric mucosa

value: Male


title: S22_8h untreated, S22


title: TDN05


title: S21_8h untreated, S21


title: TDN04


title: S12_8h LPS+50, S12


title: MDA-MB-468 IPATASERTIB REP C

description: WT


title: TDN03


title: MDA-MB-468 TAZEMETOSTAT REP C

description: WT

value: Tazemetostat


title: S11_8h LPS+50, S11


title: TDN01


title: MDA-MB-468 IPATASERTIB REP B

description: WT


title: S10_8h LPS+50, S10


title: K562, pcHiC Rep1

city: New York

first: Theodoros

last: Sakellaropoulos

address: 550 1st Avenue

institute: NYU Langone

description: Arima promoter-capture HiC

data_processing:
Base calling was performed using Illumina bcl2fastq software.
Reads were aligned and loops called using ARIMA-CHiC-c1.3.sh from https://github.com/ArimaGenomics/CHiC
Assembly: hg19
Supplementary files format and content: bedpe file of all called loops

source_name: Bone; Marrow

extract_protocol:
double cross-linked using 3mM DSG (disuccinimidyl glutarate), followed by 1% formaldehyde
Arima-HiC+ Kit version A160432 v01

value: Bone; Marrow

value: erythroleukemia cells

value: WT


title: MDA-MB-468 DMSO REP C

description: WT


title: A549, pcHiC Rep2

description: Arima promoter-capture HiC

source_name: Lung

value: Lung

value: alveolar basal epithelial cells


title: S9_8h LPS+50, S9


title: MDA-MB-468 DMSO REP B

description: WT

value: DMSO


title: A549, pcHiC Rep1

description: Arima promoter-capture HiC


title: N11

first: bo

last: tian

address: No.168, changhai road

institute: changhai hospital

description: 150 bp paired-end

data_processing:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA).RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
About xxxxx raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp1 and the low quality reads were removed to obtain the clean reads.
Then about xxxxxx clean reads for each sample were retained for subsequent analyses.The clean reads were mapped to the reference genome using HISAT22
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: paracancerous

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. 1 ug of total RNA was used for the construction of sequencing libraries.
the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

tag: patient

value: patient 11

value: paracancerous


title: K562, pcHiC Rep2

description: Arima promoter-capture HiC


title: JSN01

value: Female


title: MDA-MB-468 IPATASERTIB REP A

description: WT

value: Ipatasertib


title: SKN03


title: SKN02


title: TDH14

value: Gastric mucosa with H. pylori-associated gastritis


title: S7_8h 50ugsHVF18, S7

value: lung


title: N10

description: 150 bp paired-end

value: patient 10


title: S6_8h 50ugsHVF18, S6


title: NP_1411

city: Ithaca

first: Praveen

last: Sethupathy

state: New York

address: 618 Tower Road, T7006

institute: Cornell University

description:
CCNP_1411
10596_11196_93783_H37CVBGXB_1411_CCNP_GCCAAT

data_processing:
library strategy: Length extension chromatin run-on sequencing (leChRO-seq)
ChRO-seq mapping was performed with an established pipeline (Chu, Wang, Chou, & Danko, 2019).  Briefly, read quality was assessed using FastQC.  PCR deduplication was performed by collapsing UMIs using PRINSEQ lite 0.20.2.
Adapters were trimmed from the 3’ end of remaining reads using cutadapt 1.16 with a maximum 10% error rate, minimum 2 bp overlap, and minimum 20 quality score.
Processed reads with a minimum length of 15 bp were mapped to the genome using Burrows-Wheeler Aligner (BWA).
The resulting bigwig files were processed using dREG (Chu et al., 2019; Z. Wang, Chu, Choate, & Danko, 2019) to call peaks of active transcriptional regulatory elements.
Read counts of gene loci (hg38 GENCODE v33 coordinates) as well as the defined transcriptioinal regulatory elements were quantified using the R package bigwig (https://github.com/andrelmartins/bigWig).
Genome_build: hg38 plus a single copy of the Pol I ribosomal RNA transcription unit (GenBank U13369.1)
Supplementary_files_format_and_content: a tab-delimited text file of raw count matrix for gene loci; a tab-delimited text file of raw count matrix for transcriptional regulatory elements

molecule: nuclear RNA

source_name: primary tissues

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349131

tag: subject status

value: NASH prone (NP)

value: liver


title: TDH08

value: Male


title: NP_2374

description:
CCNP_2374
10596_11196_93782_H37CVBGXB_2374_CCNP_ACAGTG

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349130


title: N09

description: 150 bp paired-end

value: patient 9


title: S8_8h 50ugsHVF18, S8


title: liver_2279

description:
CCNR_2279
10596_11196_93781_H37CVBGXB_2279_CCNR_TGACCA

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349129


title: S5_8h 50ugsHVF18, S5


title: TDH09


title: MDA-MB-468 DMSO REP A

description: WT

tag: cell type

value: breast cancer


title: N08

description: 150 bp paired-end

value: patient 8

tag: tissue


title: NP_1860

description:
CGNP_1860
10596_11196_93780_H37CVBGXB_1860_CGNP_TTAGGC

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349128


title: N07

description: 150 bp paired-end

value: patient 7


title: S4_8h LPS, S4

value: LPS


title: TDH12


title: S3_8h LPS, S3


title: NR_1960

description:
CGNR_1960
10596_11196_93779_H37CVBGXB_1960_CGNR_CGATGT

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349127

value: NASH resistance (NR)


title: N06

description: 150 bp paired-end

value: patient 6


title: TDH07


title: TDH05


title: S2_8h LPS, S2


title: N05

description: 150 bp paired-end

value: patient 5


title: NR_2758

description:
CGNR_2758
10596_11196_93778_H37CVBGXB_2758_CGNR_ATCACG

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349126


title: TDH03


title: TDN02

value: Normal gastric mucosa


title: NP_2105

description:
CCNP_2105
10466_11196_90488_HLWKLBGX9_2105_CCNP_TAGCTT

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349125


title: S1_8h LPS, S1


title: TDH01

value: Female


title: TDH02


title: N04

description: 150 bp paired-end

value: patient 4

value: paracancerous


title: UPFL_506_Erdafitinib_Primary

city: Chapel Hill

first: William

last: Kim

state: NC

address: 450 West Dr

department: Lineberger Comprehensive Cancer Center

institute: UNC Chapel Hill

description: scRNAseq

data_processing:
75b paired-end reads were sequenced on a NextSeq 500 Desktop Sequencer using a high output flow cell kit (Illumina), yielding an average of over 28M reads per sample.
QC-passed reads were aligned to the mouse reference genome using STAR
Transcript abundance estimates for each sample were performed using SALMON
Raw SALMON read counts for all RNAseq samples were normalized by DESeq2
Illumina Novaseq_6000 for scRNAseq base calling
Transcript abundance estimates for cell were performed using cell ranger
Supplementary files format and content: Tab-delimited text files include Normalized count values for each sample
Supplementary files format and content: H5 format files of cell ranger output for each scRNAseq samples
Assembly: mm10

source_name: bladder tumor

extract_protocol:
RNA was extracted with Qiagen RNeasy Plus Mini kit
Libraries were prepared using TruSeq Stranded mRNA Sample Prep Kit (Illumina)
scRNAseq libraries were prepared using Chromium Single Cell 3' Reagent Kits (v3.1 Chemistry)

tag: strain

value: bladder tumor

tag: tissue type

value: Erdafitinib-treated primary UPFL tumor

value: Erdafitinib


title: N02

description: 150 bp paired-end

value: patient 2

tag: treatment


title: NP_1297

description:
CGNP_1297
10466_11196_90487_HLWKLBGX9_1297_CGNP_ACTTGA

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349124

value: NASH prone (NP)

value: liver


title: NP_1794

description:
CGNP_1794
10466_11196_90486_HLWKLBGX9_1794_CGNP_CAGATC

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349123


title: UPFL_361_Primary

description: scRNAseq

value: primary UPFL control

value: untreated