title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 043

city: Kobe

first: Jothivanan

last: Elumalai

state: Hyogo

address: 2-2-3, Minatojima Minamimachi, Chuo-ku

department: Biosystems Dynamics Research (BDR)

institute: RIKEN

data_processing:
We used only one end of the paired-end sequenced reads for our analysis. Raw fastq files were subjected to quality assessment with FastQC v0.11.5 , and the cutadapt program v1.15 was used to eliminate SEQXE and Illumina adapters. Mapping to the hg19 or mm9 genome was carried out using bwa v0.7.17-r1188 (bwa-aln command). The resulting mapped reads were sorted using samtools v1.7, and duplicate reads were flagged using picard-tools v2.8.1.
For single-G1 karyotype analysis: After marking the duplicate reads, copy number analysis was conducted using the AneuFinder package v1.22.0 within R v4.1.3. Initially, duplicate reads, blacklist regions (available at https://github.com/Boyle-Lab/Blacklist) and reads with a mapping quality (MAPQ) below 10 were filtered out. Uniquely mapped reads were counted within each 500-Kb genomic window, adjusted for GC content (GC.BSgenome=BSgenome.Hsapiens.UCSC.hg19 for humans and BSgenome.Mmusculus.UCSC.mm9 for mouse, method="loess"), and copy number segmentation was executed using the "findCNVs" function (method='edivisive', R=50) of the AneuFinder package. For quality control (QC), multivariate clustering was applied, and clusters with a spikiness value exceeding 1 were eliminated.
For Log2percentile RT: We followed our established procedure to generate binarized replication timing (RT) profiles for each of the 14 fractions of S-phase or single-cells under analysis, along with their respective percentage replication scores (Miura et al, Nat. Protoc. 2020). The percentage replication score of each S-phase fraction or single-cells was utilized to compute their raw, non-binarized replication timing profile, termed as "log2repliscore RT".
Assembly: hg19, mm9
Supplementary files format and content: CNV states (.txt)
Supplementary files format and content: log2percentile RT (.txt)
Library strategy: scRepli-seq

source_name: Embryo

growth_protocol: Human osteosarcoma cells (U2OS) were cultured in DMEM (Nacalai, 08459-64) supplemented with 10% FBS (Sigma, 172012) and maintained at 37°C with 5% CO2. CBMS1 mouse embryonic stem cells (mESCs) have been described (Murakami et al, Development, 2011) and grown in 2i/LIF medium as described (Hayashi et al, Nat. Protoc. 2013).

extract_protocol:
Single cells were sorted with a Sony SH800 or MA900 cell sorter. Sample preparations were performed as described (Miura et al, Nat. Protoc. 2020). DNA samples were subject to whole-genome amplification (WGA) with a SeqPlex kit (Sigma, SEQXE).
NGS libraries were constructed for amplied DNA using an NGS LTP Library Preparation Kit (KAPA, KK8232) according to the manufacturer’s instructions.

treatment_protocol: Cells were subjected to treatment with or without 0.4 μM aphidicolin for 24 hours and labelled with 10 μM EdU for 60 and 15 minutes before harvesting, respectively.

value: Embryo

value: CBMS1 mESC

value: Embryonic Stem Cells

value: Aphidicolin


title: Streptococcus pyogenes MGAS10870 wild-type RNA-seq, biological replicate 1

status: Public on Jul 13 2026

type: SRA

city: Nashville

first: Anthony

last: Flores

state: TN

address: 1161 21st Avenue S, MCN D7219

country: USA

institute: Vanderbilt University Medical Center

description:
Library name: WT_RNAseq_rep1
Wild-type MGAS10870 (emm3) or isogenic wild-type deletion mutant grown in THY to mid-exponential phase (OD600 ~0.8). Biological replicate 1 of 3. Original filename: JMF14A_R1/R2_001.fastq.gz.

library_source: transcriptomic

data_processing:
Raw paired-end FASTQ reads were quality filtered and trimmed using CLC Genomics Workbench v23 (Qiagen).
Trimmed reads were aligned to the MGAS10870 reference genome (NZ_CP067090.1, GenBank) using CLC Genomics Workbench v23 with default RNA-seq mapping parameters.
Raw read counts per gene were extracted using CLC Genomics Workbench v23.
Differential gene expression analysis was performed using DESeq2 v1.50 in R v4.5.3. Significance thresholds: |log2FC| >= log2(1.5), Bonferroni-corrected p < 0.05 and BH-FDR-adjusted padj < 0.05.
TPM (transcripts per million) values were calculated for each sample using CLC Genomics Workbench v23.
Analysis code is available at https://github.com/ar-flores/SpxA1-SpxA2-MultiOmic-GAS  (DOI: https://doi.org/10.5281/zenodo.20476011)
Assembly: NZ_CP067090.1 (Streptococcus pyogenes MGAS10870, NCBI RefSeq)
Supplementary files format and content: RNAseq_counts_matrix.txt: tab-delimited text file containing raw read counts per gene for all 9 samples (rows = genes annotated to NZ_CP067090.1; columns = sample names)
Supplementary files format and content: Per-sample TPM and RPKM files (e.g., *_TPM_matrix.txt): tab-delimited text file containing TPM- or RPKM-normalized expression values per gene for each individual sample

molecule: total RNA

organism: Streptococcus pyogenes

source_name: bacterial cells

growth_protocol: GAS strains were grown without agitation in Todd-Hewitt broth supplemented with 0.2% yeast extract (THY) at 37 degrees C under 5% CO2 to mid-exponential phase (OD600 ~0.45).

extract_protocol:
Cells were harvested by centrifugation, resuspended in RNAprotect Bacteria Reagent (Qiagen), and RNA was extracted using the RNeasy Mini Kit (Qiagen) with on-column DNase digestion. RNA quality was assessed by Bioanalyzer (Agilent). Libraries were prepared and sequenced by Genewiz (Azenta Life Sciences).
Strand-non-specific paired-end RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Libraries were sequenced on an Illumina NovaSeq 6000 platform (2x150bp paired-end reads).

treatment_protocol: Not applicable — no treatment applied prior to RNA extraction.

tag: cell type

value: bacterial cells

tag: genotype

value: wild-type

tag: batch


title: hiPSC-differentiated cells, D16, WT

city: Stockholm

first: Carmen

last: Abaurre

address: Solnavägen 9

department: MBB

country: Sweden

institute: Karolinska Institutet

description:
Library name: Sample 1
10x Genomics

library_source: transcriptomic single cell

data_processing:
BCL files received from NGI were converted to FASTQ with Illumina bcl2fastq v2.20 (RRID:SCR_015058), which was run with default parameters. Raw and filtered matrices were constructed with 10x Genomics Cell Ranger v8.0.1 using default parameters. All samples were subjected to CellBender v.0.3.2 nuclei calling and ambient RNA correction, which uses raw CellBender matrices as input. CellBender was run with default parameters and the CellBender-corrected expression matrix was used for all downstream analysis. Only nuclei with a minimum cell probability of 0.5 were retained in the nuclei matrix. Feature selection, PCA, dimensionality reduction, graph generation and embedding, clustering, annotation and regulon analysis were carried out as described in the Methods section.
Assembly: GRCh38-2020-A-2.0.0 from 10X Genomics website
Supplementary files format and content: SULF_differentiated.h5ad: HD5F object obtained after entire analysis pipeline with Scanpy, described in the manuscript's Methods.
Supplementary files format and content: (SAMPLE)_raw_feature_bc_matrix.h5.gz: CellRanger-generated filtered counts matrix for each individual sample.
Supplementary files format and content: (SAMPLE)_filtered_feature_bc_matrix.h5.gz: CellRanger-generated filtered counts matrix for each individual sample.
Supplementary files format and content: (SAMPLE)_cellbender.h5.gz: CellBender-corrected counts matrix generated for each individual sample.

organism: Homo sapiens

source_name: KOLF 2.1J iPSC

growth_protocol: hiPSC lines were maintained on Laminin 521-coated plates (Biolamina, LN521) in Essential 8 Flex medium (E8 Flex, Thermo Fisher Scientific) under standard conditions (37° C, 5% CO₂) until differentiation was initiated.

extract_protocol:
Cultured cells at D16 were dissociated using TriplE, counted, and 300,000–400,000 cells were resuspended in 500 μL lysis buffer (2% BSA, 1:200 RNase inhibitor, 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl₂, 0.1% Tergitol). To minimize mechanical stress, pipetting was limited to 1–2 gentle mixes, and lysis occurred on ice for 5 min, followed by dilution with 1 mL resuspension buffer (2% BSA in nuclease-free water with RNase inhibitor). The lysate was filtered through a 70 μm filter and centrifuged at 500 × g for 10 min at 4 °C. The supernatant was discarded, and the pellet was resuspended in 50-100 μL resuspension buffer to obtain optimal nuclei concentration. Nuclei quality was assessed visually, and concentration was determined by manual counting with Trypan Blue staining.
RNA library was constructed following the manufacturer's protocol (10X Genomics Chromium Gem-X Single Cell 3' Kit v4). Nuclei suspensions from each sample were loaded in separate lanes of the same Chromium Chip G, with a target of 20,000 nuclei per sample, and GEMs were generated in a Chromium X controller. After library preparation, next-generation sequencing was conducted by SciLifeLab National Genomics Infrastructure (NGI) on an Illumina NovaSeq XPlus instrument.

treatment_protocol:
All three iPSC lines were plated at a density of 200,000 cells/cm² in 12-well plates pre-coated with Geltrex™ (Life Technologies) and Laminin-511 (Biolamina, LN511) and maintained in E8 Flex medium. Once the cells reached confluency (typically after 48–72 h), differentiation was initiated. Cells were cultured in Neurobasal medium supplemented with B27 (Life Technologies), 2 mM L-glutamine (Invitrogen), and N2 supplement, along with the appropriate small molecules and growth factors, until D16 of differentiation.
Only SULF1/2 DKO cells were treated with FGF inhibitors PD0325901 (1 µM) and SU5402 (5 µM) (Sigma) from D4 to D14.

tag: cell line

value: KOLF 2.1J iPSC

value: hiPSC-differentiated

value: WT

tag: genetic modification

tag: growth

value: E8 flex media

tag: treatment

value: Midbrain dopaminergic differentiation

tag: time

value: Day 16


title: PFV, Me0, rep2

city: London

first: Peter

middle: P

last: Cherepanov

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description:
Library name: PFV_Me0_biol_rep2
PFV intasome integration into H3K36Me0 chromatinized yeast DNA

library_source: genomic

data_processing:
Nanopore reads containing the vDNA end (5'-CCATGACA, 5'-CTCTAGCA, or 5'-ATCTCGCA for PFV, HIV-1, and MVV, respectively; only precise match was considered) and the linker (5'-TAAGGGACT; allowing one mismatch) sequence tags in converging orientations, with at least 15 bp of intervening sequence, were cropped and brought into sense orientation with respect to integrated viral DNA end.
Cropped reads were aligned to the yeast SacSer3 assembly using BLAT version 3.5 96 with the following options: stepSize 5, repMatch 2253, minScore 20, minIdentity 0. Only matches that started immediately at the vDNA and linker junctions with overall less than 12% mismatches, (Q gap bases + T gap bases + mismatch)/match < 0.12, and were used for further analysis. Mathched with non-unique combinations of genomic positions of integration (T start) and linker ligation sites (T end) were considered PCR duplicates and counted only once. To avoid reads originating from linker ligation to ends of yeast genomic DNA fragments, all matches within 10 bp of a XbaI or NheI site were removed. Processed PSL files represent Blat alignment files pruned of duplicates and reads originated from linker ligations to XbaI or NheI genomic DNA ends. The merged processed files contain only matches with the distance between the integration site and the linked target DNA fragementation site is less than 150 bp (this distance is found in column 11 of each PSL file for each mapped integration site). The data from the merged and filtered psl files were used to construct the histograms shown in the publication.
Assembly: SacCer3
Supplementary files format and content: BLAT alignment psl files

molecule: genomic DNA

organism: Saccharomyces cerevisiae

extract_protocol:
organic extraction
Chromatinized or naked yeast DNA was incubated with purified retroviral intasomes. Chromatinized reaction products were fragmented using Fenton reaction in the presence of copper (II) cloride, mercaptopropionic acid, and hydrogen peroxide. DNA was then deproteinized,  repaired with phi29 DNA polymerase and processed for dA tailing. End-prepped DNA was ligated to a linker (obtained by annealing 5'-phosphorylated and 3'-blocked 5'-GTCCCTT AAGCGGAG with 5'- GTAATAC GACTCAC TATAGGGCC TCCGCTT AAGGGACT). The products,  PCR amplified using primers specific to the linker and viral DNA ends, were sequenced using Nanopore technology.

treatment_protocol: Genomic DNA extracted from BY4741 cells was sheared by digestion with NheI and XbaI prior to chromatinization with human histones, including H4(S47C)-phenanthroline conjugate with or without Lys36Me3 modification on histone H3. For naked target DNA control condition, the DNA was additionally sheared by sonication.

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0


title: Parental Neural Progenitor Stem Cell clone 1

city: Cleveland

first: Tyler

middle: J

last: Alban

state: OH

address: 9500 Euclid Ave

institute: Cleveland Clinic

description: Library name: Parental_1

data_processing:
Post-sequencing FASTQ files were aligned to gene code release M25 (GRCm38.p6) with STAR aligner with default parameters version 2.7.11a. Quality control was performed using RSeqQC to assess the quality of RNA alignment from BAM files. Mapped reads for each gene were counted using the featureCounts read summarization program, with annotations from Human GENECODE (GRCm38.p6)
Assembly: mm10
Supplementary files format and content: comma-separated text file with raw counts for each sample: raw_count_matrix.csv

organism: Mus musculus

source_name: NPC

extract_protocol:
Total RNA was isolated using Rneasy mini kits (Qiagen Sciences, Germantown, MD)
cDNA library was prepared using SMART-Seq v4 ultra-low input cDNA Library Construction Kit (Takara Bio, San Jose, CA) or TruSeq Library kit (Illumina, San Diego, CA)

value: NPC


title: Whole blood, VI, rep 1

city: Durham

first: Nathaniel

last: Hernandez

state: NC

address: 3 Genome Ct

department: Anesthesiology

institute: Duke University

description:
Library name: Nackley_4
Female Sprague-Dawley rat whole blood collected after 14 days of treatment

data_processing:
Sequencing reads were processed using the miRquant small RNA-seq pipeline. Adapter-trimmed reads were mapped using a two-tier Bowtie and SHRiMP strategy against the Rattus norvegicus RGSC 3.4 (rn4) reference genome. Small RNA expression was quantified as reads per million mapped reads (RPM).
Assembly: RGSC 3.4 (rn4)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: CSV file containing normalized miRNA expression values reported as reads per million (RPM), with rows representing individual small RNAs and columns representing individual biological samples.

organism: Rattus norvegicus

source_name: Whole blood

extract_protocol:
Whole blood was collected in PAXgene Blood RNA tubes (BD Biosciences). Total RNA was isolated using the PAXgene Blood miRNA Kit (Qiagen). RNA quantity and quality were assessed using a NanoDrop 1000 spectrophotometer (NanoDrop Technologies) and an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was normalized to approximately 250 ng/µL with RNase-free water prior to library preparation.
Small RNA libraries were prepared using the TriLink Small RNA Library Prep Kit according to the manufacturer's protocol. Libraries were sequenced on an Illumina HiSeq 2000 platform at the Next Generation Sequencing and Bioinformatics Core, University of Texas Health Science Center at San Antonio. Each biological sample was sequenced with three technical replicates.

tag: tissue

value: Whole blood

value: Vehicle and ICI118551/SR59230A


title: Spleen, Winter Active state, WAT1 (bio rep 1)

status: Public on Jul 12 2026

city: Shenyang

first: Wanyi

last: Dang

state: Liaoning

address: 120 Dongling Rd, Shenyang, China

country: China

institute: Shenyang Agricultural University

description: Library name: Sample 7

data_processing:
Sequenced reads were trimmed for adaptor sequence, and mapped to greater horseshoe bat (Rhinolophus ferrumequinum) transcriptomes (GCF_004115265.2_mRhiFer1) using Kallisto (v.0.46.2) with parameters -b 100. The gene abundances were obtained by kallisto-sleuth (v.0.30.0) pipeline in TPM (transcripts per million) (Bray NL et al. 2016).
Assembly: GCF_004115265.2_mRhiFer1
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

organism: Rhinolophus ferrumequinum

source_name: spleen

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany), with on-column DNase to remove contaminating genomic DNA.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: spleen


title: Spleen, Winter Active state, WAT2 (bio rep 2)

description: Library name: Sample 8


title: Patient 45, endometrium, unexplained infertility

city: Bogota

first: Maria

middle: Camila

last: Rincon

state: Bogota

department: Biomedical Engineering

country: Colombia

institute: Universidad de los Andes

description:
Library name: P45
37 year old, Previous Abortions for Trisomy 8 and Turner Syndrome

data_processing:
RNA-seq reads were mapped using HISAT2 (v.2.2.1) to the human reference genome hg38 from the Broad Institute public database (20 Broad Institute 2024). SAM files were sorted using Picard (v2.27.4). Read counts for each sample and each gene were calculated from the mapped sequences using Stringtie (v.1.3.5). The counts expression matrix was assembled using the script prepDE.py available with Stringtie. The obtained expression matrix was normalized using the VST method implemented in DESeq2
Assembly: hg38
Supplementary files format and content: FASTQ files includes raw counts for each Sample
Supplementary files format and content: csv files include TMP values for each Sample

source_name: Endometrium

extract_protocol:
Total RNA was extracted from preserved endometrium biopsies using the Monarch® Total RNA Miniprep Kit (New England Biolabs, Ipswich, MA, USA) following the instructions given for extraction from tissues (25-30mg of the sample).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

value: Endometrium

tag: subject status

value: unexplained infertility


title: Spleen, Arousal state, AS2 (bio rep 2)

description: Library name: Sample 6


title: Spleen, Arousal state, AS1 (bio rep 1)

description: Library name: Sample 5


title: Spleen, Torpor state, TP2 (bio rep 2)

description: Library name: Sample 4


title: Spleen, Torpor state, TP1 (bio rep 1)

description: Library name: Sample 3


title: Streptococcus pyogenes MGAS10870 delta-spxA2 RNA-seq, biological replicate 3

description:
Library name: spxA2KO_RNAseq_rep3
Wild-type MGAS10870 (emm3) or isogenic delta-spxA2 deletion mutant grown in THY to mid-exponential phase (OD600 ~0.8). Biological replicate 3 of 3. Original filename: JMF481C_R1/R2_001.fastq.gz.


title: Spleen, Summer Active state, SAT1 (bio rep 1)

description: Library name: Sample 1


title: Spleen, Summer Active state, SAT2 (bio rep 2)

description: Library name: Sample 2


title: PGK1_KO_replicate3

city: ChongQing

first: Guixian

last: Wu

address: No.30 Gaotanyan Main Street District

institute: Southwest Hospital, Third Military Medical University

description:
Library name: PGK1_KO_replicate3
PGK1 KO Cell
P-3

data_processing:
Data quality control was performed using fastp to remove reads with adapters. Paired reads were removed under the following conditions: when the the number of N in any sequencing read exceeded 10% of the length of that read, and when any sequencing read contained low-quality bases (Q<=20) exceeding 50% of the length of that read. Subsequent analyses were based on clean reads. The reference genome and its annotation files were downloaded from a specified website. HISAT was used to build an index, and clean reads were aligned to the reference genome.
Assembly: hg38
Supplementary files format and content: readcount_All_Samples.xlsx file includes raw counts for each Sample
Supplementary files format and content: fpkm_All_Samples.xlsx file includes FPKM values for each Sample

molecule: polyA RNA

source_name: Connective tissue

extract_protocol:
The mRNA was prepared by VAHTS mRNA Capture Beads 2.0 (N403-C4, Vazyme Biotech Co., Ltd.) following manufacturer's protocols
RNA libraries for RNA-seq were prepared using VAHTS Universal V10 RNA-seq Library Prep Kit (NR616-02, Vazyme Biotech Co., Ltd.) following manufacturer's protocols

value: Connective tissue

value: PGK1 KO


title: PGK1_KO_replicate2

description:
Library name: PGK1_KO_replicate2
PGK1 KO Cell
P-2


title: PGK1_KO_replicate1

description:
Library name: PGK1_KO_replicate1
PGK1 KO Cell
P-1


title: PGK1_WT_replicate3

description:
Library name: PGK1_WT_replicate3
WT Cell
V2-3

value: PGK1 WT


title: PGK1_WT_replicate1

description:
Library name: PGK1_WT_replicate1
WT Cell
V2-1


title: PGK1_WT_replicate2

description:
Library name: PGK1_WT_replicate2
WT Cell
V2-2


title: Streptococcus pyogenes MGAS10870 LiaSQ146A (SpxA2-OE) CovR ChIP-exo, biological replicate 1

description:
Library name: spxA2OE_ChIPexo_rep1
CovR ChIP-exo in LiaSQ146A (SpxA2-OE) MGAS10870 (emm3). Anti-CovR polyclonal antibody (N-terminal domain). Cornell ChIP-exo core facility. Biological replicate 1 of 3. FRiP=0.24. ChIP target: CovR (control of virulence response regulator).

data_processing:
Peaks called on merged BAM files using MACS3 v3.0.4: genome size 1,840,000 bp, --nomodel, --extsize 50, --shift -25, --keep-dup all, p-value 1e-10. High-confidence peaks retained at score > 5,000.
Differential CovR binding assessed using DiffBind v3.20 with DESeq2 v1.50.2 in R v4.5.3. Consensus peaks at score > 3,000 threshold; summit-centered 150bp windows for read counting; library-size normalization. FDR < 0.05 significant.
CovR binding motif occurrence assessed using FIMO v5.5.9 (MEME Suite). Dimer motif (WTWTTATAAWAAAAWNATDA) and monomer motif (ATTARA) from Horstmann et al. 2023. Fisher exact test for enrichment between peak classes.
Analysis code is available at https://github.com/ar-flores/SpxA1-SpxA2-MultiOmic-GAS  (DOI: https://doi.org/10.5281/zenodo.20476011)
Assembly: NZ_CP067090.1 (Streptococcus pyogenes MGAS10870, NCBI RefSeq)
Supplementary files format and content: BAM files: aligned reads per biological replicate (9 total), sorted and indexed. narrowPeak files: MACS3 peak calls (score > 5,000) per condition (3 files). CSV files: DiffBind consensus peaks, differential binding results, and FIMO motif hits (ST1-ST5).
Supplementary files format and content: ST1_all_700_peaks.csv: consensus peak coordinates with DESeq2-normalized counts per sample. ST2/ST3: differentially bound sites with log2FC, FDR, gene annotations. ST4: FIMO motif hits per peak. ST5: SpxA2OE vs SpxA2KO results.

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 minutes at room temperature, quenched with glycine. Cells were lysed and chromatin sheared by sonication. CovR immunoprecipitation performed using a polyclonal anti-CovR antibody (N-terminal domain). ChIP-exo library preparation and lambda-exonuclease digestion performed by the Cornell ChIP-exo core facility.
ChIP-exo libraries prepared and sequenced by the Cornell ChIP-exo core facility on an Illumina NextSeq 500 platform (75nt paired-end reads).

treatment_protocol: Not applicable — no treatment applied prior to cross-linking.

value: bacterial cells

value: LiaSQ146A (SpxA2-OE)


title: I_CKI_D7_J_rep6

city: Adelaide

first: Yan

last: Zhou

state: South Australia

address: 108 North Terrace

department: Biological science

country: Australia

institute: Adelaide University

description:
Library name: 3-18J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the compound Kushen injection treatment group; biological replicate 6.

data_processing:
Adapter and low-quality sequences were trimmed using BBDuk with parameters hdist=1, mink=11, ktrim=r, qtrim=rl, trimq=20, minlen=25, and trimpolyg=20.
Trimmed reads were aligned to the Rattus norvegicus reference genome using STAR v2.7.10a with mismatchNoverLmax set to 0.03 and alignIntronMax set to 10000.
Gene counts were generated from aligned reads and lowly expressed genes were filtered before downstream analysis.
Assembly: Rattus norvegicus reference genome mRatBN7.2 (Ensembl release 107)
Supplementary files format and content: The file contains the raw read count matrix for all genes across all samples.

source_name: jejunum epithelium

growth_protocol: Sprague Dawley rats were maintained under standard laboratory conditions with access to food and water according to the approved animal ethics protocol.

extract_protocol:
Total RNA was extracted from colon and jejunum epithelial tissues. RNA quality and quantity were assessed before library preparation. Samples passing quality-control criteria were used for bulk RNA sequencing.
RNA-seq libraries were prepared from total RNA using a transcriptome library preparation protocol and sequenced on a DNBSEQ-G400 platform using paired-end 150 bp sequencing.

treatment_protocol: Rats received fractionated abdominal irradiation at 5 × 4 Gy from day 0 to day 4. Compound Kushen powder, compound Kushen injection, or corresponding vehicle treatments were administered according to the experimental design. Colon and jejunum epithelial tissues were collected at day 4 or day 7 after irradiation.

value: jejunum epithelium

value: fractionated abdominal irradiation, 5 × 4 Gy; intraperitoneal compound Kushen injection treatment


title: I_CKI_D7_J_rep4

description:
Library name: 3-16J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the compound Kushen injection treatment group; biological replicate 4.


title: I_CKI_D7_J_rep3

description:
Library name: 3-15J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the compound Kushen injection treatment group; biological replicate 3.


title: I_CKI_D7_J_rep2

description:
Library name: 3-14J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the compound Kushen injection treatment group; biological replicate 2.


title: I_CKI_D7_J_rep5

description:
Library name: 3-17J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the compound Kushen injection treatment group; biological replicate 5.


title: I_CKI_D7_J_rep1

description:
Library name: 3-13J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the compound Kushen injection treatment group; biological replicate 1.


title: I_VC_D7_J_rep6

description:
Library name: 3-12J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the injection vehicle control group; biological replicate 6.

value: fractionated abdominal irradiation, 5 × 4 Gy; intraperitoneal vehicle treatment with 0.25% Tween-80 and 25 mM HEPES


title: I_VC_D7_J_rep5

description:
Library name: 3-11J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the injection vehicle control group; biological replicate 5.


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 037

country: Japan

value: Embryo

value: CBMS1 mESC

value: Embryonic Stem Cells

value: Aphidicolin


title: I_VC_D7_J_rep4

description:
Library name: 3-10J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the injection vehicle control group; biological replicate 4.


title: I_VC_D7_J_rep3

description:
Library name: 3-9J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the injection vehicle control group; biological replicate 3.


title: I_VC_D7_J_rep2

description:
Library name: 3-8J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the injection vehicle control group; biological replicate 2.


title: I_VC_D7_J_rep1

description:
Library name: 3-7J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the injection vehicle control group; biological replicate 1.


title: I_CKI_D7_C_rep6

description:
Library name: 3-18C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the compound Kushen injection treatment group; biological replicate 6.

source_name: colon epithelium

value: colon epithelium


title: I_CKI_D7_C_rep3

description:
Library name: 3-15C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the compound Kushen injection treatment group; biological replicate 3.


title: I_CKI_D7_C_rep4

description:
Library name: 3-16C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the compound Kushen injection treatment group; biological replicate 4.


title: I_CKI_D7_C_rep2

description:
Library name: 3-14C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the compound Kushen injection treatment group; biological replicate 2.


title: I_CKI_D7_C_rep5

description:
Library name: 3-17C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the compound Kushen injection treatment group; biological replicate 5.


title: I_CKI_D7_C_rep1

description:
Library name: 3-13C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the compound Kushen injection treatment group; biological replicate 1.


title: I_VC_D7_C_rep6

description:
Library name: 3-12C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the injection vehicle control group; biological replicate 6.


title: I_VC_D7_C_rep5

description:
Library name: 3-11C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the injection vehicle control group; biological replicate 5.


title: I_VC_D7_C_rep2

description:
Library name: 3-8C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the injection vehicle control group; biological replicate 2.


title: I_VC_D7_C_rep1

description:
Library name: 3-7C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the injection vehicle control group; biological replicate 1.


title: I_VC_D7_C_rep3

description:
Library name: 3-9C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the injection vehicle control group; biological replicate 3.


title: I_VC_D7_C_rep4

description:
Library name: 3-10C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the injection vehicle control group; biological replicate 4.


title: I_CKI_D4_J_rep6

description:
Library name: 3-24J
Jejunum epithelium sample collected at D4 after fractionated abdominal irradiation from the compound Kushen injection treatment group; biological replicate 6.


title: I_CKI_D4_J_rep5

description:
Library name: 3-23J
Jejunum epithelium sample collected at D4 after fractionated abdominal irradiation from the compound Kushen injection treatment group; biological replicate 5.


title: I_CKI_D4_J_rep4

description:
Library name: 3-22J
Jejunum epithelium sample collected at D4 after fractionated abdominal irradiation from the compound Kushen injection treatment group; biological replicate 4.


title: I_CKI_D4_J_rep2

description:
Library name: 3-5J
Jejunum epithelium sample collected at D4 after fractionated abdominal irradiation from the compound Kushen injection treatment group; biological replicate 2.


title: I_VC_D4_J_rep6

description:
Library name: 3-21J
Jejunum epithelium sample collected at D4 after fractionated abdominal irradiation from the injection vehicle control group; biological replicate 6.


title: I_CKI_D4_J_rep1

description:
Library name: 3-4J
Jejunum epithelium sample collected at D4 after fractionated abdominal irradiation from the compound Kushen injection treatment group; biological replicate 1.


title: Patient 19, endometrium, healthy control

description:
Library name: P19
23 year old, HPV positive, Suffered Toxic Shock Syndrome

value: healthy control


title: I_VC_D4_J_rep5

description:
Library name: 3-20J
Jejunum epithelium sample collected at D4 after fractionated abdominal irradiation from the injection vehicle control group; biological replicate 5.


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 042


title: I_VC_D4_J_rep4

description:
Library name: 3-19J
Jejunum epithelium sample collected at D4 after fractionated abdominal irradiation from the injection vehicle control group; biological replicate 4.


title: I_VC_D4_J_rep3

description:
Library name: 3-3J
Jejunum epithelium sample collected at D4 after fractionated abdominal irradiation from the injection vehicle control group; biological replicate 3.


title: CIAKI3

city: Nanjing

first: Mengqing

last: Ma

state: Jiangsu

address: 68 Changle Road

institute: Nanjing First Hospital, Nanjing Medical University

description:
Library name: Sample 3
10x Genomics

data_processing:
Raw sequencing data were processed using Cell Ranger 9.0.1 for quality filtering, genome alignment, barcode processing, UMI counting, and generation of gene-barcode expression matrices.
Reads were aligned to the Mus musculus reference genome from Ensembl release 112.
Gene-barcode expression matrices were generated for each sample using Cell Ranger.
Downstream single-cell analysis was performed using Seurat 4.1.1, including quality control, normalization, dimensionality reduction, clustering, and marker gene identification.
Cells were filtered based on detected gene number, UMI counts, mitochondrial gene percentage, and doublet removal. Cells with fewer than 500 detected genes or mitochondrial gene percentage greater than 25% were excluded, and DoubletFinder was used to remove potential doublets.
Assembly: Mus musculus, Ensembl release 112
Supplementary files format and content: Processed data include Cell Ranger-generated feature-barcode matrices for each sample, including matrix.mtx.gz, features.tsv.gz, and barcodes.tsv.gz files.

source_name: kidney

growth_protocol: Mice were maintained under standard laboratory conditions before contrast-induced acute kidney injury induction. Fresh kidney tissues were collected for single-cell RNA sequencing.

extract_protocol:
Fresh mouse kidney tissues were dissociated into single-cell suspensions. Cell concentration was adjusted to approximately 700–1200 cells/μL. After cell quality control, viable single cells were loaded for 10x Genomics single-cell RNA-seq library preparation.
Single-cell RNA-seq libraries were generated using the 10x Genomics platform.

treatment_protocol: A mouse model of contrast-induced acute kidney injury (CIAKI) was established. Kidney tissues were collected after CIAKI induction and processed for single-cell RNA sequencing.

value: kidney

value: wild type

value: CIAKI induction

value: batch 1


title: CIAKI4

description:
Library name: Sample 4
10x Genomics


title: I_VC_D4_J_rep1

description:
Library name: 3-1J
Jejunum epithelium sample collected at D4 after fractionated abdominal irradiation from the injection vehicle control group; biological replicate 1.


title: CIAKI2

description:
Library name: Sample 2
10x Genomics


title: I_VC_D4_J_rep2

description:
Library name: 3-2J
Jejunum epithelium sample collected at D4 after fractionated abdominal irradiation from the injection vehicle control group; biological replicate 2.


title: I_CKI_D4_C_rep6

description:
Library name: 3-24C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the compound Kushen injection treatment group; biological replicate 6.


title: Splenic NK cells from WT mouse stimulated with anti-NKp46 and anti-DNAM-1 antibodies for 48 hours, biol rep 3

city: Berkeley

first: Yeara

last: Jo

state: CA

address: 485 Weill Hall

institute: University of California, Berkeley

description:
Library name: Sample 36
Column name in ab_combo_TPM_processed.csv: WT3_NKp46_NKG2D_Ab

data_processing:
Reads were aligned to the mouse reference genome GRCm39 by using STAR aligner with the following parameters: “--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000”. Gene- and transcript-level quantification was performed using RSEM.
Assembly: GRCm39
Supplementary files format and content: csv files include TPM values for each sample

source_name: Spleen

extract_protocol:
Total RNA was extracted by using miRNeasy Micro Kit (Qiagen) following manufacturer's instructions. RNA integrity was assessed by using bioanalyzer and 50ng RNA from the samples with RIN score > 7 were used to construct sequencing libraries.
RNA-seq libraries were prepared using KAPA MRNA HyperPrep kit (Roche) following manufacturer's instructions.

value: Spleen

value: Natural Killer cells

value: WT


title: Splenic NK cells from WT mouse stimulated with anti-NKp46 and anti-DNAM-1 antibodies for 48 hours, biol rep 2

description:
Library name: Sample 35
Column name in ab_combo_TPM_processed.csv: WT3_NKp46_DNAM1_Ab


title: CBMS1 mESC, scRepli-seq, aphidicolin singleS 034


title: Splenic NK cells from WT mouse stimulated with anti-NKp46 and anti-DNAM-1 antibodies for 48 hours, biol rep 1

description:
Library name: Sample 34
Column name in ab_combo_TPM_processed.csv: WT3_medium


title: I_CKI_D4_C_rep3

description:
Library name: 3-6C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the compound Kushen injection treatment group; biological replicate 3.


title: Splenic NK cells from WT mouse stimulated with anti-NKp46 and anti-NKG2D antibodies for 48 hours, biol rep 3

description:
Library name: Sample 33
Column name in ab_combo_TPM_processed.csv: WT2_NKp46_NKG2D_Ab


title: I_CKI_D4_C_rep4

description:
Library name: 3-22C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the compound Kushen injection treatment group; biological replicate 4.


title: CIAKI1

description:
Library name: Sample 1
10x Genomics


title: Splenic NK cells from WT mouse stimulated with anti-NKp46 and anti-NKG2D antibodies for 48 hours, biol rep 2

description:
Library name: Sample 32
Column name in ab_combo_TPM_processed.csv: WT2_NKp46_DNAM1_Ab


title: I_CKI_D4_C_rep1

description:
Library name: 3-4C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the compound Kushen injection treatment group; biological replicate 1.


title: I_VC_D4_C_rep6

description:
Library name: 3-21C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the injection vehicle control group; biological replicate 6.


title: Splenic NK cells from WT mouse left in medium for 48 hours, biol rep 3

description:
Library name: Sample 30
Column name in ab_combo_TPM_processed.csv: WT1_NKp46_NKG2D_Ab


title: Splenic NK cells from WT mouse left in medium for 48 hours, biol rep 2

description:
Library name: Sample 29
Column name in ab_combo_TPM_processed.csv: WT1_NKp46_DNAM1_Ab


title: I_VC_D4_C_rep5

description:
Library name: 3-20C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the injection vehicle control group; biological replicate 5.


title: I_VC_D4_C_rep4

description:
Library name: 3-19C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the injection vehicle control group; biological replicate 4.


title: CD27-CD11b+ NK cells from subcutaneouly injected MC38 B2m tumors, biol rep 3

description:
Library name: Sample 27
Column name in tumor_TPM_processed.csv: B2MKO3_SP_tumor

source_name: Subcutaneous tumor

value: Subcutaneous tumor


title: I_VC_D4_C_rep2

description:
Library name: 3-2C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the injection vehicle control group; biological replicate 2.


title: CD27-CD11b+ NK cells from subcutaneouly injected MC38 B2m tumors, biol rep 2

description:
Library name: Sample 26
Column name in tumor_TPM_processed.csv: B2MKO2_SP_tumor


title: I_VC_D4_C_rep3

description:
Library name: 3-3C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the injection vehicle control group; biological replicate 3.


title: O_CKP_D7_J_rep6

description:
Library name: 2-27J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the compound Kushen pill treatment group; biological replicate 6.

value: jejunum epithelium

value: fractionated abdominal irradiation, 5 × 4 Gy; oral compound Kushen powder treatment


title: Splenic NK cells FACS-purified from splenocytes of WT mouse treated with ionomycin for 22 hours, biol rep 3

description:
Library name: Sample 24
Column name in vehicle_vs_iono_TPM.csv: I3


title: O_CKP_D7_J_rep5

description:
Library name: 2-26J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the compound Kushen pill treatment group; biological replicate 5.


title: Splenic NK cells FACS-purified from splenocytes of WT mouse treated with ionomycin for 22 hours, biol rep 1

description:
Library name: Sample 22
Column name in vehicle_vs_iono_TPM.csv: I1


title: WT.WM1119.3

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: Library name: WT.WM1119.3

data_processing:
Data were aligned using STAR against hg19 version of the human genome and RSEM software used for gene expression estimation using Ensemble transcriptome information
Assembly: hg19
Supplementary files format and content: RSEM estimated counts for each gene

extract_protocol:
Total RNA of HEC50B isogenic cell lines treated with vehicle control or 50 uM WM1119 for 4 days were extracted using RNeasy mini Kit (Qiagen, cat. No.: 74106) and digested with DNase I (Qiagen, cat. No.: 79254)
RNA-seq libraries were constructed using ScriptSeq complete Gold kit (Epicentre, cat. No.: SCL24EP)

value: CRISPR WT

value: inhibited


title: WT.WM1119.2

description: Library name: WT.WM1119.2


title: Splenic NK cells FACS-purified from splenocytes of WT mouse treated with vehicle for 22 hours, biol rep 3

description:
Library name: Sample 21
Column name in vehicle_vs_iono_TPM.csv: V3


title: WT.WM1119.1

description: Library name: WT.WM1119.1


title: Splenic NK cells FACS-purified from splenocytes of WT mouse treated with vehicle for 22 hours, biol rep 2

description:
Library name: Sample 20
Column name in vehicle_vs_iono_TPM.csv: V2


title: R183W.WM1119.1

description: Library name: R183W.WM1119.1

value: parental R183W


title: R183W.WM1119.2

description: Library name: R183W.WM1119.2


title: O_CKP_D7_J_rep1

description:
Library name: 1-16J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the compound Kushen pill treatment group; biological replicate 1.


title: WT.vehicle.3

description: Library name: WT.vehicle.3

value: vehicle

value: active


title: Splenic NK cells FACS-purified from splenocytes of WT mouse treated with vehicle for 22 hours, biol rep 1

description:
Library name: Sample 19
Column name in vehicle_vs_iono_TPM.csv: V1


title: O_VC_D7_J_rep6

description:
Library name: 2-24J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the oral vehicle control group; biological replicate 6.

value: fractionated abdominal irradiation, 5 × 4 Gy; oral vehicle treatment with water


title: PGK1_KO_replicate3

first: yuanze

last: zhou

address: No.30, Gaotanyan Main Street, Shapingba District

institute: The First Hospital Affiliated to Army Medical University (Southwest Hospital)

description: Library name: 241206104_P9

data_processing:
Raw sequencing reads were processed using CeleScope v2.0.7 (Singleron, Biotechnologies) with default parameters to generate gene expression matrices. Briefly, cell barcodes and unique molecular identifiers (UMIs) were extracted Read 1 (R1) and corrected. Adapter sequences and poly (A) tails were trimmed from Read 2 (R2), and the trimmed R2 reads were aligned to the GRCm38 (mm10) transcriptome using STARSolo in STAR (2.7.11a). Reads sharing the same cell barcode, UMI, and gene assignment were collapsed to generate the final gene-by-cell expression matrix for downstream analyses.
Assembly: GRCm38 (mm10)
Supplementary files format and content: barcodes.tsv/features.tsv/matrix.mtx files include raw counts and fpkm

source_name: Liver

growth_protocol: PGK1 KO or PGK1 WT Hepa1-6 cells (5 × 10⁶) were suspended in 20 μL Matrigel Basement Membrane Matrix (BD Biosciences, Franklin Lakes, NJ) and injected into the subcapsular space of the left lateral liver lobe. The incision was closed with sutures, and mice were monitored in a warmed recovery chamber until fully awake. Four weeks after implantation, mice were euthanized; livers were excised and collected.

extract_protocol:
Fresh tumor tissue were washed three times with Hanks’ Balanced Salt Solution (HBSS), minced into small pieces, and dissociated using the Singleron PythoN™ Tissue Dissociation System. The resulting cell suspension was treated with the GEXSCOPE® red blood cell lysis buﬀer (RCLB, Singleron) and centrifuged to remove red blood cells. Cell viability was assessed prior to preparing single-cell suspensions at a concentration of 2 × 10⁶ cells/mL. Single-cell suspensions were loaded onto a microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding beads were collected from the microwell chip, and captured mRNA was reverse-transcribed into cDNA, which was subsequently amplified by PCR. The amplified cDNA was fragmented and ligated to sequencing adapters.
scRNA-seq libraries were constructed according to the protocol for the GEXSCOPE® Single Cell RNA Library Kits (Singleron). Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina NovaSeq 6000 with 150bp paired-end reads.

value: Liver

value: PGK1 KO


title: R183W.vehicle.3

description: Library name: R183W.vehicle.3


title: R183W.vehicle.1

description: Library name: R183W.vehicle.1


title: O_VC_D7_J_rep4

description:
Library name: 2-22J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the oral vehicle control group; biological replicate 4.


title: PGK1_KO_replicate2

description: Library name: 241206103_P8


title: Primary human hepatocytes, GEX

city: Cambridge

first: James

last: Briggs

state: MA

address: 75 Ames St

institute: Broad Institute

description: Library name: sample_11

data_processing:
Read processing: generation of transcriptome and TF perturbation count matrices  Single-cell transcriptomes  Raw Illumina sequencing data was processed into cells x genes counts matrices using the 10X genomics cellranger-6.0.1 pipeline with default parameters. Raw BCL files were demultiplexed and converted to FASTQ format using cellranger mkfastq. Cellranger count was then used to generate counts matrices from FASTQ files. GRCh38 (version refdata-gex-GRCh38-2020-A) was used as a human reference genome for read alignment.  Single-cell TF barcodes  For single-cell TF barcode libraries, raw BCL files were demultiplexed and converted to FASTQ format using bcl2fastq2-v2.20.0 with flags: --no-lane-splitting and --mask-short-adapter-reads 10 and --sample-sheet /path/to/samplesheet.csv.  Demultiplexed FASTQ files were processed into cells x TF barcode count arrays using a custom python pipeline: process_dialout_seq.py (see GitHub repository #). Per library, the pipeline takes a R1 and R2 FASTQ path, a list of TF barcodes (from the original lentiviral pool used in the screen), and a list of cell barcodes (i.e., the pass-filter cell barcodes identified by cellranger above) as input. It outputs a dataframe of [cell barcode, TF barcode, UMI count, read count] specifying a cells vs. TF barcode count array.  This pipeline has the following main steps:  Iterate over reads and parse TF barcode, cell barcode, and UMI sequences. Output as dataframe of [TF barcode, cell barcode, UMI] sequences for pass-filter reads.  Identify key sequence (i.e., the constant sequence immediately upstream of TF barcode) in R2 Map 24-bp following key sequence to list of input TF barcodes Extract 16-bp cell barcode from R1 and map to input list of cell barcodes Extract 12-bp UMI sequence from R1 For correctly structured reads store TF barcode, cell barcode, UMI  Iterate over [cell, TF] pairs in parsed fastq and count the number of unique occurrences of each TF barcode using the UMIs. Output dataframe of [cell, TF, UMI count, read count].  Key identification, barcode mapping, and UMI counting are performed with error tolerance to account for sequencing errors. The pipeline has parameters controlling the number of sequence mismatches allowed during identification of key, TF barcode, cell barcode, and UMI sequences. We used selections of 1, 2, 1, and 1 respectively, which added tolerance to sequencing errors without endangering barcode collisions.  The pipeline is implemented to parallelize slow steps and runs in <30 minutes for a 10,000 cell dataset with 50 million reads on mid-tier Google Cloud VM instance.
Count matrix preparation  We loaded and concatenated all single-cell transcriptome count arrays into a shared AnnData object using the ScanPy54 package for single-cell analysis. We stored TF barcode counts in adata.obsm[‘TF_UMIs’] as cells x TF sparse CSR arrays. We stored corresponding TF names in adata.uns[‘TF_names’].  Cell filtering and preprocessing:  We applied the following filters to retain only high-quality cells (threshold values in Extended Data File 2): Depth filter: cell must have > min_UMIs (threshold 1k-10k UMIs) Live filter: cell must have < mito_fraction UMIs assigned to mitochondrial genes (threshold 15-20%) Doublet filter: remove cells predicted to be doublets by Scrublet55.  We scaled each cell to 1 million total UMIs to obtain units of transcripts per million (TPM).   TF barcode filtering and preprocessing:  We applied the following filters to TF barcode count data to exclude background signal (threshold values in Extended Data File 2): Depth filter: TF must be detected with > min_UMIs SNR filter: the fraction of total TF UMIs in the cell assigned to the TF must be > min_fraction  For each unique dial-out TF barcode library, the min_fraction threshold was set by inspecting per cell barcode count histograms and manually selecting a threshold that visually best separates the observed background count distribution (most barcodes observed with very few counts) from likely true signal distribution (few barcodes with significantly higher counts). The manual results were similar to those found by implementing an automated elbow identification function on the same histograms. The min_UMIs threshold was uniformly set to 5, except for one library with lower barcode detection rates that was lowered to 3.  We normalized TF expression such that pass-filter TF UMIs summed to 100 per cell and stored the resulting expression array in adata.obsm[‘TF_UMIs_filt’]. For some analysis, we then assigned an expression value of 1 to pass-filter TFs and 0 otherwise.
Assembly: GRCh38 (version refdata-gex-GRCh38-2020-A)
Supplementary files format and content: Processed .h5ad files provide annotated count matrices for scRNA-seq data. Per sample .h5ad files contain raw count data. The merged all_cells_final_v2.h5ad file contains all single cells across samples and has the following features of interest: - .X : total count normalized to 1e6 counts per cell (excluding highly expressed), then log(TPM+1) transformed - .obs['TF_subpool']: TF library used to transduce sample - .obs['timepoint']: timepoint post transduction that scSeq data was collected (or post-thaw for pHSC samples) - .obs['ddPCR_MOI']: number of TF integrations per cell measured by ddPCR - .obs['min_tot']: cell filtering threshold: minimum total number of UMIs per cell - .obs['max_mito']: cell filtering threshold: maximum allowed fraction of mitochondrial expression - .obs['min_TF_UMIs']: TF filtering threshold: minimum number of UMIs coming from expressed TFs - .obs['min_TF_frac']: TF filtering threshold: minimum fraction of UMIs per cell coming from expressed TFs - .obs['n_counts']: total UMIs detected in cell - .obs['mito_frac']: fraction of reads coming from mitochondrial genes - .obs['doublet_score']: doublet score assigned by Scrublet - .obs['sample']: scSeq library ID - .obsm['TF_UMIs_filt']: filtered to only expressed TFs, normalized so max TF per cell = 100TPMs - .obsm['TF_UMIs']: raw TF UMI expression - .uns['TF_names']: list of column names for TF expression matrices  TF_counts.csv files contain raw cells vs. TFs count matrices output from process_dialout_seq.py run on the TF dialout fastq files.

source_name: Primary hepatocytes (HUCPG, Lonza)

extract_protocol:
10X genomics 3’ transcriptome kit with v3.1 chemistry (10X genomics #1000268) processing of dissociated single cells, as per the manufacturer’s instructions.
All single-cell RNA-seq libraries were generated using the 10X genomics 3’ transcriptome kit with v3.1 chemistry (10X genomics #1000268) as per the manufacturer’s instructions. We targeted a loading concentration of 10,000 cells / lane and washed cells thoroughly in PBS-/- prior to loading to minimize background RNA contamination. We dual-indexed libraries during PCR2 using the Dual Index Kit TT (Set A; 10X genomics #1000215).  We generated corresponding single-cell TF barcode libraries by performing dial-out PCR on a sample of the 10X PCR1 product. Our primers were designed to generate a ~1.2-kb product compatible with Illumina TruSeq chemistry such that the TF barcode is sequenced by read 2 and the 10X cell barcode by read 1 (Extended Data File 5). The forward primer anneals to the 10X PCR2 adapter sequence upstream of the 10X cell barcode and adds an Illumina p5 adapter, 8-bp barcode, and TruSeq R1 primer annealing site. The reverse primer anneals immediately 5’ of the 24-bp TF barcode and adds an Illumina p7 adapter, 8-bp barcode, TruSeq R2 primer annealing site, and 12-bp stagger to increase sequence diversity. Amplification was performed using NEBNext HiFi polymerase mix (NEB #M0541L). 5% of the total 10X PCR1 product was used template – i.e., 2 uL containing ~50 ng DNA. Primers were used at a 0.25 uM final concentration. Cycling conditions were: 1. 98°C 3 minutes; 2. 20 x [98°C 10 seconds, 60°C 10 seconds, 72°C 1 minute]; 3. 72°C 1 minute. PCR product was purified for sequencing with a 0.8X SPRI selection (Beckman Coulter #B23317). Successful amplification and purification of the expected 1.2-kb product was verified by High-Sensitivity DNA Analysis (Agilent #5067-4626).  Single-cell transcriptome libraries were pooled and sequenced on an Illumina NextSeq. We typically pooled up to 40,000 cells per sequencing run and targeted 20,000 reads/cell sequencing depth. We used High-Output 500/550 v2.5 75-cycle kits with the following read distribution: R1: 28, R2: 44, i7: 10, i5: 10. Corresponding single-cell TF barcode libraries were pooled and sequenced similarly, but with the following read distribution: R1: 28, R2: 53, i7: 0, i5: 8.

value: Primary hepatocytes (HUCPG, Lonza)

tag: culture media

value: Hepatocyte Culture Media (Lonza)

tag: differentiation timepoint_(days)

tag: enrichment

tag: tf subpool

tag: min umis

tag: max mito_fraction

tag: min tf_umis

tag: min tf_fraction

tag: library type

value: GEX


title: Primary human CB CD34+, CFU cells, GEX

description: Library name: sample_10-2

source_name: Primary umbilical cord CD34+ cells (C-12921, Sigma)

value: MethoCult (StemCell)

value: CFU culture


title: O_VC_D7_J_rep3

description:
Library name: 1-12J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the oral vehicle control group; biological replicate 3.


title: PGK1_WT_replicate3

description: Library name: 241206101_V6

tag: cell type

value: PGK1 WT

tag: batch


title: Pooled screen, 773F, v4, CD34+ enriched, TF dialout

description: Library name: sample_9-4

library_source: other

molecule: other

tag: cell line

value: X-vivo 15 (Lonza)

value: CD34 MACS

value: TF dialout PCR


title: O_VC_D7_J_rep2

description:
Library name: 1-11J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the oral vehicle control group; biological replicate 2.

value: jejunum epithelium


title: Pooled screen, 773F, v4, CD34+ enriched, GEX

description: Library name: sample_9-3


title: PGK1_WT_replicate2

description: Library name: 241206100_V5


title: I_CKI_D4_C_rep5

description:
Library name: 3-23C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the compound Kushen injection treatment group; biological replicate 5.

value: colon epithelium

value: fractionated abdominal irradiation, 5 × 4 Gy; intraperitoneal compound Kushen injection treatment


title: Pooled screen, 773F, v4, bulk population, TF dialout

description: Library name: sample_9-2


title: O_VC_D7_J_rep1

description:
Library name: 1-10J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the oral vehicle control group; biological replicate 1.


title: Pooled screen, 773F, v4, bulk population, GEX

description: Library name: sample_9-1


title: I_CKI_D4_C_rep2

description:
Library name: 3-5C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the compound Kushen injection treatment group; biological replicate 2.


title: Splenic NK cells from WT mouse stimulated with anti-NKp46 and anti-NKG2D antibodies for 48 hours, biol rep 1

description:
Library name: Sample 31
Column name in ab_combo_TPM_processed.csv: WT2_medium

value: Spleen

value: Natural Killer cells

tag: genotype

value: WT


title: muscle, delt, 79f_delt

city: San Francisco

first: Steven

middle: Michael

last: Garcia

address: 1700 Owens St.

department: Orthopaedic Surgery

institute: UCSF

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0 (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
Supplementary files format and content: integrated metadata files and matrix files

source_name: muscle

extract_protocol:
Muscle was trimmed of excess fat, tendon, and connective tissue. Muscle was then mechanically and enzymatically digested in 1 mg/ml collagenase III (Worthington Biochemical Corporation, #NC0021929) in Dulbecco's Modified Eagle Medium (DMEM), 10% FBS (fetal bovine serum, Gibco, #10437028) and 1% Penicillin/Streptomycin (Gibco, #11550043) at 37°C for 70 minutes with intermittent manual needle trituration with an 18-gauge needle. Digests were washed with PBS and further digested with 0.25% trypsin at 37°C for 12–15 min. Suspensions were passed through 40 µm nylon mesh, erythrocytes were lysed with ACK lysing buffer (Quality Biological, #188-156-101) for 5–7 min on ice and washed in PBS with 2% FBS. Cells were washed and resuspended in 100 µl flow cytometry buffer (PBS with 2% FBS, 5 mM EDTA, 2 mM HEPES) per 1 gram of starting tissue weight. Antibody cocktail consisting of: anti-CD31 (eBioscience, #48-0319-42, eFluor 450) (2 µl per gram of starting muscle weight), anti-CD45 (eBioscience, #48-0459-42, eFluor 450) (2 µl), anti-CD56 (Miltenyi Biotec, #130-114-548, APC-Vio770) (8 µl), anti-CD34 (BD, #555823, PE-Cy5) (6 µl) and anti-PDGFRα (BioLegend, 323506, PE) (8 µl) was then added to the cells for 30 minutes on ice. Cells were washed and resuspended in flow cytometry buffer with 1:1000 sytox blue (ThermoFisher, #S34857). Viable CD31-/CD45-/CD56-/CD34+/PDGFRa+ FAPs were collected and spiked into a collection of all cells (sytox negative) to obtain samples with >50% FAPs. Cells were resuspended in 0.04% BSA in PBS at 1000 cells per μl to prepare 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.

treatment_protocol: For cultured FAPs: FAPs were isolated from fresh tissue digests with the surface marker combination CD31-/CD45-/CD56-/CD34+/PDGFRα+. Primary cells were cultured in growth media: Ham's F-10 Nutrient Mix (Gibco, #11550043) containing 1% Penicillin/Streptomycin (Gibco, #11550043), 10% FBS (Gibco, #10437028), and 10ng/mL bFGF (Gibco, #PHG0264). Cell media was changed every 2-3 days and cells were passaged at 70-80% confluency. For adipogenic differentiation, FAPs were grown to 80% confluency in growth media and then switched to adipogenic media (StemPro Adipogenesis Differentiation Kit, Gibco, # A1007001). Media was changed every 2 days. For fibrogenic differentiation, FAPs were grown to 80% confluency in growth media and then switched to growth media containing, 10 ng/ml of TGFβ1 (Invitrogen, #PHG9204). Media was changed every 2 days.

value: muscle

tag: location

value: deltoid


title: PGK1_WT_replicate1

description: Library name: 241206099_V4

value: Liver


title: Pooled screen, 773F, v3, CD34+ enriched, TF dialout

description: Library name: sample_8-4


title: Splenic NK cells from WT mouse left in medium for 48 hours, biol rep 1

description:
Library name: Sample 28
Column name in ab_combo_TPM_processed.csv: WT1_medium


title: O_CKP_D7_C_rep6

description:
Library name: 2-27C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the compound Kushen pill treatment group; biological replicate 6.

tag: treatment

value: fractionated abdominal irradiation, 5 × 4 Gy; oral compound Kushen powder treatment


title: O_CKP_D7_C_rep5

description:
Library name: 2-26C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the compound Kushen pill treatment group; biological replicate 5.

tag: tissue


title: Splenic NK cells FACS-purified from splenocytes of WT mouse treated with ionomycin for 22 hours, biol rep 2

description:
Library name: Sample 23
Column name in vehicle_vs_iono_TPM.csv: I2


title: O_CKP_D7_J_rep4

description:
Library name: 2-25J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the compound Kushen pill treatment group; biological replicate 4.


title: Pooled screen, 773F, v3, bulk population, TF dialout

description: Library name: sample_8-2


title: Pooled screen, 773F, v3, CD34+ enriched, GEX

description: Library name: sample_8-3

value: GEX


title: SeMSNs3-GAS

first: Jintao

last: Song

address: No. 77, Puhe Road

institute: China Medical University

description:
Library name: Sample18
G-semsn-4_FPKM

data_processing:
Remove the adapter sequences contained in the reads.
Remove the bases at the 3' end with a quality score (Q) lower than 20, that is, the base error rate is less than 0.01. Here, Q = -10 * log(error_ratio).
Remove reads with a length less than 25.
Remove the ribosome RNA reads belonging to the specific species.
Assembly: GRCm38
Supplementary files format and content: processed data.xlsx; FPKM, counts

source_name: Gastrocnemius muscle

growth_protocol: The mice were fed on a normal diet.

extract_protocol:
Extract RNA using the Boryou® Total RNA Extraction Kit. 2μg of total RNA was used to construct the sequencing libraries.
The purified Total RNA was subjected to steps such as mRNA isolation, fragmentation, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, 3' end addition of A, ligation of adapters, and enrichment, to complete the construction of the mRNA sequencing library. The library concentration was detected using the Qubit 2.0 fluorescence quantitative instrument (Thermo Fisher Scientific), and the distribution of library fragments was detected using the Agilent 4200 TapeStation (Agilent Technologies).

treatment_protocol: The SeMSNs group was given 10mg/kg by gavage daily, while the old control group was given the same amount of normal saline by gavage.

value: Gastrocnemius muscle

tag: strain

value: SeMSNs


title: I_VC_D4_C_rep1

description:
Library name: 3-1C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the injection vehicle control group; biological replicate 1.

value: fractionated abdominal irradiation, 5 × 4 Gy; intraperitoneal vehicle treatment with 0.25% Tween-80 and 25 mM HEPES


title: CD27-CD11b+ NK cells from subcutaneouly injected MC38 B2m tumors, biol rep 1

description:
Library name: Sample 25
Column name in tumor_TPM_processed.csv: B2MKO1_SP_tumor

value: Subcutaneous tumor


title: SeMSNs2-GAS

description:
Library name: Sample17
G-semsn-2_FPKM


title: Pooled screen, 773F, v3, bulk population, GEX

description: Library name: sample_8-1

tag: culture media

value: X-vivo 15 (Lonza)


title: Pooled screen, 773F, v2, CD34+ enriched, TF dialout

description: Library name: sample_7-4

tag: differentiation timepoint_(days)

value: CD34 MACS

value: TF dialout PCR


title: O_CKP_D7_C_rep4

description:
Library name: 2-25C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the compound Kushen pill treatment group; biological replicate 4.

value: colon epithelium


title: Pooled screen, 773F, v2, CD34+ enriched, GEX

description: Library name: sample_7-3

tag: enrichment


title: O_CKP_D7_J_rep3

description:
Library name: 1-18J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the compound Kushen pill treatment group; biological replicate 3.

value: jejunum epithelium


title: SeMSNs1-GAS

description:
Library name: Sample16
G-semsn-1_FPKM


title: O_CKP_D7_J_rep2

description:
Library name: 1-17J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the compound Kushen pill treatment group; biological replicate 2.


title: Pooled screen, 773F, v1, bulk population, GEX

description: Library name: sample_6-1

tag: tf subpool


title: Pooled screen, 773F, v2, bulk population, GEX

description: Library name: sample_7-1

tag: min umis


title: O_CKP_D7_C_rep2

description:
Library name: 1-17C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the compound Kushen pill treatment group; biological replicate 2.


title: Pooled screen, 773F, v2, bulk population, TF dialout

description: Library name: sample_7-2

tag: max mito_fraction


title: O_CKP_D7_C_rep3

description:
Library name: 1-18C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the compound Kushen pill treatment group; biological replicate 3.


title: WT.vehicle.2

description: Library name: WT.vehicle.2

value: CRISPR WT

value: vehicle

value: active


title: Pooled screen, 773F, v1, bulk population, TF dialout

description: Library name: sample_6-2

tag: min tf_umis


title: Old control3-GAS

description:
Library name: Sample15
G-con-3_FPKM

value: WT

value: Old control


title: Old control2-GAS

description:
Library name: Sample14
G-con-2_FPKM


title: Pooled screen, 130F, v1, CFU cells, TF dialout

description: Library name: sample_5-6

value: MethoCult (StemCell)

value: CFU culture

tag: min tf_fraction


title: Pooled screen, 130F, v1, CFU cells, GEX

description: Library name: sample_5-5

tag: library type

value: GEX


title: O_CKP_D7_C_rep1

description:
Library name: 1-16C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the compound Kushen pill treatment group; biological replicate 1.

value: fractionated abdominal irradiation, 5 × 4 Gy; oral compound Kushen powder treatment


title: WT.vehicle.1

description: Library name: WT.vehicle.1


title: R183W.vehicle.2

description: Library name: R183W.vehicle.2

value: parental R183W


title: Pooled screen, 130F, v1, CD34+ enriched, TF dialout

description: Library name: sample_5-4


title: O_VC_D7_J_rep5

description:
Library name: 2-23J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the oral vehicle control group; biological replicate 5.

value: fractionated abdominal irradiation, 5 × 4 Gy; oral vehicle treatment with water


title: O_VC_D7_C_rep6

description:
Library name: 2-24C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the oral vehicle control group; biological replicate 6.


title: aew,cheek skin,mouse No. 3

city: Kaifeng

first: ruizhen

last: wang

address: Jinming Avenue, Kaifeng City, Henan Province

institute: Henan University

data_processing:
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows: 1) Remove the reads containing the adaptor(adaptor pollution); 2) Remove reads whose N content is greater than 5%; 3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).
The filtered "Clean Reads" are saved in FASTQ format. SOAPnuke(Version v1.5.2)  Official Websitehttps://github.com/BGI-flexlab/SOAPnuke
Hierarchical Indexing for Spliced Alignment of Transcripts (HISTAT) is software for mapping RNA-seq reads.HISAT will use the global FM index to anchor the position of partial sequences in each read on the genome; then, use the partial genome indexes of these
Species: Mus_musculus；Source: NCBI；Reference Genome Version: GCF_000001635.27_GRCm39

source_name: cheek

growth_protocol: Healthy C57BL/6 mice (6-8 weeks) were selected and bred in Specific pathogen-free (SPF) animal chambers in separate cages. The room temperature was maintained at 20-27℃ and the normal day and night alternated, during which the normal diet was guaranteed.

extract_protocol:
After the completion of the experiment, the cheek tissue samples of mice were collected for RNA extraction and sent to Wuhan Huada BGI Sequencing Company for sequencing.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on DNBSeq platform (BGI-Wuhan, China).

treatment_protocol: AE and water solution were applied to the cheeks of mice at 9 a.m. and 5 p.m. every day to prepare a mouse xeroderma model. The cotton sheets soaked in AE solution ( equal volume mixture of acetone and ether ) were smeared on the shaved area of the right cheek of mice for 30 s, and then the cotton sheets soaked in distilled water were smeared on the same area for 30 s. The left cheek skin of the mice was smeared with distilled water for 60 s for 12 consecutive days. On the 12 th day, the cheek tissues of mice were collected for RNA-Seq.

value: cheek

tag: agent

value: aew


title: PATGV cells, 0hpi, replicate 2

status: Public on Jul 14 2026

city: Lyon

first: olivier

last: reynard

state: Auvergne-Rhône-Alpes

address: 21 avenue Tony Garnier

department: CIRI

country: France

institute: INSERM

data_processing:
Sequence quality control was checked using FastQC v0.11.8
Trimming was performed with Fastp 0.23.2 with options "-q 30-min_len 30"
Quantification was performed using Salmon 1.10.1 with the parameters “--gcBias --seqBias”. Index-building was performed by concatenating Nipah Bangladesh transcriptome with the Homo Sapiens transcriptome or the Pteropus Medius transcriptome
Assembly: Genbank GCF_000001405.40 for homo sapiens
Assembly: Genbank GCF_902729225.1 for pteropus giganteus
Assembly: Genbank GCA_003147825.1 for Nipah virus
Supplementary files format and content: tar file of salmon outputs including plaint text quantification file (quant.sf), transcripts used for quantification, parameter settings, version of Salmon, and estimated bias parameters

organism: Pteropus vampyrus

source_name: skin fibroblastic cell

growth_protocol: A549 cells were grown in DMEM medium supplemented with 10% of FCS and antibiotics. Bat and primary cells were grown in DMEM-F12 supplemented with 10% of FCS and antibiotic

extract_protocol:
RNA was isolated following manufacturer's instruction with Mini kit for RNA purification and treated with Dnase I (Macherey-Nagel, Cat#740955.50)
Librairies were assessed by poly-A enrichment using NEXTFLEX Poly(A) Beads 2.0 (Perkin-Elmer) and MGIEasy RNA Directional Library Prep Set User Manual (MGI-Tech) kits

value: skin fibroblastic cell

tag: cell type

value: immortalized cell


title: SeMSNs3-Kidney

description:
Library name: Sample12
k-semsn-4_FPKM

source_name: Kidney

value: Kidney

value: SeMSNs


title: Pooled screen, 130F, v1, CD34+ enriched, GEX

description: Library name: sample_5-3

tag: cell line

value: X-vivo 15 (Lonza)

value: CD34 MACS


title: SeMSNs2-Kidney

description:
Library name: Sample11
k-semsn-2_FPKM

tag: genotype


title: aew,cheek skin,mouse No. 2


title: aew,cheek skin,mouse No. 1


title: O_VC_D7_C_rep4

description:
Library name: 2-22C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the oral vehicle control group; biological replicate 4.

value: colon epithelium


title: SeMSNs1-Kidney

description:
Library name: Sample10
k-semsn-1_FPKM

value: WT


title: Pooled screen, 130F, v1, bulk population, TF dialout

description: Library name: sample_5-2

value: TF dialout PCR


title: Pooled screen, 130F, v1, bulk population, GEX

description: Library name: sample_5-1


title: O_VC_D7_C_rep5

description:
Library name: 2-23C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the oral vehicle control group; biological replicate 5.


title: Vehicle,cheek skin,mouse No. 3

value: Vehicle


title: Old control3-Kidney

description:
Library name: Sample9
K-con-3_FPKM

value: Old


title: O_VC_D7_C_rep3

description:
Library name: 1-12C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the oral vehicle control group; biological replicate 3.


title: Pooled screen, 103F, v2, CFU cells, TF dialout

description: Library name: sample_4-6

value: MethoCult (StemCell)

value: CFU culture


title: O_VC_D7_C_rep2

description:
Library name: 1-11C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the oral vehicle control group; biological replicate 2.


title: Vehicle,cheek skin,mouse No. 2


title: Old control2-Kidney

description:
Library name: Sample8
K-con-2_FPKM


title: Pooled screen, 103F, v2, CFU cells, GEX

description: Library name: sample_4-5

value: GEX


title: Vehicle,cheek skin,mouse No. 1


title: O_VC_D7_C_rep1

description:
Library name: 1-10C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the oral vehicle control group; biological replicate 1.

value: fractionated abdominal irradiation, 5 × 4 Gy; oral vehicle treatment with water


title: Old control1-Kidney

description:
Library name: Sample7
K-con-1_FPKM


title: Pooled screen, 103F, v2, CD34+ enriched, TF dialout

description: Library name: sample_4-4


title: O_CKP_D4_J_rep6

description:
Library name: 2-18J
Jejunum epithelium sample collected at D4 after fractionated abdominal irradiation from the compound Kushen pill treatment group; biological replicate 6.

value: jejunum epithelium

value: fractionated abdominal irradiation, 5 × 4 Gy; oral compound Kushen powder treatment


title: Cornea Pitx2 -/- male rep5

city: Montpellier

first: Frederic

last: Michon

state: non-US Resident

address: Institute for Neurosciences of Montpellier, 80, rue Augustin Fliche

institute: Inserm - U1298

description: Library name: M_194_mut

data_processing:
Filtered reads were aligned to the mouse reference genome (Mus_musculus_10090; UCSC mm10 v2201) with HISAT2, and gene-level counts were obtained using HTSeq-count to produce the raw count matrix.
Primary analyses were performed with BGI’s Dr. Tom multi-omics platform (https://biosys.bgi.com). Briefly, clean reads were also aligned against the gene set (including known/novel, coding/non-coding transcripts) using Bowtie2 (Langmead & Salzberg, 2012), and transcript/gene abundance was estimated with RSEM v1.3.1 (Li & Dewey, 2011).
Assembly: Mus_musculus_10090; UCSC mm10 v2201
Supplementary files format and content: tab delimited text file includes raw counts for each sample
Supplementary files format and content: csv fils include FPKM values for each sample

source_name: Cornea

growth_protocol: The mice were kept under a 12-hour light/dark cycle with free access to food and water.

extract_protocol:
Frozen corneas were shipped on dry ice to Beijing Genomics Institute (BGI, Shenzhen, China) for library construction and sequencing on the DNBseq platform. Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
Polyadenylated RNA was captured with oligo(dT)-coupled magnetic beads and fragmented. RNA integrity and fragment-size distributions were assessed on a Fragment Analyzer; only samples meeting predefined QC thresholds advanced to library preparation. Libraries were generated with the BGI Optimal Dual-mode mRNA Library Prep Kit and sequenced on a DNBSEQ-T7 (paired-end 2×100 bp; ~50 million clean reads per sample). Adapters, contaminants, and low-quality bases/reads were removed with SOAPnuke (Li et al., 2008).

value: Cornea


title: O_CKP_D4_J_rep5

description:
Library name: 2-17J
Jejunum epithelium sample collected at D4 after fractionated abdominal irradiation from the compound Kushen pill treatment group; biological replicate 5.


title: SeMSNs2-Brain

description:
Library name: Sample5
B-semsn-2_FPKM

source_name: Brain

value: Brain


title: Cornea Pitx2 -/- male rep4

department: Institute for Neurosciences of Montpellier

description: Library name: M_170_mut


title: O_CKP_D4_J_rep4

description:
Library name: 2-16J
Jejunum epithelium sample collected at D4 after fractionated abdominal irradiation from the compound Kushen pill treatment group; biological replicate 4.


title: Cornea Pitx2 +/+ male rep5

description: Library name: M_137_ctrl


title: Pooled screen, 103F, v2, bulk population, TF dialout

description: Library name: sample_4-2


title: Pooled screen, 103F, v2, bulk population, GEX

description: Library name: sample_4-1


title: SeMSNs1-Brain

description:
Library name: Sample4
B-semsn-1_FPKM


title: Cornea Pitx2 -/- male rep3

description: Library name: M_98_mut


title: Old control3-Brain

description:
Library name: Sample3
B-con-3_FPKM


title: Old control2-Brain

description:
Library name: Sample2
B-con-2_FPKM


title: Pooled screen, 103F, v1, CD34+ enriched, GEX

description: Library name: sample_3-3


title: Cornea Pitx2 -/- male rep2

description: Library name: M_91_mut


title: O_CKP_D4_J_rep1

description:
Library name: 1-19J
Jejunum epithelium sample collected at D4 after fractionated abdominal irradiation from the compound Kushen pill treatment group; biological replicate 1.


title: Old control1-Brain

description:
Library name: Sample1
B-con-1_FPKM


title: Cornea Pitx2 +/+ male rep4

description: Library name: M_85_ctrl


title: O_VC_D4_J_rep6

description:
Library name: 2-15J
Jejunum epithelium sample collected at D4 after fractionated abdominal irradiation from the oral vehicle control group; biological replicate 6.


title: Pooled screen, 103F, v1, bulk population, TF dialout

description: Library name: sample_3-2


title: O_VC_D4_J_rep5

description:
Library name: 2-14J
Jejunum epithelium sample collected at D4 after fractionated abdominal irradiation from the oral vehicle control group; biological replicate 5.


title: 4_Rep1-4

city: Hiroshima

first: Yasuo

last: Kitajima

state: Hiroshima

address: 1-2-3 Kasumi, Minami-ku

institute: Hiroshima University

description:
Library name: family-4
CaMKII-KO-Post_training

data_processing:
Read1(10bp of UMI + 9bp of barcode) was assigned to Read2(insert read) by following command "umi_tools extract -I read1.fastq --read2-in=read2.fastq --bc-pattern=NNNNNNNNNNCCCCCCCCC".
Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore (ver.0.6.10).
Reads were mapped to the GRCm38 reference using HISAT2 (ver.2.2.1).
Gene count was obtaind by featureCounts(ver.2.0.6) and UMI duplication was ramoved by using UMI tools (ver.1.1.4).
Assembly: GRCm38
Supplementary files format and content: compressed tab separated files(.tsv.gz, .txt.gz)

extract_protocol:
tissue sections were lysed in ISOGEN II reagent kit (NIPPON GENE) and extract RNA by using RNeasy Mini Kit (QIAGEN).
Libraries were prepared by BRB-Seq(Alpern D, et al.) method. Individual samples were reverse transcribed using dT primer with unique cell barcodes. Then replicate were mixed and amplified by PCR. 10nt of UMI followedby 9nt of cell barcode are in read1 and 81nt of RNA insert reads are in read2.

value: Gastrocnemius muscle


title: Pooled screen, 103F, v1, bulk population, GEX

description: Library name: sample_3-1


title: Cornea Pitx2 +/+ male rep2

description: Library name: M_78_ctrl


title: Cornea Pitx2 +/+ male rep3

description: Library name: M_79_ctrl


title: 3_Rep1-4

description:
Library name: family-3
Con-WT-Post_training


title: Pooled screen, 13F, v2, CFU cells, TF dialout

description: Library name: sample_2-2


title: O_VC_D4_J_rep4

description:
Library name: 2-13J
Jejunum epithelium sample collected at D4 after fractionated abdominal irradiation from the oral vehicle control group; biological replicate 4.


title: Cornea Pitx2 -/- male rep1

description: Library name: M_68_mut


title: Pooled screen, 13F, v2, CFU cells, GEX

description: Library name: sample_2-1


title: O_VC_D4_J_rep3

description:
Library name: 1-15J
Jejunum epithelium sample collected at D4 after fractionated abdominal irradiation from the oral vehicle control group; biological replicate 3.


title: Cornea Pitx2 +/+ male rep1

description: Library name: M_59_ctrl


title: Pooled screen, 13F, v1, CD34+ enriched, TF dialout

description: Library name: sample_1-4


title: 1_Rep1-4

description:
Library name: family-1
Con-WT-Pre_training


title: Pooled screen, 13F, v1, CD34+ enriched, GEX

description: Library name: sample_1-3


title: O_VC_D4_J_rep1

description:
Library name: 1-13J
Jejunum epithelium sample collected at D4 after fractionated abdominal irradiation from the oral vehicle control group; biological replicate 1.


title: Huh-7, Meta, macroH2A2, Rep2 (Chip)

city: Minhang

first: deng

last: yongzhuo

state: Shanghai

address: DongchuanoRoad N0.800

institute: Shanghai Jiao Tong University

description: Library name: Huh-7_Meta_macroH2A2_Chip, Rep2

data_processing:
Utilize TrimGalore to remove sequencing adapter sequences and low-quality bases from your reads (Q<20)
Use Bowtie2 to align the trimmed pair-end reads to human genome
Use Samtools to remove the unknown chromosome segments mapped reads, unmappable reads and multi-mapped reads The mapped reads are converted to bam format.
mapped reads are used to identidfy macroH2A1/2 enriched domains  by normR after normalization by the control (input nucleosome DNA). Genome is divided into 2kb bins,regimeR is used for calling peaks,  significant bins identified by Fisher’s test (P < 0.05) are use exportR to output into Bed files and BigWig files
Assembly: Homo_sapiens.GRCh38.114
Supplementary files format and content: BigWig

source_name: human hepatocellular carcinoma cells

growth_protocol: The human hepatocellular carcinoma cell line Huh-7 (CL-0120) was obtained from iCell Bioscience Inc. (Shanghai, China). Huh7 cells were cultured in Dulbecco’s Modified Eagle medium (DMEM; Gibco, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS; Gibco, Carlsbad, CA, USA) and 1% penicillin–streptomycin antibiotics (Pen/Strep; Gibco, Carlsbad, CA, USA) in an atmosphere of 95% humidified air and 5% CO2 at 37 °C.

extract_protocol:
For mitotic samples, synchronized cells were collected by mechanical shake-off, swollen in hypotonic buffer (75 mM KCl), and resuspended in polyamine buffer. Cells were homogenized using a Dounce homogenizer, filtered (10 μm and 5 μm membranes), and centrifuged to isolate purified mitotic chromosomes. Chromosomes were digested with MNase (3000 gel units/mL) at 4 °C overnight in MNase buffer; the reaction was quenched with 20 mM EDTA.  For G1/S samples, synchronized cells were harvested via trypsinization, washed with ice-cold PBS, and permeabilized in MNase buffer containing 0.5% NP-40 to release chromatin. Chromatin was digested with MNase (2000 gel units/mL) at 4 °C overnight. Both mitotic and G1/S digestion products were centrifuged at 10,000 rpm for 7 min at 4 °C, and supernatants containing mononucleosomes were collected. Mononucleosome preparations from G1/S or mitotic phases were subjected to native ChIP. Protein A/G magnetic beads were pre-incubated with target antibodies (anti-mH2A1 or anti-mH2A2) for 1 h at 4 °C, followed by overnight incubation with the mononucleosomes at 4 °C. After immunoprecipitation, beads were washed, and bound nucleosomes were eluted for subsequent sequencing library preparation.
Input mononucleosomes and ChIP-enriched nucleosomes were treated with 100 μg/mL RNase A (Invitrogen, Carlsbad, CA, USA) to remove RNA contamination, followed by overnight digestion with 1% SDS and 200 μg/mL Proteinase K (Invitrogen) at 56 °C. DNA was purified by phenol-chloroform extraction and ethanol precipitation. Sequencing libraries were prepared using approximately 1 ng of purified DNA per sample with the NEBNext® Multiplex Oligos (E7500S, NEB, Ipswich, MA, USA). Libraries were sequenced on the MGI® DNBSEQ-T7 platform.

treatment_protocol: For G1/S state synchronization, cells were first subjected to serum starvation in DMEM containing 0.5% FBS and 1% Pen/Strep for 2 days. Cells were then released into fresh complete medium supplemented with 1% Aphidicolin (Abcam, Cambridge, MA, USA) for 18 h before harvest. For mitotic synchronization, cells were cultured to approximately 80% confluence and treated with 100 ng/mL colcemid (Sigma-Aldrich, St. Louis, MO, USA) for 12 h. Mitotic cells were then collected by mechanical shake-off and used for subsequent mitotic chromosome purification..

value: human hepatocellular carcinoma cells

value: epithelial cells


title: Pooled screen, 13F, v1, bulk population, TF dialout

description: Library name: sample_1-2

value: X-vivo 15 (Lonza)


title: Huh-7, Meta, macroH2A2, Rep1 (Chip)

description: Library name: Huh-7_Meta_macroH2A2_Chip, Rep1


title: O_CKP_D4_C_rep6

description:
Library name: 2-18C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the compound Kushen pill treatment group; biological replicate 6.

value: colon epithelium


title: Cornea Pitx2 -/- female rep3

description: Library name: F_95_mut


title: Pooled screen, 13F, v1, bulk population, GEX

description: Library name: sample_1-1


title: 10L, No ASO, N, 0hr

city: Wilsonville

first: Srivathsan

middle: V

last: Ranganathan

state: OR

address: 30519 SW Ruth St

department: DOS

institute: OHSU

description: Library name: 139651

data_processing:
Fastq files assembled with Bcl2Fastq (Illumina Inc.)
Fastq files aligned with Ensembl v75 gene models (GRCh37 build of the human genome) using Kallisto (v0.46.2).
Salmon-produced transcript abundance estimates scaled using average transcript length (over all sequenced samples) and library size and converted to Ensembl-annotated gene-level count estimates (‘tximport’ Bioconductor package)
Differential expression of bulk RNAseq experiments involved filtering out Ensembl-identified genes with low counts (‘edgeR’ Bioconductor package), normalization of counts via trimmed mean of M-values method (‘edgeR’), surrogate variable analysis (‘sva’ Bioconductor package), and gene-wise modeling using empirical Bayesian limma-voom procedure (‘limma’ Bioconductor package)62,71,72. Heatmaps produced using ComplexHeatmap v2.6.2
Assembly: GRCh37
Supplementary files format and content: quant.sf format

source_name: cell line

growth_protocol: Human MOLM14 cells generously provided by Dr. Yoshinobu Matsuo (Fujisaki Cell Center, Hayashibara Biochemical Labs, Okayama, Japan). Gilteritinib resistant cultures were maintained as previously described4 in 100 nM of gilteritinib (Selleck Chemicals, Houston, TX) and RPMI (Life Technologies Inc., Carlsbad, CA) with 10% FBS (Atlanta Biologicals, Flowery Branch, GA), 2% L-glutamine, 1% penicillin/streptomycin (Life Technologies Inc.), and 0.1% amphotericin B (HyClone, South Logan, UT). Gilteritinib and media were replenished every 2-3 days.

extract_protocol:
RNA isolated with miRNeasy Mini Kit (Qiagen Inc.) according to the manufacturer’s protocol
Libraries prepared using TruSeq Stranded mRNA Kit (Illumina Inc.)

treatment_protocol: Cell lines were treated with 5 µM NRAS or control ASO or media alone every other day for 96 hours and then treated with 100 nM gilteritinib. Cell pellets were collected at timepoint 0, 4, and 24 hours after treatment.

value: cell line

value: AML cell line

value: NRAS G12D

value: No ASO

tag: aso dose_(um)

tag: gilteritinib

value: N

tag: gilt concentration_(um)

tag: time -_gilteritinib_treatment


title: U2OS, scRepli-seq, aphidicolin singleG1 013

city: Kobe

first: Jothivanan

last: Elumalai

address: 2-2-3, Minatojima Minamimachi, Chuo-ku

institute: RIKEN

data_processing:
We used only one end of the paired-end sequenced reads for our analysis. Raw fastq files were subjected to quality assessment with FastQC v0.11.5 , and the cutadapt program v1.15 was used to eliminate SEQXE and Illumina adapters. Mapping to the hg19 or mm9 genome was carried out using bwa v0.7.17-r1188 (bwa-aln command). The resulting mapped reads were sorted using samtools v1.7, and duplicate reads were flagged using picard-tools v2.8.1.
For single-G1 karyotype analysis: After marking the duplicate reads, copy number analysis was conducted using the AneuFinder package v1.22.0 within R v4.1.3. Initially, duplicate reads, blacklist regions (available at https://github.com/Boyle-Lab/Blacklist) and reads with a mapping quality (MAPQ) below 10 were filtered out. Uniquely mapped reads were counted within each 500-Kb genomic window, adjusted for GC content (GC.BSgenome=BSgenome.Hsapiens.UCSC.hg19 for humans and BSgenome.Mmusculus.UCSC.mm9 for mouse, method="loess"), and copy number segmentation was executed using the "findCNVs" function (method='edivisive', R=50) of the AneuFinder package. For quality control (QC), multivariate clustering was applied, and clusters with a spikiness value exceeding 1 were eliminated.
For Log2percentile RT: We followed our established procedure to generate binarized replication timing (RT) profiles for each of the 14 fractions of S-phase or single-cells under analysis, along with their respective percentage replication scores (Miura et al, Nat. Protoc. 2020). The percentage replication score of each S-phase fraction or single-cells was utilized to compute their raw, non-binarized replication timing profile, termed as "log2repliscore RT".
Assembly: hg19, mm9
Supplementary files format and content: CNV states (.txt)
Supplementary files format and content: log2percentile RT (.txt)
Library strategy: scRepli-seq

source_name: Bone

extract_protocol:
Single cells were sorted with a Sony SH800 or MA900 cell sorter. Sample preparations were performed as described (Miura et al, Nat. Protoc. 2020). DNA samples were subject to whole-genome amplification (WGA) with a SeqPlex kit (Sigma, SEQXE).
NGS libraries were constructed for amplied DNA using an NGS LTP Library Preparation Kit (KAPA, KK8232) according to the manufacturer’s instructions.

tag: tissue

value: Bone

value: Sarcoma-derived

tag: treatment

value: Aphidicolin


title: O_CKP_D4_C_rep5

description:
Library name: 2-17C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the compound Kushen pill treatment group; biological replicate 5.

source_name: colon epithelium


title: Huh-7, G1/S, macroH2A2, Rep2 (Chip)

description: Library name: Huh-7_G1/S_macroH2A2_Chip, Rep2


title: Cornea Pitx2 -/- female rep2

description: Library name: F_94_mut


title: CD4+ T cells from healthy control 3, C176 treated

city: Tianjin

first: Weiwei

last: Jiang

address: No. 354, Beima Road, Hongqiao District, Tianjin

department: Dermatology

institute: Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital

description: Library name: HC_c176_3

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM X PLUS sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Homo sapiens.GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: CD4+ T cells

growth_protocol: Purified CD4+ T cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BP group: Cells from BP patients cultured with standard medium. HC group: Cells from healthy controls cultured with standard medium. BP + C176 group: Cells from BP patients treated with the STING inhibitor C176 (5μM) for 24 hours. HC + C176 group: Cells from healthy controls treated with C176 (same concentration and duration).

value: CD4+ T cells

value: BP

value: STING inhibitor C176, 5μM, 24h

tag: batch


title: Huh-7, G1/S, macroH2A2, Rep1 (Chip)

description: Library name: Huh-7_G1/S_macroH2A2_Chip, Rep1


title: Cornea Pitx2 +/+ female rep5

description: Library name: F_88_ctrl

value: Cornea


title: CD4+ T cells from healthy control 2, C176 treated

description: Library name: HC_c176_2


title: O_CKP_D4_C_rep3

description:
Library name: 1-21C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the compound Kushen pill treatment group; biological replicate 3.

value: fractionated abdominal irradiation, 5 × 4 Gy; oral compound Kushen powder treatment


title: Cornea Pitx2 +/+ female rep4

description: Library name: F_87_ctrl


title: Huh-7, G1/S, macroH2A2 (input)

description: Library name: Huh-7_G1/S_macroH2A2_Control, input

value: human hepatocellular carcinoma cells


title: CD4+ T cells from healthy control 1, C176 treated

description: Library name: HC_c176_1


title: O_CKP_D4_C_rep2

description:
Library name: 1-20C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the compound Kushen pill treatment group; biological replicate 2.


title: Cornea Pitx2 +/+ female rep3

description: Library name: F_86_ctrl


title: Huh-7, Meta, macroH2A1, Rep2 (Chip)

description: Library name: Huh-7_Meta_macroH2A1_Chip, Rep2

value: epithelial cells


title: CD4+ T cells from BP patient 3, C176 treated

description: Library name: BP_c176_3


title: O_CKP_D4_C_rep1

description:
Library name: 1-19C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the compound Kushen pill treatment group; biological replicate 1.


title: Huh-7, Meta, macroH2A1, Rep1 (Chip)

description: Library name: Huh-7_Meta_macroH2A1_Chip, Rep1


title: Cornea Pitx2 +/+ female rep2

description: Library name: F_83_ctrl


title: Cornea Pitx2 -/- female rep4

description: Library name: F_96_mut


title: Huh-7, Meta, macroH2A1 (input)

description: Library name: Huh-7_Meta_macroH2A1_Control, input


title: CD4+ T cells from BP patient 1, C176 treated

description: Library name: BP_c176_1