title: CHIKV non-infected, long RNA, rep1

description:
Library name: CONTROL-IP-1_S4
CHIKV-long-RNA_diffexpr.csv
CHIKV-long-RNA_diffpeaks.csv


title: WT_Pair-fed-2

status: Public on Apr 29 2026

type: SRA

city: Hefei

first: Jinghao

last: Yao

state: Anhui

address: NO. 218 Jixi Road

department: Oncology

country: China

institute: First Affiliated Hospital of Anhui Medical University

description:
Library name: Sample 2
Column name in Ctrl_E-vs-Ctrl_PF.txt: FPKM_Ctrl_PF2
Ctrl_E-vs-Ctrl_PF.txt

library_source: transcriptomic

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count .
Assembly: mm10
Supplementary files format and content: FPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

tag: tissue

value: Liver

tag: genotype

value: WT

tag: treatment

value: Pair-fed


title: pool-5,well-3,GEX

city: San Francisco

first: Ravi

last: Patel

state: CA

address: 513 Parnassus Ave

department: CoLabs

country: USA

institute: University of California San Francisco

description:
Library name: XVIR1-POOL-SCG18_GEX
Pool of XVIR1-HS11-SNEGB4,XVIR1-HS14-NCTLB3,XVIR1-HS16-NCTLB4,XVIR1-HS17-SNEGB2,XVIR1-HS20-NCTLB2,XVIR1-HS21-NCTLB2,XVIR1-HS22-NCTLB1,XVIR1-HS37-NCTLB7,XVIR1-HS41-SNEGB5,XVIR1-HS42-SNEGB4,XVIR1-HS44-NCTLB5,XVIR1-HS5-SNEGB9,XVIR1-HS7-SNEGB1

data_processing:
Sequencer-obtained bcl files were demultiplexed using mkfastq program from Cell Ranger v6.0.2   (10x Genomics). Feature-barcode matrices were obtained for each library by aligning the raw fastqs of gene expression to GRCh38 reference genome (Ensembl v98) and the raw fastqs of surface protein expression to a TotalSeq-A antibody reference panel using the Cell Ranger count. Raw feature-barcode matrices were imported and analyzed using Seurat (v4.0.3).
Each library was demultiplexed to map individual cells to their sample of origin using freemuxlet (vAug2021), SNP profiles were mapped to the genotypes of patients from bulk RNA-seq using bcftools gtcheck (v1.10.2), and inter-sample doublets and empty droplets were removed.
DoubletFinder (v2.0.3)22 was used to filter barcodes containing heterotypic intra-sample doublets.
Barcodes containing less than 100 genes and genes that are detected in fewer than 3 cells were removed. We further filtered out the barcodes based on library-specific cutoffs for the number of genes per cell (nFeature_RNA <300-400 and >4,000), the number of unique molecular indexes (UMIs) per cell (nCount_RNA <700-2,000 and >20,000; nCount_ADT >20,000), mitochondrial content (>20%), and ribosomal content (<2-13% and >60%) to remove poor quality cells. The RNA and ADT count data for the resulting high-quality cell-barcodes are provided here.
Assembly: GRCh38
Supplementary files format and content: *.h5 files contain raw count data in 10X H5 format
Supplementary files format and content: CITEseq_cell_metadata.rds is an R object file containing metadata for single-cells, including patient, sample, library, and pool ids, study group, timepoint, cell annotations, and additional sample-specific metadata
Library strategy: CITE-seq

organism: Homo sapiens

source_name: PBMC

extract_protocol:
PBMCs were isolated from whole blood using Ficoll-Paque PLUS density gradient and were stored in freezing medium (9:1 FBS/DMSO) in liquid nitrogen (<-135C). Thawed PBMC suspensions from 16 individual patients were pooled together with equivalent numbers of live cells.  10^6 pooled cells were Fc blocked  for 10 min at room temperature followed by staining with a custom TotalSeqTM-A antibody panel for 45 minutes at 4°C. Cells were washed 3 times with Cell Staining Buffer resuspended in DPBS (w/o Ca2+, Mg2+)  with 0.04% BSA at 2,000 cells/uL and loaded onto a 10X Genomics Chromium Controller.
Stained cells were loaded onto a Chromium Next GEM Chip G at 65,000 cells per well, 4 wells per pool (except for one pool  with only 2 wells per pool (XVIR1-POOL-SC[G/C]2 and XVIR1-POOL-SC[G/C]3)) and processed for single-cell encapsulation and cDNA library generation using the Chromium Single Cell 3′ v3.1 Reagent Kits (User guide CG000206 Rev D; 10X Genomics) and Single Index Kit T Set A according to the manufacturer’s instructions. Gene Expression (GEX) and surface protein-targeting Antibody Derived Tag (ADT) libraries were pooled at 2.5:1 and the libraries were sequenced on Illumina NovaSeq 6000 (S4-200, ~2.5B reads per library) at the Center for Advanced Technology at UCSF at a depth of 25,000 reads per cell for GEX and 10,000 reads per cell for ADT using the recommended cycle numbers: Read 1 28 cycles, i7 index 8 cycles, Read 2 91 cycles.

value: PBMC


title: CHIKV non-infected, long RNA, rep3

city: Helsingør

first: Niels-Ulrik

last: Frigaard

address: Strandpromenaden 5

department: Department of Biology

country: Denmark

institute: University of Copenhagen

description:
Library name: CONTROL-IP-3_S6
CHIKV-long-RNA_diffexpr.csv
CHIKV-long-RNA_diffpeaks.csv

data_processing:
Read quality was controlled using fastx toolkits cutadapt: remove adapters, discard reads of Phred score lower than 10 (or 20) and shorten reads to a fixed length of 130 nts or 60 nts for long and short RNA-seq, respectively.
Read mapping to virus genomes and GRCh38 with Bowtie v1.2.2 (paramters -n 1 -l 8 -a --best --strata --phred33-qual) for small RNA-seq and STAR v2.5.2a (parameters --outSAMstrandField intronMotif --outSJfilterCountUniqueMin 3 2 2 2).
Filter ribosomal RNAs (RepeatMasker v4.0.5 and repeat library db20140131).
Gene quantification (Gencode human v45 or v27) with Subread featureCounts or HTSeq, and differential gene expression analysis with DESeq2 or edgeR.
Peak calling of bin size 100 nts and step size 50 nts using Piranha v1.2.1 (parameters -s -p 0.5), and differential peak analysis using DiffBind and DESeq2 or edgeR.
Assembly: GRCh38, HCV J6/JFH1 cl2, YFV 17D, pCHIKV
Supplementary files format and content: csv files including differential expressed genes called with DESeq2 or edgeR for each of the four experiments
Supplementary files format and content: csv files including differential expressed peaks called with DiffBind for each of the four experiments

molecule: cytoplasmic RNA

growth_protocol: Huh-7.5 hepatoma cells were maintained in Dulbecco’s Modified  Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and keptT at 37°C and 5% CO2.

extract_protocol:
Briefly, in the modified RAP-RNA protocol, RNA molecules in close proximity were cross-linked using UV365 in the presence of the psoralen molecule, 4′-aminomethyltrioxsalen (AMT). Cells were then fractionated into nuclear and cytoplasmic constituents, and cytoplasmic viral RNA was enriched using pull-down with specific DNA probes. The enriched RNA was then DNAse treated to remove the DNA probes, and reverse cross-linked using UV254.
To allow efficient identification of both short and long RNA interactors, two parallel strand-specific RNA-library methods were applied, based on poly-adenylation and template switching (CATS small-RNAseq-kit (Diagenode)), or random hexamer priming (NEBnext Ultra II), respectively.

treatment_protocol: Cells were infected with the HCV genotype 2a recombinant, J6/JFH1-c2 (72 hpi, MOI=1), YFV strain 17D (24 hpi, MOI=1), or CHIKV strain LR (24 hpi, MOI=1).

tag: cell line

tag: cell type

value: Hepatoma cells

value: Non-infected

tag: batch


title: WT_Pair-fed-1

description:
Library name: Sample 1
Column name in Ctrl_E-vs-Ctrl_PF.txt: FPKM_Ctrl_PF1
Ctrl_E-vs-Ctrl_PF.txt


title: pool-5,well-3,ADT

description:
Library name: XVIR1-POOL-SCC18_ADT
Pool of XVIR1-HS11-SNEGB4,XVIR1-HS14-NCTLB3,XVIR1-HS16-NCTLB4,XVIR1-HS17-SNEGB2,XVIR1-HS20-NCTLB2,XVIR1-HS21-NCTLB2,XVIR1-HS22-NCTLB1,XVIR1-HS37-NCTLB7,XVIR1-HS41-SNEGB5,XVIR1-HS42-SNEGB4,XVIR1-HS44-NCTLB5,XVIR1-HS5-SNEGB9,XVIR1-HS7-SNEGB1

library_source: other

molecule: protein


title: CHIKV infected, long RNA, rep3

description:
Library name: CHIK-IP-3_S3
CHIKV-long-RNA_diffexpr.csv
CHIKV-long-RNA_diffpeaks.csv

value: CHIKV infected


title: PNR-7-02_TDP1_DIG

city: Philadelphia

first: Paul

middle: M

last: Lieberman

state: Pennsylvania

address: 3601 Spruce Street

institute: The Wistar Institute

description: Library name: Sample 12

library_source: genomic

data_processing:
DNA sequening reads were aligned to human gamma herpesvirus 8 BCBL-1 genome (GCA_027939675.1) using Bowtie 2 program (version 2.2.2)
Assembly: human gamma herpesvirus 8 BCBL-1 genome (GCA_027939675.1)
Supplementary files format and content: Bedgraph

molecule: genomic DNA

organism:
Homo sapiens
Human gammaherpesvirus 8

extract_protocol:
Genomic DNA from 5 × 107 cells treated with DMSO or PNR07-02 was purified and treated with 5 μg of pancreatic RNase (Roche) followed by with or without 1 μg of TDP1 in 80 mM KCl, 50 mM Tris–HCl pH 8.0, 2 mM EDTA,2 mM DTT for 1 h at 37 °C, adjusted to 0.5% SDS and incubated for 1 h at 55 °C with proteinase K (200 μg/mL). DNA was extracted twice with phenol and precipitated with ethanol in the presence of 2 M ammonium acetate.
The Epicentre DNA END-Repair kit (Epicentre Biotechnologies, Madison, WI, USA) was used to generate blunt-ended DNA. SSB and DSB DNA libraries were prepared using NEBNext utra II DNA library prep kit for Illumina (NEB). The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina Genome Analyzer (Illumina, San Diego, USA) following manufacturer protocols.

value: B lymphocyte (PEL-derived)

value: KSHV+


title: PNR-7-02_noTDP1_DIG

description: Library name: Sample 10


title: Liver tumor, MKO_PD1, rep3

city: Hong Kong

first: Alfred Sze-Lok

last: Cheng

address: Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, CUHK

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Library name: MKO_PD1_G36

data_processing:
Reads were aligned to the mouse reference genome (mm10) using STAR (v2.7.10a). The read counts were calculated using subread-featureCounts (v2.0.3) and then obtain the values of transcripts per million (TPM).
Assembly: mm10
Supplementary files format and content: csv files include TPM values for each Sample

molecule: polyA RNA

source_name: liver tumor

extract_protocol:
Total RNA was extracted from RIL-175/PD-1R tumors derived from LysM-Cre and TREM2-MKO mice using TRIzol (Invitrogen) according to manual instruction and further purified with the RNeasy MinElute Cleanup Kit (Qiagen). RNA integrity and concentration were assessed on the Agilent 4200 TapeStation System.
Librariy construction for RNA-seq were prepared by Novogene Co., Ltd following standard protocols.

value: liver tumor


title: pool-5,well-2,GEX

description:
Library name: XVIR1-POOL-SCG17_GEX
Pool of XVIR1-HS11-SNEGB4,XVIR1-HS14-NCTLB3,XVIR1-HS16-NCTLB4,XVIR1-HS17-SNEGB2,XVIR1-HS20-NCTLB2,XVIR1-HS21-NCTLB2,XVIR1-HS22-NCTLB1,XVIR1-HS37-NCTLB7,XVIR1-HS41-SNEGB5,XVIR1-HS42-SNEGB4,XVIR1-HS44-NCTLB5,XVIR1-HS5-SNEGB9,XVIR1-HS7-SNEGB1


title: WT_EtOH-fed-1

description:
Library name: Sample 4
Column name in Ctrl_E-vs-Ctrl_PF.txt: FPKM_Ctrl_E1
Ctrl_E-vs-Ctrl_PF.txt
M3_E-vs-Ctrl_E.txt

value: Ethanol-fed


title: CHIKV infected, long RNA, rep2

description:
Library name: CHIK-IP-2_S2
CHIKV-long-RNA_diffexpr.csv
CHIKV-long-RNA_diffpeaks.csv


title: DMSO_TDP1_Biotin

description: Library name: Sample 5

value: DMSO


title: pool-5,well-2,ADT

description:
Library name: XVIR1-POOL-SCC17_ADT
Pool of XVIR1-HS11-SNEGB4,XVIR1-HS14-NCTLB3,XVIR1-HS16-NCTLB4,XVIR1-HS17-SNEGB2,XVIR1-HS20-NCTLB2,XVIR1-HS21-NCTLB2,XVIR1-HS22-NCTLB1,XVIR1-HS37-NCTLB7,XVIR1-HS41-SNEGB5,XVIR1-HS42-SNEGB4,XVIR1-HS44-NCTLB5,XVIR1-HS5-SNEGB9,XVIR1-HS7-SNEGB1


title: CHIKV infected, long RNA, rep1

description:
Library name: CHIK-IP-1_S1
CHIKV-long-RNA_diffexpr.csv
CHIKV-long-RNA_diffpeaks.csv


title: Liver tumor, MKO_PD1, rep2

description: Library name: MKO_PD1_G31


title: YFV non-infected, long RNA, rep3

description:
Library name: ControlRep3_S6
YFV-long-RNA_diffexpr.csv
YFV-long-RNA_diffpeaks.csv


title: pool-5,well-1,ADT

description:
Library name: XVIR1-POOL-SCC16_ADT
Pool of XVIR1-HS11-SNEGB4,XVIR1-HS14-NCTLB3,XVIR1-HS16-NCTLB4,XVIR1-HS17-SNEGB2,XVIR1-HS20-NCTLB2,XVIR1-HS21-NCTLB2,XVIR1-HS22-NCTLB1,XVIR1-HS37-NCTLB7,XVIR1-HS41-SNEGB5,XVIR1-HS42-SNEGB4,XVIR1-HS44-NCTLB5,XVIR1-HS5-SNEGB9,XVIR1-HS7-SNEGB1


title: DMSO_noTDP1_Biotin

description: Library name: Sample 3


title: Liver tumor, Cre_PD1, rep3

description: Library name: Cre_PD1_G53


title: Liver tumor, MKO_PD1, rep1

description: Library name: MKO_PD1_G34


title: pool-5,well-1,GEX

description:
Library name: XVIR1-POOL-SCG16_GEX
Pool of XVIR1-HS11-SNEGB4,XVIR1-HS14-NCTLB3,XVIR1-HS16-NCTLB4,XVIR1-HS17-SNEGB2,XVIR1-HS20-NCTLB2,XVIR1-HS21-NCTLB2,XVIR1-HS22-NCTLB1,XVIR1-HS37-NCTLB7,XVIR1-HS41-SNEGB5,XVIR1-HS42-SNEGB4,XVIR1-HS44-NCTLB5,XVIR1-HS5-SNEGB9,XVIR1-HS7-SNEGB1


title: DMSO_TDP1_noBiotin

description: Library name: Sample 1


title: pool-4,well-4,GEX

description:
Library name: XVIR1-POOL-SCG15_GEX
Pool of XVIR1-HS11-SNEGB3,XVIR1-HS14-NCTLB2,XVIR1-HS15-NCTLB8,XVIR1-HS16-NCTLB3,XVIR1-HS17-SNEGB1,XVIR1-HS19-NCTLB2,XVIR1-HS20-NCTLB1,XVIR1-HS4-SNEGB3,XVIR1-HS42-SNEGB3,XVIR1-HS44-NCTLB4,XVIR1-HS9-SNEGB3


title: DMSO_TDP1_DIG

description: Library name: Sample 11


title: YFV non-infected, long RNA, rep2

description:
Library name: ControlRep2_S5
YFV-long-RNA_diffexpr.csv
YFV-long-RNA_diffpeaks.csv


title: pool-4,well-4,ADT

description:
Library name: XVIR1-POOL-SCC15_ADT
Pool of XVIR1-HS11-SNEGB3,XVIR1-HS14-NCTLB2,XVIR1-HS15-NCTLB8,XVIR1-HS16-NCTLB3,XVIR1-HS17-SNEGB1,XVIR1-HS19-NCTLB2,XVIR1-HS20-NCTLB1,XVIR1-HS4-SNEGB3,XVIR1-HS42-SNEGB3,XVIR1-HS44-NCTLB4,XVIR1-HS9-SNEGB3


title: Liver tumor, Cre_PD1, rep2

description: Library name: Cre_PD1_G10


title: YFV non-infected, long RNA, rep1

description:
Library name: ControlRep1_S4
YFV-long-RNA_diffexpr.csv
YFV-long-RNA_diffpeaks.csv


title: pool-4,well-3,ADT

description:
Library name: XVIR1-POOL-SCC14_ADT
Pool of XVIR1-HS11-SNEGB3,XVIR1-HS14-NCTLB2,XVIR1-HS15-NCTLB8,XVIR1-HS16-NCTLB3,XVIR1-HS17-SNEGB1,XVIR1-HS19-NCTLB2,XVIR1-HS20-NCTLB1,XVIR1-HS4-SNEGB3,XVIR1-HS42-SNEGB3,XVIR1-HS44-NCTLB4,XVIR1-HS9-SNEGB3


title: Liver tumor, Cre_PD1, rep1

description: Library name: Cre_PD1_G7


title: YFV infected, long RNA, rep3

description:
Library name: YFVrep3_S3
YFV-long-RNA_diffexpr.csv
YFV-long-RNA_diffpeaks.csv

value: YFV infected


title: DMSO_noTDP1_DIG

description: Library name: Sample 9


title: PNR-7-02_TDP1_noDIG

description: Library name: Sample 8


title: DMSO_TDP1_noDIG

description: Library name: Sample 7


title: YFV infected, long RNA, rep2

description:
Library name: YFVrep2_S2
YFV-long-RNA_diffexpr.csv
YFV-long-RNA_diffpeaks.csv


title: pool-4,well-3,GEX

description:
Library name: XVIR1-POOL-SCG14_GEX
Pool of XVIR1-HS11-SNEGB3,XVIR1-HS14-NCTLB2,XVIR1-HS15-NCTLB8,XVIR1-HS16-NCTLB3,XVIR1-HS17-SNEGB1,XVIR1-HS19-NCTLB2,XVIR1-HS20-NCTLB1,XVIR1-HS4-SNEGB3,XVIR1-HS42-SNEGB3,XVIR1-HS44-NCTLB4,XVIR1-HS9-SNEGB3


title: WI3_S254_L004_R1_001

city: Québec

first: David

last: Gosselin

state: Quebec

address: CRCHUL - 2705 Boulevard Laurier, Bloc T - 2-34

department: Molecular Medicine

country: Canada

institute: Université Laval

data_processing:
Alignment: Only R1 sequencing files were mapped and used for differential expression analysis. FASTQ files from sequencing experiments were mapped to the mouse mm10 reference genome. STAR (2.7.0f) with default parameters was used to map RNA-seq experiments. The aligned read .sam files for each experiments were then converted into tag diretories using HOMER (v4.11; http://homer.ucsd.edu/homer/ ; makeTagDirectory.pl ), with the -flip option specified, for downsteam analyses.
RNA-seq: For differential expression analyses, a table read count including relevant samples was first created using the analyzeRepeats.pl program of HOMER (v4.11; http://homer.ucsd.edu/homer/) with the following parameters: rna -noadj -condenseGenes -count exons -pc 3. Non-coding RNA and pseudogenes were then removed to retain only protein-coding mRNAs and the resulting dataset was used as input file for HOMER’s getDiffExpression.pl program, which leveraged R/DESeq2 for to assess differential expression. For data interpretation, only genes with 16 or more normalized reads were considered. Alternatively, Transcript Per Million-normalized datasets were generated using the analyzeRepeats.pl program of HOMER with the following parameters: rna -TPM -condenseGenes -count exons -pc 3. The base-2 logarithm of the TPM values was taken after adding a pseudocount of 1 TPM to each gene.
Only the R1 reads were mapped and used for differential analyses
Assembly: mm10
Supplementary files format and content: Microglia_RNA_dUTP_rawdata.txt; abundance measurements; raw counts for all samples (replicates = biological replicates)
Supplementary files format and content: Microglia_RNA_dUTP_TPMnormalization.txt; abundance measurements; Transcript per million normalization (replicates = biological replicates)

extract_protocol:
Brain samples were homogenized in Qiazol buffer (Qiagen, Germantown, MD, USA), and total RNA was extracted using the miRNeasy micro kit on-column DNase (Qiagen) treatment.
The NEBNext Ultra II directional RNA library prep kit for Illumina (New Englands Biolabs Inc., MA, USA) was used to prepare mRNA sequencing libraries, according to manufacturer's instruction.

treatment_protocol: To investigate the role of DKK1 following ischemic stroke in mice, we induced DKK1 by doxyxycline 3 days after MCAo. We analyzed DKK1/ON and WT/DOX ipsilateral lesioned tissue and contralateral intact tissue of the brain hemispheres 28 days after MCAo.

tag: disease

value: Ischemic stroke

value: Doxyxycline (200 mg/kg)


title: Foxp3KO Treg_2 (RNA-seq)

city: Hongo, Bunkyo-ku

first: Ryuichi

last: Murakami

state: Tokyo

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: The University of Tokyo

description:
Freshly sorted
DK22174_01_12

data_processing:
RNA-seq reads were mapped to mouse reference genome (mm10) using STAR v2.6.1c
RNA-seq reads per gene were counted using --quantMode GeneCounts option in STAR
Assembly: mm10
Supplementary files format and content: raw read counts

source_name: lymph nodes and spleen

extract_protocol:
Total RNA was extracted using Isogen and poly(A) mRNA was enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module
NEBNext Ultra Directional RNA Library Prep Kit for Illumina or NEBNext UltraII RNA Library Prep Kit for Illumina

value: lymph nodes and spleen

value: Treg (CD4+hCD2+GFP-)

tag: strain


title: WI2_S253_L004_R1_001


title: YFV infected, long RNA, rep1

description:
Library name: YFVrep1_S1
YFV-long-RNA_diffexpr.csv
YFV-long-RNA_diffpeaks.csv


title: pool-4,well-2,ADT

description:
Library name: XVIR1-POOL-SCC13_ADT
Pool of XVIR1-HS11-SNEGB3,XVIR1-HS14-NCTLB2,XVIR1-HS15-NCTLB8,XVIR1-HS16-NCTLB3,XVIR1-HS17-SNEGB1,XVIR1-HS19-NCTLB2,XVIR1-HS20-NCTLB1,XVIR1-HS4-SNEGB3,XVIR1-HS42-SNEGB3,XVIR1-HS44-NCTLB4,XVIR1-HS9-SNEGB3


title: Foxp3KO Treg_1 (RNA-seq)

description:
Freshly sorted
DK22174_01_10


title: WI1_S252_L004_R1_001


title: HCV non-infected, long RNA, batch 2, rep5

description:
Library name: NT2_S11
HCV-long-RNA_diffexpr.csv
HCV-long-RNA_diffpeaks.csv


title: HCV non-infected, long RNA, batch 2, rep4

description:
Library name: NT1_S10
HCV-long-RNA_diffexpr.csv
HCV-long-RNA_diffpeaks.csv


title: pool-4,well-2,GEX

description:
Library name: XVIR1-POOL-SCG13_GEX
Pool of XVIR1-HS11-SNEGB3,XVIR1-HS14-NCTLB2,XVIR1-HS15-NCTLB8,XVIR1-HS16-NCTLB3,XVIR1-HS17-SNEGB1,XVIR1-HS19-NCTLB2,XVIR1-HS20-NCTLB1,XVIR1-HS4-SNEGB3,XVIR1-HS42-SNEGB3,XVIR1-HS44-NCTLB4,XVIR1-HS9-SNEGB3


title: WT Treg_6 (RNA-seq) (Foxp3KO control)

description:
Freshly sorted
DK22174_01_11


title: HCV non-infected, long RNA, batch 2, rep6

description:
Library name: NT3_S12
HCV-long-RNA_diffexpr.csv
HCV-long-RNA_diffpeaks.csv


title: pool-3,well-4,ADT

description:
Library name: XVIR1-POOL-SCC11_ADT
Pool of XVIR1-HS11-SNEGB6,XVIR1-HS15-NCTLB7,XVIR1-HS16-NCTLB2,XVIR1-HS17-SNEGB9,XVIR1-HS19-NCTLB1,XVIR1-HS20-NCTLB6,XVIR1-HS37-NCTLB6,XVIR1-HS4-SNEGB1,XVIR1-HS41-SNEGB4,XVIR1-HS43-SNEGB4,XVIR1-HS44-NCTLB3,XVIR1-HS5-SNEGB4,XVIR1-HS9-SNEGB1


title: WC2_S250_L004_R1_001


title: pool-4,well-1,GEX

description:
Library name: XVIR1-POOL-SCG12_GEX
Pool of XVIR1-HS11-SNEGB3,XVIR1-HS14-NCTLB2,XVIR1-HS15-NCTLB8,XVIR1-HS16-NCTLB3,XVIR1-HS17-SNEGB1,XVIR1-HS19-NCTLB2,XVIR1-HS20-NCTLB1,XVIR1-HS4-SNEGB3,XVIR1-HS42-SNEGB3,XVIR1-HS44-NCTLB4,XVIR1-HS9-SNEGB3


title: WC3_S251_L004_R1_001


title: pool-4,well-1,ADT

description:
Library name: XVIR1-POOL-SCC12_ADT
Pool of XVIR1-HS11-SNEGB3,XVIR1-HS14-NCTLB2,XVIR1-HS15-NCTLB8,XVIR1-HS16-NCTLB3,XVIR1-HS17-SNEGB1,XVIR1-HS19-NCTLB2,XVIR1-HS20-NCTLB1,XVIR1-HS4-SNEGB3,XVIR1-HS42-SNEGB3,XVIR1-HS44-NCTLB4,XVIR1-HS9-SNEGB3


title: WC1_S249_L004_R1_001


title: pool-3,well-4,GEX

description:
Library name: XVIR1-POOL-SCG11_GEX
Pool of XVIR1-HS11-SNEGB6,XVIR1-HS15-NCTLB7,XVIR1-HS16-NCTLB2,XVIR1-HS17-SNEGB9,XVIR1-HS19-NCTLB1,XVIR1-HS20-NCTLB6,XVIR1-HS37-NCTLB6,XVIR1-HS4-SNEGB1,XVIR1-HS41-SNEGB4,XVIR1-HS43-SNEGB4,XVIR1-HS44-NCTLB3,XVIR1-HS5-SNEGB4,XVIR1-HS9-SNEGB1


title: WT Treg_5 (RNA-seq) (Foxp3KO control)

description:
Freshly sorted
DK22174_01_09


title: HCV infected, long RNA, batch 2, rep4

description:
Library name: HH+1_S1
HCV-long-RNA_diffexpr.csv
HCV-long-RNA_diffpeaks.csv

value: HCV infected


title: Zebrafish,hsd17b7_KO

city: Nantong City

first: Xin

last: Wang

state: Jiangsu Province

address: No.9, Seyuan Road

institute: Nantong University

description:
Library name: Sample 2
10X Genomics single-cell RNA-seq library from hsd17b7 mutant zebrafish larvae

library_source: transcriptomic single cell

data_processing:
Raw base call files were demultiplexed and converted to FASTQ format using the Cell Ranger pipeline (10x Genomics).
Reads were aligned to the zebrafish reference genome, and gene expression matrices were generated using Cell Ranger according to the manufacturer’s instructions.
Downstream quality control and analysis were performed using Seurat in R.
Assembly: Danio rerio reference genome (GRCz11)
Supplementary files format and content: Processed data files include gene expression matrices generated by the 10x Genomics Cell Ranger pipeline, provided as compressed Matrix Market files (matrix.mtx.gz) with corresponding feature (features.tsv.gz) and cell barcode (barcodes.tsv.gz) annotation files.

organism: Danio rerio

source_name: hair cell

growth_protocol: Zebrafish larvae were raised under standard laboratory conditions according to established protocols.

extract_protocol:
Inner ear and lateral line sensory hair cells were isolated from 4 days post-fertilization (dpf) Tg(Brn3c:mGFP) zebrafish larvae of both wild-type and hsd17b7 mutant backgrounds. Tissues were enzymatically dissociated using trypsin to generate single-cell suspensions, followed by centrifugation, resuspension, and cell counting. GFP-positive cells were enriched by fluorescence-activated cell sorting (FACS) prior to single-cell RNA sequencing library preparation.
Single-cell RNA sequencing libraries were prepared using the 10x Genomics Chromium Single Cell 3′ v4 reagent kit according to the manufacturer’s instructions. Briefly, single-cell suspensions were loaded onto Chromium microfluidic chips, where individual cells were encapsulated with barcoded gel beads in oil emulsions (GEMs) using a Chromium Controller (10x Genomics). Barcoded RNA was reverse-transcribed, and sequencing libraries were constructed following standard 10x Genomics protocols.

treatment_protocol: No chemical or pharmacological treatment was applied.

value: hair cell


title: Zebrafish,hsd17b7_ctrl

description:
Library name: Sample 1
10X Genomics single-cell RNA-seq library from wild-type zebrafish larvae

value: Wild-type


title: HCV infected, long RNA, batch 2, rep6

description:
Library name: HH+3_S3
HCV-long-RNA_diffexpr.csv
HCV-long-RNA_diffpeaks.csv

value: WT


title: DI1_S258_L004_R1_001


title: DC3_S257_L004_R1_001


title: Liver tumor, MKO_PD1, Input rep2

description: Library name: MKO_PD1_Input5

data_processing:
ChIP-seq data were processed following the steps of the ENCODE ChIP-seq pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2). Raw paired-end reads are first processed through Trimmomatic for quality control and adapter trimming, followed by alignment to the mm10 genome using Bowtie2. SAMtools performs post-alignment filtering to remove low-quality reads (MAPQ<30), unmapped reads, and improperly paired reads, while Picard marks PCR duplicates. MACS2 is then used for peak calling, with IDR analysis performed to evaluate reproducibility between replicates. The resulting peaks are filtered against mm10 blacklist regions, and signal tracks are generated as fold-enrichment and p-value bigWig files.
Assembly: mm10
Supplementary files format and content: Signal tracks of fold-enrichment bigWig file generated from bamCoverage tools
Supplementary files format and content: narrow peak files (extended bed format) generated using MACS2

source_name: Liver tumor

extract_protocol:
Tumor tissues from mice were ground in liquid nitrogen, cross-linked with 1% formaldehyde for 10 minutes, and quenched with glycine to a final concentration of 125 mM. Fixed cells were lysed in SDS lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, and 1% SDS) and subjected to DNA fragmentation using the Covaris ME220. The fragmented cell lysates were diluted 10-fold with dilution buffer (10 mM Tris-HCl pH 7.4, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, and 0.01% SDS) and pre-cleared using Protein A+G magnetic beads (Life Technologies) at 4 °C for 1 hour. Meanwhile, antibodies against H3K36ac (Cell Signaling Technology) were conjugated to Protein A+G magnetic beads at 4 °C for 1 hour. Supernatants were collected at 2,000 rpm for 10 minutes and incubated with the antibody-conjugated beads at 4 °C overnight. After washing, chromatin-antibody complexes were eluted in elution buffer (0.1 M NaHCO3, 1% SDS) and reverse cross-linked with 1 mg/mL proteinase K and 200 mM NaCl at 65 °C overnight. Immunoprecipitated DNA was purified using DNA cleanup columns (TIANGEN). Whole-genome amplification was performed using the WGA4 kit (Sigma-Aldrich) and BpmI-WGA primers and digested with BpmI (New England Biolab) before the NEBNext ChIP-seq library prep reagent set (New England Biolab).
Libraries were contructed following manufactor's intructions (NEBNext ChIP-seq Library Prep Reagent Set for Illumina)

value: Liver tumor

value: anti-PD-1 treatment

tag: antibody

value: Input


title: pool-3,well-3,ADT

description:
Library name: XVIR1-POOL-SCC10_ADT
Pool of XVIR1-HS11-SNEGB6,XVIR1-HS15-NCTLB7,XVIR1-HS16-NCTLB2,XVIR1-HS17-SNEGB9,XVIR1-HS19-NCTLB1,XVIR1-HS20-NCTLB6,XVIR1-HS37-NCTLB6,XVIR1-HS4-SNEGB1,XVIR1-HS41-SNEGB4,XVIR1-HS43-SNEGB4,XVIR1-HS44-NCTLB3,XVIR1-HS5-SNEGB4,XVIR1-HS9-SNEGB1

value: PBMC


title: Liver tumor, MKO_PD1, Input rep3

description: Library name: MKO_PD1_Input6


title: DI2_S259_L004_R1_001


title: Liver tumor, MKO_PD1, Input rep1

description: Library name: MKO_PD1_Input2


title: pool-3,well-3,GEX

description:
Library name: XVIR1-POOL-SCG10_GEX
Pool of XVIR1-HS11-SNEGB6,XVIR1-HS15-NCTLB7,XVIR1-HS16-NCTLB2,XVIR1-HS17-SNEGB9,XVIR1-HS19-NCTLB1,XVIR1-HS20-NCTLB6,XVIR1-HS37-NCTLB6,XVIR1-HS4-SNEGB1,XVIR1-HS41-SNEGB4,XVIR1-HS43-SNEGB4,XVIR1-HS44-NCTLB3,XVIR1-HS5-SNEGB4,XVIR1-HS9-SNEGB1


title: HCV non-infected, long RNA, batch 1, rep3

description:
Library name: WGS806_S4
HCV-long-RNA_diffexpr.csv
HCV-long-RNA_diffpeaks.csv

value: Hepatoma cells

value: Non-infected


title: HCV infected, long RNA, batch 2, rep5

description:
Library name: HH+2_S2
HCV-long-RNA_diffexpr.csv
HCV-long-RNA_diffpeaks.csv


title: pool-3,well-2,ADT

description:
Library name: XVIR1-POOL-SCC9_ADT
Pool of XVIR1-HS11-SNEGB6,XVIR1-HS15-NCTLB7,XVIR1-HS16-NCTLB2,XVIR1-HS17-SNEGB9,XVIR1-HS19-NCTLB1,XVIR1-HS20-NCTLB6,XVIR1-HS37-NCTLB6,XVIR1-HS4-SNEGB1,XVIR1-HS41-SNEGB4,XVIR1-HS43-SNEGB4,XVIR1-HS44-NCTLB3,XVIR1-HS5-SNEGB4,XVIR1-HS9-SNEGB1


title: HCV non-infected, long RNA, batch 1, rep2

description:
Library name: 9_S4
HCV-long-RNA_diffexpr.csv
HCV-long-RNA_diffpeaks.csv


title: DC1_S255_L004_R1_001


title: Liver tumor, MKO_PD1, H3K36ac rep3

description: Library name: MKO_PD1_IP6


title: Liver tumor, MKO_PD1, H3K36ac rep1

description: Library name: MKO_PD1_IP2


title: WT Tconv_2 (RNA-seq)

description:
Library name: WT Tconv_2 (RNA-seq)
Freshly sorted
S04063
rawcount_RNAseq_allsamples2.csv

data_processing:
RNA-seq reads were mapped to mouse reference genome (mm10) using STAR v2.6.1c
RNA-seq reads per gene were counted using --quantMode GeneCounts option in STAR
mm10
Assembly: mm10
Supplementary files format and content: rawcount_RNAseq_allsamples.csv: raw read counts
Supplementary files format and content: rawcount_RNAseq_allsamples2.csv: raw read counts, including additional samples

value: Treg (CD4+hCD2-)


title: Liver tumor, MKO_PD1, H3K36ac rep2

description: Library name: MKO_PD1_IP5


title: Liver tumor, Cre_PD1, Input rep3

description: Library name: Cre_PD1_Input11

value: LysM-Cre


title: DI3_S260_L004_R1_001


title: HCV infected, long RNA, batch 1, rep1

description:
Library name: 6_S1
HCV-long-RNA_diffexpr.csv
HCV-long-RNA_diffpeaks.csv


title: HCV non-infected, long RNA, batch 1, rep1

description:
Library name: 7_S2
HCV-long-RNA_diffexpr.csv
HCV-long-RNA_diffpeaks.csv


title: DC2_S256_L004_R1_001


title: pool-3,well-1,GEX

description:
Library name: XVIR1-POOL-SCG8_GEX
Pool of XVIR1-HS11-SNEGB6,XVIR1-HS15-NCTLB7,XVIR1-HS16-NCTLB2,XVIR1-HS17-SNEGB9,XVIR1-HS19-NCTLB1,XVIR1-HS20-NCTLB6,XVIR1-HS37-NCTLB6,XVIR1-HS4-SNEGB1,XVIR1-HS41-SNEGB4,XVIR1-HS43-SNEGB4,XVIR1-HS44-NCTLB3,XVIR1-HS5-SNEGB4,XVIR1-HS9-SNEGB1


title: pool-3,well-2,GEX

description:
Library name: XVIR1-POOL-SCG9_GEX
Pool of XVIR1-HS11-SNEGB6,XVIR1-HS15-NCTLB7,XVIR1-HS16-NCTLB2,XVIR1-HS17-SNEGB9,XVIR1-HS19-NCTLB1,XVIR1-HS20-NCTLB6,XVIR1-HS37-NCTLB6,XVIR1-HS4-SNEGB1,XVIR1-HS41-SNEGB4,XVIR1-HS43-SNEGB4,XVIR1-HS44-NCTLB3,XVIR1-HS5-SNEGB4,XVIR1-HS9-SNEGB1


title: pool-3,well-1,ADT

description:
Library name: XVIR1-POOL-SCC8_ADT
Pool of XVIR1-HS11-SNEGB6,XVIR1-HS15-NCTLB7,XVIR1-HS16-NCTLB2,XVIR1-HS17-SNEGB9,XVIR1-HS19-NCTLB1,XVIR1-HS20-NCTLB6,XVIR1-HS37-NCTLB6,XVIR1-HS4-SNEGB1,XVIR1-HS41-SNEGB4,XVIR1-HS43-SNEGB4,XVIR1-HS44-NCTLB3,XVIR1-HS5-SNEGB4,XVIR1-HS9-SNEGB1


title: pool-2,well-4,ADT

description:
Library name: XVIR1-POOL-SCC7_ADT
Pool of XVIR1-HS11-SNEGB2,XVIR1-HS14-NCTLB6,XVIR1-HS15-NCTLB1,XVIR1-HS16-NCTLB7,XVIR1-HS17-SNEGB3,XVIR1-HS19-NCTLB5,XVIR1-HS21-NCTLB1,XVIR1-HS37-NCTLB3,XVIR1-HS5-SNEGB3,XVIR1-HS9-SNEGB5


title: HCV infected, long RNA, batch 1, rep3

description:
Library name: WGS805_S3
HCV-long-RNA_diffexpr.csv
HCV-long-RNA_diffpeaks.csv


title: WT Teff_2 (RNA-seq)

description:
Freshly sorted
S06555

value: Teff (CD4+hCD2-CCR7loCD62Llo)


title: WT Tconv_1 (RNA-seq)

description:
Library name: WT Tconv_1 (RNA-seq)
Freshly sorted
S04044
rawcount_RNAseq_allsamples2.csv


title: HCV infected, long RNA, batch 1, rep2

description:
Library name: 8_S3
HCV-long-RNA_diffexpr.csv
HCV-long-RNA_diffpeaks.csv


title: HCV infected, short RNA, rep2

description:
Library name: WGS799_S11
HCV-short-RNA_diffexpr.csv
HCV-short-RNA_diffpeaks.csv


title: pool-2,well-3,ADT

description:
Library name: XVIR1-POOL-SCC6_ADT
Pool of XVIR1-HS11-SNEGB2,XVIR1-HS14-NCTLB6,XVIR1-HS15-NCTLB1,XVIR1-HS16-NCTLB7,XVIR1-HS17-SNEGB3,XVIR1-HS19-NCTLB5,XVIR1-HS21-NCTLB1,XVIR1-HS37-NCTLB3,XVIR1-HS5-SNEGB3,XVIR1-HS9-SNEGB5


title: HCV non-infected, short RNA, rep1

description:
Library name: WGS798_S10
HCV-short-RNA_diffexpr.csv
HCV-short-RNA_diffpeaks.csv


title: pool-2,well-3,GEX

description:
Library name: XVIR1-POOL-SCG6_GEX
Pool of XVIR1-HS11-SNEGB2,XVIR1-HS14-NCTLB6,XVIR1-HS15-NCTLB1,XVIR1-HS16-NCTLB7,XVIR1-HS17-SNEGB3,XVIR1-HS19-NCTLB5,XVIR1-HS21-NCTLB1,XVIR1-HS37-NCTLB3,XVIR1-HS5-SNEGB3,XVIR1-HS9-SNEGB5


title: Liver tumor, Cre_PD1, Input rep2

description: Library name: Cre_PD1_Input10


title: pool-2,well-4,GEX

description:
Library name: XVIR1-POOL-SCG7_GEX
Pool of XVIR1-HS11-SNEGB2,XVIR1-HS14-NCTLB6,XVIR1-HS15-NCTLB1,XVIR1-HS16-NCTLB7,XVIR1-HS17-SNEGB3,XVIR1-HS19-NCTLB5,XVIR1-HS21-NCTLB1,XVIR1-HS37-NCTLB3,XVIR1-HS5-SNEGB3,XVIR1-HS9-SNEGB5


title: HCV non-infected, short RNA, rep2

description:
Library name: WGS800_S12
HCV-short-RNA_diffexpr.csv
HCV-short-RNA_diffpeaks.csv


title: Liver tumor, Cre_PD1, Input rep1

description: Library name: Cre_PD1_Input4


title: pool-2,well-2,ADT

description:
Library name: XVIR1-POOL-SCC5_ADT
Pool of XVIR1-HS11-SNEGB2,XVIR1-HS14-NCTLB6,XVIR1-HS15-NCTLB1,XVIR1-HS16-NCTLB7,XVIR1-HS17-SNEGB3,XVIR1-HS19-NCTLB5,XVIR1-HS21-NCTLB1,XVIR1-HS37-NCTLB3,XVIR1-HS5-SNEGB3,XVIR1-HS9-SNEGB5


title: WT eTreg_2 (RNA-seq)

description:
Freshly sorted
S06552

value: eTreg (CD4+hCD2+CCR7loCD62Llo)


title: WT Tnaive_2 (RNA-seq)

description:
Freshly sorted
S06556

value: Tnaive (CD4+hCD2-CCR7hiCD62LhiCD44lo)


title: WT Teff_1 (RNA-seq)

description:
Freshly sorted
S06549

value: lymph nodes and spleen


title: S_Xnr_24.0

city: Exeter

first: Nick

last: Owens

state: Exeter

address: Barrack Road

country: United Kingdom

institute: University of Exeter Medical School

description: Library name: Sample_S23

data_processing:
Paired end reads were aligned to X. laevis gene models v7.2 by JGI with Bowtie allowing for up to 3 mismatches in seed and leaving the other parameters at the default value. Gene hits was counted using RSEM with default parameters. Expected read counts reported by RSEM are provided in the processed data.
Assembly: X. Laevis 7.2
Supplementary files format and content: tab-delimited files of RSEM expected counts (unnormalised).

organism: Xenopus laevis

source_name: Animal cap

growth_protocol: Xenopus laevis embryos were obtained by mating of frogs primed with human chorionic gonadotrophin (Sigma) or by in vitro fertilisation (Sive, 2000). Jelly membrane was removed with 2% cysteine-HCl, pH 7.8 (Sive, 2000). Embryos were grown in 10% Normal Amphibian Media (NAM) and staged as described.(Sive, 2000). Whole embryos (WE) or explants were cultured until age match control siblings had reached desired stage

extract_protocol:
RNA was extracted using the acid-guanidinium thiocyanate phenol chloroform method (Chomczynski and Sacchi, 1987) and cDNA was synthesised using the RevertAid reverse transcriptase kit (ThermoFisher).
The Xenopus RNA samples were converted to cDNA libraries using a Bioo NextFlex directional v.2 kit and were sequenced at Bristol University’s sequencing facility. The human RNA samples were converted to cDNA libraries using Illumina Truseq stranded mRNA library kit and sequenced at the Genome Research Hub, School of Biosciences, Cardiff University.

value: Animal cap

tag: condition

value: Xnr

tag: time


title: Current smoker, COPD, rep-3

city: Tokyo

first: Keiko

last: Kan-O

address: Kawadacho 8-1, Shinjuku-ku

department: Department of Respiratory Medicine

institute: Tokyo Women's Medical University

description: Library name: Sample8

data_processing:
ATAC libraries were built using ATAC-seq kit (Active Motifs). The resulting readswere aligned using STAR method.
Assembly: hg19
Supplementary files format and content: Bigwig

molecule: other

source_name: Bronchia

extract_protocol: ATAC-seq kit (Active Motifs) were used for library preparation.

treatment_protocol: Primary bronchial epithelial cells were cultured in air/liquid culture conditions for more than 4 weeks.  The patients were classified as never-smoker (healthy) with normal lung function, ex-smokers with COPD, or current smokers with COPD.

value: Bronchia

value: Bronchial epithelial cells

value: Current smoker, COPD


title: Current smoker, COPD, rep-1

description: Library name: Sample6

growth_protocol: Primary bronchial epithelial cells were cultured in air/liquid culture conditions for more than 4 weeks.


title: S_G4D_24.0

description: Library name: Sample_S21


title: pool-2,well-1,GEX

description:
Library name: XVIR1-POOL-SCG4_GEX
Pool of XVIR1-HS11-SNEGB2,XVIR1-HS14-NCTLB6,XVIR1-HS15-NCTLB1,XVIR1-HS16-NCTLB7,XVIR1-HS17-SNEGB3,XVIR1-HS19-NCTLB5,XVIR1-HS21-NCTLB1,XVIR1-HS37-NCTLB3,XVIR1-HS5-SNEGB3,XVIR1-HS9-SNEGB5


title: HCV infected, short RNA, rep1

description:
Library name: WGS797_S9
HCV-short-RNA_diffexpr.csv
HCV-short-RNA_diffpeaks.csv

value: WT

value: HCV infected


title: Liver tumor, Cre_PD1, H3K36ac rep2

description: Library name: Cre_PD1_IP10

value: Liver tumor

value: anti-PD-1 treatment


title: pool-2,well-2,GEX

description:
Library name: XVIR1-POOL-SCG5_GEX
Pool of XVIR1-HS11-SNEGB2,XVIR1-HS14-NCTLB6,XVIR1-HS15-NCTLB1,XVIR1-HS16-NCTLB7,XVIR1-HS17-SNEGB3,XVIR1-HS19-NCTLB5,XVIR1-HS21-NCTLB1,XVIR1-HS37-NCTLB3,XVIR1-HS5-SNEGB3,XVIR1-HS9-SNEGB5

value: PBMC


title: WT Tnaive_1 (RNA-seq)

description:
Freshly sorted
S06550


title: Liver tumor, Cre_PD1, H3K36ac rep3

description: Library name: Cre_PD1_IP11


title: S_AC_24.0

description: Library name: Sample_S19

value: AC


title: pool-2,well-1,ADT

description:
Library name: XVIR1-POOL-SCC4_ADT
Pool of XVIR1-HS11-SNEGB2,XVIR1-HS14-NCTLB6,XVIR1-HS15-NCTLB1,XVIR1-HS16-NCTLB7,XVIR1-HS17-SNEGB3,XVIR1-HS19-NCTLB5,XVIR1-HS21-NCTLB1,XVIR1-HS37-NCTLB3,XVIR1-HS5-SNEGB3,XVIR1-HS9-SNEGB5


title: Current smoker, COPD, rep-2

description: Library name: Sample7


title: WT cTreg_2 (RNA-seq)

description:
Freshly sorted
S06553

value: cTreg (CD4+hCD2+CCR7hiCD62LhiCD44lo)


title: Foxp3R397W Treg_2 (RNA-seq)

description:
Freshly sorted
S04040

value: Treg (CD4+hCD2+GFP-)


title: Liver tumor, Cre_PD1, H3K36ac rep1

description: Library name: Cre_PD1_IP4

value: LysM-Cre


title: pool-1,well-2,GEX

description:
Library name: XVIR1-POOL-SCG3_GEX
Pool of XVIR1-HS14-NCTLB7,XVIR1-HS15-NCTLB2,XVIR1-HS16-NCTLB1,XVIR1-HS19-NCTLB3,XVIR1-HS20-NCTLB4,XVIR1-HS22-NCTLB2,XVIR1-HS3-SNEGB2,XVIR1-HS4-SNEGB2,XVIR1-HS5-SNEGB1,XVIR1-HS6-SNEGB2,XVIR1-HS7-SNEGB4,XVIR1-HS8-SNEGB3


title: WT eTreg_1 (RNA-seq)

description:
Freshly sorted
S06546

value: eTreg (CD4+hCD2+CCR7loCD62Llo)


title: WT cTreg_1 (RNA-seq)

description:
Freshly sorted
S06547


title: Foxp3R397W Treg_1 (RNA-seq)

description:
Freshly sorted
S04039


title: S_G4_24.0

description: Library name: Sample_S20


title: Ex smoker, COPD, rep-2

description: Library name: Sample5

value: Ex smoker, COPD


title: Never smoker, healthy, rep-3

description: Library name: Sample3

value: Never smoker, healthy


title: WT Treg_4 (RNA-seq) (R397W control)

description:
Freshly sorted
S04038

value: lymph nodes and spleen


title: WT Treg_3 (RNA-seq) (R397W control)

description:
Freshly sorted
S04037


title: S_Xnr_7.5

description: Library name: Sample_S17

value: Animal cap

value: Xnr


title: pool-1,well-1,ADT

description:
Library name: XVIR1-POOL-SCC2_ADT
Pool of XVIR1-HS14-NCTLB7,XVIR1-HS15-NCTLB2,XVIR1-HS16-NCTLB1,XVIR1-HS19-NCTLB3,XVIR1-HS20-NCTLB4,XVIR1-HS22-NCTLB2,XVIR1-HS3-SNEGB2,XVIR1-HS4-SNEGB2,XVIR1-HS5-SNEGB1,XVIR1-HS6-SNEGB2,XVIR1-HS7-SNEGB4,XVIR1-HS8-SNEGB3


title: pool-1,well-2,ADT

description:
Library name: XVIR1-POOL-SCC3_ADT
Pool of XVIR1-HS14-NCTLB7,XVIR1-HS15-NCTLB2,XVIR1-HS16-NCTLB1,XVIR1-HS19-NCTLB3,XVIR1-HS20-NCTLB4,XVIR1-HS22-NCTLB2,XVIR1-HS3-SNEGB2,XVIR1-HS4-SNEGB2,XVIR1-HS5-SNEGB1,XVIR1-HS6-SNEGB2,XVIR1-HS7-SNEGB4,XVIR1-HS8-SNEGB3


title: Ex smoker, COPD, rep-1

description: Library name: Sample4

value: Bronchia

value: Bronchial epithelial cells


title: Never smoker, healthy, rep-2

description: Library name: Sample2


title: S_G4D_7.5

description: Library name: Sample_S15


title: Never smoker, healthy, rep-1

description: Library name: Sample1


title: pool-1,well-1,GEX

description:
Library name: XVIR1-POOL-SCG2_GEX
Pool of XVIR1-HS14-NCTLB7,XVIR1-HS15-NCTLB2,XVIR1-HS16-NCTLB1,XVIR1-HS19-NCTLB3,XVIR1-HS20-NCTLB4,XVIR1-HS22-NCTLB2,XVIR1-HS3-SNEGB2,XVIR1-HS4-SNEGB2,XVIR1-HS5-SNEGB1,XVIR1-HS6-SNEGB2,XVIR1-HS7-SNEGB4,XVIR1-HS8-SNEGB3


title: S_AC_7.5

description: Library name: Sample_S13


title: BATFcKO Treg_YFP_2 (RNA-seq)

description:
Freshly sorted
S04867

value: Treg (CD4+YFP+hCD2-)


title: S_G4_7.5

description: Library name: Sample_S14


title: Current smoker, COPD, rep-3

description: Library name: Sample8

data_processing:
RNA libraries were built using NEBNext Ultra II RNA library prep kit for illumina (NEB). The resulting readswere aligned using STAR method.
Assembly: hg19
Supplementary files format and content: txt

extract_protocol:
Total RNA was extracted using Rneasy mini kit followed by manufacturer's instructions (Qiagen).
poly(A) was extracted and RNA libraries were built using NEBNext Ultra II RNA library prep kit for illumina (NEB).

value: Current smoker, COPD


title: S_G4D_5.0

description: Library name: Sample_S09_reseq


title: BATFKO Treg_2 (RNA-seq)

description:
Freshly sorted
S04051

value: Treg (CD4+hCD2+)


title: Cap.area9_tonsil

city: Paris

first: Alba

last: Diaz Herrero

address: 1 Av. Claude Vellefaux, 75010 Paris

country: France

institute: INSERM

data_processing:
Raw sequencing data were processed using the 10X Genomics Space Ranger pipeline
Assembly: GRCh38
Supplementary files format and content: aligned_fiducials.jpeg : aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpeg: image of the tissue and spots
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: tonsil

extract_protocol:
Formalin-fixed paraffin-embedded (FFPE) tissue sections are placed onto a Visium gene expression slide
Spatial transcriptome sequecing libraries were prepared with 10X Genomics Visium Spatial Gene Expression Slides and Reagent kit following corresponding User Guides

value: tonsil


title: BATFcKO Treg_YFP_1 (RNA-seq)

description:
Freshly sorted
S04863


title: S_Xnr_5.0

description: Library name: Sample_S11_reseq


title: Cap.area7_DLBCL

source_name: DLBCL resection

value: DLBCL resection


title: Cap.area8_LN

source_name: lymph node

value: lymph node


title: Current smoker, COPD, rep-1

description: Library name: Sample6


title: Current smoker, COPD, rep-2

description: Library name: Sample7


title: Cap.area6_DLBCL


title: WT Treg_YFP_2 (RNA-seq)

description:
Freshly sorted
S04865


title: BATFKO Treg_1 (RNA-seq)

description:
Freshly sorted
S04042


title: S_G4_5.0

description: Library name: Sample_S08_reseq


title: Ex smoker, COPD, rep-2

description: Library name: Sample5


title: S_AC_5.0

description: Library name: Sample_S07_reseq

value: AC


title: Cap.area5_DLBCL

source_name: DLBCL biopsies

value: DLBCL biopsies


title: Ex smoker, COPD, rep-1

description: Library name: Sample4


title: S_Xnr_2.5

description: Library name: Sample_S05


title: WT Treg_YFP_1 (RNA-seq)

description:
Freshly sorted
S04861


title: WT Treg_2 (RNA-seq)

description:
Freshly sorted
S04050


title: Cap.area3_DLBCL


title: Never smoker, healthy, rep-2

description: Library name: Sample2


title: Never smoker, healthy, rep-1

description: Library name: Sample1


title: S_AC_2.5

description: Library name: Sample_S01


title: Never smoker, healthy, rep-3

description: Library name: Sample3


title: Cap.area2_tonsil


title: S_G4_2.5

description: Library name: Sample_S02


title: WT Treg_1 (RNA-seq)

description:
Freshly sorted
S04041


title: Cap.area4_DLBCL


title: Cap.area1_LN


title: Müllerian duct cells, E11.0, female, right Müllerian duct only, CellPlex

status: Public on Apr 28 2026

city: Clayton

first: Monash

middle: Bioinformatics

last: Platform

state: VIC

address: Wellington Road

country: Australia

institute: Monash Genomics & Bioinformatics Platform

description: Library name: E11.0_female_right_duct_CellPlex

data_processing:
The raw data was processed with using cellranger multi (cellranger version 8.0.1). It was aligned against the Ensembl Gallus gallus reference genome (Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.112) and demultiplexed with CMOs (CMO301-CMO312).
The data was then loaded into R for quality control. The isOutlier function from the scran package was used to determine outlier thresholds for each demultiplexed sample for the following metrics: the number of detected genes, the number of UMIs and the percentage of UMIs to mitochondrial genes. Doublet detection was run using the scDblFinder package.
The dataset was filtered to remove outlier cells and doublets. It was then proccessed through the standard Seurat analysis workflow. 15 principal components were used for dimensionality reduction and a resolution of 0.8 was used for clustering. The FindAllMarkers function from Seurat was used to calculate cluster markers with the ROC test used.
The data was re-processed in Scanpy using a subset of MDM cell populations. Pseudotime analysis was performed using Palantir and cluster 17 (from the Seurat anaylsis) was selected as the starting cell population.
Assembly: Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.112
Supplementary files format and content: CellRanger output files: mRNA_barcodes.tsv.gz, mRNA_features.tsv.gz, mRNA_matrix.mtx.gz

organism: Gallus gallus

source_name: Mullerian duct

extract_protocol:
The Müllerian duct tissues were dissociated by adding 300µL of 0.25% Trypsin-EDTA to each tube, and incubating at 37°C for 18 minutes, shaking at 750RPM. The digestion was stopped with 75µL of neat Fetal Calf Serum (FCS). The dissociated cells were filtered by loading onto 35µm Cell Strainer FACS tubes. The strainer was washed twice by adding 200µL 10% FCS in PBS, and centrifuging at 600G, room temperature, for 1 minute. The cells were pelleted by spinning at 600G, room temperature for 3 minutes. The 10% FCS in PBS was removed, and the cells were resuspended in 1mL 0.04% BSA in PBS. The cells were spun at 400G, room temperature, for 5 minutes. The following CMOs (10X Genomics) were used to label three technical replicates for each sample: E6.5 Mixed Sex (CMO 304-306), E8.5 Female (CMO 307-309), E8.5 Male (CMO 310-312), E11.0 Female left duct (CMO 301-303), E11.0 Female right duct (CMO 304-306 for whole ducts, CMO 307 for duct tips). The CMO labelling protocol was carried out in accordance with the manufacturer’s instructions (10X Genomics document CG000391 Revision B). Each technical replicate was resuspended in 100µL CMO and incubated for 5 mins at room temperature. Following CMO labelling, the dissociated cells were washed three times in 1% BSA in PBS, on ice. Each technical replicate was diluted to 1000 cells/µL and determined to be of >95% viability using trypan blue staining and the Countess 3 Cell Counter. Each technical replicate was pooled in equal proportions into a single sample.
For each sample, 16,500 cells at 1000 cells/µL were loaded to obtain a targeted recovery of 10,000 cells post-sequencing. Single-cell analysis was carried out using the 10X Genomics Chromium Controller and Chromium Single Cell 3′ Library & Gel Bead Kit V3.1, as per the manufacturer’s instructions (10X Genomics document CG000388 Revision D). Samples were subjected to 11 cycles of PCR for cDNA amplification and 13/14 cycles for library amplification. Completed libraries were pooled in an equimolar ratio along with a 5% PhilX Control Library V3, per the manufacturer’s instructions (Illumina document 15048776 V11). The prepared libraries were sequenced using an Illumina Novaseq at Azenta Life Sciences, using SBS chemistry, in paired-end (PE)-150 configuration, targeting 20,000 read pairs per cell for gene expression libraries and 5000 read pairs per cell for Cell Multiplexing libraries.

value: Mullerian duct

value: WT

value: mixed sample (E11.0 female right whole duct replicate 1, EE11.0 female right whole duct replicate 2, E11.0 female right duct whole replicate 3, E11.0 female right duct tip replicate 1)

tag: library type

value: CMO

tag: cmo

value: CMO304 (E11.0 female right whole duct replicate 1), CMO305 (E11.0 female right whole duct replicate 2), CMO306 (E11.0 female right whole duct replicate 3), CMO307(E11.0 female right tip duct replicate 1)


title: Müllerian duct cells, E8.5, male, CellPlex

description: Library name: E8.5_male_CellPlex

value: mixed sample (E8.5 male replicate 1, E8.5 male replicate 2, E8.5 male replicate 3)

value: CMO310 (E8.5 male replicate 1), CMO311 (E8.5 male replicate 2), CMO312 (E8.5 male replicate 3)


title: Müllerian duct cells, E8.5, female, CellPlex

description: Library name: E8.5_female_CellPlex

value: mixed sample (E8.5 female replicate 1, E8.5 female replicate 2, E8.5 female replicate 3)

value: CMO307 (E8.5 female replicate 1), CMO308 (E8.5 female replicate 2), CMO309 (E8.5 female replicate 3)


title: Müllerian duct cells, E11.0, female, left Müllerian duct only, CellPlex

description: Library name: E11.0_female_left_duct_CellPlex

value: mixed sample (E11.0 female left duct replicate 1, EE11.0 female left duct replicate 2, E11.0 female left duct replicate 3)

value: CMO301 (E11.0 female left duct replicate 1), CMO302 (E11.0 female left duct replicate 2), CMO303 (E11.0 female left duct replicate 3)


title: DM_15D

city: Chicago

first: Andrius

last: Kazlauskas

state: IL

address: 1905 W Taylor St

department: Department of Ophthalmology and Visual Sciences

institute: University of Illinois at Chicago

description:
Library name: sample 4
10x Genomics

data_processing:
The fastq files were demultiplexed and aligned to Mus musculus genome assembly GRCm38 (mm10/ Ensembl98) using cellranger-7.0.1.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Retina

extract_protocol:
Eyeballs were enucleated, and the retinas were carefully dissected. For single-cell RNA sequencing (scRNA-Seq), the dissected retinal samples were prepared following the 10X Genomics guidelines (#1000414, CG000553, 10X Genomics). In brief, the retinal tissue, separated from the choroid and retinal pigment epithelium (RPE) layer, was fixed in fixation buffer for 24 hours. Following fixation, the retinal tissue was dissociated into a single-cell suspension using dissociation buffer for 20 minutes. The resulting suspension was filtered through a 40 μm strainer to ensure a single-cell population.
The samples were processed following the user Guide (CG000691, 10x Genomics) for Chromium Fixed RNA Profiling assay using the Chromium X (10x Genomics). Briefly, between 4,000 and 10,000 cells from the retinal single-cell suspension were captured for each condition after hybridization with Mouse WTA Probes. Libraries were made, checked using High Sensitivity D5000 ScreenTape and the TapeStation 4150 (Agilent), quantified using KAPA library quantification kit, and sequenced into a 10B lane NovaSeq X Plus (Illumina).

treatment_protocol: Diabetes was induced in eight-week-old male C57BL/6J mice (Jax #000664, Jackson Laboratory, Bar Harbor, ME, USA) by administering five consecutive daily intraperitoneal injections of streptozotocin (60 mg/kg/day) (S0130, Sigma-Aldrich, Burlington, MA, USA) in 47 mM sodium citrate (pH 4.5). Age-matched non-diabetic (non-DM) control mice received an equivalent volume of citrate buffer. Fasting blood glucose levels were measured two days after the final streptozotocin dose. Mice that had a fasting blood glucose level exceeding 250 mg/dL at this time point, which they maintained for 5 days or 15 days, were considered diabetic.

value: Retinal cells

value: Retina

tag: age

value: 8- week old

tag: Sex

value: Male

value: STZ induced diabetes


title: Control _5D

description:
Library name: sample 1
10x Genomics

value: Control


title: Müllerian duct cells, E8.5, male, GEX

description: Library name: E8.5_male_GEX

value: Mullerian duct

value: mRNA


title: Control_15D

description:
Library name: sample 2
10x Genomics


title: Müllerian duct cells, E8.5, female, GEX

description: Library name: E8.5_female_GEX

value: WT


title: Müllerian duct cells embryonic day (E) 6.5, male and female, GEX

description: Library name: E6.5_mixed_sex_GEX

value: mixed sample (E4.5 replicate 1, E4.5 replicate 2, E4.5 replicate 3)


title: dorsal trachea, control group

city: Shanghai

first: Wendong

last: Weng

address: No.320, Yueyang Rd.

institute: Center for Excellence in Molecular Cell Science

description:
Library name: Ctrl_D
10X Genomics

data_processing:
The demultiplxing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v10.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-what-is-cell-ranger)
Assembly: Mouse GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: dorsal trachea

extract_protocol:
Tracheal cells were dissociated using a papain-based enzymatic digestion protocol. For whole-trachea cell isolation, each trachea was longitudinally bisected and further cut into pieces, then incubated in papain dissociation solution (Worthington) prepared in EBSS (5 mL per three tracheae) supplemented with DNase I. Samples were incubated at 37 °C for 45 minutes. Following digestion, tissues were mechanically triturated to release single cells, filtered through a 100-µm cell strainer, and centrifuged at 500 × g for 5 minutes at 4 °C. Cell pellets were resuspended in EBSS containing ovo-mucoid protease inhibitor and DNase I and incubated on a rotating platform at 4 °C for 20 minutes to quench residual papain activity. Cells were then subjected to red blood cell lysis, washed, collected by centrifugation.
scRNA-seq libraries were generated according to the manufacturer’s instructions using the Chromium GEM-X Single Cell 5′ v3 Gene Expression platform (10x Genomics). Briefly, single-cell suspensions were resuspended in the master mix and loaded together with gel beads and partitioning oil into a Chromium chip to generate Gel Beads-in-Emulsion (GEMs).Polyadenylated RNA transcripts from individual cells were reverse-transcribed into cDNA incorporating Illumina read 1 sequences, a cell barcode, and a unique molecular identifier (UMI). After GEM recovery, cDNA was amplified by PCR, and amplified products were purified using Silane Dynabeads. Size selection was performed using SPRIselect reagent to obtain appropriately sized fragments for library construction. During library preparation, Illumina R2 sequences, P5 and P7 adapters, and sample indices were added.

treatment_protocol: Tamoxifen induction and conditional gene knockout

value: dorsal trachea

value: tamoxifen

value: P63-CreER; Ki67-lsl-Dre; Rosa26-rsr-GFP; Ctnnb1-fl/+


title: Müllerian duct cells, E11.0, female, left Müllerian duct only, GEX

description: Library name: E11.0_female_left_duct_GEX


title: ventral trachea, Ctnnb1 KO in P63+ basal cells

description:
Library name: KO_V
10X Genomics

source_name: ventral trachea

value: ventral trachea

value: tamoxifen with Ctnnb1 KO

value: P63-CreER; Ki67-lsl-Dre; Rosa26-rsr-GFP; Ctnnb1-fl/fl


title: Müllerian duct cells, E11.0, female, right Müllerian duct only, GEX

description: Library name: E11.0_female_right_duct_GEX

value: mixed sample (E11.0 female right duct tip only replicate 1, E11.0 female right whole duct replicate 1, EE11.0 female right whole duct replicate 2, E11.0 female right duct whole replicate 3)


title: TGFB1_KO Rep 3

city: Piscataway

first: Michael

last: Verzi

state: NJ

address: 145 Bevier Road,

department: Department of Genetics

institute: Rutgers University

description:
Library name: Sample 12
TGFB1_KO_123

data_processing:
Alignment: RNA-seq: Kallisto v0.46.1
RNA-seq Transcript Import: tximport 1.28.0
DESeq2 1.40.1
Assembly: RefSeq mm9
Supplementary files format and content: RNA-Seq: FPKM table outputted by DESeq2 for fragment counts normalized per kilobase of feature length per million mapped fragments

source_name: Mesenchyme

extract_protocol:
QIAGEN RNeasy Micro Kit
Library preparation was performed by Novogene. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: Mesenchyme


title: Mullerian duct cells E6.5, male and female, CellPlex

description: Library name: E6.5_mixed_sex_CellPlex

value: CMO

value: CMO304 (E6.5 mixed replicate 1), CMO305 (E6.5 mixed replicate 2), CMO306 (E6.5 mixed replicate 3)


title: dorsal trachea, Ctnnb1 KO in P63+ basal cells

description:
Library name: KO_D
10X Genomics


title: ventral trachea, control group

description:
Library name: Ctrl_V
10X Genomics


title: Vehicle_Tgfbr2KO Rep 1

description:
Library name: Sample 7
V_KO_31


title: Vehicle_Tgfbr2KO Rep 3

description:
Library name: Sample 9
V_KO_123


title: TGFB1_KO Rep 2

description:
Library name: Sample 11
TGFB1_KO_121


title: TGFB1_KO Rep 1

description:
Library name: Sample 10
TGFB1_KO_31


title: Vehicle_Tgfbr2KO Rep 2

description:
Library name: Sample 8
V_KO_121


title: TGFB1 Rep 2

description:
Library name: Sample 5
TGFB1_121


title: TGFB1 Rep 3

description:
Library name: Sample 6
TGFB1_123


title: Vehicle Rep 2

description:
Library name: Sample 2
V_121


title: DM_5D

description:
Library name: sample 3
10x Genomics

value: Retinal cells

value: Retina

value: 8- week old

value: Male


title: Mesenchyme_only_Control Rep 1

description:
Library name: Sample 1
cocultureCONTROL

data_processing:
Alignment: RNA-seq: Kallisto v0.46.1
RNA-seq Transcript Import: tximport 1.28.0
DESeq2 1.40.1
Assembly: RefSeq mm9
Supplementary files format and content: RNA-Seq: FPKM table outputted by DESeq2 for fragment counts normalized per kilobase of feature length per million mapped fragments
Supplementary files format and content: Results table outputted by DESeq2 that extracts Log2FC values, p values, adjusted p values, baseMean values, and test statistic values.

source_name: Control Rep 1


title: TGFB1 Rep 1

description:
Library name: Sample 4
TGFB1_31


title: Cdx2het_Bcathet_Day9

description:
Library name: Sample 8
755_DAY9_EXON3

source_name: Epithelium

value: Epithelium

value: Day 9

value: paired-end


title: Coculture_BcatGOF Rep 1

description:
Library name: Sample 7
cocultureMUTANT

source_name: Mutant Rep 1


title: Bcathet_Day8

description:
Library name: Sample 4
754_DAY8_CDX2HET_EXON3

value: Day 8


title: Control_Day8

description:
Library name: Sample 1
691_DAY8_CONTROL


title: Control_Day9

description:
Library name: Sample 2
701_DAY9_CONTROL


title: Bcathet_Day9

description:
Library name: Sample 5
759_DAY9_CDX2HET_EXON3


title: Coculture_Wildtype Rep 2

description:
Library name: Sample 5
MIX_CC_WildType

source_name: Wildtype Rep 2


title: Coculture_Wildtype Rep 3

description:
Library name: Sample 6
889_468WildType

source_name: Wildtype Rep 3


title: Vehicle Rep 1

description:
Library name: Sample 1
V_31


title: Cdx2het_Bcathet_Day10

description:
Library name: Sample 9
756_DAY10_EXON3

value: Day 10


title: Vehicle Rep 3

description:
Library name: Sample 3
V_123


title: S_G4D_2.5

description: Library name: Sample_S03

value: Animal cap


title: Bcathet_Day10

description:
Library name: Sample 6
757_DAY10_CDX2HET_EXON3


title: Coculture_Wildtype Rep 1

description:
Library name: Sample 4
cocultureWILDTYPE

source_name: Wildtype Rep 1


title: Control_Day10

description:
Library name: Sample 3
693_DAY10_CONTROL


title: Cdx2het_Bcathet_Day8

description:
Library name: Sample 7
761_DAY8_EXON3


title: Control Rep 1

description: Library name: Sample 3


title: β-cateninGOF/+ Rep 1

description: Library name: Sample 1


title: Mesenchyme_only_Control Rep 2

description:
Library name: Sample 2
MIX_CC_control

source_name: Control Rep 2


title: Control Rep 3

description: Library name: Sample 6


title: Coculture_BcatGOF Rep 2

description:
Library name: Sample 8
MIX_CC_Mutant

source_name: Mutant Rep 2


title: LUAD_P10, lung adenocarcinoma, Stereo-XCR-seq

city: Shenzhen

first: Zhong

last: Liu

address: 9 Yunhua Road, Meisha Street, Yantian District

institute: BGI

description:
Library name: LUAD_P10
Stereo-XCR-seq spatial transcriptomics data of LUAD patient P10

data_processing:
Raw sequencing reads were processed, quality-filtered, and aligned to the human reference genome. UMI-based counting was applied for gene expression quantification, and expression matrices were normalized for downstream analysis.
Spatial coordinates and gene expression matrices were integrated and stored in H5AD format for downstream analysis.
Assembly: GRCh38/hg38
Supplementary files format and content: H5AD (Hierarchical Data Format 5 with AnnData structure) containing normalized gene expression matrices, spatial coordinates, and metadata for each sample.
Library strategy: Spatial Transcriptomics

source_name: lung

extract_protocol:
Fresh frozen tissue sections were mounted on Stereo-seq chips, fixed, and permeabilized to release mRNA, which was captured by spatially barcoded probes. In situ reverse transcription was then performed to synthesize barcoded cDNA.
Stereo-seq cDNA library was generated by in situ reverse transcription on the chip, followed by standard library construction and sequencing. The Stereo-XCR-seq library was further obtained through enrichment of T/B cell receptor transcripts via circularization and sscirPCR.

value: lung


title: LUAD_P9, lung adenocarcinoma, Stereo-XCR-seq

description:
Library name: LUAD_P9
Stereo-XCR-seq spatial transcriptomics data of LUAD patient P9


title: Control Rep 2

description: Library name: Sample 5


title: Mesenchyme_only_Control Rep 3

description:
Library name: Sample 3
889

source_name: Control Rep 3


title: β-cateninGOF/+ Rep 3

description: Library name: Sample 4


title: LUAD_P11, lung adenocarcinoma, Stereo-XCR-seq

description:
Library name: LUAD_P11
Stereo-XCR-seq spatial transcriptomics data of LUAD patient P11


title: LUAD_P7, lung adenocarcinoma, Stereo-XCR-seq

description:
Library name: LUAD_P7
Stereo-XCR-seq spatial transcriptomics data of LUAD patient P7


title: LUAD_P6, lung adenocarcinoma, Stereo-XCR-seq

description:
Library name: LUAD_P6
Stereo-XCR-seq spatial transcriptomics data of LUAD patient P6


title: human-chimp hybrids 3 rep3

city: Rehovot

first: Simon

last: Fishilevich

address: 234 Herzl St

country: Israel

institute: Weizmann Institute of Science

description: Library name: HC3-3

data_processing:
Remove sequencing adapters with SeqPrep
Map reads to reference genomes with STAR
Remove duplicate reads with Picard
Remove reads which exhibit mapping bias with WASP (Hornet)
Count allele specific and total reads
Assembly: human:GRCh38; chimp: PanTro6; Gorilla: gorGor6
Supplementary files format and content: Read counts aligned to GRCh38 per gene per sample, aligned to human variants (human_counts), chimp or gorilla variants (chimp_counts or gorilla_counts), no variants (no_ase_counts) and ambiguous calls (ambig_ase_counts).

organism:
Pan troglodytes
Homo sapiens

source_name: iPSC-derived limb osteochondral progenitor cells

extract_protocol:
Qiagen Rneasy Mini Kit with on-column DNAse digestion (Qiagen)
Illumina TruSeq Stranded mRNA library prep kit (Illumina)


title: human-chimp hybrids 2 rep1

description: Library name: HC2-1

value: iPSC-derived limb osteochondral progenitor cells


title: LUAD_P8, lung adenocarcinoma, Stereo-XCR-seq

description:
Library name: LUAD_P8
Stereo-XCR-seq spatial transcriptomics data of LUAD patient P8


title: msgn1 overexpression, rep3

city: New Haven

first: Miriam

last: Genuth

state: CT

address: 260 Whitney Ave

department: Molecular Cell and Developmental Biology

institute: Yale University

description:
Library name: msgn1OE_3
column name in genecountmatrix: msgn1_rep3

data_processing:
Low quality reads were trimmed, and adaptor contamination was removed using Trim Galore (v0.5.0). Trimmed reads were mapped to the zebrafish reference genome (GRCz11) using HISAT2 (v2.1.0)
Assembly: GRCz11
Supplementary files format and content: csv file of raw gene counts for each replicate

source_name: tailbud

extract_protocol:
RNA was extracted with trizol.
library was created using the Watchmaker mRNA Library Prep Kit

treatment_protocol: Embryos were heatshocked at 28 degrees for 30 minutes at the 2-3 somite stage and then allowed to recover for 3 hours. The tailbud was obtained from 10 embryos per replicate by cutting immediately posterior to the last formed somite.

value: tailbud

value: heat shock


title: human-chimp hybrids 1 rep1

description: Library name: HC1-1


title: LUAD_P5, lung adenocarcinoma, Stereo-XCR-seq

description:
Library name: LUAD_P5
Stereo-XCR-seq spatial transcriptomics data of LUAD patient P5


title: β-cateninGOF/+ Rep 2

description: Library name: Sample 2


title: LUAD_P1, lung adenocarcinoma, Stereo-XCR-seq

description:
Library name: LUAD_P1
Stereo-XCR-seq spatial transcriptomics data of LUAD patient P1


title: human-chimp hybrids 2 rep2

description: Library name: HC2-2


title: human-chimp hybrids 3 rep2

description: Library name: HC3-2


title: wildtype, rep2

description:
Library name: wt_2
column name in genecountmatrix.csv: wt_rep2

value: wildtype


title: LUAD_P4, lung adenocarcinoma, Stereo-XCR-seq

description:
Library name: LUAD_P4
Stereo-XCR-seq spatial transcriptomics data of LUAD patient P4


title: msgn1 overexpression, rep1

description:
Library name: msgn1OE_1
column name in genecountmatrix: msgn1_rep1


title: LUAD_P3, lung adenocarcinoma, Stereo-XCR-seq

description:
Library name: LUAD_P3
Stereo-XCR-seq spatial transcriptomics data of LUAD patient P3


title: LUAD_P2, lung adenocarcinoma, Stereo-XCR-seq

description:
Library name: LUAD_P2
Stereo-XCR-seq spatial transcriptomics data of LUAD patient P2


title: msgn1 overexpression, rep2

description:
Library name: msgn1OE_2
column name in genecountmatrix: msgn1_rep2


title: tbx16 overexpression, rep 1

description:
Library name: tbx16OE_1
column name in genecountmatrix: tbx16_rep1


title: human-gorilla hybrids 2 rep3

description: Library name: hg2-3

organism:
Gorilla gorilla
Homo sapiens


title: human-gorilla hybrids 1 rep2

description: Library name: hg1-2


title: human-gorilla hybrids 2 rep1

description: Library name: hg2-1


title: wildtype, rep3

description:
Library name: wt_3
column name in genecountmatrix.csv: wt_rep3


title: wildtype, rep1

description:
Library name: wt_1
column name in genecountmatrix.csv: wt_rep1


title: Head regenerating tip, 23hpa, repA

city: Basel

first: Panagiotis

last: Papasaikas

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute

description: Library name: 1984F47_23A

data_processing:
Reads were aligned against the NCBI Hydra vulgaris NCBI  high contiguity assembly Hydra_vulgaris_105_v3  (GCF_022113875.1) using the STAR software (v2.7.10a). Command prototype: STAR --genomeDir INDEXDIR --sjdbGTFfile GTF --readFilesIn fqpath --outSJfilterReads Unique --outFilterType BySJout --outFilterMultimapNmax 5 --alignSJoverhangMin 8 --alignSJDBoverhangMin 4 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate --seedSearchStartLmax 50  --quantMode GeneCounts --sjdbGTFtagExonParentTranscript transcript_id --sjdbGTFtagExonParentGene gene_id --genomeChrBinNbits 12 --genomeSAsparseD 2
Genes were quantified using the STAR software (v2.7.10a) GeneCounts quantification mode (--quantMode).
Assembly: NCBI Hydra vulgaris Release Hydra_vulgaris_105_v3  (GCF_022113875.1)
Supplementary files format and content: tab-delimited file with raw (not normalized) counts for each biological sample (96 columns) and Hydra gene feature (28608 rows).

organism: Hydra vulgaris

source_name: Whole tissue

growth_protocol: Animals are maintained in Hydra medium solution [1 mM CaCl2, 0.2 mM NaHCO3, 0.02 mM KCl, 0.02 mM MgCl2, and 0.2 mM tris-HCl (pH 7.4)] at 18°C and fed three times per week with freshly hatched Artemia nauplii.

extract_protocol:
RNA was purified using the Norgen Biotek Single Cell RNA Purification kit according to the manufacturer's protocol. RNA quality was assessed using an Agilent Bioanalyzer.
5ng of RNA was used as input to generate RNA sequencing libraries using SmartSeq2 .

treatment_protocol: We bisected Hydras and collected samples from the oral end of regenerating Hydras at one-hour intervals over a 48-hour period.

value: Whole tissue

tag: time after_bisection

value: 23 hours


title: tbx16 overexpression, rep 2

description:
Library name: tbx16OE_2
column name in genecountmatrix: tbx16_rep2


title: human-gorilla hybrids 1 rep1

description: Library name: hg1-1


title: Head regenerating tip, 23hpa, repB

description: Library name: 1984F48_23B


title: human-chimp hybrids 1 rep2

description: Library name: HC1-2


title: Head regenerating tip, 22hpa, repA

description: Library name: 1984F43_22A

value: 22 hours


title: Head regenerating tip, 21hpa, repA

description: Library name: 1984F39_21A

value: 21 hours


title: Head regenerating tip, 11hpa, repA

description: Library name: 1984F45_11A

value: 11 hours


title: Head regenerating tip, 22hpa, repB

description: Library name: 1984F44_22B


title: tbx16 overexpression, rep3

description:
Library name: tbx16OE_3
column name in genecountmatrix: tbx16_rep3


title: Head regenerating tip, 21hpa, repB

description: Library name: 1984F40_21B


title: Head regenerating tip, 9hpa, repB

description: Library name: 1984F38_9B

value: 9 hours


title: Head regenerating tip, 11hpa, repB

description: Library name: 1984F46_11B


title: Head regenerating tip, 10hpa, repA

description: Library name: 1984F41_10A

value: 10 hours


title: Head regenerating tip, 8hpa, repA

description: Library name: 1984F33_8A

value: 8 hours


title: Head regenerating tip, 19hpa, repB

description: Library name: 1984F32_19B

value: 19 hours


title: Head regenerating tip, 9hpa, repA

description: Library name: 1984F37_9A


title: Head regenerating tip, 20hpa, repA

description: Library name: 1984F35_20A

value: 20 hours


title: Head regenerating tip, 10hpa, repB

description: Library name: 1984F42_10B


title: Head regenerating tip, 8hpa, repB

description: Library name: 1984F34_8B


title: Head regenerating tip, 7hpa, repA

description: Library name: 1984F29_7A

value: 7 hours


title: Head regenerating tip, 7hpa, repB

description: Library name: 1984F30_7B


title: Head regenerating tip, 19hpa, repA

description: Library name: 1984F31_19A


title: Head regenerating tip, 18hpa, repB

description: Library name: 1984F28_18B

value: 18 hours


title: Head regenerating tip, 6hpa, repB

description: Library name: 1984F26_6B

value: 6 hours


title: Head regenerating tip, 17hpa, repB

description: Library name: 1984F24_17B

value: 17 hours


title: Head regenerating tip, 18hpa, repA

description: Library name: 1984F27_18A


title: Head regenerating tip, 5hpa, repA

description: Library name: 1984F21_5A

value: 5 hours


title: Head regenerating tip, 6hpa, repA

description: Library name: 1984F25_6A


title: Head regenerating tip, 16hpa, repA

description: Library name: 1984F19_16A

value: 16 hours


title: Head regenerating tip, 4hpa, repA

description: Library name: 1984F17_4A

value: 4 hours


title: Head regenerating tip, 20hpa, repB

description: Library name: 1984F36_20B

value: Whole tissue


title: Head regenerating tip, 16hpa, repB

description: Library name: 1984F20_16B


title: Head regenerating tip, 4hpa, repB

description: Library name: 1984F18_4B


title: Head regenerating tip, 5hpa, repB

description: Library name: 1984F22_5B


title: Head regenerating tip, 17hpa, repA

description: Library name: 1984F23_17A


title: Head regenerating tip, 2hpa, repB

description: Library name: 1984F10_2B

value: 2 hours


title: Head regenerating tip, 2hpa, repA

description: Library name: 1984F9_2A


title: Head regenerating tip, 15hpa, repA

description: Library name: 1984F15_15A

value: 15 hours


title: Head regenerating tip, 3hpa, repA

description: Library name: 1984F13_3A

value: 3 hours


title: Head regenerating tip, 3hpa, repB

description: Library name: 1984F14_3B


title: Head regenerating tip, 13hpa, repA

description: Library name: 1984F7_13A

value: 13 hours


title: Head regenerating tip, 13hpa, repB

description: Library name: 1984F8_13B


title: Head regenerating tip, 15hpa, repB

description: Library name: 1984F16_15B


title: Head regenerating tip, 1hpa, repA

description: Library name: 1984F5_1A

value: 1 hour


title: Head regenerating tip, 1hpa, repB

description: Library name: 1984F6_1B


title: Head regenerating tip, 14hpa, repA

description: Library name: 1984F11_14A

value: 14 hours


title: Head regenerating tip, 0hpa, repB

description: Library name: 1984F2_0B

value: 0 hour


title: Head regenerating tip, 14hpa, repB

description: Library name: 1984F12_14B


title: Head regenerating tip, 12hpa, repA

description: Library name: 1984F3_12A

value: 12 hours


title: Head regenerating tip, 0hpa, repA

description: Library name: 1984F1_0A


title: Head regenerating tip, 12hpa, repB

description: Library name: 1984F4_12B


title: Colon, W6, Immune fraction, Feature barcodes

city: Stockholm

first: Jennifer

last: Fransson

address: Karolinska Institutet

country: Sweden

institute: Karolinska Institutet

data_processing:
Reads were analyzed using CellRanger v 6.0.2 (10X Genomics). The first run did not capture the feature barcodes of some samples due to a mistake, for which reason .tsv-files containing the feature barcode counts for those samples.
Gene expression matrices were analyzed using the Seurat 4.1.1 pipeline
Assembly: mm10
Supplementary files format and content: .h5-files for each sample and .tsv-files with feature barcode counts for some samples.

source_name: colon

extract_protocol:
Colonic cells were isolated as previously described with minor alterations (Villablanca et al., 2011). Briefly, colonic tissue was cleaned from fat, opened longitudinally and cut into 1 cm pieces. Tissues from mice from the same treatment group and time point were pooled. Tissues were incubated for 30 min at 37 °C in 20 ml HBSS with 5% FCS, 5 mM EDTA, 1 mM DTT and 15 mM HEPES while shaking gently. The epithelium-enriched supernatant was then filtered through a 100 µm strainer, washed in PBS with 5% FCS and 1 mM EDTA, and cells were recovered at the interface of a 44-67% Percoll gradient. The remaining tissue was washed twice in PBS and digested in 10 ml of serum-free HBSS with Liberase TL (0.15 mg/ml, Roche) and 0.1 mg/ml DNase I (Roche) at 37 °C at 600 rpm for 60 min. After filtration through a 100 μm cell strainer, lamina propria-enriched cells were washed with PBS with 5% FCS and 1 mM EDTA and separated on a 44-67% Percoll gradient. Both epithelium-enriched and lamina propria-enriched fractions were stained with TER-119 Pacific Blue, CD45.2 PE/Cyanine7 and EpCAM FITC surface antibodies (BioLegend) for cell type assignment. Cells from the lamina propria were additionally labeled with TotalSeq antibodies (BioLegend) targeting CD90.2, CD3, CD4, KLRG1, CD127, Ly-6C, CD64, CD11b, CD11c, CD103 and Ly-6G according to manufacturer’s instructions. After additional staining with DAPI for live/dead cell identification, cells were sorted using Sony SH800 Cell Sorter into 15mL tubes filled with complete RPMI medium with 10% FCS. Epithelial cells were sorted from the epithelium-enriched fraction by gating EpCAM+/CD45- cells. Immune and stromal cells were sorted from the lamina propria-enriched fraction, by gating EpCAM-/CD45+ and EpCAM-/CD45- cells, respectively. Approximately 16000 cells per sample were loaded onto the 10X Genomics Chromium Controller and processed with the Chromium Next GEM Single Cell 3ʹ v3.1 (Dual Index) with Feature Barcode technology for Cell Surface Protein (10X Genomics).
Libraries were constructed following the manufacturer’s guidelines (Chromium Next GEM Single Cell 3ʹ v3.1 (Dual Index) with Feature Barcode technology for Cell Surface Protein (10X Genomics)), with TotalSeq-derived barcodes being retained only for the immune cell fractions.
Sequencing was performed by Novogene Co. Ltd (UK) (Rag2-/- samples) or NGI Sweden (SCID samples) on NovaSeq 6000 sequencers with a targeted sequencing depth of 300M reads per gene expression sample and 50M reads per TotalSeq-derived sample. Read length was PE150 (Novogene) or 28-10-10-150 for gene expression samples and 28-10-10-25 (NGI) for TotalSeq-derived samples.

value: colon

value: Immune

value: SCID

value: CD45RBhi transfer

value: no


title: Colon, W7, Immune fraction, Feature barcodes


title: Colon, W2, Immune fraction, Feature barcodes


title: Colon, W3, Immune fraction, Feature barcodes


title: Colon, W0, Immune fraction, Feature barcodes


title: Colon, W5, Immune fraction, Feature barcodes


title: Colon, W1, Immune fraction, Feature barcodes


title: Colon, D60, Immune fraction, Feature barcodes

value: Rag2 KO


title: Colon, D20, Immune fraction, Feature barcodes


title: Colon, D40, Immune fraction, Feature barcodes


title: Colon, D0, Immune fraction, Feature barcodes


title: Colon, D50, Immune fraction, Feature barcodes


title: Colon, D60, Immune fraction, gene expression


title: Colon, W4, Immune fraction, Feature barcodes


title: Colon, D60, Epithelial fraction, gene expression

value: Epithelial


title: Colon, D50, Stroma fraction, gene expression

value: Stroma


title: Colon, D60, Epithelial fraction, anti-IL-12p40-treated, gene expression

value: CD45RBhi transfer + anti-IL-12p40-treated

value: yes


title: Colon, D40, Immune fraction, gene expression


title: Colon, D10, Immune fraction, Feature barcodes


title: Colon, D40, Epithelial fraction, anti-IL-12p40-treated, gene expression


title: Colon, D50, Epithelial fraction, gene expression


title: Colon, D60, Stroma fraction, gene expression


title: Colon, D10, Immune fraction, gene expression


title: Colon, D20, Epithelial fraction, gene expression


title: Colon, D20, Stroma fraction, gene expression


title: Colon, D20, Immune fraction, gene expression


title: Colon, D0, Stroma fraction, gene expression


title: Colon, D30, Epithelial fraction, anti-IL-12p40-treated, gene expression


title: Colon, D0, Immune fraction, gene expression


title: Colon, W7, Immune fraction, gene expression

value: BALB/c SCID


title: Colon, W7, Immune fraction, anti-IL-12p40-treated, gene expression


title: Colon, D0, Epithelial fraction, gene expression


title: Colon, W7, Epithelial fraction, anti-IL-12p40-treated, gene expression


title: Colon, D40, Epithelial fraction, gene expression


title: Colon, D10, Epithelial fraction, gene expression


title: Colon, W7, Stroma fraction, gene expression


title: Colon, W6, Immune fraction, gene expression


title: Colon, W7, Epithelial fraction, gene expression


title: Colon, W6, Epithelial fraction, gene expression


title: Colon, W7, Stroma fraction, anti-IL-12p40-treated, gene expression


title: Colon, W6, Stroma fraction, gene expression


title: Colon, W5, Epithelial fraction, anti-IL-12p40-treated, gene expression


title: Colon, W5, Immune fraction, gene expression


title: Colon, W5, Stroma fraction, gene expression


title: Colon, W4, Immune fraction, gene expression


title: Colon, W5, Epithelial fraction, gene expression


title: Colon, W4, Stroma fraction, gene expression


title: Colon, W4, Epithelial fraction, gene expression


title: Colon, W3, Epithelial fraction, anti-IL-12p40-treated, gene expression


title: Colon, W3, Epithelial fraction, gene expression


title: Colon, W0, Stroma fraction, gene expression


title: Colon, W2, Epithelial fraction, gene expression


title: Colon, W2, Stroma fraction, gene expression


title: Colon, W3, Immune fraction, gene expression


title: Colon, W1, Epithelial fraction, gene expression


title: Colon, W1, Stroma fraction, gene expression


title: Colon, W1, Immune fraction, gene expression


title: Colon, Week 7, replicate 2

description:
W7dcRF5
SCID_counts.tsv
SCID_tpm.tsv

data_processing:
Read quality was inspected using FastQC and further processed for abundance estimation using Kallisto.
Read abundances and TPM values estimated with Kallisto were compiled into gene expression matrices and processed separately for each genotype.
Assembly: mm10
Supplementary files format and content: .csv-files with count and TPM matrices

extract_protocol:
Tissue biopsies (approximately 0.5 cm long) were collected from the distal colon and stored at -80°C in RNAlater (Invitrogen). To extract RNA, tissue was lysed in RLT Plus Buffer (QIAGEN) + 2% b-mercaptoethanol by bead-beating (Precellys). RNA was isolated with the RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer's instructions and quantified using a Nanodrop spectrophotometer (ThermoFisher).
cDNA libraries were constructed by Novogene Co. Ltd (UK).
cDNA libraries were sequenced by Novogene Co. Ltd (UK) at a sequencing depth of 20 million reads per sample using paired-end 150 bp reads on a NovaSeq 6000 sequencer with a v1.0 reagent kit. Samples were sequenced using paired-end 150bp sequencing, aiming at a coverage of 20M reads.

tag: agent

tag: rin

tag: cage

value: F

tag: lipocalin feces_ng_g

tag: histological colitis_score


title: Colon, Week 7, anti-IL-12p40-treated, replicate 2

description:
W7dcRD6
SCID_counts.tsv
SCID_tpm.tsv

tag: tissue

tag: genotype

tag: treatment

value: D


title: Colon, W0, Immune fraction, gene expression

tag: cell type


title: Colon, Week 7, anti-IL-12p40-treated, replicate 1

description:
W7dcRD3
SCID_counts.tsv
SCID_tpm.tsv


title: Colon, W0, Epithelial fraction, gene expression


title: Colon, W3, Stroma fraction, gene expression


title: Colon, Week 6, replicate 3

description:
W6dcRF6
SCID_counts.tsv
SCID_tpm.tsv


title: Colon, Week 5, anti-IL-12p40-treated, replicate 3

description:
W5dcRE6
SCID_counts.tsv
SCID_tpm.tsv

value: E


title: Colon, Week 6, replicate 1

description:
W6dcRB3
SCID_counts.tsv
SCID_tpm.tsv

value: B


title: Colon, W2, Immune fraction, gene expression


title: Colon, Week 7, anti-IL-12p40-treated, replicate 3

description:
W7dcRE3
SCID_counts.tsv
SCID_tpm.tsv


title: Colon, Week 7, replicate 3

description:
W7dcRH1
SCID_counts.tsv
SCID_tpm.tsv

value: H


title: Colon, Week 5, anti-IL-12p40-treated, replicate 2

description:
W5dcRD5
SCID_counts.tsv
SCID_tpm.tsv


title: Colon, Week 5, replicate 2

description:
W5dcRB4
SCID_counts.tsv
SCID_tpm.tsv


title: Colon, Week 6, replicate 2

description:
W6dcRF2
SCID_counts.tsv
SCID_tpm.tsv


title: Colon, Week 7, replicate 1

description:
W7dcRC5
SCID_counts.tsv
SCID_tpm.tsv

value: C


title: Colon, Week 5, anti-IL-12p40-treated, replicate 1

description:
W5dcRD4
SCID_counts.tsv
SCID_tpm.tsv

value: colon


title: Colon, Week 4, replicate 3

description:
W4dcRG3
SCID_counts.tsv
SCID_tpm.tsv

value: G


title: Colon, Week 4, replicate 2

description:
W4dcRC6
SCID_counts.tsv
SCID_tpm.tsv


title: Colon, Week 5, replicate 3

description:
W5dcRC2
SCID_counts.tsv
SCID_tpm.tsv


title: Colon, Week 5, replicate 1

description:
W5dcRA2
SCID_counts.tsv
SCID_tpm.tsv

value: A


title: Colon, Week 4, replicate 1

description:
W4dcRA1
SCID_counts.tsv
SCID_tpm.tsv

value: CD45RBhi transfer


title: Colon, Week 3, replicate 3

description:
W3dcRH2
SCID_counts.tsv
SCID_tpm.tsv


title: Colon, Week 3, anti-IL-12p40-treated, replicate 3

description:
W3dcRE5
SCID_counts.tsv
SCID_tpm.tsv


title: Colon, Week 3, replicate 2

description:
W3dcRC4
SCID_counts.tsv
SCID_tpm.tsv


title: Colon, Week 2, replicate 1

description:
W2dcRA3
SCID_counts.tsv
SCID_tpm.tsv


title: Colon, Week 2, replicate 3

description:
W2dcRG4
SCID_counts.tsv
SCID_tpm.tsv


title: Colon, Week 3, anti-IL-12p40-treated, replicate 2

description:
W3dcRE1
SCID_counts.tsv
SCID_tpm.tsv


title: Colon, Week 3, anti-IL-12p40-treated, replicate 1

description:
W3dcRD2
SCID_counts.tsv
SCID_tpm.tsv


title: Colon, Week 2, replicate 2

description:
W2dcRC3
SCID_counts.tsv
SCID_tpm.tsv


title: Colon, Week 1, replicate 3

description:
W1dcRG1
SCID_counts.tsv
SCID_tpm.tsv


title: Colon, Week 1, replicate 1

description:
W1dcRB2
SCID_counts.tsv
SCID_tpm.tsv


title: Colon, Week 0, replicate 2

description:
W0dcRB1
SCID_counts.tsv
SCID_tpm.tsv


title: Colon, Day 60, anti-IL-12p40-treated, replicate 3

description:
D60dcRG3
Rag2_counts.tsv
Rag2_tpm.csv


title: Colon, Week 0, replicate 1

description:
W0dcRA6
SCID_counts.tsv
SCID_tpm.tsv


title: Colon, Week 0, replicate 3

description:
W0dcRF4
SCID_counts.tsv
SCID_tpm.tsv


title: WT & Knockdown iNeuron treated with1080min of Cisplatin and 20uM EdU and subjected to scEdU-seq plate 7

city: Utrecht

first: Jeroen

last: van den Berg

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: Library name: JvB-184-iNeuron-Cisplatin-knockdown-1080E-F-pl7

data_processing:
Unless otherwise mentioned all data analysis was done in bash and R. First the cell barcode was extracted from position 4-11 in read-1, after which only read pairs were kept where the barcode had an exact match with a cell barcode and where position 12 corresponded to T (complementary A was added during single-base overhang ligation). The cell barcode and the umi (position 1-3 in read-1) were put in the name of the read pair. The reads were then trimmed using trimgalore (wrapper for cutadapt) using the default settings and the --paired flag. Trimmed reads were mapped with STAR version 2.710b to un-masked GRCh38 with following settings; --outFilterMultimapNmax 1 --peOverlapNbasesMin 10 --alignIntronMax 1. Only properly mapped read pairs were kept and deduplicated by grouping on cell barcode, umi, chromosome, and mapping position of read-1 within 10 bases, after which the longest insert size is kept per group.
https://github.com/FelixKrueger/TrimGalore
https://github.com/alexdobin/STAR
https://github.com/marcelm/cutadapt
For single-cell data, cells with > 2,000 reads were defined as EdU positive cells, after excluding reads in blacklist. Read counts from the transcribed and non-transcribed strands were quantified using intersect command in the bedtools suite (version 2.31.1)68 with “different strandedness” and “strandedness” parameters, respectively. Remaining reads were assigned to intergenic regions.
Transcribed-strand reads from EdU-positive cells were quantified within each gene body and normalized by TPM. Correlations with gene expression levels were calculated by Person correlation coefficient.
Assembly: hg38
Supplementary files format and content: count tables with cell barcode, chromosome, start position and insert size

source_name: embryonic

growth_protocol: The WTC11 human iPSC cell line was previously engineered to express mouse neurogenin-2 (NGN2) via a doxycycline-induced promoter that was integrated into the AAVS1 safe harbor site. Additionally, these cells were engineered to express CAG-dCas9-BFP-KRAB at the Clybl promoter for use in targeted gene knockdowns. To differentiate iPSCs into neurons, iPSCs were grown on matrigel pre-coated plates in N2 medium (KnockOut DMEM/F12 medium; Life Technologies Corporation, cat. No. 12660012) with N2 supplement (Life Technologies, cat. No. 17502048), 1x MEM nonessential amino acids (Thermo Scientific, cat. No. 11140050), 1x GlutaMAX (Thermofisher Scientific, cat. No. 35050061), 10 µM ROCK inhibitor (Y-27632; Selleckchem, cat. No. S1049), and 2 µg/mL doxycycline (Clontech, cat. No. 631311). N2 medium was removed and changed daily for two additional days. 3 days post-plating, cells (“day3 neurons”) were dissociated in accutase for 10-15 minutes at 37°C to obtain single-cell suspension, washed in PBS, and replated onto new plates freshly coated with poly-L-ornithine (PLO) (0.1 mg/mL; Sigma, cat. No. P3655) in BrainPhys medium (STEMCELL Technologies, cat. no. A3582801) to complete differentiation. BrainPhys medium was supplemented with B27 Plus Supplement (ThermoFisher Scientific, cat. no. 450-03), 1 mg/mL mouse laminin (Sigma, cat. no. L2020-1MG), 10 ng/mL BDNF (PeproTech, cat. no. 450-02), 10 ng/mL NT-3 (PeproTech, cat. no. 450-03), and 2 μg/ml doxycycline (Clontech, cat. no. 631311). For SAR-seq experiments, 10-15 million day3 neurons were plated onto 10-cm plates. For scSAR-seq and all FACS experiments, 2-3 million day3 neurons were plated per well onto 6-well plates. For immunofluorescence imaging experiments, 50,000 d3 neurons were plated per well onto µ-Slide 18 well glass bottom slides (Ibidi, 81817). For viability experiments, 200,000 d3 neurons were plated per well onto 24-well plates.  For nascent RNA imaging experiments, 500,000 d3 neurons were plated per well onto 12-well plates. Usually, cells were treated on day 6 (3 days after plating on PLO-coated plates) unless otherwise noted. In cases where neurons were grown longer-term, half media changes were done every 3-4 days.

extract_protocol:
Proteinase K digestion
scEdU-seq (Nature Methods, 2024)

treatment_protocol: i3Neurons were treated with 20 µM cisplatin for 24 hours with 20 µM EdU

value: embryonic

tag: cell line

value: Neuronal

value: Wild-type

value: Cisplatin

tag: batch

tag: sample group


title: Colon, Week 1, replicate 2

description:
W1dcRF3
SCID_counts.tsv
SCID_tpm.tsv

tag: time


title: WT & Knockdown iNeuron treated with1080min of Cisplatin and 20uM EdU and subjected to scEdU-seq plate 6

description: Library name: JvB-184-iNeuron-Cisplatin-knockdown-1080E-F-pl6


title: WT & Knockdown iNeuron treated with1080min of Cisplatin and 20uM EdU and subjected to scEdU-seq plate 8

description: Library name: JvB-184-iNeuron-Cisplatin-knockdown-1080E-F-pl8


title: Colon, Day 60, replicate 3

description:
D60dcRE3
Rag2_counts.tsv
Rag2_tpm.csv

value: Rag2 KO


title: WT & Knockdown iNeuron treated with1080min of Cisplatin and 20uM EdU and subjected to scEdU-seq plate 5

description: Library name: JvB-184-iNeuron-Cisplatin-knockdown-1080E-F-pl5


title: Colon, Week 3, replicate 1

description:
W3dcRB5
SCID_counts.tsv
SCID_tpm.tsv


title: WT & Knockdown iNeuron treated with1080min of Cisplatin and 20uM EdU and subjected to scEdU-seq plate 4

description: Library name: JvB-184-iNeuron-Cisplatin-knockdown-1080E-F-pl4


title: Colon, Day 60, replicate 2

description:
D60dcRD4
Rag2_counts.tsv
Rag2_tpm.csv


title: Colon, Day 60, anti-IL-12p40-treated, replicate 1

description:
D60dcRC1
Rag2_counts.tsv
Rag2_tpm.csv

value: CD45RBhi transfer + anti-IL-12p40-treated


title: Colon, Day 60, anti-IL-12p40-treated, replicate 2

description:
D60dcRC4
Rag2_counts.tsv
Rag2_tpm.csv


title: WT & Knockdown iNeuron treated with1080min of Cisplatin and 20uM EdU and subjected to scEdU-seq plate 3

description: Library name: JvB-184-iNeuron-Cisplatin-knockdown-1080E-F-pl3


title: WT & Knockdown iNeuron treated with1080min of Cisplatin and 20uM EdU and subjected to scEdU-seq plate 2

description: Library name: JvB-184-iNeuron-Cisplatin-knockdown-1080E-F-pl2


title: Colon, Day 60, replicate 1

description:
D60dcRB8
Rag2_counts.tsv
Rag2_tpm.csv


title: WT & Knockdown iNeuron treated with1080min of Cisplatin and 20uM EdU and subjected to scEdU-seq plate 1

description: Library name: JvB-184-iNeuron-Cisplatin-knockdown-1080E-F-pl1


title: WT iNeuron treated with1080min of Cisplatin and a timecourse 20uM EdU and subjected to scEdU-seq plate 5

description: Library name: JvB-183-iNeuron-Cisplatin-timecrouse-1080E-F-pl5


title: WT iNeuron treated with1080min of Cisplatin and a timecourse 20uM EdU and subjected to scEdU-seq plate 6

description: Library name: JvB-183-iNeuron-Cisplatin-timecrouse-1080E-F-pl6


title: WT iNeuron treated with1080min of Cisplatin and a timecourse 20uM EdU and subjected to scEdU-seq plate 4

description: Library name: JvB-183-iNeuron-Cisplatin-timecrouse-1080E-F-pl4


title: Colon, Day 50, replicate 1

description:
D50dcRB3
Rag2_counts.tsv
Rag2_tpm.csv


title: Colon, Day 40, anti-IL-12p40-treated, replicate 2

description:
D40dcRG5
Rag2_counts.tsv
Rag2_tpm.csv


title: Colon, Day 40, anti-IL-12p40-treated, replicate 1

description:
D40dcRG1
Rag2_counts.tsv
Rag2_tpm.csv


title: Colon, Day 40, replicate 3

description:
D40dcRF1
Rag2_counts.tsv
Rag2_tpm.csv


title: WT iNeuron treated with1080min of Cisplatin and a timecourse 20uM EdU and subjected to scEdU-seq plate 3

description: Library name: JvB-183-iNeuron-Cisplatin-timecrouse-1080E-F-pl3


title: Colon, Day 50, replicate 3

description:
D50dcRE4
Rag2_counts.tsv
Rag2_tpm.csv


title: WT iNeuron treated with 1440min of Cisplatin and 20uM EdU and subjected to scEdU-seq plate 7

description: Library name: JvB-172-iNeuron-20uM-Cisplatin-1440E-F-pl7


title: WT iNeuron treated with 1440min of Cisplatin and 20uM EdU and subjected to scEdU-seq plate 8

description: Library name: JvB-172-iNeuron-20uM-Cisplatin-1440E-F-pl8


title: Colon, Day 50, replicate 2

description:
D50dcRD5
Rag2_counts.tsv
Rag2_tpm.csv


title: Colon, Day 30, anti-IL-12p40-treated, replicate 3

description:
D30dcRG4
Rag2_counts.tsv
Rag2_tpm.csv


title: Colon, Day 40, anti-IL-12p40-treated, replicate 3

description:
D40dcRC6
Rag2_counts.tsv
Rag2_tpm.csv


title: WT iNeuron treated with1080min of Cisplatin and a timecourse 20uM EdU and subjected to scEdU-seq plate 1

description: Library name: JvB-183-iNeuron-Cisplatin-timecrouse-1080E-F-pl1


title: Colon, Day 40, replicate 2

description:
D40dcRD1
Rag2_counts.tsv
Rag2_tpm.csv


title: Colon, Day 40, replicate 1

description:
D40dcRB7
Rag2_counts.tsv
Rag2_tpm.csv


title: WT iNeuron treated with 1440min of Cisplatin and 20uM EdU and subjected to scEdU-seq plate 6

description: Library name: JvB-172-iNeuron-20uM-Cisplatin-1440E-F-pl6


title: WT iNeuron treated with 1440min of Cisplatin and 20uM EdU and subjected to scEdU-seq plate 3

description: Library name: JvB-172-iNeuron-20uM-Cisplatin-1440E-F-pl3


title: WT iNeuron treated with 1440min of Cisplatin and 20uM EdU and subjected to scEdU-seq plate 5

description: Library name: JvB-172-iNeuron-20uM-Cisplatin-1440E-F-pl5


title: WT iNeuron treated with 1440min of Cisplatin and 20uM EdU and subjected to scEdU-seq plate 2

description: Library name: JvB-172-iNeuron-20uM-Cisplatin-1440E-F-pl2


title: Colon, Day 30, anti-IL-12p40-treated, replicate 2

description:
D30dcRG2
Rag2_counts.tsv
Rag2_tpm.csv


title: WT iNeuron treated with 1440min of Cisplatin and 20uM EdU and subjected to scEdU-seq plate 4

description: Library name: JvB-172-iNeuron-20uM-Cisplatin-1440E-F-pl4


title: WT iNeuron treated with1080min of Cisplatin and a timecourse 20uM EdU and subjected to scEdU-seq plate 2

description: Library name: JvB-183-iNeuron-Cisplatin-timecrouse-1080E-F-pl2


title: SKOV3 cells, STM3675, 24 h, rep2

city: Cambridge

first: Harry

last: Fischl

address: Babraham Research Campus

institute: Storm Therapeutics

description:
Library name: SKOV3_STM3675_24h_rep2
rRNA depleted total RNA-seq

data_processing:
Unique molecular identifiers (UMIs) were extracted from single-end RNA-seq fastq files. Fastq files were then trimmed of adapters using cutadapt (Martin, 2011) according to Lexogen’s recommendations and aligned to the human GRCh38 genome using the STAR aligner (Dobin et al., 2013). Bam files were deduplicated using UMI tools (Smith et al., 2017) (--method=unique). Normalised bigwig tracks were generated by dividing the signal at each nucleotide by the total genome signal and multiplying by 1 billion.
Assembly: GRCh38
Supplementary files format and content: .bw files show normalized signal for positive and negative strands

extract_protocol:
RNA was extracted using Trizol according to the manufacturer's instructions
RNA was generated into RNA-seq libraries by Lexogen using Ribocop rRNA-depletion and CORALL Total RNA-seq library generation and sequenced to a depth of greater than 100 million SE100 reads.

treatment_protocol: A549, CAOV3, COV644, EFO21, OE21 and SKOV3 treated with DMSO and CAOV3 cells treated with 1 uM STM3675 for 24h

value: Ovarian carcinoma


title: Colon, Day 30, replicate 2

description:
D30dcRE6
Rag2_counts.tsv
Rag2_tpm.csv


title: SKOV3 cells, STM3675, 24 h, rep1

description:
Library name: SKOV3_STM3675_24h_rep1
rRNA depleted total RNA-seq


title: Colon, Day 30, anti-IL-12p40-treated, replicate 1

description:
D30dcRC3
Rag2_counts.tsv
Rag2_tpm.csv


title: Colon, Day 30, replicate 1

description:
D30dcRB4
Rag2_counts.tsv
Rag2_tpm.csv


title: WT iNeuron treated with 1440min of Cisplatin and 20uM EdU and subjected to scEdU-seq plate 1

description: Library name: JvB-172-iNeuron-20uM-Cisplatin-1440E-F-pl1


title: Colon, Day 10, replicate 2

description:
D10dcRE2
Rag2_counts.tsv
Rag2_tpm.csv


title: Colon, Day 10, replicate 3

description:
D10dcRF4
Rag2_counts.tsv
Rag2_tpm.csv

value: F


title: Colon, Day 10, replicate 1

description:
D10dcRB5
Rag2_counts.tsv
Rag2_tpm.csv


title: SKOV3 cells, STM3675, 24 h, rep3

description:
Library name: SKOV3_STM3675_24h_rep3
rRNA depleted total RNA-seq


title: Colon, Day 20, replicate 3

description:
D20dcRF5
Rag2_counts.tsv
Rag2_tpm.csv


title: Colon, Day 20, replicate 1

description:
D20dcRB6
Rag2_counts.tsv
Rag2_tpm.csv


title: OE21 cells, DMSO, 24 h, rep3

description:
Library name: OE21_DMSO_24h_rep3
rRNA depleted total RNA-seq

value: Oesophageal carcinoma

value: DMSO 24h


title: OE21 cells, STM3675, 24 h, rep2

description:
Library name: OE21_STM3675_24h_rep2
rRNA depleted total RNA-seq


title: SKOV3 cells, DMSO, 24 h, rep3

description:
Library name: SKOV3_DMSO_24h_rep3
rRNA depleted total RNA-seq


title: Colon, Day 20, replicate 2

description:
D20dcRD2
Rag2_counts.tsv
Rag2_tpm.csv

value: D


title: OE21 cells, STM3675, 24 h, rep3

description:
Library name: OE21_STM3675_24h_rep3
rRNA depleted total RNA-seq


title: SKOV3 cells, DMSO, 24 h, rep1

description:
Library name: SKOV3_DMSO_24h_rep1
rRNA depleted total RNA-seq


title: SKOV3 cells, DMSO, 24 h, rep2

description:
Library name: SKOV3_DMSO_24h_rep2
rRNA depleted total RNA-seq