title: vehicle, KO, 24h, Rep2

description: Library name: BMDM_58


title: Dex, KO, 24h, Rep2

status: Public on Aug 26 2025

type: SRA

city: Rozzano

first: Massimo

last: Locati

state: Milano

address: Via Alessandro Manzoni, 56

country: Italy

institute: IRCCS Humanitas Research Hospital

description: Library name: BMDM_59

library_source: transcriptomic

data_processing:
Reads were trimmed for adapter sequences using fastp.
Trimmed reads were mapped to GRCm38 using HISAT2 and transcript-level quantification was performed using Salmon.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes normalized counts per each sample.

molecule: total RNA

organism: Mus musculus

source_name: Macrophages

growth_protocol: Murine bone marrow-derived macrophages (BMDMs) were generated by 6 days of culture with 50 ng/ml recombinant murine (rm) M-CSF in Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 10% FBS, 1% Penicillin/Streptomycin, and 1% L-Glutamine in 100 mm dishes.

extract_protocol:
At the end of the treatment, the medium was removed, and cells were washed with 1X PBS and lysed with Trizol. RNA was extracted using the ReliaPrep™ RNA Cell Miniprep System (Promega – Z6012) according to the manufacturer's instructions.
RNA-seq libraries were prepared using SMART-Seq® mRNA LP kit (Takara Bio) following the manufacturer’s protocol.

treatment_protocol: At the end of the differentiation, BMDMs were detached with Accutase and plated in 12-well plates. The following day, cells were stimulated with or without 1 µM Dexamethasone for 2 h, 8 h, and 24 h.

tag: cell type

value: Macrophages

tag: genotype

value: MS4A4A KO

tag: treatment

value: Dex

tag: timepoint


title: bulkATAC_D8_CD4_TEMRA_P

city: New Delhi

first: Veena

middle: S.

last: Patil

state: Delhi

address: Aruna Asaf Ali Marg

country: India

institute: National Institute of Immunology

description:
Library name: bATAC_D8_P
aggregated .bw file for 10 donors

library_source: genomic

data_processing:
Raw demultiplexed FASTQ files (n = 60; 10 donors, 6 cell types – CD4-Naïve TN, CD4-TSCM, CD4-TCM, CD4-TEM, CD4-TEMRA-P and CD4-TEMRA-E) were quality filtered, and adaptor trimmed using trim_galore, and trimmed reads were mapped to the GRCh38 (hg38) human reference sequence using Bowtie2.
Publicly available pipelines from snakemake and nfcore were followed to analyze ATAC-Seq data.
De-duplicated reads (using picard markduplicates) were filtered for reads mapping to ENCODE blacklisted region, mitochondrial genome and low-quality reads (bedtools and samtools).
Reads passing all quality checks were called for peaks using MACS2 narrowPeak caller. BAM files for each cell type across 10 donors were merged using samtools.
Assembly: GRCh38 (hg38)
Supplementary files format and content: N_out.bw, SCM_out.bw, CM_out.bw, EM_out.bw, P_out.bw and E_out.bw. bigWig files for each cell type is the aggregated file from 10 donors.

molecule: genomic DNA

organism: Homo sapiens

source_name: PBMC

growth_protocol: CD4-Naïve (TN), CD4-TSCM, CD4-TCM, CD4-TEM, CD4-TEMRA-P and CD4-TEMRA-E were isolated from PBMCs using flow cytometry (FACS). The FACS sorted cells were used for nuclei isolation using Omni ATAC-Seq protocol by Corces et.al., 2017.

extract_protocol:
Cells sorted in collection media (1:1 FBS:PBS) were counted, and 55,000 cells were taken in LoBind 0.6 mL microcentrifuge tubes (Eppendorf) and washed with 0.5 mL chilled PBS. Cell pellet was resuspended in 50 uL chilled freshly-made lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL-CA630, 0.1% Tween-20, 0.01% Digitonin, 1X Protease Inhibtor, 20 mM NaBu) supplemented with 1 U/uL recombinant RNase Inhibtor. After 5 minutes of lysis on ice, 0.2 mL of wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20) supplemented with 1 U/uL recombinant RNase Inhibitor, was added. Pelleted nuclei were transposed using Tn5 transposase from Illumina, in a 50 uL reaction mix supplemented with 1X PBS, 0.1% Tween-20 and 0.01% Digitonin, at 37°C for 30 minutes.
Tagmented DNA was purified using Zymo DNA Clean and Concentrator-5 kit followed by amplification using barcoded Nextera XT primers with KAPA Hi-Fi HotStart Ready Mix. After the initial 5 cycles of amplification, cycle threshold determination (CTD) was performed using SYBR and ROX. Based on the CTD the additional cycles (CTD-2 cycle) were performed on the amplified DNA. Final libraries were purified and size-selected using double sided purification by Ampure XP beads (0.5X / 1.8X).
Pooled libraries were sequenced using NovaSeq 6000 (Illumina) for 150-bp paired-end sequencing.

treatment_protocol: No particular treatment was done to the PBMCs. PBMCs were immuno stained and sorted using FACS.

tag: tissue

value: PBMC

tag: cell type_surface_markers

tag: donor #


title: bulkATAC_D10_CD4_TEMRA_P

description:
Library name: bATAC_D10_P
aggregated .bw file for 10 donors


title: Dex, WT, 24h, Rep2

description: Library name: BMDM_54

value: WT


title: vehicle, WT, 24h, Rep2

description: Library name: BMDM_53

value: vehicle


title: bulkATAC_D9_CD4_TEMRA_P

description:
Library name: bATAC_D9_P
aggregated .bw file for 10 donors


title: bulkATAC_D6_CD4_TEMRA_P

description:
Library name: bATAC_D6_P
aggregated .bw file for 10 donors


title: bulkATAC_D5_CD4_TEMRA_P

description:
Library name: bATAC_D5_P
aggregated .bw file for 10 donors


title: Dex, WT, 8h, Rep2

description: Library name: BMDM_44


title: bulkATAC_D4_CD4_TEMRA_P

description:
Library name: bATAC_D4_P
aggregated .bw file for 10 donors


title: Dex, KO, 8h, Rep2

description: Library name: BMDM_49


title: bulkATAC_D7_CD4_TEMRA_P

description:
Library name: bATAC_D7_P
aggregated .bw file for 10 donors


title: vehicle, WT, 8h, Rep2

description: Library name: BMDM_43


title: vehicle, KO, 8h, Rep2

description: Library name: BMDM_48


title: bulkATAC_D3_CD4_TEMRA_P

description:
Library name: bATAC_D3_P
aggregated .bw file for 10 donors


title: Untr, KO, 0_baseline, Rep2

description: Library name: BMDM_64

value: Untr


title: B4

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description: Library name: Sample 1

data_processing:
The fastq sequences were mapped with a standard STAR pipeline (version: 2.7.3a). The duplicated reads were filtered out using UMI-tools (version: 1.1.4). The gene expression counts summary was calculated using featureCounts function from the Subread package (version 1.4.6-p5)
Assembly: mm10
Supplementary files format and content: Tab-seprated values files

source_name: Kidney

extract_protocol:
Kidney tissue was lysed in RLT buffer and homogenized. RNAeasy Micro or Mini kit (Qiagen) was used to extract mRNA according to the manufacturer’s protocol.
Library preparation and sequencing was performed as described previously (Hagemann-Jensen M, et al. Single-cell RNA counting at allele and isoform resolution using Smart-seq3. Nature biotechnology. 2020;38(6):708-14.).

value: Kidney

tag: age

value: adult

value: IgG

tag: treatment group

value: CL


title: Dex, KO, 2h, Rep2

description: Library name: BMDM_39


title: Dex, WT, 2h, Rep2

description: Library name: BMDM_34


title: vehicle, WT, 2h, Rep2

description: Library name: BMDM_33


title: vehicle, KO, 2h, Rep2

description: Library name: BMDM_38


title: bulkATAC_D9_CD4_TEM

description:
Library name: bATAC_D9_EM
aggregated .bw file for 10 donors


title: Dex, KO, 24h, Rep1

description: Library name: BMDM_29


title: vehicle, KO, 24h, Rep1

description: Library name: BMDM_28


title: bulkATAC_D2_CD4_TEMRA_P

description:
Library name: bATAC_D2_P
aggregated .bw file for 10 donors


title: Dex, WT, 24h, Rep1

description: Library name: BMDM_24


title: vehicle, WT, 24h, Rep1

description: Library name: BMDM_23


title: bulkATAC_D7_CD4_TEM

description:
Library name: bATAC_D7_EM
aggregated .bw file for 10 donors


title: bulkATAC_D6_CD4_TEM

description:
Library name: bATAC_D6_EM
aggregated .bw file for 10 donors


title: WJL3015_RLF_N025

city: Stanford

first: Richard

middle: L

last: Frock

state: California

address: 269 Campus Drive

department: Radiation Oncology

country: USA

institute: Stanford University

description:
Library name: WJL3015
5'Smu bait priming

data_processing:
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203) and Liang et al., 2021 PNAS (PMC8166026).
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (https://expressionanalysis.github.io/ea-utils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) to map translocations
Reads were aligned to the bait and the prey region using Bowtie2. The cross library contamination in the co-tagged PCR was filtered by the inner barcodes from I7-nested primers.
Assembly: mm9
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)

source_name: Spleen

growth_protocol: CD19-enriched murine splenic B cells proficient or deficient in Xrcc4 (with CD21-Cre), Polq, Shld1, or in combination and were were cultured at 37 °C, 5% CO2, in RPMI 1640 supplemented with 12% FBS, penicillin (100 U/ml)/streptomycin (100 μg/ml) and 50 μM 2-mercaptoethanol.

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
Libraries were generated as described in Dong et al., Nature 2015 (PMC4592165) (Bait priming),  Hu et al., 2016 Nature Protocols (PMC4895203) (LAM-HTGTS protocol) and Liang et al, 2021 PNAS (PMC8166026) (JoinT-seq analysis) using Illumina NovoSeq sequencing

treatment_protocol: Ig heavy chain locus class switch recombination was induced at 0.6 × 10^6 cells/mL over 4-5 days using the following cytokine combinations: IgG1 with anti-IgD dextran (3ng/mL), IL-4 (10 ng/ml ) and LPS (25 μg/ml).

value: Spleen

value: Primary B cells

value: anti-IgD dextran, IL-4, LPS


title: vehicle, KO, 8h, Rep1

description: Library name: BMDM_18


title: Dex, KO, 8h, Rep1

description: Library name: BMDM_19


title: WJL3014_RLF_N025

description:
Library name: WJL3014
5'Smu bait priming


title: vehicle, WT, 8h, Rep1

description: Library name: BMDM_13


title: bulkATAC_D4_CD4_TEM

description:
Library name: bATAC_D4_EM
aggregated .bw file for 10 donors


title: Dex, WT, 8h, Rep1

description: Library name: BMDM_14


title: vehicle, KO, 2h, Rep1

description: Library name: BMDM_08


title: bulkATAC_D3_CD4_TEM

description:
Library name: bATAC_D3_EM
aggregated .bw file for 10 donors


title: bulkATAC_D10_CD4_TEM

description:
Library name: bATAC_D10_EM
aggregated .bw file for 10 donors


title: bulkATAC_D2_CD4_TEM

description:
Library name: bATAC_D2_EM
aggregated .bw file for 10 donors


title: WJL3012_RLF_N025

description:
Library name: WJL3012
5'Smu bait priming

value: Shld1-/- Polq-/-


title: bulkATAC_D1_CD4_TEMRA_P

description:
Library name: bATAC_D1_P
aggregated .bw file for 10 donors


title: Dex, WT, 2h, Rep1

description: Library name: BMDM_04


title: vehicle, WT, 2h, Rep1

description: Library name: BMDM_03


title: WJL3013_RLF_N025

description:
Library name: WJL3013
5'Smu bait priming


title: bulkATAC_D8_CD4_TEM

description:
Library name: bATAC_D8_EM
aggregated .bw file for 10 donors


title: WJL3011_RLF_N025

description:
Library name: WJL3011
5'Smu bait priming


title: bulkATAC_D1_CD4_TEM

description:
Library name: bATAC_D1_EM
aggregated .bw file for 10 donors


title: WJL3010_RLF_N025

description:
Library name: WJL3010
5'Smu bait priming

value: PolQ-/-


title: bulkATAC_D5_CD4_TEM

description:
Library name: bATAC_D5_EM
aggregated .bw file for 10 donors


title: bulkATAC_D10_CD4_TCM

description:
Library name: bATAC_D10_CM
aggregated .bw file for 10 donors


title: Untr, WT, 0_baseline, Rep1

description: Library name: BMDM_01


title: bph_bpn_bpniv_bpnlv_2023_038

city: Columbia

first: Wenbin

last: Tan

state: SC

address: 6311 Garners Ferry Road

department: Cell Biology and Anatomy

institute: University of South Carolina School of Medicine

description: Library name: DSP-1001660021860-E-D03

data_processing:
During library preparation, the DSP barcodes are tagged with their ROI location, then sequenced on an Illumina sequencer. DNA oligonucleotide sequences contain ROI indices mapping them back to their tissue location, an RNA target identification sequence matching them to their ISH probes, and a unique molecular identifier (UMI) to deduplicate reads.
Sequenced oligonucleotides are processed and then imported back into the GeoMx DSP analysis software for integration with the slide images and ROI selections for spatially-resolved RNA expression. GeoMx software uniquely combines whole tissue visualization at single cell resolution with advanced ROI selection to enable comprehensive spatial profiling of tissue sections.
Assembly: GRCH38
Supplementary files format and content: xlsx spread sheet and pdf; DEG and GSEA profiles among subgroup comparisons
Library strategy: Spatial Transcriptomics

source_name: thoracic aorta

extract_protocol:
3-5 um tissue sectioned were stained with RNAscope probes and GeoMx DSP oligo-conjugated RNA detection probes.
GeoMx RNA assays contain in situ hybridization (ISH) probes conjugated to unique DNA indexing-oligonucleotides (DSP barcodes) via a UV-photocleavable linker. After selecting regions of interest (ROIs) on the GeoMx DSP, the DSP barcodes are UV-cleaved and collected. During library preparation, the DSP barcodes are tagged with their ROI location, then sequenced on an Illumina sequencer. Slides were exposed to an in situ hybridization (ISH) probe overnight at 37 degrees and conjugated to unique DNA indexing-oligonucleotides (DSP barcodes) via a UV-photocleavable linker. DNA oligonucleotide sequences contain ROI indices mapping them back to their tissue location, an RNA target identification sequence matching them to their ISH probes, and a unique molecular identifier (UMI) to deduplicate reads. Sequenced oligonucleotides are processed and then imported back into the GeoMx DSP analysis software for integration with the slide images and ROI selections for spatially-resolved RNA expression.

value: thoracic aorta

tag: subject id

value: blood vessels

tag: disease state

value: normotension (control)

tag: subgroup

value: BPN24 LVTF VSM

tag: batch

tag: sample id_roi


title: bph_bpn_bpniv_bpnlv_2023_036

description: Library name: DSP-1001660021860-E-D01

value: BPH

value: hipertension

value: BPH LVTF1 VSM


title: Dex, KO, 2h, Rep1

description: Library name: BMDM_09

value: Macrophages

value: MS4A4A KO

value: Dex


title: WJL3007_RLF_N025

description:
Library name: WJL3007
5'Smu bait priming


title: bulkATAC_D8_CD4_TCM

description:
Library name: bATAC_D8_CM
aggregated .bw file for 10 donors

value: PBMC


title: WJL3006_RLF_N025

description:
Library name: WJL3006
5'Smu bait priming


title: bph_bpn_bpniv_bpnlv_2023_033

description: Library name: DSP-1001660021860-E-C10

value: BPN

value: BPN LVCO VSM


title: bph_bpn_bpniv_bpnlv_2023_034

description: Library name: DSP-1001660021860-E-C11

value: BPN LVCO endothelium


title: bph_bpn_bpniv_bpnlv_2023_031

description: Library name: DSP-1001660021860-E-C08

value: BPN LVTF1 VSM


title: bulkATAC_D6_CD4_TCM

description:
Library name: bATAC_D6_CM
aggregated .bw file for 10 donors


title: bph_bpn_bpniv_bpnlv_2023_032

description: Library name: DSP-1001660021860-E-C09


title: bph_bpn_bpniv_bpnlv_2023_030

description: Library name: DSP-1001660021860-E-C07

value: BPN LVTF1 endothelium


title: WJL3005_RLF_N025

description:
Library name: WJL3005
5'Smu bait priming

value: Spleen

value: Primary B cells

value: PolQ-/-

value: anti-IgD dextran, IL-4, LPS


title: bph_bpn_bpniv_bpnlv_2023_029

description: Library name: DSP-1001660021860-E-C06

value: thoracic aorta

value: blood vessels

value: BPH LVTF2 VSM


title: WJL3004_RLF_N025

description:
Library name: WJL3004
5'Smu bait priming

value: WT


title: Untr, KO, 0_baseline, Rep1

description: Library name: BMDM_02

value: Macrophages

value: Untr


title: bph_bpn_bpniv_bpnlv_2023_028

description: Library name: DSP-1001660021860-E-C05

value: BPH

value: hipertension

value: BPH LVTF2 endothelium


title: bulkATAC_D5_CD4_TCM

description:
Library name: bATAC_D5_CM
aggregated .bw file for 10 donors

value: PBMC


title: bph_bpn_bpniv_bpnlv_2023_039

description: Library name: DSP-1001660021860-E-D04

value: normotension (control)

value: BPN24 LVTF endothelium


title: bulkATAC_D4_CD4_TCM

description:
Library name: bATAC_D4_CM
aggregated .bw file for 10 donors


title: bph_bpn_bpniv_bpnlv_2023_026

description: Library name: DSP-1001660021860-E-C03

value: BPH LVCO2 endothelium


title: bph_bpn_bpniv_bpnlv_2023_037

description: Library name: DSP-1001660021860-E-D02

value: BPH LVTF1 VSM


title: WJL3009_RLF_N025

description:
Library name: WJL3009
5'Smu bait priming

value: Spleen

value: Primary B cells


title: bph_bpn_bpniv_bpnlv_2023_027

description: Library name: DSP-1001660021860-E-C04


title: bulkATAC_D9_CD4_TCM

description:
Library name: bATAC_D9_CM
aggregated .bw file for 10 donors


title: bph_bpn_bpniv_bpnlv_2023_035

description: Library name: DSP-1001660021860-E-C12

value: BPH LVTF1 endothelium


title: bph_bpn_bpniv_bpnlv_2023_025

description: Library name: DSP-1001660021860-E-C02

value: thoracic aorta

value: BPH LVCO2 VSM


title: bulkATAC_D3_CD4_TCM

description:
Library name: bATAC_D3_CM
aggregated .bw file for 10 donors


title: WJL2617_RLF_N024

description:
Library name: WJL2617
5'Smu bait priming

value: Polq-/-

value: anti-IgD dextran, IL-4, LPS


title: bulkATAC_D7_CD4_TCM

description:
Library name: bATAC_D7_CM
aggregated .bw file for 10 donors


title: bph_bpn_bpniv_bpnlv_2023_024

description: Library name: DSP-1001660021860-E-C01

value: blood vessels

value: BPN3 LVTF VSM


title: bph_bpn_bpniv_bpnlv_2023_023

description: Library name: DSP-1001660021860-E-B12

value: BPN21 LVTF VSM


title: bulkATAC_D2_CD4_TCM

description:
Library name: bATAC_D2_CM
aggregated .bw file for 10 donors


title: bph_bpn_bpniv_bpnlv_2023_022

description: Library name: DSP-1001660021860-E-B11

value: BPN21 LVTF endothelium


title: WJL2616_RLF_N024

description:
Library name: WJL2616
5'Smu bait priming

value: WT


title: bph_bpn_bpniv_bpnlv_2023_020

description: Library name: DSP-1001660021860-E-B09


title: bph_bpn_bpniv_bpnlv_2023_021

description: Library name: DSP-1001660021860-E-B10


title: WJL2615_RLF_N024

description:
Library name: WJL2615
5'Smu bait priming

value: CD21 xrcc4-/-


title: bulkATAC_D1_CD4_TCM

description:
Library name: bATAC_D1_CM
aggregated .bw file for 10 donors

value: PBMC


title: WJL2614_RLF_N024

description:
Library name: WJL2614
5'Smu bait priming

value: CD21 xrcc4-/- polq-/-


title: bph_bpn_bpniv_bpnlv_2023_019

description: Library name: DSP-1001660021860-E-B08

value: normotension (control)

value: BPN26 LVCO VSM


title: WJL2618_RLF_N024

description:
Library name: WJL2618
5'Smu bait priming

value: Spleen


title: bulkATAC_D10_CD4_TSCM

description:
Library name: bATAC_D10_SCM
aggregated .bw file for 10 donors


title: bph_bpn_bpniv_bpnlv_2023_017

description: Library name: DSP-1001660021860-E-B06

value: BPN26 LVCO endothelium


title: bulkATAC_D9_CD4_TSCM

description:
Library name: bATAC_D9_SCM
aggregated .bw file for 10 donors


title: bph_bpn_bpniv_bpnlv_2023_015

description: Library name: DSP-1001660021860-E-B04

value: hipertension

value: BPH1 LVCO VSM


title: WJL2619_RLF_N024

description:
Library name: WJL2619
5'Smu bait priming

value: Primary B cells


title: bph_bpn_bpniv_bpnlv_2023_018

description: Library name: DSP-1001660021860-E-B07

value: thoracic aorta


title: bph_bpn_bpniv_bpnlv_2023_016

description: Library name: DSP-1001660021860-E-B05


title: bph_bpn_bpniv_bpnlv_2023_013

description: Library name: DSP-1001660021860-E-B02

value: BPH2 LVCO VSM


title: bph_bpn_bpniv_bpnlv_2023_014

description: Library name: DSP-1001660021860-E-B03

value: blood vessels

value: BPH1 LVCO endothelium


title: WJL2613_RLF_N024

description:
Library name: WJL2613
5'Smu bait priming

value: Polq-/-

value: anti-IgD dextran, IL-4, LPS


title: bulkATAC_D7_CD4_TSCM

description:
Library name: bATAC_D7_SCM
aggregated .bw file for 10 donors


title: bph_bpn_bpniv_bpnlv_2023_012

description: Library name: DSP-1001660021860-E-B01


title: bulkATAC_D6_CD4_TSCM

description:
Library name: bATAC_D6_SCM
aggregated .bw file for 10 donors


title: bulkATAC_D8_CD4_TSCM

description:
Library name: bATAC_D8_SCM
aggregated .bw file for 10 donors


title: bph_bpn_bpniv_bpnlv_2023_009

description: Library name: DSP-1001660021860-E-A10


title: bph_bpn_bpniv_bpnlv_2023_010

description: Library name: DSP-1001660021860-E-A11

value: BPH3 LVTF VSM


title: bulkATAC_D5_CD4_TSCM

description:
Library name: bATAC_D5_SCM
aggregated .bw file for 10 donors


title: bph_bpn_bpniv_bpnlv_2023_011

description: Library name: DSP-1001660021860-E-A12


title: WJL2610_RLF_N024

description:
Library name: WJL2610
5'Smu bait priming

value: CD21 xrcc4-/-


title: WJL2609_RLF_N024

description:
Library name: WJL2609
5'Smu bait priming


title: bph_bpn_bpniv_bpnlv_2023_006

description: Library name: DSP-1001660021860-E-A07


title: bph_bpn_bpniv_bpnlv_2023_007

description: Library name: DSP-1001660021860-E-A08


title: bulkATAC_D4_CD4_TSCM

description:
Library name: bATAC_D4_SCM
aggregated .bw file for 10 donors

value: PBMC


title: bulkATAC_D3_CD4_TSCM

description:
Library name: bATAC_D3_SCM
aggregated .bw file for 10 donors


title: WJL2608_RLF_N024

description:
Library name: WJL2608
5'Smu bait priming


title: WJL2612_RLF_N024

description:
Library name: WJL2612
5'Smu bait priming

value: WT


title: bph_bpn_bpniv_bpnlv_2023_004

description: Library name: DSP-1001660021860-E-A05

value: BPH3 LVTF endothelium


title: bph_bpn_bpniv_bpnlv_2023_003

description: Library name: DSP-1001660021860-E-A04

value: BPH5 LVTF VSM


title: bulkATAC_D2_CD4_TSCM

description:
Library name: bATAC_D2_SCM
aggregated .bw file for 10 donors


title: WJL2607_RLF_N024

description:
Library name: WJL2607
5'Smu bait priming

value: Spleen


title: bph_bpn_bpniv_bpnlv_2023_002

description: Library name: DSP-1001660021860-E-A03

value: BPH5 LVTF endothelium


title: bulkATAC_D1_CD4_TSCM

description:
Library name: bATAC_D1_SCM
aggregated .bw file for 10 donors


title: WJL2606_RLF_N024

description:
Library name: WJL2606
5'Smu bait priming


title: bph_bpn_bpniv_bpnlv_2023_001

description: Library name: DSP-1001660021860-E-A02

value: hipertension


title: 72 hpi, Donor 3, Uganda infected

city: Bochum

first: André

last: Gömer

address: University Street 150

department: MMV

country: Germany

institute: Ruhr University Bochum

description: Library name: PHH24

data_processing:
CLC Genomics Workbench (Qiagen, Aarhaus)
Single reads were mapped to the Hg38 genome scaffold, with gene and transcript annotations.
For each sample, read counts for each human gene were normalised (RPKM, TPM)
Hg38 mappings were used in to identify differentialy expressed genes (DEGs) in the host between conditions (FDR <0.05)
Assembly: Hg38
Supplementary files format and content: Each sample has  .xlsx file containing processed data after Hg38 Mapping. This includes columns for Name; Chromosome; Region; Expression value; TPM; RPKM; Exons; Gene ID; Gene length; ENSEMBL; Biotype; Unique gene reads; Total gene reads; Transcripts annotated; Uniquely identified transcripts; Exon length; Unique exon reads; Total exon reads; Ratio of unique to total (exon reads); Unique exon-exon reads; Total exon-exon reads; Unique intron reads; Total intron reads; Ratio of intron to total gene reads

source_name: Liver

growth_protocol: PHH were thawed and seeded at a density of 2.5×105 live cells/well on collagen-coated 24-well plates one day prior to YFV infection. In line with the provider’s recommendations, plated PHHs were maintained in a 37°C incubator with 5% CO2 in either William’s E Medium (CM4000, ThermoFisher) or Human Hepatocyte Maintenance Medium (HHMM-500, PRIMACYT), with the recommended supplements added to maintenance media immediately prior to use

extract_protocol:
Total RNA was extracted using Direct-zol RNA miniprep kit (Zymo Research) according to manufacturer’s instructions. RNA quality and quantity were analyzed using the NanoDrop One (Thermo Scientific) and Agilent Bioanalyser
PHH sequencing library preparation was performed according to NNSR priming method as described previously with the following modifications. One μg of total RNA was used for mRNA isolation using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB). An RNA fragmentation step of 5 minutes at 95oC in the buffer of the Maxima H- reverse transcriptase (RT) (Thermo Scientific) was performed before the RT reaction, which was done in the presence of Actinomycin D. After the RT, Thermolabile Exonuclease I (NEB) was used to digest the RT primer. Following RNase H (NEB) treatment the 2nd strand cDNA synthesis was performed with Klenow exo(-) (NEB). After a 1.5-volume magnetic bead purification, 10% of the sample volume was subjected to RT-qPCR to determine the number of amplification cycles required for the barcoding PCRs.

treatment_protocol: PHH were infected with YFV (3 distinct strains MOI 0.5) or left uninfected

value: Liver

value: Primary human hepatocyte

value: YFV infected 72 hpi


title: No Template Control

description: Library name: DSP-1001660021860-E-A01

source_name: No Template Control

value: No Template Control


title: WJL2611_RLF_N024

description:
Library name: WJL2611
5'Smu bait priming

value: Primary B cells

value: CD21 xrcc4-/- polq-/-


title: endhothelial scRNA-seq

city: Cincinnati

first: Yunguan

last: Wang

state: oh

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

description: Library name: endothelial_scRNA-seq_multiplexed

library_source: transcriptomic single cell

data_processing:
The Parsebio split-pipe software was used to demultiplex reads, align to reference genome and quantify gene expression in single cells. The human genome Hg38 was used as the reference genome.
Assembly: HG38
Supplementary files format and content: all_genes.csv, gene annotations
Supplementary files format and content: sample_loading_table.xlsm, sample loading table used by split-pipe
Supplementary files format and content: count_matrix.mtx, cell by gene matrix
Supplementary files format and content: cell_metadata.csv, processed cell annotations

molecule: nuclear RNA

growth_protocol: Cells were used in passages 4 and 5, and maintained in normal human EC growth medium (Cell Applications, #211-500).

extract_protocol:
Human male and female normal and hypertensive HAoECs were infected by sendai virus expressing egfp or OSK factors for 0, 3, and 7 days. The cells were trypsinized and collected. Multiplex scRNA-seq was performed.
Parse Evercode™ single-cell library kit was used for library construction (Pars Bioscience, Seattle, WA, USA). Approximately 4500 cells per sample were processed. Paired-end sequencing was performed on a NovaSeq 6000 system (Illumina, San Diego, CA, USA) for 50 K reads per cell.

treatment_protocol: At 60% confluence, the HAoEC were randomly infected with sendai virus (SeV) carried polycistronic Klf4-Oct3/4-Sox2 and Klf4 vectors (Thermo Fisher Scientific, #A16517), here referred as OSK-SeV, to induce cell reprogram. The MOI of Klf4-Oct3/4-Sox2 and Klf4 was respectively 5:3. The HAoEC was also infected with control SeV with EmGFP (Thermo Fisher Scientific, A16519), named as EGFP-SeV (control condition). Some experiments were performed with SeV with no EGFP to avoid green fluorescence interference. In this case, PBS was used as control condition, and OSK-SeV with no EGFP referred to the OSK factors overexpression in HAoEC. The ECs were collected at day 5 for further analysis.

value: thoracic aorta

tag: cell line

value: primary human aortic endothelia cell

value: endothelial cell


title: Trp53_wildtype_non-irradiated_replicate_5

city: Zurich

first: Jonas

last: Fullin

address: Rämistrasse 100

department: Department  of Medical Oncology and Hematology

country: Switzerland

institute: University of Zurich

description: Library name: non-irradiated_wild-type_5

data_processing:
Quality control, mapping and differential gene expression analysis was performed using the SUSHI bioinformatics pipeline. Gene set enrichment analysis was performed using the GSEA software developed jointly by UC San Diego and the Broad Institute.
Assembly: NCBI
Supplementary files format and content: excel, normalized counts

molecule: polyA RNA

source_name: Bone marrow

extract_protocol:
PicoPure RNA Isolation Kit (ThermoFisher)
Illumina Stranded mRNA Prep, Ligation

value: Bone marrow


title: Trp53_wildtype_non-irradiated_replicate_4

description: Library name: non-irradiated_wild-type_4


title: bph_bpn_bpniv_bpnlv_2023_008

description: Library name: DSP-1001660021860-E-A09

value: blood vessels

value: BPH2 LVCO VSM


title: 72 hpi, Donor 2, Uganda infected

description: Library name: PHH20


title: GIST-PDS-3

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

description: Library name: PDS_3_S24

data_processing:
Quality of sequenced reads was accessed through FastQC v0.11.5.
Unwanted adapter and rRNA matching reads were filtered out with Trimmomatic = 0.38.
Trimmed reads were aligned to human genome assembly hg38 (UCSC) with STAR 2.7.11a
Then counted with HTSeq v2.0.5 against Gencode v43 basic annotation
Further analyses, including FPKM normalization, were conducted in R environment (edgeR v4.2.1).
Assembly: Hg38 UCSC
Supplementary files format and content: Tables with raw and FPKM normalized counts per transcript and gene, respectively.

source_name: GIST 430

growth_protocol: GIST cells were grown in a humidified atmosphere of 5% CO2 at 37 °C (LamSystems, Miass, Russia).

extract_protocol:
Total RNA was isolated from the GIST cell lines using the TRIzol reagent (RNAiso, Invitrogen, Carlsbad, CA, USA).
The quantity and purity of RNA was estimated on a NanoPhotometer (Implen), and 800 ng of RIN ≥7 of total RNA was used for library construction using NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra II™ Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA) according to the manu-facturer’s instruction.

treatment_protocol: GIST T-1 cell line was established from a metastatic pleural tumor from stomach GIST and contains heterozygous 57-base pair deletion (V570-Y578) in KIT exon 11. IM-resistant GIST T-1R subline was established in our laboratory after a continuous induction from 0.4 nM to 1000nM IM in a stepwise increasing concentration manner. The knockdown of CLDN1 and FGFR2 was performed using a SMARTpool (Dharmacon, Lafayette, CO, USA). A non-targeting siRNA (Dharmacon, Lafayette, CO, USA) was used for negative control. Briefly, 10 μl of Lipofectamine 2000 (Thermo Fisher Scientific, Waltham, MA, USA) and 10 μl of siRNA (20 μM) or negative control were mixed with Opti-MEM (Gibco, NY, USA) to a final volume of 400 μl per well at room temperature for 30 min according to the manufacturer’s protocol. Next, a transfection mix was introduced into 70% confluent GIST T-1R culture for 10 h. After the mix was removed, the cells were cultured in a complete culture medium for 48 h before RNA extraction.

value: GIST 430


title: 72 hpi, Donor 3, Asibi infected

description: Library name: PHH23


title: Trp53_wildtype_non-irradiated_replicate_3

description: Library name: non-irradiated_wild-type_3


title: GIST-PDS-2

description: Library name: PDS_2_S23


title: bph_bpn_bpniv_bpnlv_2023_005

description: Library name: DSP-1001660021860-E-A06

value: BPH3 LVTF VSM


title: 72 hpi, Donor 1, Asibi infected

description: Library name: Asibi_3


title: Trp53_wildtype_non-rradiated_replicate_2

description: Library name: non-irradiated_wild-type_2


title: Trp53_wildtype_non-irradiated_replicate_1

description: Library name: non-irradiated_wild-type_1


title: 72 hpi, Donor 2, 17D infected

description: Library name: PHH18


title: 72 hpi, Donor 1, 17D infected

description: Library name: 17D


title: 72 hpi, Donor 3, 17D infected

description: Library name: PHH22


title: GIST-PDS-1

description: Library name: PDS_1_S22


title: GIST-T1R-3

description: Library name: cntrl_3_S18

value: no treatment


title: monoallelic_Trp53_mutation_non-irradiated_replicate_4

description: Library name: non-irradiated_monoallelic_4


title: 72 hpi, Donor 3, mock

description: Library name: PHH21

value: Uninfected 72 hpi


title: 48 hpi, Donor 3, Uganda infected

description: Library name: PHH16

value: YFV infected 48 hpi


title: GIST-T1R-2

description: Library name: cntrl_2_S17


title: GIST-T1R-1

description: Library name: cntrl_1_S16


title: 72 hpi, Donor 1, mock

description: Library name: mock3d

value: Liver


title: monoallelic_Trp53_mutation_non-irradiated_replicate_3

description: Library name: non-irradiated_monoallelic_3


title: 72 hpi, Donor 1, Uganda infected

description: Library name: Uganda_3

value: Primary human hepatocyte


title: monoallelic_Trp53_mutation_non-irradiated_replicate_2

description: Library name: non-irradiated_monoallelic_2


title: 48 hpi, Donor 2, Uganda infected

description: Library name: PHH12


title: 48 hpi, Donor 1, Uganda infected

description: Library name: Uganda_2


title: 72 hpi, Donor 2, mock

description: Library name: PHH17


title: siCLDN1-GIST-3

description: Library name: cldn3_S21


title: monoallelic_Trp53_mutation_non-irradiated_replicate_1

description: Library name: non-irradiated_monoallelic_1


title: 48 hpi, Donor 2, Asibi infected

description: Library name: PHH11


title: siCLDN1-GIST-2

description: Library name: cldn2_S20


title: 48 hpi, Donor 3, Asibi infected

description: Library name: PHH15


title: 72 hpi, Donor 2, Asibi infected

description: Library name: PHH19

value: YFV infected 72 hpi


title: 48 hpi, Donor 1, Asibi infected

description: Library name: Asibi_2


title: biallelic_Trp53_mutation_non-irradiated_replicate_5

description: Library name: non-irradiated_biallelic_5


title: 48 hpi, Donor 3, 17D infected

description: Library name: PHH14


title: 48 hpi, Donor 2, 17D infected

description: Library name: PHH10


title: siCLDN1-GIST-1

description: Library name: cldn1_S19


title: hZ_Z2, RCAS-hZic3 injected, zeugopod

status: Public on Aug 27 2025

city: Shenyang

first: Bai

last: Shibin

address: 120 Dongling Road

country: China

institute: Shenyang Agriculture University

description: treatment

data_processing:
Reads were mapped to the NCBI Gallus gallus genome assembly (bGalGal1.mat.broiler.GRCg7b) with inserted human-Zic3 cDNA sequences using HISAT2 version 2.2.1.
Transcript assembly by StringTie v2.1.7
Use prepDE.py3 script of StringTie to get raw counts and TPM counts
Assembly: bGalGal1.mat.broiler.GRCg7b
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

organism: Gallus gallus

source_name: hindlimb zeugopod

extract_protocol:
Total RNA was extracted using the RNeasy micro kit (Qiagen, Hilden, Germany), with on-column DNase to remove contaminating genomic DNA. RNA concentration and purity were measured using NanoDrop 2000. (Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit from the Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

value: hindlimb zeugopod

value: tissue

value: RCAS-hZic3 overexpression


title: 48 hpi, Donor 1, 17D infected

description: Library name: 17D_2


title: biallelic_Trp53_mutation_non-irradiated_replicate_4

description: Library name: non-irradiated_biallelic_4


title: biallelic_Trp53_mutation_non-irradiated_replicate_3

description: Library name: non-irradiated_biallelic_3


title: 48 hpi, Donor 3, mock

description: Library name: PHH13

value: Uninfected 48 hpi


title: 48 hpi, Donor 2, mock

description: Library name: PHH9


title: bulkTCR_D1_tcrb_P

description: Library name: D1_tcrb_P

data_processing:
The sequencing data was mapped and analyzed using MIGEC software (version 1.2.9) with default settings.
Sample fastq were obtained with command Checkout (parameters -cute) from MIGEC software.
Histogram, AssembleBatch, CdrBlastBatch and FilterCDRBlastResultsBatch functions from MIGEC were used to define TCR sequences.
Downstream analysis was performed using V(D)J tools with default settings.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Processed data is supplied as Supplementary Information in the manuscript.
Library strategy: TCR-Seq

growth_protocol: Various T memory cell types including CD4-Naive were sorted from PBMCs using flow cytometry (FACS). The sorted cells were lysed using TRIzol (Invitrogen) for RNA extraction. No particular cell growth procedure was required.

extract_protocol:
TCR-seq was performed as described previously by Shugay et. al., 2014 with 5ng of total RNA. Total RNA was purified using a RNEasy Micro kit (Qiagen, #74004), QC-ed using Fragment Analyzer and quantified using standard curve method via qPCR.
TCR-seq was performed as described previously by Shugay et. al., 2014 with 5ng of total RNA.
TCRα and TCRβ specific libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina following manufacturer’s recommendations. Pooled libraries were sequenced using NovaSeq 6000 (Illumina) for 150-bp paired-end sequencing.

treatment_protocol: No particular treatment was done to the PBMCs. PBMCs were immuno stained and sorted using FACS for RNA isolation.

value: PBMC

tag: attribute


title: 24 hpi, Donor 3, Uganda infected

description: Library name: PHH8

value: YFV infected 24 hpi


title: bulkTCR_D1_tcrb_EM

description: Library name: D1_tcrb_EM


title: 24 hpi, Donor 3, Asibi infected

description: Library name: PHH7


title: biallelic_Trp53_mutation_non-irradiated_replicate_2

description: Library name: non-irradiated_biallelic_2

value: Bone marrow


title: 24 hpi, Donor 1, Asibi infected

description: Library name: Asibi_1


title: biallelic_Trp53_mutation_non-irradiated_replicate_1

description: Library name: non-irradiated_biallelic_1


title: 24 hpi, Donor 3, 17D infected

description: Library name: PHH6


title: 24 hpi, Donor 2, Uganda infected

description: Library name: PHH4


title: 24 hpi, Donor 1, Uganda infected

description: Library name: Uganda_1


title: bulkTCR_D1_tcrb_N

description: Library name: D1_tcrb_N


title: 24 hpi, Donor 2, Asibi infected

description: Library name: PHH3


title: 24 hpi, Donor 2, 17D infected

description: Library name: PHH2


title: bulkTCR_D1_tcrb_E

description: Library name: D1_tcrb_E


title: Trp53_wildtype_irradiated_replicate_5

description: Library name: irradiated_wild-type_5


title: Trp53_wildtype_irradiated_replicate_3

description: Library name: irradiated_wild-type_3


title: bulkTCR_D1_tcrb_CD8RA

description: Library name: D1_tcrb_CD8RA


title: bulkTCR_D1_tcrb_CM

description: Library name: D1_tcrb_CM


title: Trp53_wildtype_irradiated_replicate_2

description: Library name: irradiated_wild-type_2


title: Trp53_wildtype_irradiated_replicate_4

description: Library name: irradiated_wild-type_4


title: 24 hpi, Donor 3, mock

description: Library name: PHH5

value: Uninfected 24 hpi


title: 24 hpi, Donor 1, 17D infected

description: Library name: 17D_1


title: bulkTCR_D1_tcrb_SCM

description: Library name: D1_tcrb_SCM


title: 24 hpi, Donor 2, mock

description: Library name: PHH1


title: 48 hpi, Donor 1, mock

description: Library name: mockD2


title: bulkTCR_D1_tcra_SCM

description: Library name: D1_tcra_SCM


title: bulkTCR_D1_tcra_P

description: Library name: D1_tcra_P


title: Trp53_wildtype_irradiated_replicate_1

description: Library name: irradiated_wild-type_1


title: 24 hpi, Donor 1, mock

description: Library name: mockD1


title: monoallelic_Trp53_mutation_irradiated_replicate_5

description: Library name: irradiated_monoallelic_5


title: bulkTCR_D1_tcra_N

description: Library name: D1_tcra_N


title: MDA-MB-231, nanoparticles, no laser, rep4

city: Kuopio

first: Tiit

last: Örd

address: Neulaniementie 2

country: Finland

institute: A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland

data_processing:
Fastq files were processed using the nf-core RNA-Seq pipeline (version 3.14; https://nf-co.re/rnaseq/) using the default workflow (STAR for alignment, salmon for quantification) with the GRCh38 human genome and Ensembl release 98 transcript definitions.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample (gene quantification using salmon).

growth_protocol: Human MDA-MB-231 breast cancer cells were cultured in RPMI 1640 cell culture medium (Biowest) supplemented with 10% fetal bovine serum (Gibco) and 1% penicillin-streptomycin (Gibco). The culture was maintained at 37 °C in a humidified atmosphere of 5% CO2. The cells were detached using 0.25% trypsin-EDTA (Gibco), centrifuged at 1200 rcf for 5 min, seeded at 30000 cells per well into a 96-well plate and grown for 24 h.

extract_protocol:
Total RNA was extracted using the Monarch Total RNA Miniprep Kit (New England Biolabs). Two wells were pooled for each sample to increase RNA yield.
RNA-seq libraries were prepared using the QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with UDI (Lexogen). The libraries were quantified with the Qubit dsDNA HS Assay (Fisher Scientific) and their length was assessed using a Fragment Analyzer with the HS NGS Fragment Kit (Agilent).

treatment_protocol: The cell culture medium was replaced with the fresh medium containing the biomimetic nanoparticles (NPs; 200 µl, 0.1 mg/ml). The cells were incubated with the NPs for 4 h. One well of the 96-well plate was irradiated at a time for 10 min with a 808 nm continuous wave laser and the temperature of the laser was controlled at 46, 50 or 54 °C. After laser irradiations, the cells were washed once with Hanks’ balanced salt solution (Biowest).

value: breast cancer

tag: treatment with_nanoparticles

value: 4 h incubation with nanoparticles

tag: temperature for_laser_treatment

value: No laser

tag: replicate

tag: library column_name_in_matrix


title: monoallelic_Trp53_mutation_irradiated_replicate_4

description: Library name: irradiated_monoallelic_4

tag: treatment


title: scATAC_exvivoTSCM_6donors

description:
Library name: scTSCM_ATAC
10X Genomics ATAC v1; open chromatin

library_source: genomic single cell

data_processing:
Demultiplexed raw FASTQ files corresponding single-cell open chromatin libraries from each lane of 10X Genomics run were mapped to the human reference genome GRCh38 using 10X Genomics’ cellranger (v2.1.0) atac pipeline.
R-based Seurat package (v5.0.1) and Signac (v1.13.9) were used for analysis.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Default ouput files as part of cellranger multi pipeline. "barcodes.tsv" contains barcodes for all captured nuclei. "peaks.bed" contains peaks corresponding to all open chromatin across nuclei. "matrix.mtx" contains the count matrix for all nuclei for all corresponding peaks.

growth_protocol: CD4-TSCM compartment was directly sorted using flow cytometry (FACS) from PBMCs into collection medium (1:1 FBS:PBS). The sorted cells were washed with 1X PBS and subjected to scATAC-Seq using manufacturer's protocol (10X Genomics). No particular cell growth procedure was required.

extract_protocol:
PBMCs were thawed and cells of interest were sorted based on experimental requirement after staining with fluorescence conjugated cell-surface protein antibodies. Ex vivo sorted cells were thoroughly washed using 1X PBS and maintained at a viability >95%.
scATAC-Seq with 10x Genomics v1. About 25,000 transposed nuclei were loaded onto Chromium NextGEM Chip H. Manufacturers’ recommendations were followed to generate libraries.
Libraries were sequenced on NextSeq 2000 (Illumina) for sequencing according to manufacturer's recommendations.

treatment_protocol: No particular treatment was done to the PBMCs. PBMCs were immuno stained and sorted using FACS for scATAC-Seq experiment.

tag: tissue

tag: cell type

value: ex vivo TSCM cells

value: donor_#:D1 to D6

tag: library type

value: ATAC


title: scRNA_invitrodiff_Naive_TSCM_Day10_Th1_GEX

description:
Library name: scdiff_n_scm_D10_Th1_GEX
10X Genomics 5' v2; gene expression (GEX)

data_processing:
Demultiplexed raw FASTQ files corresponding to 5ʹ single-cell gene expression, associated V(D)J and cell surface protein libraries from each lane of 10X Genomics run were mapped to the human reference genome GRCh38 using 10X Genomics’ cellranger (v7.1.0) multi pipeline.
Individual 10X Genomics run was processed independently using the R-based Seurat package (v5.0.1) before integrating multiple datasets to mitigate batch effects or were merged if the experiments were performed concomitantly.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Default ouput files as part of cellranger multi pipeline. "barcodes.tsv.gz" contains barcodes for all captured cells. "features.tsv" contains annotated transcripts. "matrix.mtx.gz" contains the count matrix for all cells for all corresponding annotated transcripts.
Supplementary files format and content: Captured TCR data is supplied as a supplementary file in the manuscript.

growth_protocol: CD4-Naive (CD3+CD4+CD45RA+CCR7+CD95-) and CD4-TSCM (CD3+CD4+CD45RA+CCR7+CD95+) were isolated from PBMCs of healthy human donors and activated for 48 hrs using aCD3/aCD28 Dynabeads in a Th1 polarizing milieu of cytokines and antibodies. The cells were then cultured in the Th1 polarizing condition.

extract_protocol:
On the mentioned day (D10), the cells were taken from culture and washed thoroughly with 1X PBS, and maintained at >95% viability. Cells were stained with hashtag oligos (TotalSeqC, BioLegend) for demarcating donors.
scRNA-Seq with 10x Genomics 5' v2. About 25,000 cells per lane were loaded onto Chromium NextGEM Chip K. Manufacturers’ recommendations were followed to generate libraries for transcriptome, TCR repertoire and cell surface proteins.
Libraries were sequenced on NovaSeq 6000 (Illumina) for 150-bp paired-end sequencing.

treatment_protocol: Th1 polarizing milieu of cytokines and antobodies (refer to methods section of manuscript).

value: in vitro differentiated and Th1 polarized naive and TSCM CD4 T cells cultured for 10 days

tag: donor #

value: D1 to D6

value: mRNA


title: bulkTCR_D1_tcra_EM

description: Library name: D1_tcra_EM


title: scRNA_invitrodiff_Naive_TSCM_Day10_Th1_ADT

description:
Library name: scdiff_n_scm_D10_Th1_ADT
10X Genomics 5' v2; cell surface protein (CSP)

value: ADT


title: MDA-MB-231, nanoparticles, no laser, rep2


title: monoallelic_Trp53_mutation_irradiated_replicate_3

description: Library name: irradiated_monoallelic_3


title: MDA-MB-231, nanoparticles, no laser, rep3


title: MDA-MB-231, nanoparticles, no laser, rep1


title: bulkTCR_D1_tcra_E

description: Library name: D1_tcra_E


title: monoallelic_Trp53_mutation_irradiated_replicate_2

description: Library name: irradiated_monoallelic_2


title: MDA-MB-231, no nanoparticles, no laser, rep4

value: No nanoparticles


title: bulkTCR_D1_tcra_CM

description: Library name: D1_tcra_CM


title: MDA-MB-231, no nanoparticles, no laser, rep3


title: bulkTCR_D1_tcra_CD8RA

description: Library name: D1_tcra_CD8RA


title: monoallelic_Trp53_mutation_irradiated_replicate_1

description: Library name: irradiated_monoallelic_1


title: MDA-MB-231, no nanoparticles, no laser, rep2


title: MDA-MB-231, no nanoparticles, no laser, rep1


title: biallelic_Trp53_mutation_irradiated_replicate_4

description: Library name: irradiated_biallelic_4


title: scRNA_invitrodiff_Naive_TSCM_Day10_Th1_VDJ

description:
Library name: scdiff_n_scm_D10_Th1_VDJ
10X Genomics 5' v2; TCR repertoire (VDJ)

value: TCR


title: bulkTCR_D4_tcrb_SCM

description: Library name: D4_tcrb_SCM


title: MDA-MB-231, nanoparticles, laser 54 °C, rep3

value: 54 °C


title: MDA-MB-231, nanoparticles, laser 54 °C, rep2


title: MDA-MB-231, nanoparticles, laser 54 °C, rep1


title: bulkTCR_D4_tcrb_P

description: Library name: D4_tcrb_P

value: PBMC


title: MDA-MB-231, nanoparticles, laser 54 °C, rep4


title: MDA-MB-231, nanoparticles, laser 50 °C, rep4

value: 50 °C


title: biallelic_Trp53_mutation_irradiated_replicate_2

description: Library name: irradiated_biallelic_2

value: Bone marrow


title: MDA-MB-231, nanoparticles, laser 50 °C, rep3


title: bulkTCR_D4_tcrb_N

description: Library name: D4_tcrb_N


title: biallelic_Trp53_mutation_irradiated_replicate_1

description: Library name: irradiated_biallelic_1


title: biallelic_Trp53_mutation_irradiated_replicate_3

description: Library name: irradiated_biallelic_3


title: MDA-MB-231, nanoparticles, laser 50 °C, rep1


title: AML sample from mouse with monoallelic transgenes mouse 5

description: Library name: AML_monoallelic_5

source_name: bone marrow

extract_protocol:
RNeasy Plus Mini Kit (Qiagen)
Smartseq II

value: bone marrow


title: MDA-MB-231, nanoparticles, laser 50 °C, rep2

value: breast cancer


title: MDA-MB-231, nanoparticles, laser 46 °C, rep4

value: 4 h incubation with nanoparticles

value: 46 °C


title: bulkTCR_D4_tcrb_E

description: Library name: D4_tcrb_E


title: AML sample from mouse with monoallelic transgenes mouse 4

description: Library name: AML_monoallelic_4


title: bulkTCR_D4_tcrb_CM

description: Library name: D4_tcrb_CM


title: MDA-MB-231, nanoparticles, laser 46 °C, rep2


title: AML sample from mouse with monoallelic transgenes mouse 3

description: Library name: AML_monoallelic_3


title: MDA-MB-231, nanoparticles, laser 46 °C, rep3


title: bulkTCR_D4_tcrb_CD8RA

description: Library name: D4_tcrb_CD8RA


title: hPSC, shPIN1, untreated

city: Portland

first: Ellen

last: Langer

state: OR

address: 2720 SW Moody Ave

department: DOS (Department of Oncological Sciences)

institute: Oregon Health and Science University

description: Library name: hPSC_shPIN1_Untreated

data_processing:
bcl2fastq to process raw sequencing reads to FASTQ format
universal demultiplexer (unidex) to generate index-matched FASTQ files for each sample/experimental condition
scitools fastq-sci2geo to generate FASTQ index files for each demultiplexed sample
Assembly: hg38
Supplementary files format and content: Barcode-matched and demultiplexed sciATAC-seq data as FASTQ files (R1, R2, and index) for each sample/experimental condition. All barcodes are included regardless of per-cell quality metrics.
Supplementary files format and content: Metadata included as tab-separated files that detail the 1) sample/experimental group, 2) PhenoGraph cluster, and 3) UMAP coordinates of processed barcodes used in the analysis. An additional file containing all possible barcodes from combinatorial indexing and their corresponding sample/experimental group is included.

source_name: pancreatic stellate cells

growth_protocol: Primary human pancreatic stellate cells were purchased from Sciencell and grown in 2D in Stellate Cell Media.

extract_protocol:
Nuclei isolation using sci-ATAC-seq protocols
sci-ATAC-seq protocol

treatment_protocol: PSCs were infected with an shSCR (control) or shPIN1 (knockdown) lentivirus and stable pools selected with puromycin. Cells were plated overnight, and then treated +/- 5 ng/mL TGFB for 8 hours prior to collection.

value: pancreatic stellate cells


title: hPSC, shSCR, TGFB

description: Library name: hPSC_shSCR_TGFb

value: shSCR+TGFB


title: bulkTCR_D4_tcra_SCM

description: Library name: D4_tcra_SCM


title: hPSC, shPIN1, TGFB

description: Library name: hPSC_shPIN1_TGFb


title: hPSC, shSCR, untreated

description: Library name: hPSC_shSCR_Untreated

value: shSCR


title: AML sample from mouse with monoallelic transgenes mouse 2

description: Library name: AML_monoallelic_2


title: AML sample from mouse with monoallelic transgenes mouse 1

description: Library name: AML_monoallelic_1


title: hPSC, shPIN1, TGFB, rep5

state: Oregon

address: 2720 S Moody Ave

department: CEDAR

institute: OHSU

description: Library name: PSCPINT5

data_processing:
Base calling using bcl2fastq
Adapter trimming and quality filtering were performed using Trimmomatic v0.39. Reads shorter than 36 bases after trimming were discarded.
Trimmed reads were aligned to the GRCh38 human reference genome using STAR v2.7.11b with default parameters.
Aligned BAM files were subsequently processed with featureCounts v2.0.8 to generate gene-level count matrices. All downstream differential expression analyses were performed using DESeq2 v1.46.0.
Assembly: GRCh38
Supplementary files format and content: Knockdown_proteincoding_fpkm.txt (FPKM  of all protein coding genes, text file, Genes exhibiting zero counts across all samples were filtered out prior to downstream analysis.)
Supplementary files format and content: Knockdown_COUNTS.txt (text file, counts table)

extract_protocol:
Qiagen Rneasy kit
For paired end RNA-seq, mRNA 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 then underwent end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and RT-PCR for quantification and bioanalyzer for size distribution. Quantified libraries were pooled and sequenced on an Illumina NovoSeq X plus. For single end RNA-seq, sequencing libraries were constructed using a TruSeq Stranded mRNA kit (Illumina, San Diego, CA). Briefly, poly(A)+ RNA was isolated using oligo-dT-coated magnetic beads. The recovered RNA was then chemically fragmented. First strand cDNA was generated using random hexamers as primers for reverse transcriptase. Strand-specific second strand cDNA synthesis was performed and a single ‘A’ nucleotide was then added to each end. Illumina adaptors were ligated to the cDNAs. Limited-round (15-cycle) PCR was used to amplify the material to yield the final libraries. Library concentration was determined using real-time PCR with primers complementary to the Illumina adaptors. Sample libraries were diluted and applied to an IlluminaNextSeq500 HiOutput flow cell. Llibraries were prepared with indexing barcodes to permit multiplexing in a single lane. The 75-cycle single read sequencing was used to assemble the reads into standard fastq formatted data.

treatment_protocol: PSCs were infected with an shSCR (control) or shPIN1 (knockdown) lentivirus and stable pools selected with puromycin. Cells were plated overnight, and then treated +/- 5 ng/mL TGFB for 24 hours prior to collection.

tag: shRNA

value: TGFB


title: hPSC, shPIN1, untreated, rep5

description: Library name: PSCPINU5

value: Untreated


title: bulkTCR_D4_tcra_P

description: Library name: D4_tcra_P


title: Healthy MEPs with wild-type Trp53 mutation mouse 3

description: Library name: AML_healthy_control_wt_3


title: hPSC, shSCR, TGFB, rep5

description: Library name: PSCSCRT5


title: bulkTCR_D4_tcrb_EM

description: Library name: D4_tcrb_EM


title: bulkTCR_D4_tcra_N

description: Library name: D4_tcra_N


title: hPSC, shSCR, untreated, rep5

description: Library name: PSCSCRU5


title: Healthy MEPs with wild-type Trp53 mutation mouse 2

description: Library name: AML_healthy_control_wt_2


title: hPSC, shPIN1, TGFB, rep4

description: Library name: PSCPINT4


title: bulkTCR_D4_tcra_EM

description: Library name: D4_tcra_EM


title: Healthy MEPs with wild-type Trp53 mutation mouse 1

description: Library name: AML_healthy_control_wt_1


title: MDA-MB-231, nanoparticles, laser 46 °C, rep1


title: bulkTCR_D4_tcra_E

description: Library name: D4_tcra_E


title: Healthy MEPs with monoallelic Trp53 mutation mouse 3

description: Library name: AML_healthy_control_monoallelic_3


title: hPSC, shSCR, untreated, rep4

description: Library name: PSCSCRU4


title: hPSC, shPIN1, untreated, rep4

description: Library name: PSCPINU4


title: bulkTCR_D4_tcra_CM

description: Library name: D4_tcra_CM


title: Bulk CD8 Lymph Node RNA-Seq 0074

city: Durban

first: Veron

last: Ramsuran

state: KZN

address: Mazisi Kunene Road

country: South Africa

institute: UKZN

description: Library name: 208_30_0074_LN_Bulk_CD8-47048

data_processing:
Lane merged and trimed
MACS2 with IDR 0.1
Diffbind R package and DESeq2 for differential peak accessibility analysis
Assembly: hg19
Supplementary files format and content: TSV with peak numbers, loci and counts
Supplementary files format and content: TSV with Transcript tpm values

source_name: Lymph node

extract_protocol:
Standard Bulk RNA-Seq and ATAC-Seq protocol following FACS sorting of cells from Lymph node or Peripheral blood
ATAC-Seq and RNA-Seq

value: Lymph node

value: CD8+ T cell


title: Bulk CD8 Peripheral Blood RNA-Seq 0069

description: Library name: 208_30_0069_PB_Bulk_CD8-47061

source_name: Peripheral Blood

value: Peripheral Blood


title: bulkTCR_D4_tcra_CD8RA

description: Library name: D4_tcra_CD8RA


title: Bulk CD8 Lymph Node RNA-Seq 0068

description: Library name: 208_30_0068_LN_Bulk_CD8-45050


title: Healthy MEPs with monoallelic Trp53 mutation mouse 1

description: Library name: AML_healthy_control_monoallelic_1


title: Healthy MEPs with monoallelic Trp53 mutation mouse 2

description: Library name: AML_healthy_control_monoallelic_2


title: Bulk CD8 Peripheral Blood RNA-Seq 0074

description: Library name: 208_30_0074_111_30_0037_0_PB_Bulk_CD8-47050


title: bulkTCR_D3_tcrb_SCM

description: Library name: D3_tcrb_SCM


title: Bulk CD8 Peripheral Blood RNA-Seq 0068

description: Library name: 208_30_0068_111_30_0010_PB_Bulk_CD8-45052


title: Healthy MEPs with biallelic Trp53 mutation mouse 3

description: Library name: AML_healthy_control_biallelic_3


title: Bulk CD8 Lymph Node RNA-Seq 0054

description: Library name: 208_30_0054_LN_Bulk_CD8-45053


title: bulkTCR_D3_tcrb_P

description: Library name: D3_tcrb_P


title: Bulk CD8 Peripheral Blood RNA-Seq 0054

description: Library name: 208_30_0054_127_33_1192_879_PB_Bulk_CD8-45055


title: Bulk CD8 Peripheral Blood ATAC-Seq 1192

description:
Library name: cd8.pb.bulk_1192
cd8.pb.bulk.bed
pbln_atac_counts_2025.tsv


title: Healthy MEPs with biallelic Trp53 mutation mouse 2

description: Library name: AML_healthy_control_biallelic_2


title: bulkTCR_D3_tcrb_N

description: Library name: D3_tcrb_N


title: Bulk CD8 Peripheral Blood ATAC-Seq 0063

description:
Library name: cd8.pb.bulk_0063
cd8.pb.bulk.bed
pbln_atac_counts_2025.tsv


title: Healthy MEPs with biallelic Trp53 mutation mouse 1

description: Library name: AML_healthy_control_biallelic_1


title: Bulk CD8 Peripheral Blood ATAC-Seq 0816

description:
Library name: cd8.pb.bulk_0816
cd8.pb.bulk.bed
pbln_atac_counts_2025.tsv


title: hPSC, shSCR, TGFB, rep4

description: Library name: PSCSCRT4


title: Bulk CD8 Peripheral Blood ATAC-Seq 0037

description:
Library name: cd8.pb.bulk_0037
cd8.pb.bulk.bed
pbln_atac_counts_2025.tsv


title: bulkTCR_D3_tcrb_EM

description: Library name: D3_tcrb_EM


title: Bulk CD8 Peripheral Blood ATAC-Seq 0010

description:
Library name: cd8.pb.bulk_0010
cd8.pb.bulk.bed
pbln_atac_counts_2025.tsv


title: Bulk CD8 Lymph Node ATAC-Seq 0074

description:
Library name: cd8.ln.bulk_0074
cd8.ln.bulk.bed
pbln_atac_counts_2025.tsv


title: bulkTCR_D3_tcrb_E

description: Library name: D3_tcrb_E


title: Bulk CD8 Lymph Node ATAC-Seq 0068

description:
Library name: cd8.ln.bulk_0068
cd8.ln.bulk.bed
pbln_atac_counts_2025.tsv


title: AML sample from mouse with biallelic transgenes mouse 5

description: Library name: AML_biallelic_5_Replacement_1


title: Bulk CD8 Lymph Node ATAC-Seq 0054

description:
Library name: cd8.ln.bulk_0054
cd8.ln.bulk.bed
pbln_atac_counts_2025.tsv


title: bulkTCR_D3_tcrb_CM

description: Library name: D3_tcrb_CM


title: Bulk CD8 Lymph Node ATAC-Seq 0052

description:
Library name: cd8.ln.bulk_0052
cd8.ln.bulk.bed
pbln_atac_counts_2025.tsv


title: AML sample from mouse with biallelic transgenes mouse 3

description: Library name: AML_biallelic_3_Replacement_1


title: bulkTCR_D3_tcrb_CD8RA

description: Library name: D3_tcrb_CD8RA


title: bulkTCR_D3_tcra_SCM

description: Library name: D3_tcra_SCM


title: AML sample from mouse with biallelic transgenes mouse 2

description: Library name: AML_biallelic_2_Replacement_1


title: Panc02 cell, treated with TNFa-2

city: Bei Jing

first: Jie

last: Zhao

address: Shuangqing Street

department: Department of Basic Medical Sciences

institute: Tsinghua University

data_processing:
Sequence reads were trimmed for adaptor sequence/low qualitily sequencing by trim_galore, and then mapped to mm10 by Hisat2, count extraction were performed by featurecounts.
Assembly: mm10
Supplementary files format and content: csv file including raw counts for each sample

extract_protocol:
RNA was harvested using TRIzol, then total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina MiSeqReagent kit following manufacturer‘s protocols.

value: pancreatic cancer cells

tag: genotype

value: WT

value: TNFa


title: Bulk CD8 Lymph Node ATAC-Seq 0040

description:
Library name: cd8.ln.bulk_0040
cd8.ln.bulk.bed
pbln_atac_counts_2025.tsv


title: Panc02 cell, untreat-2

value: untreat


title: N153SLSL/LSLPcp2-cre  mouse3

city: DALLAS

last: YAN

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description: Library name: NS3

data_processing:
1) Trim the ends of sequences with remaining adapter or quality scores < 25. Remove any sequence less than 35bp after trimming, then generate a file for capturing information about how many sequences were trimmed. 2) Trimmed Fastq files are aligned to the selected reference genome using STAR (Dobin et al. 2012) 3) Marks Duplicates using SAMBAMBA 4) Features (genes, transcripts and exons) are counted using featureCounts (Liao et al 2014) and StringTie (Pertea et al. 2015) using the Gencode feature table(Harrow et al. 2012) 5) Basic pairwise differential expression analysis is performed using EdgeR (Robinson et al. 2010) and DESeq 6) Abundances of transcripts are calculated using ballgown (Frazee et al. 2014) 7) Identify gene fusions or fused transcripts using STAR-Fusion.
Assembly: mouse GRCm39
Supplementary files format and content: Tab-delimited text file including raw counts for each samples
Supplementary files format and content: Tab-delimited text file including FPKM for each samples

source_name: cerebellum

extract_protocol:
Cerebellar tissues were homogenized and total RNA was isolated with TRI Reagent™  (MilliporeSigma).
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.

value: cerebellum

tag: age

value: 2 months

tag: Sex

value: Female


title: AML sample from mouse with biallelic transgenes mouse 1

description: Library name: AML_biallelic_1_Replacement_1

value: bone marrow


title: Panc02 cell, treated with TNFa-3


title: Bulk CD8 Lymph Node ATAC-Seq 0037

description:
Library name: cd8.ln.bulk_0037
cd8.ln.bulk.bed
pbln_atac_counts_2025.tsv


title: bulkTCR_D3_tcra_P

description: Library name: D3_tcra_P

value: PBMC


title: bulkTCR_D3_tcra_N

description: Library name: D3_tcra_N


title: N153SLSL/LSLPcp2-cre  mouse2

description: Library name: NS2

value: Male


title: Panc02 cell, untreat-3


title: Panc02 cell, untreat-1


title: bulkTCR_D3_tcra_EM

description: Library name: D3_tcra_EM


title: N153SLSL/LSLPcp2-cre  mouse1

description: Library name: NS1


title: Panc02 cell, sgCad-2, co-cultured with BMDMs

value: Cad knockout

value: co-culutre with BMDMs


title: Panc02 cell, sgCad-1


title: AML sample from mouse with biallelic transgenes mouse 4

description: Library name: AML_biallelic_4


title: Panc02 cell, sgCad-2


title: Panc02 cell, sgCad-1, co-cultured with BMDMs


title: N153SLSL/LSL  mouse3

description: Library name: C3


title: bulkTCR_D3_tcra_E

description: Library name: D3_tcra_E


title: LSS3

city: changsha

first: ruijiang

last: Zeng

address: No.139 Renmin Road Central

institute: The Second Xiangya Hospital of Central South University

description:
Library name: SAMPLE 6
B3

data_processing:
Total RNA qualification
mRNA enrichment
Double-strand cDNA synthesis
End repair, ploy-A & adaptor addition
Fragment selection and PCR
Library qualty assessement
Assembly: illumina sequencing
Supplementary files format and content: hg38
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: hVECs

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: hVECs


title: LSS2

description:
Library name: SAMPLE 5
B2


title: N153SLSL/LSL  mouse2

description: Library name: C2


title: LSS1

description:
Library name: SAMPLE 4
B1


title: OSS3

description:
Library name: SAMPLE 3
A3


title: N153SLSL/LSL  mouse1

description: Library name: C1


title: Panc02 cell, treated with TNFa-1


title: OSS2

description:
Library name: SAMPLE 2
A2


title: OSS1

description:
Library name: SAMPLE 1
A1


title: bulkTCR_D10_tcrb_P

description: Library name: D10_tcrb_P


title: T-bet-Eomes-RORγt Triple Knockout 3

city: Orlando

first: Kunal

last: Dhume

state: FLorida

address: 6900 lake Nona Blvd

department: Burnett School of Biomedical Sciences

institute: University Of Central Florida

description:
Library name: Sample 6
column name in rsem_counts.txt: Triple6424

data_processing:
Bcl-convert (v4.2.4) was used to perform demultiplexing, quality control, and adapter trimming.
Read mapping was performed with mouse as a reference genome and using STAR with default parameters.
RSEM2 was used on default parameters to perform feature quantification
Assembly: mm10
Supplementary files format and content: tab-delimited file includes raw counts for each sample

source_name: Primary Transgenic OT-II CD4 T Cells

growth_protocol: Cells were maintained in RPMI 1640 media supplemented with 2 mM L-glutamine, 100 IU penicillin, 100 μg/mL penicillin/streptomycin (Invitrogen), 10 mM HEPES (Gibco), 50 μM 2-mercaptoethanol (MilliporeSigma), and 7.5% FBS (Hyclone)

extract_protocol:
Total RNA was obtained from day 4 in vitro primed CD4 T cells that were resuspended in TRIzol. RNA was further purified by phase separation using cholorform and RNeasy kit (Qiagen). Cells were Dnase treated to remove impurities.
Libraries were prepped using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus Kit and 10bp unique dual indices (UDI).  Paired end 150 bp reads were sequenced using a NovaSeq X Plus. Bcl-convert (v4.2.4) was used to perform demultiplexing, quality control, and adapter trimming. Sequencing reads were distributed as compressed fastq files.

treatment_protocol: To generate Th17 effector cells in vitro, naive T-bet-Eomes Double Knockout Cells or T-bet-Eomes-RORγt OT-II CD4 T cells were plated with an equal number of irradiated antigen presenting cells with OVAII peptide, IL-2 at 11ng/mL,anti-IFNγ Ab (clone XMG1.2) at 15 μg/mL, anti-IL-4 Ab (clone 11B11) at 15 μg/mL, TNF at 10 ng/mL, TGF-β at 0.5 ng/mL, IL-21 at 50 ng/mL, IL-1b at 10 ng/mL, IL-23 at 25 ng/mL and IL-6 at 20 ng/mL.

value: Primary Transgenic OT-II CD4 T Cells

value: CD4 T cell Th17 Cells

value: T-bet-Eomes-RORgt Triple Knockout

value: Th17 Differentiation

tag: batch

value: Day 4 Effectors


title: T-bet-Eomes-RORγt Triple Knockout 2

description:
Library name: Sample 5
column name in rsem_counts.txt: Triple61824


title: bulkTCR_D10_tcrb_N

address: Aruna Asaf Ali Marg

institute: National Institute of Immunology

description: Library name: D10_tcrb_N


title: RT4R-2

description: Library name: sample5

data_processing:
Total RNA qualification
mRNA enrichment
Double-strand cDNA synthesis
End repair, ploy-A & adaptor addition
Fragment selection and PCR
Assembly: Library qualty assessement
Supplementary files format and content: hg38
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: bladder cancer

growth_protocol: RT4 cells were cultured in MEM medium supplemented with 10% fetal bovine serum (FBS) and incubated at 37 °C in 5% CO2.

treatment_protocol: Treat with PBS or cisplatin

value: bladder cancer

value: WT

value: Cisplatin treatment


title: RT4R-3

description: Library name: sample6


title: RT4-2

description: Library name: sample2

value: PBS treatment


title: RT4R-1

description: Library name: sample4


title: T-bet-Eomes Double Knockout 3

description:
Library name: Sample 3
column name in rsem_counts.txt: Double6424

value: T-bet-Eomes Double Knockout


title: bulkTCR_D10_tcrb_E

description: Library name: D10_tcrb_E

source_name: PBMC


title: Short Tx-Group 2, HTO

city: New Haven

first: Edward

last: Doherty

state: CT

address: 300 Cedar street

department: Internal Medicine

institute: Yale School of Medicine

description:
Library name: short_citeseq
10x Genomics Chromium

library_source: other

data_processing:
Raw scRNA-seq data were processed with Cell Ranger v7.1.0 (10x Genomics) for alignment to mm10, quantification, and gene–cell matrix generation, followed by downstream analysis in Seurat v5.1.0 (R v4.3.2) including demultiplexing by hashtag oligo enrichment, quality filtering, normalization, scaling, dimensionality reduction (PCA/UMAP), clustering (Louvain algorithm), and differential expression analysis (DESeq2). Additional analyses included myeloid subset analysis, functional enrichment (GSEA/ORA via clusterProfiler), custom gene module scoring, statistical testing (ggpubr), cell–cell communication inference (CellChat), and transcription factor activity estimation (decoupler).
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: CITE-seq

molecule: protein

source_name: Melanoma tumor

extract_protocol:
Yummer 1.7 melanoma tumor tissue was digested in RPMI/2% FBS supplemented with 0.1 mg/mL collagenase (Sigma) and 1:1000 DNase I (Sigma) for 30 min at 37ºC and then mechanically dissociated. Dissociated tumors were passed through a 70 μM filter and washed in RPMI medium to create a single cell suspension. The cell suspension was subjected to fluorescence-activated cell sorting (FACS) for CD45 expression, yielding CD45+ (immune cell) and CD45- (tumor cell) populations. Post-sorting, the cells were recombined to enrich for immune cells using 20% CD45- and 80% CD45+ cells to achieve a final population of 100,000 cells.
This enriched cell suspension was processed using the Chromium 5′ Single-Cell Gene Expression system (10X Genomics) to generate scRNA seq libraries following the manufacturer’s protocol. Briefly, single-cell suspensions with ≥85% viability were incubated with a pool of oligonucleotide-conjugated antibodies (BioLegend TotalSeq™) for sample indexing. Labeled cells were loaded into a Chromium Next GEM Chip G to generate Gel Bead-In-Emulsions (GEMs), enabling barcoding of individual cells and transcripts. Reverse transcription, cDNA amplification, and separate library construction for gene expression and feature barcodes were performed as described in the 10x Genomics protocol. Libraries were quantified, pooled, and sequenced on an Illumina NovaSeq platform with recommended read configurations.

value: Melanoma tumor

value: Yummer 1.7 melanoma cells

value: Tumor/infiltrating immune cells

value: mixed sample (HTO:Isotype, anti-PD1, anti-MIF, anti-PD1-MIF)


title: RT4-1

description: Library name: sample1


title: T-bet-Eomes-RORγt Triple Knockout 1

description:
Library name: Sample 4
column name in rsem_counts.txt: Triple61224


title: Short Tx-Group 2, GEX

description:
Library name: short_MMT
10x Genomics Chromium

data_processing:
Raw scRNA-seq data were processed with Cell Ranger v7.1.0 (10x Genomics) for alignment to mm10, quantification, and gene–cell matrix generation, followed by downstream analysis in Seurat v5.1.0 (R v4.3.2) including demultiplexing by hashtag oligo enrichment, quality filtering, normalization, scaling, dimensionality reduction (PCA/UMAP), clustering (Louvain algorithm), and differential expression analysis (DESeq2). Additional analyses included myeloid subset analysis, functional enrichment (GSEA/ORA via clusterProfiler), custom gene module scoring, statistical testing (ggpubr), cell–cell communication inference (CellChat), and transcription factor activity estimation (decoupler).
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files


title: bulkTCR_D10_tcrb_EM

city: New Delhi

last: Patil

description: Library name: D10_tcrb_EM

value: PBMC


title: bulkTCR_D3_tcra_CM

description: Library name: D3_tcra_CM


title: bulkTCR_D10_tcrb_CM

description: Library name: D10_tcrb_CM


title: T-bet-Eomes Double Knockout 2

description:
Library name: Sample 2
column name in rsem_counts.txt: Double61824


title: bulkTCR_D3_tcra_CD8RA

description: Library name: D3_tcra_CD8RA


title: Long Tx-Group 1, HTO

description:
Library name: long_citeseq
10x Genomics Chromium


title: Long Tx-Group 1, GEX

description:
Library name: long_MMT
10x Genomics Chromium


title: bulkTCR_D10_tcrb_CD8RA

description: Library name: D10_tcrb_CD8RA


title: ESC passage #15 Rep2

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
The raw reads were processed to remove adapter sequences and trimmed by Cutadapt (default Q ≥ 20).
Only reads with the desired size range (18–28 nucleotides) were considered to identify likely miRNAs.
The obtained reads were mapped against annotated sequences in the mouse miRBase database.
DESeq2 (version 1.30.0) was used to identify differentially expressed miRNAs. Only miRNAs with a maximum adjusted p-value of 0.1 and a minimum combined mean of five read counts were considered to be significantly differentially expressed. Benjamini-Hochberg adjusted p-values were used to determine the false-discovery rates.
Assembly: mm10
Supplementary files format and content: library size normalized counts

source_name: ESC sample

growth_protocol: ESCs were cultured on gelatinized tissue-culture plates in N2B27 medium that consisted of a 1:1 ratio of DMEM/F12 and Neurobasal media, supplemented with 0.1 mM β-mercaptoethanol, 2 mM L-glutamine, 0.1 mM non-essential amino acids, 50 U/ml penicillin, 50 μg/ml streptomycin, and mouse leukemia inhibitory factor in the presence of R2i chemicals (1 μM PD0325901 and 10 μM SB431542). The media refreshment or passaging of the cells was done every other day.

extract_protocol:
Total RNA of ICMs, ICM outgrowths at days 0.5 (=12 hours), 1, 2, 3 and 5, and passage-2, -4, and -15 ESCs was isolated using PureLink miRNA Isolation Kit (Invitrogen) with two-column isolation protocol to separate the small RNA (< 200 nucleotides) and total RNA (> 200 nucleotides) fractions.
A total of 3 μl of small RNA (3–10 ng RNA) was used as the input in a TruSeq Small RNA Library Kit (Illumina) reaction to prepare the small RNA libraries. The cDNA pool was amplified and the libraries were pooled based on the amount of fragments that ranged from 145–160 bp that corresponded to 15–30 bp insert sizes. The size selection of this pool was performed in a PippinHT system (Sage Science) on 3% agarose cassettes with a target size set to 154 bp.

treatment_protocol: The mice were superovulated by administration of HCG (7.5 IU) and PMSG (7.5 IU). E3.5 blastocysts were harvested by flushing the mouse uteri following superovulation. Removal of zona pellucida and immunosurgery for ICM isolation were carried out by placing blastocysts in acidic Tyrode’s solution (pH 2.2) using FBS-coated, pulled glass Pasteur pipettes followed by washing for three times in DMEM/F12 media. Zona-free E3.5 blastocysts were incubated in anti-mouse antisera for 45-60 minutes in a humidified incubator. Next, the embryos were rinsed three times in DMEM/F12 media and incubated in 25-μl droplets of guinea pig complement under mineral oil for 20 minutes, after which they were washed three times in DMEM/F12 media. The ICMs were then isolated from the blastocysts via gentle pipetting using FBS-coated, pulled glass Pasteur pipettes and transferred to gelatin-coated central-well embryo-culture dishes in R2i media. The ICMs were allowed to outgrow into various developmental stages and ESCs at different passages before being collected for small-RNA sequencing. Freshly isolated ICMs, ICMs 12 hours after seeding, ICM outgrowths at days 1, 2, 3, and 5, and passage-2, -4, and -15 ESCs were collected for time-course tracking of the miRNA expression profiles.

tag: strain

value: NMRI

tag: culture media

tag: tissue source

value: Blastocyst

value: ESC


title: bulkTCR_D10_tcrb_SCM

first: Veena

description: Library name: D10_tcrb_SCM

tag: attribute


title: ESC passage #15 Rep1


title: Z2-FKBP_D6DTag24h_RNA_rep3

city: Santander

first: Alvaro

last: Rada-Iglesias

state: Cantabria

address: Albert Einstein 22, PCTCAN

country: Spain

institute: Institute of Biomedicine and Biotechnology of Cantabria

description:
Library name: Sample 57
Column name in counts_allSamples.tsv: Z2-FKBP_D6DTag24h_RNA_rep3

data_processing:
Reads quality control and removal of low quality regions and/or adapters was performed with fastqc (https://www.bioinformatics. babraham.ac.uk/projects/fastqc/), MultiQC and Trimmomatic. Next, reads were mapped to the mouse reference assembly (mm10) using Hisat2. Those reads with a mapping quality below 10 were discarded with Samtools. Subsequently, the number of read counts per gene was calculated with HTseq−count taking as reference gencode.vM25.annotation.gtf. Due to differences in the strandedness of the RNA-Seq libraries generated by the different sequencing companies employed (evaluated with infer_experiment.py tool from RSeQC), specific parameters had to be adjusted when running Hisat2 and HTseq-count. For the samples sequenced via CNAG (WT and Z2KO D3 and D5 samples, as well as Z3K0 D0 samples), the library was prepared as fr-secondstrand. Accordingly, the --rna-strandedness parameter in Hisat2 was set to FR and the HTseq-count --stranded parameter was set to yes. For the remaining samples (sequenced via Macrogene), the library was fr-firststrand. For these, Hisat2 --rna-strandedness was set to RF and HTseq-count --stranded parameter was set to reverse. A matrix including raw counts per gene for each sample is available in GEO.  Differential expression analyses were done with DESeq2. Prior to performing differential expression analyses, counts per million (CPM) were obtained for each gene using the function cpm() available in the edgeR package. Only genes minimally expressed in at least one of the compared conditions were considered (CPM > 1 for all replicates).Overall, differential expression analyses were done between: • WT D0 mESC and Z2KO D0 mESC. • WT D3 mESC and Z2KO D3 mESC. • WT D5 AntNPCs and Z2KO D5 AntNPCs. • WT D6 AntNPCs and Zic2-/- D6 AntNPCs. • WT D0 mESC and Z3KO D0 mESC. • Zic2FKBPV36+DMSO and Zic2FKBPV36+dTAG-13 for each depletion experiment D6.
Assembly: mm10
Supplementary files format and content: counts_allSamples.tsv: tab-delimited text file which includes raw counts per gene for each sample.

source_name: Z2-FKBP E14Tg2a AntNPCs D6

growth_protocol: mESC maintenance and AntNPCs differentiation protocol. E14Tg2a (E14) mouse ESC were cultured on gelatin-coated plates using Knock-out DMEM (Life Technologies, 10829018) supplemented with 15% FBS (Life Technologies, 10082147), leukemia inhibitory factor (LIF), antifungal and antibiotics (Sigma-Aldrich, A5955), β-mercaptoethanol (ThermoFisher Scientific, 21985023), Glutamax (ThermoFisher Scientific, 35050038) and MEM NEAA (ThermoFisher Scientific, 11140035). Cells were cultured at 37°C with 5% CO2. For the AntNPC differentiation, mESCs were plated at 20.000 cells/cm2 on geltrex-coated plates (ThermoFisher, A1413302) and grown in N2B27 medium: Advanced Dulbecco’s Modified Eagle Medium F12 (Life Technologies, 21041025) and Neurobasal medium (Life Technologies,12348017) (1:1), supplemented with 1 × N2 (R&D Systems, AR009), 1 × B27 (Life Technologies, 12587010), 2mM l-glutamine (Life Technologies, 25030024) and 0.1 mM 2-mercaptoethanol (Life Technologies, 31350010)). During the six days of differentiation, the N2B27 medium was additionally supplemented with the following components: bFGF (ThermoFisher Scientific, PHG0368) 10 ng/ml from day 0 to day 2, Xav939 (Sigma-Aldrich, X3004-5MG) 5 µM from day 2 to day 6, BSA (ThermoFisher Scientific, 15260037) 1 mg/ml at day 0 and 40 µg/mL the remaining days.

extract_protocol:
Total RNA was isolated with the NZY Total RNA Isolation Kit (NZYTech, MB13402) following the manufacturer’s protocol. For RNA-seq applications, 7.5 µg of RNA were treated using the TURBO DNA-free Kit (Thermo Fisher Scientific, AM1907), and RNA integrity (RIN) was assessed on an Agilent 4200 TapeStation. Only samples with RIN > 8 were used for sequencing.
Total RNA from D0 (n=3), D3 (n=4), D5 (n=4) and D6 (n=3) WT and Zic2-/- (Z2KO) cells and Zic2FKBPV36 D6 DMSO-treated and dTAG13-treated D6 (n=3 for all conditions, except for the DMSO 48h treatment where n=2) was purified and DNAse-treated. Libraries for WT and Z2KO D3 and D5 samples, as well as Z3K0 D0 samples, were prepared using stranded mRNA-seq protocols and sequenced on an Illumina NovaSeq platform at CNAG (Barcelona, Spain) with 50 bp PE reads (>40M reads/sample), while the rest of the samples were processed (i.e. quality control and library preparation) and sequenced by Macrogen Inc. (Korea) using the TruSeq Stranded mRNA protocol (150 bp PE reads). For the analyses performed on the heterozygous Zic2+/- AntNPCs (Z2HET), an independent dataset composed by WT (n=3), Z2KO (n=3) and Z2HET (n=3) belonging to an independent differentiation was used. These samples were also processed and sequenced by Macrogen Inc. (Korea) as previously described.

treatment_protocol: Zic2 and Zic3 deletions using CRISPR-Cas9.Pairs of sgRNAs were designed to flank Zic2 coding region using Benchling’s genome engineering toolbox (https://www. benchling.com/). Guides were selected for high on target efficiency and minimal off target potential. Complementary oligonucleotides containing BbsI (NEB, R0539L) overhangs were synthesized and annealed (see Supplementary Data 4) by heating to 95°C for 5 min, followed by gradual cooling down to 25°C at -5 °C/min. Annealed oligos were ligated into BbsI-digested pX330A-hCas9-longchimeric-gRNA-G2P vector using T4 DNA ligase (NEB, M0202L) and transformed into chemically competent E. coli (TOP10) via heat shock. Colonies were plated on LB-ampicillin agar and screened by colony PCR to confirm the presence of the desired insert (see Colony PCR section). Plasmids were purified using the NZY Miniprep Kit (NZYTech, MB01001) and verified by Sanger sequencing with the pX330A_R primer (see Supplementary Data 4). Verified clones were stored as glycerol stocks at -140°C. mESCs were plated on gelatin-coated 12- or 6-well plates and co-transfected with Lipofectamine 3000 transfection reagent (Thermo Fisher Scientific, L3000001) and one or two sgRNA-expressing pX330A vectors. For 12-well plates, 150.000 mESC were transfected with 1.5 µl of Lipofectamine 3000. Transfection efficiency was assessed via GFP fluorescence 24 h later. Cells with 70–90% transfection efficiency underwent puromycin (Sigma-Aldrich, P8833-25MG) selection (2 µg puromycin/ml during 48 h). Puromycin-resistant cells were serially diluted and plated in 96-well plates for clonal expansion. After 10–12 days, individual colonies were split into duplicate wells: one for gDNA extraction and PCR based genotyping and another for expansion and maintenance of each clone. Positive Zic2 knock-out mESC clones were expanded and cryopreserved at -140 °C for future use. Genomic insertions by CRISPR-Cas9 through homology directed repair. To generate the DNA double strand break that would favour a genomic insertion through homology directed repair (HDR), a single gRNA was designed in order to cut as close as possible to the insertion site according to the instructions of the genome engineering toolbox from Benchling (https://www.benchling.com/). The steps followed for the design were the same as the ones described for the Genomic Deletions section. In order to introduce the desired insertion, a ssDNA repair template was designed and synthe_x0002_sized as an Ultramer™ (for fragments up to 200 bp; IDT) or as a Megamer™ (for fragments up to 500 bp; IDT). The repair template contained the sequence of the epitope (i.e. Flag-HA, FKBPV36-HA) flanked with two homology arms, complementary to the sequences upstream and downstream of gRNA-Cas9 cutting site. mESC were transfected as de_x0002_scribed above, inluding the ssDNA sequence as an additional component of the transfection reactions. Subsequent steps to derive mESC clonal lines with the desired genomic insertion were as the ones described in previous sections. For ZIC2 targeted depletion experiments (performed using the ZIC2-FKBP cell line), mESC were differentiated to AntNPCs as previously described. Additionally, samples were treated with either DMSO (control) or d-TAG13 (treated, final concentration 500nM) for the three different dTAG-13 depletion conditions:  (1) continuous from D0 to D6,(2) during the final 48 hours (D4–D6), and (3) during the last  24 hours (D5–D6).

tag: cell line

value: Z2-FKBP E14Tg2a AntNPCs D6

value: Differentiation to AntNPCs + D-TAG13 treatment 24h


title: RT4-3

description: Library name: sample3


title: ESC passage #4 Rep1


title: bulkTCR_D10_tcra_SCM

description: Library name: D10_tcra_SCM


title: Z2-FKBP_D6DTag24h_RNA_rep2

description:
Library name: Sample 56
Column name in counts_allSamples.tsv: Z2-FKBP_D6DTag24h_RNA_rep2


title: ESC passage #2 Rep2


title: day 5 Rep2

source_name: ICM outgrowth

value: ICM outgrowth


title: Z2-FKBP_D6DTag24h_RNA_rep1

description:
Library name: Sample 55
Column name in counts_allSamples.tsv: Z2-FKBP_D6DTag24h_RNA_rep1


title: bulkTCR_D10_tcra_N

description: Library name: D10_tcra_N


title: ESC passage #2 Rep1


title: Z2-FKBP_D6Dmso24h_RNA_rep2

description:
Library name: Sample 53
Column name in counts_allSamples.tsv: Z2-FKBP_D6Dmso24h_RNA_rep2

value: Differentiation to AntNPCs + DMSO treatment 24h


title: bulkTCR_D10_tcra_E

description: Library name: D10_tcra_E


title: Z2-FKBP_D6Dmso24h_RNA_rep3

description:
Library name: Sample 54
Column name in counts_allSamples.tsv: Z2-FKBP_D6Dmso24h_RNA_rep3


title: day 3 Rep2


title: Z2-FKBP_D6Dmso24h_RNA_rep1

description:
Library name: Sample 52
Column name in counts_allSamples.tsv: Z2-FKBP_D6Dmso24h_RNA_rep1


title: bulkTCR_D10_tcra_CM

description: Library name: D10_tcra_CM


title: T-bet-Eomes Double Knockout 1

description:
Library name: Sample 1
column name in rsem_counts.txt: Double61224

value: Primary Transgenic OT-II CD4 T Cells

value: CD4 T cell Th17 Cells

value: Th17 Differentiation

value: Day 4 Effectors


title: day 0.5 Rep2


title: day 1 Rep2


title: bulkTCR_D10_tcra_CD8RA

description: Library name: D10_tcra_CD8RA


title: ESC passage #4 Rep2


title: day 0.5 Rep1


title: Z2-FKBP_D6DTag48h_RNA_rep2

description:
Library name: Sample 50
Column name in counts_allSamples.tsv: Z2-FKBP_D6DTag48h_RNA_rep2

value: Differentiation to AntNPCs + D-TAG13 treatment 48h


title: Z2-FKBP_D6DTag48h_RNA_rep3

description:
Library name: Sample 51
Column name in counts_allSamples.tsv: Z2-FKBP_D6DTag48h_RNA_rep3


title: day 0 (ICM) Rep2

source_name: Isolated ICM

value: Isolated ICM


title: bulkTCR_D10_tcra_P

description: Library name: D10_tcra_P


title: bulkTCR_D9_tcrb_SCM

description: Library name: D9_tcrb_SCM


title: day 0 (ICM) Rep1


title: Z2-FKBP_D6DTag48h_RNA_rep1

description:
Library name: Sample 49
Column name in counts_allSamples.tsv: Z2-FKBP_D6DTag48h_RNA_rep1


title: day 3 Rep1


title: bulkTCR_D10_tcra_EM

description: Library name: D10_tcra_EM


title: day 5 Rep1


title: day 2 Rep2


title: bulkTCR_D9_tcrb_P

description: Library name: D9_tcrb_P


title: Z2-FKBP_D6Dmso48h_RNA_rep2

description:
Library name: Sample 48
Column name in counts_allSamples.tsv: Z2-FKBP_D6Dmso48h_RNA_rep2

value: Differentiation to AntNPCs + DMSO treatment 48h


title: bulkTCR_D9_tcrb_N

description: Library name: D9_tcrb_N


title: day 1 Rep1


title: day 2 Rep1


title: Z2-FKBP_D6DTagTotal_RNA_rep3

description:
Library name: Sample 46
Column name in counts_allSamples.tsv: Z2-FKBP_D6DTagTotal_RNA_rep3

value: Differentiation to AntNPCs + D-TAG13 treatment total


title: Z2-FKBP_D6Dmso48h_RNA_rep1

description:
Library name: Sample 47
Column name in counts_allSamples.tsv: Z2-FKBP_D6Dmso48h_RNA_rep1


title: DNA_HAP1_scRR1_G1_113

city: Tsu-shi

first: Rawin

last: Poonperm

state: Mie

address: 1577 Kurimamachiya

department: Graduate School of Bioresources

institute: Mie University

data_processing:
Computation associated with the transcriptome profiling of (scRNA-seq) single cells: All RNA-seq, scRNA-seq, and scRR-seq-RNA data were analyzed using a complete nextflow pipeline, ramdaq v.1.9.2 (Yoshimura, M., Ozaki, H. & Kelly, T. ramdaq. Dataset on Zenodo (2023). doi:10.5281/zenodo.7655298). Human gencode v38 and mouse gencode vM25 were used as references.  Computation associated with the RT profiling (scRepli-seq) of single cells: For non-haplotype/allele-specific analyses, we followed our established pipeline for scRepli-seq RT analysis as described (Takahashi et al., Nat Genet 2019). We mapped scRR-seq-DNA data to hg38 and mm10 reference genomes for human and mouse cells, respectively, using bwa (v.0.7.17-r1188). We then analyzed scRR-seq-DNA data of the whole genome for each single cell in 40-kb nonoverlapping bins (or 80-kb bins as indicated) using AneuFinder (v.1.2.1). For binarization, different options were applied to each cell depending on their FACS sorting gates (2-HMM option for G1 FACS gate: most.frequent.state = ‘1-somy’; 2-HMM option for S-phase FACS gates: most.frequent.state = ‘2-somy’).  Computation associated with the detection of CNVs in single cells: We mapped G1 IMR-90 scRR-seq-DNA data to hg38 reference genome using bwa (v.0.7.17-r1188). We then analyzed scRR-seq-DNA data of the whole genome for each single cell in 50-kb, 100-kb, 200-kb, and 500-kb nonoverlapping bins. Using AneuFinder (v.1.2.1), we analyzed CNVs using Aneufinder wrapper with the following parameters: method=‘dnacopy’, correction.method = ‘mappability’, blacklist = ENCODE Blacklist version 231, mappability.reference = merged G1 reads).
Assembly: hg38
Supplementary files format and content: txt, bedGraph
Library strategy: scRepli-seq

extract_protocol:
Single cells were collected into 0.2 ml PCR tubes by cell sorter or manually picked and lysed in RamDA-seq lysis buffer (TOYOBO, #RMD-101) containing 2 mg/ml Dynabeads™ MyOne™ Carboxylic Acid (Invitrogen, #65011). Genomic DNA was trapped on the beads, while RNA was released into the lysis buffer. The isolated DNA on magnetic beads was subjected to whole-genome amplification (WGA) and Next-Generation Sequencing (NGS) library preparation, as described in scRepli-seq (Takahashi et al., Nat Genet 2019). The DNA-seq (scRepli-seq) data was used to assess genome-wide DNA copy numbers, karyotype G1-phase cells, and analyze the replication state of S-phase cells. In parallel, the RNA isolated in the supernatant was subjected to scRamDA-seq (Hayashi et al., Nat Commun 2018) using the GenNext®RamDA-seq™ Single Cell Kit (TOYOBO, #RMD-101) according to the manufacturer’s instructions with modifications.
Sample and library preparation for scRR-seq-DNA (scRepli-seq): Genomic DNA was subjected to WGA with a SeqPlex kit (Sigma, SEQXE) in a 30-µl reaction volume, per the manufacturer’s instructions. Amplified gDNA was purified and size-selected with Agencourt AMPure XP SPRI beads (1.7× reaction volume), and the SEQXE adapter sequence was removed by the primer removal enzyme Eco57I (Sigma, SEQXE). The gDNA was then purified with Agencourt AMPure XP SPRI beads (2.0× reaction volume) and eluted in 20 µl of 1/10× Elution Buffer (Qiagen). The DNA fragment size peak should be within 150–200 bp, which was confirmed by a capillary electrophoresis system, MultiNA (Shimadzu). We could easily distinguish single cells from zero or two cells by quantification of DNA with MultiNA, which provided reassurance that the gDNA was indeed derived from single cells. Then NGS libraries were constructed using the NGS LTP Library Preparation Kit (KAPA, KK8232) with a SeqCap adapter kit A/B (Roche, 07141530001/07141548001) or NEXTflex DNA barcode (Bio Scientific, NOVA), or the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England BioLabs , #E7645) with NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1, Set 2) (New England BioLabs , #E7600S, #E7780S ) or NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1, Set 2, Set 3, Set 4) (New England BioLabs , #E7355L, E7500L, E7710L, E7730L). Finally, the samples were subjected to NGS on an Illumina HiSeq X Ten system or Novaseq X Plus system (150-bp length, paired-end read).  Library preparation for scRR-seq-RNA scRamDA-seq NGS libraries were generated by using the Nextera® XT Library Prep Kit 24 Samples (illumina, #15032350, #15032352) with Nextera® XT Index Kit v2 Set A 96 indexes-samples (Illumina, #15052163) according to the manufacturer’s instructions with modifications. Finally, the samples were subjected to NGS on an Illumina HiSeq X Ten system or Novaseq X Plus system (150-bp length, paired-end read).


title: bulkTCR_D9_tcrb_E

description: Library name: D9_tcrb_E

data_processing:
The sequencing data was mapped and analyzed using MIGEC software (version 1.2.9) with default settings.
Sample fastq were obtained with command Checkout (parameters -cute) from MIGEC software.
Histogram, AssembleBatch, CdrBlastBatch and FilterCDRBlastResultsBatch functions from MIGEC were used to define TCR sequences.
Downstream analysis was performed using V(D)J tools with default settings.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Processed data is supplied as Supplementary Information in the manuscript.
Library strategy: TCR-Seq


title: DNA_HAP1_scRR1_MidS_109


title: DNA_HAP1_scRR1_MidS_110


title: Z2-FKBP_D6DTagTotal_RNA_rep2

description:
Library name: Sample 45
Column name in counts_allSamples.tsv: Z2-FKBP_D6DTagTotal_RNA_rep2


title: DNA_HAP1_scRR1_MidS_106


title: DNA_HAP1_scRR1_MidS_105


title: DNA_HAP1_scRR1_MidS_107


title: bulkTCR_D9_tcrb_CM

description: Library name: D9_tcrb_CM


title: DNA_HAP1_scRR1_MidS_104


title: DNA_HAP1_scRR1_MidS_108


title: DNA_HAP1_scRR1_G1_114


title: DNA_HAP1_scRR1_G1_115


title: Z2-FKBP_D6DTagTotal_RNA_rep1

description:
Library name: Sample 44
Column name in counts_allSamples.tsv: Z2-FKBP_D6DTagTotal_RNA_rep1


title: DNA_HAP1_scRR1_MidS_103


title: bulkTCR_D9_tcrb_CD8RA

description: Library name: D9_tcrb_CD8RA


title: DNA_HAP1_scRR1_MidS_102


title: DNA_HAP1_scRR1_G1_111


title: bulkTCR_D9_tcra_SCM

description: Library name: D9_tcra_SCM


title: Z2-FKBP_D6DmsoTotal_RNA_rep2

description:
Library name: Sample 42
Column name in counts_allSamples.tsv: Z2-FKBP_D6DmsoTotal_RNA_rep2

value: Differentiation to AntNPCs + DMSO treatment total


title: DNA_HAP1_scRR1_G1_112


title: bulkTCR_D9_tcrb_EM

description: Library name: D9_tcrb_EM

value: PBMC


title: bulkTCR_D9_tcra_P

description: Library name: D9_tcra_P


title: DNA_HAP1_scRR1_MidS_101


title: DNA_HAP1_scRR1_MidS_096


title: DNA_HAP1_scRR1_MidS_095


title: Z2-FKBP_D6DmsoTotal_RNA_rep1

description:
Library name: Sample 41
Column name in counts_allSamples.tsv: Z2-FKBP_D6DmsoTotal_RNA_rep1


title: bulkTCR_D9_tcra_N

description: Library name: D9_tcra_N


title: Z2HET_D6HetDif_RNA_rep3

description:
Library name: Sample 40
Column name in counts_allSamples.tsv: Z2HET_D6HetDif_RNA_rep3

source_name: Z2HET E14Tg2a AntNPCs D6

value: Z2HET E14Tg2a AntNPCs D6

value: Differentiation to AntNPCs


title: DNA_HAP1_scRR1_MidS_091


title: Z2HET_D6HetDif_RNA_rep1

description:
Library name: Sample 38
Column name in counts_allSamples.tsv: Z2HET_D6HetDif_RNA_rep1


title: bulkTCR_D9_tcra_EM

description: Library name: D9_tcra_EM


title: DNA_HAP1_scRR1_MidS_084


title: bulkTCR_D9_tcra_CM

description: Library name: D9_tcra_CM


title: DNA_HAP1_scRR1_MidS_087


title: DNA_HAP1_scRR1_MidS_089


title: Z2HET_D6HetDif_RNA_rep2

description:
Library name: Sample 39
Column name in counts_allSamples.tsv: Z2HET_D6HetDif_RNA_rep2


title: Z2KO_D6HetDif_RNA_rep3

description:
Library name: Sample 37
Column name in counts_allSamples.tsv: Z2KO_D6HetDif_RNA_rep3

source_name: Z2KO E14Tg2a AntNPCs D6

value: Z2KO E14Tg2a AntNPCs D6


title: DNA_HAP1_scRR1_MidS_081


title: DNA_HAP1_scRR1_MidS_083


title: bulkTCR_D9_tcra_CD8RA

description: Library name: D9_tcra_CD8RA


title: bulkTCR_D9_tcra_E

description: Library name: D9_tcra_E


title: Z2KO_D6HetDif_RNA_rep2

description:
Library name: Sample 36
Column name in counts_allSamples.tsv: Z2KO_D6HetDif_RNA_rep2


title: Z2-FKBP_D6DmsoTotal_RNA_rep3

description:
Library name: Sample 43
Column name in counts_allSamples.tsv: Z2-FKBP_D6DmsoTotal_RNA_rep3

value: Z2-FKBP E14Tg2a AntNPCs D6