title: DNA_HAP1_scRR1_MidS_079


title: bulkTCR_D8_tcrb_SCM

status: Public on Aug 26 2025

type: SRA

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: D8_tcrb_SCM

library_source: transcriptomic

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

molecule: polyA RNA

organism: Homo sapiens

source_name: PBMC

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.

tag: tissue

value: PBMC

tag: cell type

tag: attribute


title: DNA_HAP1_scRR1_MidS_007

city: Tsu-shi

first: Rawin

last: Poonperm

state: Mie

address: 1577 Kurimamachiya

department: Graduate School of Bioresources

country: Japan

institute: Mie University

library_source: genomic

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

molecule: genomic DNA

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).

tag: cell line


title: Z2KO_D6HetDif_RNA_rep1

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 35
Column name in counts_allSamples.tsv: Z2KO_D6HetDif_RNA_rep1

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.

organism: Mus musculus

source_name: Z2KO 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).

value: Z2KO E14Tg2a AntNPCs D6

tag: genotype

tag: treatment

value: Differentiation to AntNPCs


title: bulkTCR_D8_tcrb_P

description: Library name: D8_tcrb_P


title: DNA_HAP1_scRR1_MidS_077


title: DNA_HAP1_scRR1_MidS_078


title: DNA_HAP1_scRR1_MidS_094


title: DNA_HAP1_scRR1_MidS_074


title: bulkTCR_D8_tcrb_N

description: Library name: D8_tcrb_N


title: DNA_HAP1_scRR1_MidS_086


title: DNA_HAP1_scRR1_MidS_073


title: DNA_HAP1_scRR1_MidS_072


title: WT_D6HetDif_RNA_rep2

description:
Library name: Sample 33
Column name in counts_allSamples.tsv: WT_D6HetDif_RNA_rep2

source_name: E14Tg2a AntNPCs D6

value: E14Tg2a AntNPCs D6

value: WT


title: DNA_HAP1_scRR1_MidS_080


title: bulkTCR_D8_tcrb_E

description: Library name: D8_tcrb_E


title: DNA_HAP1_scRR1_MidS_071


title: Z3KO_D0_RNA_rep2

description:
Library name: Sample 30
Column name in counts_allSamples.tsv: Z3KO_D0_RNA_rep2

source_name: Z3KO E14Tg2a mESC D0

value: Z3KO E14Tg2a mESC D0

value: Culture in Serum + LIF


title: Z3KO_D0_RNA_rep3

description:
Library name: Sample 31
Column name in counts_allSamples.tsv: Z3KO_D0_RNA_rep3


title: bulkTCR_D8_tcrb_EM

description: Library name: D8_tcrb_EM


title: bulkTCR_D8_tcrb_CD8RA

description: Library name: D8_tcrb_CD8RA


title: DNA_HAP1_scRR1_MidS_070


title: Col-0 adr1 triple knockout control biol rep 2

city: Singapore

first: Donghui

last: HU

state: Singapore

address: 16 Science Drive 4 Block S1A #06-12

department: department of biological sciences

country: Singapore

institute: National University of Singapore

description:
Library name: Col-0_adr1s_2
Aerial tissue from Col-0 plants with ADR1 triple knockout

data_processing:
Raw sequencing reads were quality-trimmed using fastp (v0.23.2)
RNA-Seq reads were mapped to the Arabidopsis thaliana TAIR10 reference genome using HISAT2 (v2.2.1)
Read counting was performed with featureCounts (v2.0.1) and differential gene expression analysis was conducted using DESeq2 (v1.34.0)
ATAC-Seq reads were aligned to TAIR10 using Bowtie2 (v2.4.4), processed with SAMtools (v1.15), and peak calling was performed with MACS2 (v2.2.7)
WGCNA was performed using the WGCNA R package (v1.70-3) on the top 20% most variable genes across samples
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text files containing normalised gene expression values (RNA-Seq) and differential accessibility results (ATAC-Seq)
Supplementary files format and content: WGCNA module assignments and differential expression results with log2 fold changes and adjusted p-values

molecule: total RNA

organism: Arabidopsis thaliana

source_name: shoot

growth_protocol: Arabidopsis thaliana seeds were surface sterilised with 70% ethanol + 0.05% Triton X-100 for 20 minutes, followed by 70% ethanol for 10 minutes, then rinsed five times with sterile water. After stratification at 4°C for 4 days in darkness, seeds were sown on half-strength Murashige and Skoog (½MS) medium containing 1% sucrose and 0.8% agar, pH 5.7. Plants were grown under long-day conditions (16h light/8h dark cycle) at 22°C ± 2°C with 60-70% relative humidity and light intensity of 110-130 μmol m⁻² s⁻¹.

extract_protocol:
For RNA-Seq: Aerial tissues were harvested at 12 DAS (DM1-DM2d) or 14 DAS (DM6-DM7), flash-frozen in liquid nitrogen and ground using TissueLyser II with 3mm stainless steel beads at 30 Hz for 40 seconds. Total RNA was extracted using the LogSpin method. For ATAC-Seq: 50 mg of frozen tissue was ground in liquid nitrogen and homogenised in Buffer A, filtered through cell strainers, and nuclei were purified using Percoll gradient centrifugation.
For RNA-Seq: Strand-specific RNA-Seq libraries were prepared using standard protocols and sequenced on Illumina NovaSeq 6000 platform, generating approximately 30 million 150 bp paired-end reads per sample. For ATAC-Seq: Libraries were prepared using the Hyperactive ATAC-Seq Library Prep Kit (Vazyme, TD711-01) from approximately 50,000 nuclei and sequenced on Illumina platforms, generating 25-30 million paired-end reads per sample.

treatment_protocol: DM autoimmune lines were generated by transforming Col-0 with constructs containing DANGEROUS MIX gene pairs. ADR1 triple knockout lines were generated using CRISPR-Cas9 mediated knockout of ADR1, ADR1-L1, and ADR1-L2 using multiplexed approach with guide RNAs designed by MINORg.

value: shoot

value: Col-0 adr1 triple

value: ADR1 knockout in wild-type background

tag: batch


title: Col-0 adr1 triple knockout control biol rep 1

description:
Library name: Col-0_adr1s_1
Aerial tissue from Col-0 plants with ADR1 triple knockout


title: bulkTCR_D8_tcrb_CM

description: Library name: D8_tcrb_CM


title: DNA_HAP1_scRR1_MidS_069


title: Col-0 adr1 triple knockout control biol rep 3

description:
Library name: Col-0_adr1s_3
Aerial tissue from Col-0 plants with ADR1 triple knockout


title: bulkTCR_D8_tcra_SCM

description: Library name: D8_tcra_SCM


title: WT_D6HetDif_RNA_rep3

description:
Library name: Sample 34
Column name in counts_allSamples.tsv: WT_D6HetDif_RNA_rep3


title: Z3KO_D0_RNA_rep1

description:
Library name: Sample 29
Column name in counts_allSamples.tsv: Z3KO_D0_RNA_rep1


title: Z2KO_D6_RNA_rep3

description:
Library name: Sample 28
Column name in counts_allSamples.tsv: Z2KO_D6_RNA_rep3


title: DNA_HAP1_scRR1_MidS_068


title: DNA_HAP1_scRR1_MidS_066


title: DM6-DM7 adr1 triple knockout shoot tissue biol rep 2

description:
Library name: DM6_DM7_adr1s_2
Aerial tissue from DM6-DM7 plants with ADR1 triple knockout

value: DM6-DM7 adr1 triple

value: ADR1 knockout in autoimmune background


title: bulkTCR_D8_tcra_P

description: Library name: D8_tcra_P


title: DM6-DM7 adr1 triple knockout shoot tissue biol rep 1

description:
Library name: DM6_DM7_adr1s_1
Aerial tissue from DM6-DM7 plants with ADR1 triple knockout


title: bulkTCR_D8_tcra_N

description: Library name: D8_tcra_N


title: DM1-DM2d adr1 triple knockout shoot tissue biol rep 3

description:
Library name: DM1_DM2d_adr1s_3
Aerial tissue from DM1-DM2d plants with ADR1 triple knockout

value: DM1-DM2d adr1 triple


title: DNA_HAP1_scRR1_MidS_064


title: Z2KO_D6_RNA_rep2

description:
Library name: Sample 27
Column name in counts_allSamples.tsv: Z2KO_D6_RNA_rep2


title: WT_D6HetDif_RNA_rep1

description:
Library name: Sample 32
Column name in counts_allSamples.tsv: WT_D6HetDif_RNA_rep1


title: bulkTCR_D8_tcra_EM

description: Library name: D8_tcra_EM


title: Z2KO_D6_RNA_rep1

description:
Library name: Sample 26
Column name in counts_allSamples.tsv: Z2KO_D6_RNA_rep1


title: DNA_HAP1_scRR1_MidS_063


title: DM1-DM2d adr1 triple knockout shoot tissue biol rep 2

description:
Library name: DM1_DM2d_adr1s_2
Aerial tissue from DM1-DM2d plants with ADR1 triple knockout


title: DM6-DM7 adr1 triple knockout shoot tissue biol rep 3

description:
Library name: DM6_DM7_adr1s_3
Aerial tissue from DM6-DM7 plants with ADR1 triple knockout


title: WT_D6_RNA_rep3

description:
Library name: Sample 25
Column name in counts_allSamples.tsv: WT_D6_RNA_rep3


title: DM1-DM2d adr1 triple knockout shoot tissue biol rep 1

description:
Library name: DM1_DM2d_adr1s_1
Aerial tissue from DM1-DM2d plants with ADR1 triple knockout


title: bulkTCR_D8_tcra_E

description: Library name: D8_tcra_E


title: Col-0 wild-type control shoot tissue at 14 DAS biol rep 3

description:
Library name: Col-0_Shoot_14DAS_3
Aerial tissue from Col-0 wild-type plants at 14 days after sowing

value: control


title: DNA_HAP1_scRR1_MidS_060


title: DNA_HAP1_scRR1_MidS_061


title: Z2KO_D5_RNA_rep4

description:
Library name: Sample 22
Column name in counts_allSamples.tsv: Z2KO_D5_RNA_rep4

source_name: Z2KO E14Tg2a AntNPCs D5

value: Z2KO E14Tg2a AntNPCs D5


title: Col-0 wild-type control shoot tissue at 14 DAS biol rep 1

description:
Library name: Col-0_Shoot_14DAS_1
Aerial tissue from Col-0 wild-type plants at 14 days after sowing


title: WT_D6_RNA_rep1

description:
Library name: Sample 23
Column name in counts_allSamples.tsv: WT_D6_RNA_rep1


title: Col-0 wild-type control shoot tissue at 14 DAS biol rep 2

description:
Library name: Col-0_Shoot_14DAS_2
Aerial tissue from Col-0 wild-type plants at 14 days after sowing


title: DNA_HAP1_scRR1_MidS_005


title: bulkTCR_D8_tcra_CD8RA

description: Library name: D8_tcra_CD8RA


title: bulkTCR_D7_tcrb_SCM

description: Library name: D7_tcrb_SCM


title: DNA_HAP1_scRR1_MidS_059


title: DM6-DM7 autoimmune line shoot tissue at 14 DAS biol rep 3

description:
Library name: DM6_DM7_Shoot_14DAS_3
Aerial tissue from DM6-DM7 autoimmune plants at 14 days after sowing

value: autoimmunity


title: DNA_HAP1_scRR1_MidS_057


title: bulkTCR_D8_tcra_CM

description: Library name: D8_tcra_CM


title: DM6-DM7 autoimmune line shoot tissue at 14 DAS biol rep 2

description:
Library name: DM6_DM7_Shoot_14DAS_2
Aerial tissue from DM6-DM7 autoimmune plants at 14 days after sowing


title: bulkTCR_D7_tcrb_N

description: Library name: D7_tcrb_N


title: Z2KO_D5_RNA_rep2

description:
Library name: Sample 20
Column name in counts_allSamples.tsv: Z2KO_D5_RNA_rep2


title: Z2KO_D5_RNA_rep1

description:
Library name: Sample 19
Column name in counts_allSamples.tsv: Z2KO_D5_RNA_rep1


title: Z2KO_D5_RNA_rep3

description:
Library name: Sample 21
Column name in counts_allSamples.tsv: Z2KO_D5_RNA_rep3


title: bulkTCR_D7_tcrb_P

description: Library name: D7_tcrb_P


title: DNA_HAP1_scRR1_MidS_055


title: DM6-DM7 autoimmune line shoot tissue at 14 DAS biol rep 1

description:
Library name: DM6_DM7_Shoot_14DAS_1
Aerial tissue from DM6-DM7 autoimmune plants at 14 days after sowing


title: bulkTCR_D7_tcrb_EM

description: Library name: D7_tcrb_EM


title: DNA_HAP1_scRR1_MidS_054


title: WT_D5_RNA_rep4

description:
Library name: Sample 18
Column name in counts_allSamples.tsv: WT_D5_RNA_rep4

source_name: E14Tg2a AntNPCs D5

value: E14Tg2a AntNPCs D5


title: Col-0 wild-type control shoot tissue at 12 DAS biol rep 2

description:
Library name: Col-0_12DAS_Shoot_2
Aerial tissue from Col-0 wild-type plants at 12 days after sowing


title: bulkTCR_D7_tcrb_E

description: Library name: D7_tcrb_E

value: PBMC


title: DNA_HAP1_scRR1_MidS_053


title: WT_D5_RNA_rep3

description:
Library name: Sample 17
Column name in counts_allSamples.tsv: WT_D5_RNA_rep3


title: WT_D6_RNA_rep2

description:
Library name: Sample 24
Column name in counts_allSamples.tsv: WT_D6_RNA_rep2


title: bulkTCR_D7_tcrb_CM

description: Library name: D7_tcrb_CM


title: bulkTCR_D7_tcrb_CD8RA

description: Library name: D7_tcrb_CD8RA


title: WT_D5_RNA_rep2

description:
Library name: Sample 16
Column name in counts_allSamples.tsv: WT_D5_RNA_rep2


title: WT_D5_RNA_rep1

description:
Library name: Sample 15
Column name in counts_allSamples.tsv: WT_D5_RNA_rep1


title: DNA_HAP1_scRR1_MidS_050


title: DM1-DM2d autoimmune line shoot tissue at 12 DAS biol rep 2

description:
Library name: DM1_DM2d_12DAS_Shoot_2
Aerial tissue from DM1-DM2d autoimmune plants at 12 days after sowing


title: DM1-DM2d autoimmune line shoot tissue at 12 DAS biol rep 3

description:
Library name: DM1_DM2d_12DAS_Shoot_3
Aerial tissue from DM1-DM2d autoimmune plants at 12 days after sowing


title: bulkTCR_D7_tcra_SCM

description: Library name: D7_tcra_SCM


title: DNA_HAP1_scRR1_MidS_051


title: DNA_HAP1_scRR1_MidS_043


title: DM1-DM2d autoimmune line shoot tissue at 12 DAS biol rep 1

description:
Library name: DM1_DM2d_12DAS_Shoot_1
Aerial tissue from DM1-DM2d autoimmune plants at 12 days after sowing


title: bulkTCR_D7_tcra_P

description: Library name: D7_tcra_P


title: DNA_HAP1_scRR1_MidS_038


title: Z2KO_D3_RNA_rep3

description:
Library name: Sample 13
Column name in counts_allSamples.tsv: Z2KO_D3_RNA_rep3

source_name: Z2KO E14Tg2a D3

value: Z2KO E14Tg2a D3


title: Z2KO_D3_RNA_rep4

description:
Library name: Sample 14
Column name in counts_allSamples.tsv: Z2KO_D3_RNA_rep4

value: Differentiation to AntNPCs


title: bulkTCR_D7_tcra_N

description: Library name: D7_tcra_N


title: Control replicate 3

description:
Library name: control_3
Untreated control seedlings

data_processing:
Raw sequencing reads were quality-trimmed using fastp (v0.23.2)
Trimmed reads were mapped to Arabidopsis thaliana TAIR10 reference genome using HISAT2 (v2.2.1)
Read counting was performed with featureCounts (v2.0.1)
Differential gene expression analysis was conducted using DESeq2 (v1.34.0) in R (v4.1.0)
Gene Ontology enrichment analysis was performed using clusterProfiler (v4.2.2)
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text files containing normalised gene expression values and differential expression statistics with gene identifiers, log2 fold changes, adjusted p-values, and associated metadata
Supplementary files format and content: Gene count matrices in tab-delimited format with samples as columns and genes as rows, containing raw and normalised read counts

source_name: aerial tissue

growth_protocol: Arabidopsis thaliana Col-0 seeds were surface sterilised with 70% ethanol + 0.05% Triton X-100 for 20 minutes, followed by 70% ethanol for 10 minutes, then rinsed five times with sterile water. After stratification at 4°C for 4 days, seeds were sown on half-strength Murashige and Skoog medium containing 1% sucrose and 0.8% agar, pH 5.7. Seedlings were grown under long-day conditions (16h light/8h dark cycle) at 22°C ± 2°C with 60-70% relative humidity and light intensity of 110-130 μmol m⁻² s⁻¹.

extract_protocol:
Aerial tissues were harvested at 6, 12, and 20 hours post-inoculation, immediately frozen in liquid nitrogen, and ground using TissueLyser II with 3mm stainless steel beads at 30 Hz for 40 seconds. Total RNA was extracted using the LogSpin method.
Strand-specific RNA-Seq libraries were prepared using standard protocols and sequenced on Illumina NovaSeq 6000 platform, generating approximately 30 million 150 bp paired-end reads per sample. Three biological replicates were prepared for each condition.

treatment_protocol: Transient pathogen flood assay was performed following Ishiga et al. (2011). Six-day-old seedlings grown vertically were transferred to horizontal plates for an additional 6 days. Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2 or avrRps4 were cultured overnight, collected by centrifugation, and resuspended in 10 mM MgCl₂ to OD₆₀₀ = 0.1. Silwet L-77 was added to 0.028% (w/v). Bacterial suspension was gently poured onto plates to submerge seedlings for 2-3 minutes, then drained. Mock treatments used 10 mM MgCl₂ with 0.028% Silwet L-77.

value: aerial tissue

value: untreated


title: Z2KO_D3_RNA_rep2

description:
Library name: Sample 12
Column name in counts_allSamples.tsv: Z2KO_D3_RNA_rep2


title: Control replicate 2

description:
Library name: control_2
Untreated control seedlings


title: bulkTCR_D7_tcra_EM

description: Library name: D7_tcra_EM


title: DNA_HAP1_scRR1_MidS_036


title: DNA_HAP1_scRR1_MidS_035


title: Z2KO_D3_RNA_rep1

description:
Library name: Sample 11
Column name in counts_allSamples.tsv: Z2KO_D3_RNA_rep1


title: bulkTCR_D7_tcra_E

description: Library name: D7_tcra_E


title: DNA_HAP1_scRR1_MidS_034


title: Col-0 wild-type control shoot tissue at 12 DAS biol rep 1

description:
Library name: Col-0_12DAS_Shoot_1
Aerial tissue from Col-0 wild-type plants at 12 days after sowing


title: WT_D3_RNA_rep4

description:
Library name: Sample 10
Column name in counts_allSamples.tsv: WT_D3_RNA_rep4

source_name: E14Tg2a D3

value: E14Tg2a D3

value: WT


title: AvrRps4 treatment 20 hours replicate 3

description:
Library name: AvrRps4-20h_3
AvrRps4-treated seedlings harvested at 20 hours post-inoculation

value: Pst DC3000 avrRps4


title: bulkTCR_D7_tcra_CM

description: Library name: D7_tcra_CM


title: DNA_HAP1_scRR1_MidS_032


title: WT_D3_RNA_rep3

description:
Library name: Sample 9
Column name in counts_allSamples.tsv: WT_D3_RNA_rep3


title: bulkTCR_D7_tcra_CD8RA

description: Library name: D7_tcra_CD8RA


title: DNA_HAP1_scRR1_MidS_031


title: AvrRps4 treatment 20 hours replicate 2

description:
Library name: AvrRps4-20h_2
AvrRps4-treated seedlings harvested at 20 hours post-inoculation


title: WT_D3_RNA_rep2

description:
Library name: Sample 8
Column name in counts_allSamples.tsv: WT_D3_RNA_rep2


title: AvrRps4 treatment 20 hours replicate 1

description:
Library name: AvrRps4-20h_1
AvrRps4-treated seedlings harvested at 20 hours post-inoculation


title: DNA_HAP1_scRR1_MidS_029


title: WT_D3_RNA_rep1

description:
Library name: Sample 7
Column name in counts_allSamples.tsv: WT_D3_RNA_rep1


title: DNA_HAP1_scRR1_MidS_028


title: bulkTCR_D6_tcrb_P

description: Library name: D6_tcrb_P


title: AvrRpt2 treatment 20 hours replicate 3

description:
Library name: AvrRpt2-20h_3
AvrRpt2-treated seedlings harvested at 20 hours post-inoculation

value: Pst DC3000 avrRpt2


title: bulkTCR_D6_tcrb_N

description: Library name: D6_tcrb_N


title: AvrRpt2 treatment 20 hours replicate 2

description:
Library name: AvrRpt2-20h_2
AvrRpt2-treated seedlings harvested at 20 hours post-inoculation


title: Z2KO_D0_RNA_rep3

description:
Library name: Sample 6
Column name in counts_allSamples.tsv: Z2KO_D0_RNA_rep3

source_name: Z2KO E14Tg2a mESC D0

value: Z2KO E14Tg2a mESC D0

value: Culture in Serum + LIF


title: DNA_HAP1_scRR1_MidS_026


title: Control replicate 1

description:
Library name: control_1
Untreated control seedlings


title: AvrRpt2 treatment 20 hours replicate 1

description:
Library name: AvrRpt2-20h_1
AvrRpt2-treated seedlings harvested at 20 hours post-inoculation


title: bulkTCR_D6_tcrb_EM

description: Library name: D6_tcrb_EM


title: Z2KO_D0_RNA_rep2

description:
Library name: Sample 5
Column name in counts_allSamples.tsv: Z2KO_D0_RNA_rep2


title: DNA_HAP1_scRR1_MidS_025


title: Z2KO_D0_RNA_rep1

description:
Library name: Sample 4
Column name in counts_allSamples.tsv: Z2KO_D0_RNA_rep1


title: DNA_HAP1_scRR1_MidS_024


title: bulkTCR_D6_tcrb_E

description: Library name: D6_tcrb_E


title: WT_D0_RNA_rep3

description:
Library name: Sample 3
Column name in counts_allSamples.tsv: WT_D0_RNA_rep3

source_name: E14Tg2a mESC D0

value: E14Tg2a mESC D0


title: bulkTCR_D6_tcrb_CM

description: Library name: D6_tcrb_CM


title: DNA_HAP1_scRR1_MidS_023


title: Mock treatment 20 hours replicate 2

description:
Library name: Mock-20h_2
Mock-treated seedlings harvested at 20 hours post-treatment

value: Mock (10 mM MgCl₂)


title: Mock treatment 20 hours replicate 3

description:
Library name: Mock-20h_3
Mock-treated seedlings harvested at 20 hours post-treatment


title: bulkTCR_D6_tcrb_SCM

description: Library name: D6_tcrb_SCM


title: WT_D0_RNA_rep2

description:
Library name: Sample 2
Column name in counts_allSamples.tsv: WT_D0_RNA_rep2


title: DNA_HAP1_scRR1_MidS_021


title: Mock treatment 20 hours replicate 1

description:
Library name: Mock-20h_1
Mock-treated seedlings harvested at 20 hours post-treatment


title: AvrRps4 treatment 12 hours replicate 3

description:
Library name: AvrRps4-12h_3
AvrRps4-treated seedlings harvested at 12 hours post-inoculation


title: bulkTCR_D6_tcrb_CD8RA

description: Library name: D6_tcrb_CD8RA


title: WT_D0_RNA_rep1

description:
Library name: Sample 1
Column name in counts_allSamples.tsv: WT_D0_RNA_rep1


title: bulkTCR_D6_tcra_SCM

description: Library name: D6_tcra_SCM


title: DNA_HAP1_scRR1_MidS_020


title: bulkTCR_D6_tcra_N

description: Library name: D6_tcra_N


title: Newborn_Polr2b.fl.fl.GFP_K14Cre_GFP_Rep2

city: Ithaca

first: Tudorita

last: Tumbar

state: NY

address: 526 Campus Rd

department: Molecular biology and genetics

country: USA

institute: Cornell University

description: Library name: Sample 4

library_source: other

data_processing:
PReCIS-seq reads were first trimmed with fastp (v0.23.2), then mapped to the mouse rDNA using bowtie2 (v2.4.4) to deplete nascent rRNA. The rRNA-depleted reads were then mapped to the mm39 reference genome using STAR (v2.7.10b) and UMI duplicate reads were removed using umi_tools (v 1.1.2). The de-duplicated BAM files were then converted to CPM-normalized bigWig files using samtools and visualized using Integrated Genome Viewer (IGV). Promoter-proximal and gene body counts were obtained using the BRGenomics package in R and are provided as supplementary data files.
Assembly: mm39
Supplementary files format and content: Strand specific bigWig files
Library strategy: PRO-Seq

molecule: other

source_name: Skin

growth_protocol: PReCIS-seq was performed by harvesting whole dorsal skin tissue at postnatal day 0.

extract_protocol:
For mouse skin samples, samples were flash-frozen in liquid N2, followed by dry pulverization of frozen tissue through a cell crusher and douncing. Chromatin was isolated using NUN buffer and fragmented with DNase I, and nascent RNA was biotin-labeled through a run-on reaction. Cell-type-specific nascent RNAs were enriched through GFP pull-down and library preparation steps were then followed as previously described for PRO-seq assay. All input samples were processed without GFP pull-down that served as controls for cell-type specific nascent RNA enrichment.
Nascent RNA libraries were generated using the PRO-seq protocol.

value: Skin

value: Keratinocytes

value: Polr2b.fl.fl.GFP; K14Cre


title: AvrRps4 treatment 12 hours replicate 1

description:
Library name: AvrRps4-12h_1
AvrRps4-treated seedlings harvested at 12 hours post-inoculation


title: Newborn_Polr2b.fl.fl.GFP_K14Cre_GFP_Rep1

description: Library name: Sample 3


title: AvrRps4 treatment 12 hours replicate 2

description:
Library name: AvrRps4-12h_2
AvrRps4-treated seedlings harvested at 12 hours post-inoculation


title: AvrRpt2 treatment 12 hours replicate 3

description:
Library name: AvrRpt2-12h_3
AvrRpt2-treated seedlings harvested at 12 hours post-inoculation


title: DNA_HAP1_scRR1_MidS_018


title: bulkTCR_D6_tcra_EM

description: Library name: D6_tcra_EM


title: Newborn_Polr2b.fl.fl.GFP_K14Cre_Input_Rep1

description: Library name: Sample 1

value: All cells in skin


title: AvrRpt2 treatment 12 hours replicate 2

description:
Library name: AvrRpt2-12h_2
AvrRpt2-treated seedlings harvested at 12 hours post-inoculation


title: RNA_HAP1_scRR1_MidS_110

library_source: transcriptomic single cell

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


title: bulkTCR_D6_tcra_E

description: Library name: D6_tcra_E

value: PBMC


title: Newborn_Polr2b.fl.fl.GFP_K14Cre_Input_Rep2

description: Library name: Sample 2


title: DNA_HAP1_scRR1_MidS_017


title: AvrRpt2 treatment 12 hours replicate 1

description:
Library name: AvrRpt2-12h_1
AvrRpt2-treated seedlings harvested at 12 hours post-inoculation


title: Glu-tag cells, sh-IRS23

city: Shijiazhuang

first: Meng

last: Zhang

state: Hebei

address: Changan district No.12 Jiankang Road Shijiazhuang, 050031, Hebei Province China

department: Gastroenterology

country: China

institute: The Fourth Hospital of Hebei Medical University

description:
Library name: sample 6
Glu-tag IRS2-knockdown cells, rep1

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes gene counts for each sample
Supplementary files format and content: tab-delimited text file includes fpkm value for each sample

source_name: Small intestine

extract_protocol:
RNA was extracted from cell lines using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: Small intestine

value: Glu-tag cells

value: IRS2 Knockdown


title: bulkTCR_D6_tcra_CM

description: Library name: D6_tcra_CM


title: Glu-tag cells, sh-IRS22

description:
Library name: sample 5
Glu-tag IRS2-knockdown cells, rep1


title: RNA_HAP1_scRR1_MidS_109


title: Glu-tag cells, sh-IRS21

description:
Library name: sample 4
Glu-tag IRS2-knockdown cells, rep1


title: Mock treatment 12 hours replicate 3

description:
Library name: Mock-12h_3
Mock-treated seedlings harvested at 12 hours post-treatment

value: aerial tissue


title: Mock treatment 12 hours replicate 2

description:
Library name: Mock-12h_2
Mock-treated seedlings harvested at 12 hours post-treatment


title: RNA_HAP1_scRR1_MidS_108


title: Glu-tag cells, sh-control3

description:
Library name: sample 3
Glu-tag control cells, rep1


title: DNA_HAP1_scRR1_MidS_001


title: bulkTCR_D5_tcrb_SCM

description: Library name: D5_tcrb_SCM


title: RNA_HAP1_scRR1_MidS_107


title: bulkTCR_D6_tcra_CD8RA

description: Library name: D6_tcra_CD8RA


title: bulkTCR_D6_tcra_P

description: Library name: D6_tcra_P


title: bulkTCR_D5_tcrb_N

description: Library name: D5_tcrb_N


title: bulkTCR_D5_tcrb_P

description: Library name: D5_tcrb_P


title: RNA_HAP1_scRR1_MidS_106


title: Mock treatment 12 hours replicate 1

description:
Library name: Mock-12h_1
Mock-treated seedlings harvested at 12 hours post-treatment


title: AvrRps4 treatment 6 hours replicate 3

description:
Library name: AvrRps4-6h_3
AvrRps4-treated seedlings harvested at 6 hours post-inoculation


title: RNA_HAP1_scRR1_MidS_105


title: Glu-tag cells, sh-control2

description:
Library name: sample 2
Glu-tag control cells, rep1


title: Glu-tag cells, sh-control1

description:
Library name: sample 1
Glu-tag control cells, rep1


title: AvrRps4 treatment 6 hours replicate 2

description:
Library name: AvrRps4-6h_2
AvrRps4-treated seedlings harvested at 6 hours post-inoculation


title: bulkTCR_D5_tcrb_E

description: Library name: D5_tcrb_E


title: AvrRps4 treatment 6 hours replicate 1

description:
Library name: AvrRps4-6h_1
AvrRps4-treated seedlings harvested at 6 hours post-inoculation


title: AvrRpt2 treatment 6 hours replicate 3

description:
Library name: AvrRpt2-6h_3
AvrRpt2-treated seedlings harvested at 6 hours post-inoculation


title: bulkTCR_D5_tcrb_CM

description: Library name: D5_tcrb_CM


title: bulkTCR_D5_tcrb_EM

description: Library name: D5_tcrb_EM


title: RNA_HAP1_scRR1_MidS_103


title: AvrRpt2 treatment 6 hours replicate 2

description:
Library name: AvrRpt2-6h_2
AvrRpt2-treated seedlings harvested at 6 hours post-inoculation


title: RNA_HAP1_scRR1_MidS_102


title: AvrRpt2 treatment 6 hours replicate 1

description:
Library name: AvrRpt2-6h_1
AvrRpt2-treated seedlings harvested at 6 hours post-inoculation


title: bulkTCR_D5_tcrb_CD8RA

description: Library name: D5_tcrb_CD8RA


title: RNA_HAP1_scRR1_MidS_096


title: RNA_HAP1_scRR1_MidS_101


title: bulkTCR_D5_tcra_SCM

description: Library name: D5_tcra_SCM


title: SPOP CKI mice heart repeat1

city: Monrovia

first: Hao

last: Wu

state: CA

address: 702 Oakdale Ave

institute: harbin medicine univercity

description:
Library name: SPOPCKI1
SPOPCKI1

data_processing:
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels. Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . padj<=0.05
Assembly: mm10
Supplementary files format and content: format:xls.  concent: gene id; gene name; pvalue; padj

source_name: heart tissue

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

value: heart tissue

tag: Sex

value: Male

value: cardiac cell populations

value: CKI


title: SPOP CKI mice heart repeat5

description:
Library name: SPOPCKI5
SPOPCKI5


title: SPOP CKI mice heart repeat3

description:
Library name: SPOPCKI3
SPOPCK3


title: SPOP CKI mice heart repeat4

description:
Library name: SPOPCKI4
SPOPCKI4


title: bulkTCR_D5_tcra_P

description: Library name: D5_tcra_P


title: WT mice heart repeat5

description:
Library name: WT5
WT5


title: SPOP CKI mice heart repeat2

description:
Library name: SPOPCKI2
SPOPCKI2


title: RNA_HAP1_scRR1_MidS_104


title: Mock treatment 6 hours replicate 3

description:
Library name: Mock-6h_3
Mock-treated seedlings harvested at 6 hours post-treatment


title: RNA_HAP1_scRR1_MidS_094


title: RNA_HAP1_scRR1_MidS_095


title: Mock treatment 6 hours replicate 2

description:
Library name: Mock-6h_2
Mock-treated seedlings harvested at 6 hours post-treatment


title: Mock treatment 6 hours replicate 1

description:
Library name: Mock-6h_1
Mock-treated seedlings harvested at 6 hours post-treatment


title: WT mice heart repeat4

description:
Library name: WT4
WT4


title: WT mice heart repeat2

description:
Library name: WT2
WT2


title: bulkTCR_D5_tcra_EM

description: Library name: D5_tcra_EM


title: bulkTCR_D5_tcra_E

description: Library name: D5_tcra_E


title: WT mice heart repeat3

description:
Library name: WT3
WT3


title: RNA_HAP1_scRR1_MidS_089


title: RNA_HAP1_scRR1_MidS_091


title: con_2_input

city: Fujian

first: Dongcheng

address: Overseas Education College of Fujian Medical University, No. 1 Xuefu North Road, University Town, Fuzhou, Fujian Province, P.R.China

institute: Fujian Medical University

data_processing:
The raw MeRIP-seq data were aligned to genome reference sequences by Hisat2. The aligned reads were used for m6A-modification peak calling and the significant methylation was identified by exomepeak2 , and the m6A peak calling can be visualized by IGV software.
The MetaTX was used to examine the distribution pattern of epitranscriptome profiles. The STREME  was used to determine if the m6A peaks contained the consensus of m6A motif sequences.
For mRNA-seq, the mRNA expression level was analyzed by StringTie, and differentially expressed mRNAs were calculated by DEseq.
The substrates of m6A regulators were obtained from starBase v2.0.
The statistical enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for differentially expressed genes (DEGs) and differentially methylated mRNAs were applied by DAVID and KOBAS.
Assembly: human NCBI
Supplementary files format and content: DEseq output

source_name: liver

extract_protocol:
Total RNA was extracted according to manufacturer’s instruction.
The stranded RNA sequencing library was constructed by KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched

value: liver

value: human hepatocellular carcinoma cell line

value: control


title: WT mice heart repeat1

description:
Library name: WT1
WT1


title: con_1_input


title: TIGAR KO VSMC + PDGF-BB 2

city: nanjing

first: li

middle: chen

last: yu

address: Longmian Avenue

institute: nanjing medical university

description: Library name: K2-P

data_processing:
Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences and low-quality reads. The clean reads were then aligned to mouse genome (mm10_Ensembl100) using the Hisat2. HTseq was used to get gene counts and FPKM method was used to determine the gene expression.
Assembly: mm10_Ensembl100
Supplementary files format and content: tab_delimited text files include FPKM values for each Sample

source_name: vascular

growth_protocol: primary mice VSMCs were isolated from 4-6 weeks old WT or Tigar KO mice, and cultured in Dulbecco’s modified Eagle’s medium (DMEM)/F12 medium (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS; Gibco) and 1% penicillin-streptomycin (PS; Gibco), and cells between passages 4 to 6 were used for experiments.

extract_protocol:
Total RNA was isolated from primary VSMCs of WT or Tigar KO mice treated with PDGF-BB (40 μg/L) for 6 hours using Trizol reagent, following the manufacturer’s instructions. RNA quality was assessed using the Agilent 2200 system and stored at -80 °C. RNA with a RNA integrity number (RIN) > 7.0 was deemed suitable for cDNA library construction.
cDNA libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina, Inc.) according to the manufacturer’s protocol.

treatment_protocol: VSMCs from WT and TIGAR KO mice were treated or untreated with PDGF-BB (315-18, Peprotech) for 6 hours

value: vascular

value: primary culture cell

value: VSMC

value: TIGAR knockout

value: with PDGF-BB


title: bulkTCR_D5_tcra_CD8RA

description: Library name: D5_tcra_CD8RA

source_name: PBMC

value: PBMC


title: TIGAR KO VSMC + PDGF-BB 3

description: Library name: K3-P


title: con_2_IP

data_processing:
The raw MeRIP-seq data were aligned to genome reference sequences by Hisat2. The aligned reads were used for m6A-modification peak calling and the significant methylation was identified by exomepeak2 , and the m6A peak calling can be visualized by IGV software.
The MetaTX was used to examine the distribution pattern of epitranscriptome profiles. The STREME  was used to determine if the m6A peaks contained the consensus of m6A motif sequences.
For mRNA-seq, the mRNA expression level was analyzed by StringTie, and differentially expressed mRNAs were calculated by DEseq.
The substrates of m6A regulators were obtained from starBase v2.0.
The statistical enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for differentially expressed genes (DEGs) and differentially methylated mRNAs were applied by DAVID and KOBAS.
Assembly: human NCBI
Supplementary files format and content: DEseq output
Library strategy: MeRIP-seq


title: bulkTCR_D5_tcra_N

description: Library name: D5_tcra_N


title: TIGAR KO VSMC + PDGF-BB 1

description: Library name: K1-P


title: con_3_input


title: con_1_IP


title: con_3_IP


title: bulkTCR_D2_tcrb_SCM

description: Library name: D2_tcrb_SCM


title: TIGAR KO VSMC - 3

description: Library name: K3

value: without PDGF-BB


title: bulkTCR_D2_tcrb_N

description: Library name: D2_tcrb_N


title: RNA_HAP1_scRR1_MidS_083


title: RNA_HAP1_scRR1_MidS_084


title: RNA_HAP1_scRR1_MidS_081


title: bulkTCR_D5_tcra_CM

description: Library name: D5_tcra_CM


title: RNA_HAP1_scRR1_MidS_080


title: To_3_input

value: toosendanin


title: TIGAR KO VSMC - 2

description: Library name: K2


title: bulkTCR_D2_tcrb_EM

description: Library name: D2_tcrb_EM


title: RNA_HAP1_scRR1_MidS_087


title: To_2_input


title: bulkTCR_D2_tcrb_E

description: Library name: D2_tcrb_E


title: RNA_HAP1_scRR1_MidS_086


title: RNA_HAP1_scRR1_MidS_007


title: TIGAR KO VSMC - 1

description: Library name: K1


title: To_1_input


title: bulkTCR_D2_tcrb_P

description: Library name: D2_tcrb_P


title: RNA_HAP1_scRR1_MidS_079


title: To_2_IP


title: WT VSMC + PDGF-BB 2

description: Library name: W2-P

value: WT


title: RNA_HAP1_scRR1_MidS_078


title: WT VSMC + PDGF-BB 1

description: Library name: W1-P


title: bulkTCR_D2_tcrb_CD8RA

description: Library name: D2_tcrb_CD8RA


title: bulkTCR_D2_tcra_SCM

description: Library name: D2_tcra_SCM


title: RNA_HAP1_scRR1_MidS_077


title: To_1_IP


title: RNA_HAP1_scRR1_MidS_074


title: RNA_HAP1_scRR1_MidS_073


title: bulkTCR_D2_tcra_EM

description: Library name: D2_tcra_EM


title: WT VSMC - 2

description: Library name: W2


title: SN005

city: London

first: Rachel

last: Lai

address: Du Cane Road

department: Infectious Disease

country: United Kingdom

institute: Imperial College London

data_processing:
STAR v2.7.1a
featureCounts v1.5.2
DESeq2 v3.19
Assembly: GRCh38
Supplementary files format and content: Normalised spliced estimates in .csv
Supplementary files format and content: Normalised unspliced estimates in .csv

source_name: Whole blood

growth_protocol: Not applicable

extract_protocol:
Whole blood were collected in PAXgene tubes and total RNA extracted using PAXgene Blood RNA Kit (from PreAnalytiX) and quantified by absorbance method
Total RNA library using Tecan's Ovation Universal Human Blood kit with rRNA and globin RNA removal

treatment_protocol: Not applicable

value: Whole blood

tag: condition

value: TB-IRIS

value: Placebo


title: RNA_HAP1_scRR1_MidS_071


title: bulkTCR_D2_tcra_E

description: Library name: D2_tcra_E


title: bulkTCR_D2_tcra_CM

description: Library name: D2_tcra_CM


title: SN087

value: non-TB-IRIS


title: RNA_HAP1_scRR1_MidS_070


title: bulkTCR_D2_tcrb_CM

description: Library name: D2_tcrb_CM


title: To_3_IP


title: WT VSMC + PDGF-BB 3

description: Library name: W3-P


title: SN162


title: RNA_HAP1_scRR1_MidS_069


title: bulkTCR_D2_tcra_P

description: Library name: D2_tcra_P


title: WT VSMC - 3

description: Library name: W3


title: bulkTCR_D2_tcra_CD8RA

description: Library name: D2_tcra_CD8RA


title: scRNA_invitrodiff_Day20_Th1_ADT

description:
Library name: scdiff_D20_Th1_ADT
10X Genomics 5' v2; cell surface protein (CSP)

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 T cells (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 days (D10 and D20), 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 CD4 T cells cultured for 20 days

value: donor_#:D1 to D6

tag: library type

value: ADT


title: SN114


title: SN073


title: WT VSMC - 1

description: Library name: W1


title: SN260


title: RNA_HAP1_scRR1_MidS_072


title: scRNA_invitrodiff_Day20_Th1_VDJ

description:
Library name: scdiff_D20_Th1_VDJ
10X Genomics 5' v2; TCR repertoire (VDJ)

value: TCR


title: Tracheal cells, E12.5

city: Kobe

first: Shogo

last: Nakayama

state: Hyogo

address: Chuo-ku, Minatojima-minamimachi2-2-3, Lung Development and Regeneration

institute: RIKEN BDR

description:
Library name: E12_trachea
10x Genomics

data_processing:
The 10x Genomics Cell Ranger software (v5.0.1) was used for demultiplexing, read alignment and unique molecule identifier (UMI) counting. Read-depth normalization between sequencing lanes was performed using 10x Genomics Cell Ranger aggr.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Whole trachea

extract_protocol:
To prepare single-cell suspensions of mouse tracheal cells, tracheas were dissected from E11.5-E14.5 embryos. Dissected tracheas were incubated on a microtube shaker with mixture of 0.25% Trypsin-EDTA (Thermo Fisher Scientific) and 4 mg/mL collagenase type Ⅱ (Worthington) at 37 ˚C for 15 – 45 min with trituration by a P1000 pipette every 15 min. 1 mL PBS containing 10% FBS was added to quench the enzymes. The cell-suspensions were loaded onto a 40 µm cell strainer (Falcon) to purify the single cells. Single-cell suspensions were pelleted by centrifugation at 300 x g for 3 min in a swinging-bucket rotor. The supernatant was removed, and cells were resuspended in PBS with 0.5% bovine serum albumin (BSA).
Single cell sequencing library construction were performed using the 10x Genomics Chromium Single Cell 3’ Library & Gel Bead Kit following the manufacturer’s instructions. Libraries were sequenced on a HiSeq X (Illumina).

value: Whole trachea

tag: age

value: Embryonic day 12.5


title: Tracheal cells, E13.5

description:
Library name: E13_trachea
10x Genomics

value: Embryonic day 13.5


title: Tracheal cells, E11.5

description:
Library name: E11_trachea
10x Genomics

value: Embryonic day 11.5


title: RNA_HAP1_scRR1_MidS_066


title: DNA_CBMS1_scRR1_WholeS_099

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: mm10
Supplementary files format and content: txt, bedGraph
Library strategy: scRepli-seq

value: embryonic stem cell


title: SN033


title: scRNA_invitrodiff_Day20_Th1_GEX

description:
Library name: scdiff_D20_Th1_GEX
10X Genomics 5' v2; gene expression (GEX)

value: PBMC

value: mRNA


title: RNA_HAP1_scRR1_MidS_064


title: scRNA_invitrodiff_Day10_Th1_ADT

description:
Library name: scdiff_D10_Th1_ADT
10X Genomics 5' v2; cell surface protein (CSP)

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


title: RNA_HAP1_scRR1_MidS_063


title: SN250


title: DNA_CBMS1_scRR1_WholeS_096


title: SN059


title: RNA_HAP1_scRR1_MidS_068


title: RNA_HAP1_scRR1_MidS_061


title: scRNA_invitrodiff_Day10_Th1_VDJ

description:
Library name: scdiff_D10_Th1_VDJ
10X Genomics 5' v2; TCR repertoire (VDJ)


title: DNA_CBMS1_scRR1_WholeS_095


title: SN195


title: RNA_HAP1_scRR1_MidS_060


title: scRNA_invitrodiff_Day10_Th1_GEX

description:
Library name: scdiff_D10_Th1_GEX
10X Genomics 5' v2; gene expression (GEX)


title: DNA_CBMS1_scRR1_WholeS_094


title: SN227


title: scRNA_exvivoTEMRA_10donors_5v2_ADT

description:
Library name: scTEMRA_8donors_ADT
10X Genomics 5' v2; cell surface protein (CSP)

growth_protocol: T cell compartment of interest were isolated from PBMCs and directly sorted by flow cytometry (FACS) into collection medium (1:1 FBS:PBS). The sorted cells were washed with 1X PBS and subjected to scRNA-Seq using manufacturer's protocol (10X Genomics). No particular cell growth procedure was required.

extract_protocol:
PBMCs were thawed and stained with hashtag oligo-conjugated antibodies (BioLegend) to assign donor identities 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%. To analyse a limited repertoire of cell surface proteins, the cells were further stained with oligo-tagged cell surface protein antibodies (TotalSeqC antibodies, BioLegend) based on experimental requirement. For scRNA-Seq of CD4-TEMRA, TEMRA-P and TEMRA-E were sorted individually, followed by staining of TEMRA-E with oligo-conjugated αCD4 TotalSeq C antibody to be able to demarcate them in downstream analyses, and pooled in 1:1 ratio.
scRNA-Seq with 10x Genomics 5'. About 25,000 cells per lane were loaded onto Chromium NextGEM Chip G (ex vivo CD4) or Chip K (ex vivo TSCM and TEMRA) depending on kit version v1.1 or v2 respectively. 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: No particular treatment was done to the PBMCs. PBMCs were immuno stained and sorted using FACS for scRNA-Seq experiment.

value: ex vivo TEMRA cells

value: donor_#:D1 to D8


title: RNA_HAP1_scRR1_MidS_005


title: DNA_CBMS1_scRR1_WholeS_093


title: SN258

value: Whole blood


title: RNA_HAP1_scRR1_MidS_059


title: DNA_CBMS1_scRR1_WholeS_091


title: scRNA_exvivoTEMRA_10donors_5v2_TCR

description:
Library name: scTEMRA_8donors_TCR
10X Genomics 5' v2; TCR repertoire (VDJ)


title: SN319

value: Placebo


title: DNA_CBMS1_scRR1_WholeS_098


title: RNA_HAP1_scRR1_MidS_057


title: RNA_HAP1_scRR1_MidS_055


title: DNA_CBMS1_scRR1_WholeS_090


title: SN237

value: TB-IRIS


title: scRNA_exvivoTSCM_10donors_5v2_TCR

description:
Library name: scTSCM_8donors_TCR
10X Genomics 5' v2; TCR repertoire (VDJ)

value: ex vivo TSCM cells


title: scRNA_exvivoTSCM_10donors_5v2_ADT

description:
Library name: scTSCM_8donors_ADT
10X Genomics 5' v2; cell surface protein (CSP)


title: SN204

value: non-TB-IRIS


title: RNA_HAP1_scRR1_MidS_054


title: scRNA_exvivoTSCM_10donors_5v2_GEX

description:
Library name: scTSCM_8donors_GEX
10X Genomics 5' v2; gene expression (GEX)


title: DNA_CBMS1_scRR1_WholeS_087


title: DNA_CBMS1_scRR1_WholeS_086


title: SN158


title: scRNA_exvivoCD4_10donors_5v1_ADT

description:
Library name: scCD4_10donors_ADT
10X Genomics 5' v1.1; cell surface protein (CSP)

value: ex vivo CD4 cells

value: donor_#:D1 to D10

value: ADT


title: DNA_CBMS1_scRR1_WholeS_085


title: RNA_HAP1_scRR1_MidS_051


title: SN015


title: SN149


title: RNA_HAP1_scRR1_MidS_050


title: scRNA_exvivoTEMRA_10donors_5v2_GEX

description:
Library name: scTEMRA_8donors_GEX
10X Genomics 5' v2; gene expression (GEX)


title: DNA_CBMS1_scRR1_WholeS_084


title: SN248


title: Tracheal cells, E14.5

description:
Library name: E14_trachea
10x Genomics

value: Whole trachea

value: Embryonic day 14.5


title: scRNA_exvivoCD4_10donors_5v1_GEX

description:
Library name: scCD4_10donors_GEX
10X Genomics 5' v1.1; gene expression (GEX)


title: DNA_CBMS1_scRR1_WholeS_082


title: SN219


title: RNA_HAP1_scRR1_MidS_043


title: DNA_CBMS1_scRR1_WholeS_089


title: RNA_HAP1_scRR1_MidS_038


title: DNA_CBMS1_scRR1_WholeS_080


title: scATAC_invitrodiff_Day10_Th1_6donors

description:
Library name: scdiff_D10_Th1_ATAC
10X Genomics ATAC v1; open chromatin

library_source: genomic single cell

data_processing:
Demultiplexed raw FASTQ files corresponding to 5ʹ 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.

extract_protocol:
On the mentioned days (D10 and D20), the cells were taken from culture and washed thoroughly with 1X PBS, and maintained at >95% viability.
scATAC-Seq with 10x Genomics ATAC v1. About 25,000 transposed nuclei per lane were loaded onto Chromium NextGEM Chip H. Manufacturers’ recommendations were followed to generate libraries for open chromatin.
Libraries were sequenced on NovaSeq 6000 (Illumina) for sequencing according to manufacturer's recommendations.

value: donor_#:D1 to D6

value: ATAC


title: RNA_HAP1_scRR1_MidS_053


title: SN301


title: bulkRNASeq_D10_CD8_TEMRA

description: Library name: bRNA_D10_CD8RA

data_processing:
Raw demultiplexed FASTQ files (n=70; 10 donors, 7 cell types) were adaptor trimmed using trim_galore (https://github.com/FelixKrueger/TrimGalore) and mapped to GRCh38 (hg38) human reference genome using STAR.
Sequencing read coverage per gene was counted using HTSeq-count (http://www huber.embl.de/users/anders/HTSeq/). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
Assembly: GRCh38 (hg38)
Supplementary files format and content: "counts_A1ReadsPerGene.out.tab" contains raw counts of sequencing reads obtained with HTSeq-count.

extract_protocol:
RNA-seq was performed as described previously by Picelli et al, 2013, and Patil et al 2018, using Smart-Seq2 method with 3 ng 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.
Barcoded Illumina sequencing libraries were constructed as per the protocol described by Illumina (Nextera XT library preparation kit, Illumina).
Libraries were sequenced on NovaSeq 6000 (Illumina) for 150-bp paired-end sequencing.

value: PBMC


title: SN107


title: DNA_CBMS1_scRR1_WholeS_079

value: embryonic stem cell


title: RNA_HAP1_scRR1_MidS_036


title: bulkRNASeq_D9_CD8_TEMRA

description: Library name: bRNA_D9_CD8RA


title: RNA_HAP1_scRR1_MidS_035


title: SN057


title: bulkRNASeq_D8_CD8_TEMRA

description: Library name: bRNA_D8_CD8RA


title: RNA_HAP1_scRR1_MidS_034


title: DNA_CBMS1_scRR1_WholeS_078


title: scATAC_invitrodiff_Day20_Th1_6donors

description:
Library name: scdiff_D20_Th1_ATAC
10X Genomics ATAC v1; open chromatin

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


title: DNA_CBMS1_scRR1_WholeS_077


title: SN193


title: RNA_HAP1_scRR1_MidS_032


title: bulkRNASeq_D7_CD8_TEMRA

description: Library name: bRNA_D7_CD8RA


title: DNA_CBMS1_scRR1_WholeS_076


title: bulkRNASeq_D6_CD8_TEMRA

description: Library name: bRNA_D6_CD8RA


title: SN039


title: RNA_HAP1_scRR1_MidS_031


title: RNA_HAP1_scRR1_MidS_029


title: bulkRNASeq_D5_CD8_TEMRA

description: Library name: bRNA_D5_CD8RA


title: DNA_CBMS1_scRR1_WholeS_075


title: RNA_HAP1_scRR1_MidS_028


title: bulkRNASeq_D4_CD8_TEMRA

description: Library name: bRNA_D4_CD8RA


title: DNA_CBMS1_scRR1_WholeS_074


title: DNA_CBMS1_scRR1_WholeS_073


title: SN285


title: RNA_HAP1_scRR1_MidS_026


title: SN148


title: SN257


title: bulkRNASeq_D1_CD8_TEMRA

description: Library name: bRNA_D1_CD8RA


title: bulkRNASeq_D3_CD8_TEMRA

description: Library name: bRNA_D3_CD8RA


title: bulkRNASeq_D2_CD8_TEMRA

description: Library name: bRNA_D2_CD8RA


title: DNA_CBMS1_scRR1_WholeS_072


title: SN133


title: SN284


title: DNA_CBMS1_scRR1_WholeS_071


title: bulkRNASeq_D10_CD4_TEM

description: Library name: bRNA_D10_EM


title: DNA_CBMS1_scRR1_WholeS_069


title: DNA_CBMS1_scRR1_WholeS_070


title: RNA_HAP1_scRR1_MidS_025


title: SN170


title: RNA_HAP1_scRR1_MidS_023


title: RNA_HAP1_scRR1_MidS_024


title: SN321


title: RNA_HAP1_scRR1_MidS_020


title: DNA_CBMS1_scRR1_WholeS_066


title: DNA_CBMS1_scRR1_WholeS_065


title: RNA_HAP1_scRR1_MidS_021


title: SN141


title: RNA_HAP1_scRR1_MidS_001


title: bulkRNASeq_D8_CD4_TEM

description: Library name: bRNA_D8_EM


title: SN302


title: bulkRNASeq_D7_CD4_TEM

description: Library name: bRNA_D7_EM


title: bulkRNASeq_D5_CD4_TEM

description: Library name: bRNA_D5_EM


title: DNA_CBMS1_scRR3_WholeS_061


title: RNA_HAP1_scRR1_MidS_017


title: DNA_CBMS1_scRR3_WholeS_063


title: RNA_HAP1_scRR1_MidS_018


title: bulkRNASeq_D6_CD4_TEM

description: Library name: bRNA_D6_EM


title: SN247


title: SN218


title: bulkRNASeq_D4_CD4_TEM

description: Library name: bRNA_D4_EM


title: DNA_CBMS1_scRR3_WholeS_057


title: SN029


title: bulkRNASeq_D9_CD4_TEM

description: Library name: bRNA_D9_EM


title: DNA_RPE1_scRR3_G0_WholeS_002

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, hg19
Supplementary files format and content: txt, bedGraph
Library strategy: scRepli-seq


title: DNA_RPE1_scRR3_G0_WholeS_015


title: bulkRNASeq_D3_CD4_TEM

description: Library name: bRNA_D3_EM


title: DNA_CBMS1_scRR3_WholeS_055


title: SN300


title: DNA_RPE1_scRR3_Lot2_WholeS_09


title: DNA_CBMS1_scRR3_WholeS_053


title: DNA_CBMS1_scRR3_WholeS_060


title: SN225


title: bulkRNASeq_D2_CD4_TEM

description: Library name: bRNA_D2_EM


title: DNA_CBMS1_scRR3_WholeS_052


title: DNA_RPE1_scRR3_Lot2_WholeS_08


title: SN256


title: SN147


title: bulkRNASeq_D10_CD4_TCM

description: Library name: bRNA_D10_CM


title: DNA_RPE1_scRR3_Lot2_WholeS_016


title: DNA_CBMS1_scRR3_WholeS_050


title: bulkRNASeq_D9_CD4_TCM

description: Library name: bRNA_D9_CM


title: DNA_CBMS1_scRR3_WholeS_048


title: SN316


title: DNA_RPE1_scRR3_Lot2_WholeS_015


title: SN132


title: bulkRNASeq_D8_CD4_TCM

description: Library name: bRNA_D8_CM


title: bulkRNASeq_D7_CD4_TCM

description: Library name: bRNA_D7_CM


title: SN068


title: DNA_CBMS1_scRR3_WholeS_047


title: DNA_CBMS1_scRR3_WholeS_046


title: SN266


title: DNA_RPE1_scRR3_Lot2_WholeS_014


title: bulkRNASeq_D1_CD4_TEM

description: Library name: bRNA_D1_EM


title: bulkRNASeq_D6_CD4_TCM

description: Library name: bRNA_D6_CM


title: DNA_CBMS1_scRR3_WholeS_045


title: SN019


title: bulkRNASeq_D5_CD4_TCM

description: Library name: bRNA_D5_CM


title: SN156


title: DNA_RPE1_scRR3_Lot2_WholeS_012


title: bulkRNASeq_D4_CD4_TCM

description: Library name: bRNA_D4_CM


title: DNA_RPE1_scRR3_Lot1_WholeS_009


title: DNA_CBMS1_scRR3_WholeS_040


title: DNA_CBMS1_scRR3_WholeS_038


title: SN240


title: SN217


title: bulkTCR_D2_tcra_N

description: Library name: D2_tcra_N

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_RPE1_scRR3_Lot1_WholeS_007


title: bulkRNASeq_D3_CD4_TCM

description: Library name: bRNA_D3_CM


title: DNA_CBMS1_scRR3_WholeS_037


title: SN299


title: DNA_RPE1_scRR3_Lot1_WholeS_006


title: DNA_CBMS1_scRR3_WholeS_036


title: DNA_RPE1_scRR3_Lot2_WholeS_013


title: SN102


title: bulkRNASeq_D1_CD4_TCM

description: Library name: bRNA_D1_CM


title: DNA_RPE1_scRR3_Lot2_WholeS_011


title: DNA_CBMS1_scRR3_WholeS_032


title: DNA_RPE1_scRR3_Lot1_WholeS_003


title: bulkRNASeq_D10_CD4_TEMRA_E

description: Library name: bRNA_D10_E


title: SN191


title: SN224


title: DNA_CBMS1_scRR3_WholeS_030


title: DNA_RPE1_scRR3_Lot1_WholeS_013


title: DNA_RPE1_scRR3_Lot1_WholeS_019


title: DNA_CBMS1_scRR3_WholeS_029


title: SN082


title: bulkRNASeq_D9_CD4_TEMRA_E

description: Library name: bRNA_D9_E


title: DNA_RPE1_scRR1_Lot2_WholeS_095


title: DNA_RPE1_scRR1_Lot2_WholeS_074


title: SN178


title: bulkRNASeq_D7_CD4_TEMRA_E

description: Library name: bRNA_D7_E


title: DNA_CBMS1_scRR3_WholeS_027


title: bulkRNASeq_D2_CD4_TCM

description: Library name: bRNA_D2_CM


title: DNA_CBMS1_scRR3_WholeS_026


title: bulkRNASeq_D6_CD4_TEMRA_E

description: Library name: bRNA_D6_E


title: DNA_RPE1_scRR1_Lot2_WholeS_066


title: SN255


title: DNA_CBMS1_scRR3_WholeS_024


title: bulkRNASeq_D5_CD4_TEMRA_E

description: Library name: bRNA_D5_E


title: SN278


title: DNA_CBMS1_scRR3_WholeS_023


title: SN146


title: DNA_CBMS1_scRR3_WholeS_022


title: SN293


title: DNA_RPE1_scRR1_Lot2_WholeS_064


title: bulkRNASeq_D4_CD4_TEMRA_E

description: Library name: bRNA_D4_E


title: DNA_RPE1_scRR1_Lot2_WholeS_058


title: bulkRNASeq_D3_CD4_TEMRA_E

description: Library name: bRNA_D3_E


title: bulkRNASeq_D8_CD4_TEMRA_E

description: Library name: bRNA_D8_E


title: SN066


title: DNA_RPE1_scRR1_Lot2_WholeS_054


title: bulkRNASeq_D2_CD4_TEMRA_E

description: Library name: bRNA_D2_E


title: DNA_CBMS1_scRR3_WholeS_021


title: SN046


title: DNA_CBMS1_scRR3_WholeS_019


title: DNA_RPE1_scRR1_Lot2_WholeS_051


title: bulkRNASeq_D1_CD4_TEMRA_E

description: Library name: bRNA_D1_E


title: SN263


title: DNA_RPE1_scRR1_Lot2_WholeS_070


title: DNA_RPE1_scRR1_Lot2_WholeS_049


title: bulkRNASeq_D10_CD4_TEMRA_P

description: Library name: bRNA_D10_P


title: DNA_CBMS1_scRR3_WholeS_013


title: SN199


title: bulkRNASeq_D9_CD4_TEMRA_P

description: Library name: bRNA_D9_P


title: DNA_CBMS1_scRR1_WholeS_128


title: SN275


title: DNA_RPE1_scRR1_Lot2_WholeS_045


title: DNA_CBMS1_scRR1_WholeS_127


title: SN308


title: DNA_RPE1_scRR1_Lot2_WholeS_044


title: bulkRNASeq_D7_CD4_TEMRA_P

description: Library name: bRNA_D7_P


title: DNA_CBMS1_scRR1_WholeS_126


title: DNA_RPE1_scRR1_Lot2_WholeS_043


title: DNA_CBMS1_scRR1_WholeS_125


title: SN027


title: bulkRNASeq_D5_CD4_TEMRA_P

description: Library name: bRNA_D5_P


title: DNA_RPE1_scRR1_Lot2_WholeS_004


title: DNA_CBMS1_scRR1_WholeS_124


title: SN018


title: DNA_CBMS1_scRR3_WholeS_016


title: SN245


title: bulkRNASeq_D4_CD4_TEMRA_P

description: Library name: bRNA_D4_P


title: SN120


title: bulkRNASeq_D3_CD4_TEMRA_P

description: Library name: bRNA_D3_P


title: DNA_CBMS1_scRR1_WholeS_123


title: DNA_RPE1_scRR1_Lot2_WholeS_048


title: DNA_RPE1_scRR1_Lot2_WholeS_035


title: DNA_RPE1_scRR1_Lot2_WholeS_037


title: bulkRNASeq_D8_CD4_TEMRA_P

description: Library name: bRNA_D8_P


title: bulkRNASeq_D2_CD4_TEMRA_P

description: Library name: bRNA_D2_P


title: DNA_RPE1_scRR1_Lot2_WholeS_031


title: SN080


title: SN223


title: DNA_CBMS1_scRR1_WholeS_120


title: bulkRNASeq_D1_CD4_TEMRA_P

description: Library name: bRNA_D1_P


title: DNA_RPE1_scRR1_Lot2_WholeS_028


title: bulkRNASeq_D6_CD4_TEMRA_P

description: Library name: bRNA_D6_P


title: bulkRNASeq_D10_CD4_TSCM

description: Library name: bRNA_D10_SCM


title: DNA_RPE1_scRR1_Lot2_WholeS_026


title: DNA_CBMS1_scRR1_WholeS_119


title: SN274


title: bulkRNASeq_D9_CD4_TSCM

description: Library name: bRNA_D9_SCM


title: bulkRNASeq_D8_CD4_TSCM

description: Library name: bRNA_D8_SCM


title: DNA_RPE1_scRR1_Lot2_WholeS_024


title: DNA_CBMS1_scRR1_WholeS_116


title: SN130


title: DNA_RPE1_scRR1_Lot2_WholeS_020


title: DNA_CBMS1_scRR1_WholeS_121


title: bulkRNASeq_D7_CD4_TSCM

description: Library name: bRNA_D7_SCM


title: bulkRNASeq_D6_CD4_TSCM

description: Library name: bRNA_D6_SCM


title: DNA_RPE1_scRR1_Lot2_WholeS_002


title: SN198


title: DNA_CBMS1_scRR1_WholeS_115


title: SN061


title: DNA_CBMS1_scRR1_WholeS_113


title: DNA_CBMS1_scRR1_WholeS_111


title: bulkRNASeq_D4_CD4_TSCM

description: Library name: bRNA_D4_SCM


title: DNA_CBMS1_scRR3_WholeS_012


title: DNA_RPE1_scRR1_Lot2_WholeS_011


title: SN035


title: SN307


title: DNA_RPE1_scRR1_Lot1_WholeS_008


title: DNA_CBMS1_scRR1_WholeS_110


title: DNA_CBMS1_scRR1_WholeS_118


title: bulkRNASeq_D3_CD4_TSCM

description: Library name: bRNA_D3_SCM


title: SN008


title: bulkRNASeq_D2_CD4_TSCM

description: Library name: bRNA_D2_SCM


title: DNA_RPE1_scRR1_Lot2_WholeS_016


title: DNA_CBMS1_scRR3_WholeS_011


title: DNA_RPE1_scRR1_Lot1_WholeS_005


title: SN151


title: bulkRNASeq_D5_CD4_TSCM

description: Library name: bRNA_D5_SCM


title: bulkRNASeq_D1_CD4_TSCM

description: Library name: bRNA_D1_SCM


title: DNA_CBMS1_scRR1_WholeS_108


title: bulkRNASeq_D10_CD4_Naive

description: Library name: bRNA_D10_N


title: SN214


title: DNA_CBMS1_scRR1_WholeS_109


title: DNA_RPE1_scRR1_Lot1_WholeS_003


title: DNA_RPE1_scRR1_Lot1_WholeS_006


title: DNA_CBMS1_scRR1_WholeS_104


title: SN051


title: DNA_RPE1_scRR1_Lot1_WholeS_016


title: DNA_CBMS1_scRR1_WholeS_103


title: SN188


title: DNA_RPE1_scRR1_Lot1_WholeS_015


title: bulkRNASeq_D9_CD4_Naive

description: Library name: bRNA_D9_N


title: DNA_CBMS1_scRR1_WholeS_102


title: SN207


title: SN116


title: DNA_RPE1_scRR1_Lot1_WholeS_007


title: DNA_RPE1_scRR1_Lot1_WholeS_014


title: DNA_CBMS1_scRR1_WholeS_101


title: bulkRNASeq_D7_CD4_Naive

description: Library name: bRNA_D7_N


title: SN296


title: bulkRNASeq_D6_CD4_Naive

description: Library name: bRNA_D6_N


title: DNA_CBMS1_scRR3_WholeS_007


title: SN272


title: RNA_RPE1_scRR3_G0_WholeS_002

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, hg19
Supplementary files format and content: txt, bedGraph


title: bulkRNASeq_D5_CD4_Naive

description: Library name: bRNA_D5_N


title: DNA_RPE1_scRR1_Lot1_WholeS_013


title: DNA_CBMS1_scRR3_WholeS_005


title: bulkRNASeq_D4_CD4_Naive

description: Library name: bRNA_D4_N


title: bulkRNASeq_D8_CD4_Naive

description: Library name: bRNA_D8_N


title: DNA_CBMS1_scRR3_WholeS_004


title: RNA_RPE1_scRR3_G0_WholeS_015


title: SN144


title: bulkRNASeq_D3_CD4_Naive

description: Library name: bRNA_D3_N


title: bulkRNASeq_D2_CD4_Naive

description: Library name: bRNA_D2_N


title: DNA_CBMS1_scRR3_WholeS_001


title: RNA_RPE1_scRR3_Lot2_WholeS_08


title: DNA_CBMS1_scRR3_WholeS_002


title: bulkRNASeq_D1_CD4_Naive

description: Library name: bRNA_D1_N


title: RNA_RPE1_scRR3_Lot2_WholeS_09


title: SN136


title: RNA_CBMS1_scRR1_WholeS_099

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: mm10
Supplementary files format and content: txt, bedGraph


title: SN127


title: RNA_RPE1_scRR3_Lot2_WholeS_016


title: SN042


title: SN160


title: bulkATAC_D10_CD4_TEMRA_E

description:
Library name: bATAC_D10_E
aggregated .bw file for 10 donors
E_out.bw

data_processing:
Raw demultiplexed FASTQ files (n = 20; 10 donors, 2 cell types – CD4-Naïve TN 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 and E_out.bw. bigWig files for each cell type is the aggregated file from 10 donors.

growth_protocol: CD4-Naive 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.


title: SN175


title: RNA_CBMS1_scRR1_WholeS_098


title: RNA_RPE1_scRR3_Lot2_WholeS_015


title: SN023


title: bulkATAC_D9_CD4_TEMRA_E

description:
Library name: bATAC_D9_E
aggregated .bw file for 10 donors
E_out.bw


title: RNA_RPE1_scRR3_Lot2_WholeS_014


title: RNA_CBMS1_scRR1_WholeS_096


title: SN242


title: RNA_RPE1_scRR3_Lot2_WholeS_013


title: bulkATAC_D8_CD4_TEMRA_E

description:
Library name: bATAC_D8_E
aggregated .bw file for 10 donors
E_out.bw


title: RNA_CBMS1_scRR1_WholeS_095


title: bulkATAC_D7_CD4_TEMRA_E

description:
Library name: bATAC_D7_E
aggregated .bw file for 10 donors
E_out.bw


title: SN091


title: RNA_RPE1_scRR3_Lot2_WholeS_012


title: RNA_CBMS1_scRR1_WholeS_094


title: RNA_RPE1_scRR3_Lot2_WholeS_011


title: RNA_CBMS1_scRR1_WholeS_093


title: RNA_RPE1_scRR3_Lot1_WholeS_007


title: bulkATAC_D4_CD4_TEMRA_E

description:
Library name: bATAC_D4_E
aggregated .bw file for 10 donors
E_out.bw


title: bulkATAC_D6_CD4_TEMRA_E

description:
Library name: bATAC_D6_E
aggregated .bw file for 10 donors
E_out.bw


title: RNA_CBMS1_scRR1_WholeS_090


title: RNA_RPE1_scRR3_Lot1_WholeS_009


title: bulkATAC_D3_CD4_TEMRA_E

description:
Library name: bATAC_D3_E
aggregated .bw file for 10 donors
E_out.bw


title: RNA_RPE1_scRR3_Lot1_WholeS_006


title: bulkATAC_D2_CD4_TEMRA_E

description:
Library name: bATAC_D2_E
aggregated .bw file for 10 donors
E_out.bw


title: RNA_CBMS1_scRR1_WholeS_089


title: RNA_RPE1_scRR3_Lot1_WholeS_003


title: RNA_CBMS1_scRR1_WholeS_091


title: bulkATAC_D5_CD4_TEMRA_E

description:
Library name: bATAC_D5_E
aggregated .bw file for 10 donors
E_out.bw


title: RNA_CBMS1_scRR1_WholeS_087


title: RNA_CBMS1_scRR1_WholeS_086


title: bulkATAC_D10_CD4_Naive

description:
Library name: bATAC_D10_N
aggregated .bw file for 10 donors
N_out.bw


title: bulkATAC_D1_CD4_TEMRA_E

description:
Library name: bATAC_D1_E
aggregated .bw file for 10 donors
E_out.bw


title: RNA_RPE1_scRR3_Lot1_WholeS_013


title: RNA_RPE1_scRR3_Lot1_WholeS_019


title: VEZF1-2A-3

city: 重庆

first: Yang

middle: jia

last: yao

address: Medical College Road

department: Key Laboratory of Molecular Biology for Infectious Diseases

institute: Chongqing Medical University

data_processing:
UID-mRNA-seq PE-150
Assembly: GRCh38_release101
Supplementary files format and content: tab-delimited text files include raw counts for each sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: we used lentivirus-encoded sgRNA to eliminate endogenous VEZF1 in HepG2 cells followed by re-expression of VEZF1WT or VEZF12A.RNA-seq was performed.


title: VEZF1-2A-2


title: RNA_CBMS1_scRR1_WholeS_085

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: RNA_CBMS1_scRR1_WholeS_084


title: VEZF1-2A-1


title: bulkATAC_D8_CD4_Naive

description:
Library name: bATAC_D8_N
aggregated .bw file for 10 donors
N_out.bw


title: 1P

type: RNA

city: Nanjing

first: yueming

last: sun

state: jiangsu

address: Nanjing medical university

institute: The First Affiliated Hospital of Nanjing Medical University

description: mRNA expression in paired adjacent normal tissue

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: adjacent normal tissue

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

growth_protocol: The colorectal cancer tissue and adjacent tissue were obtained after surgery, respectively.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Fresh tissues were acquired after surgery and immediately frozen in -80℃.Total RNA containing small RNA was extracted by using  the Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA) according to manufacter’s protocol.

value: adjacent normal tissue


title: RNA_RPE1_scRR1_Lot2_WholeS_074


title: RNA_CBMS1_scRR1_WholeS_082


title: bulkATAC_D7_CD4_Naive

description:
Library name: bATAC_D7_N
aggregated .bw file for 10 donors
N_out.bw


title: 3P


title: 4T

description: mRNA expression in colorectal cancer tissue

source_name: colorectal cancer tissues

value: colorectal cancer tissue


title: 3T


title: 4P


title: VEZF1-WT-3


title: RNA_RPE1_scRR1_Lot2_WholeS_070


title: 1T


title: RNA_CBMS1_scRR1_WholeS_080


title: RNA_RPE1_scRR1_Lot2_WholeS_095


title: bulkATAC_D6_CD4_Naive

description:
Library name: bATAC_D6_N
aggregated .bw file for 10 donors
N_out.bw


title: bulkATAC_D9_CD4_Naive

description:
Library name: bATAC_D9_N
aggregated .bw file for 10 donors
N_out.bw


title: RNA_RPE1_scRR1_Lot2_WholeS_066


title: VEZF1-WT-1


title: VEZF1-WT-2