title: snRNA-seq, visceral adipose tissue, 10x channel AD4 (donor DM_01)

description:
Library name: AD4
Single-nucleus RNA-seq of visceral adipose tissue, 10x Genomics channel AD4, single donor DM_01. Metabolic group: obesity with type 2 diabetes. Sequenced across 4 lanes; all lane-level FASTQ files belong to this one library.
VAT_snRNA_matrix.mtx.gz
VAT_snRNA_barcodes.tsv.gz
VAT_snRNA_features.tsv.gz
VAT_snRNA_metadata.tsv


title: MJM3381 replicate 4

status: Public on Aug 14 2026

type: SRA

city: Madison

first: Mark

middle: J

last: Mandel

state: WI

address: 1550 Linden Drive

department: Medical Microbiology and Immunology

country: USA

institute: University of Wisconsin-Madison

description: Library name: Sample4

library_source: transcriptomic

data_processing:
Read demultiplexing, read trimming, and run analytics were performed using DRAGEN v4.2.7, an on-board analysis software on the NextSeq2000.
Processed with fastp V0.23.4
Fastp-processed sequence files were aligned to the V. fischeri ES114 reference genome ENSEMBL_GCA_000011805 (MJM3381 and MJM5250) or to ENSEMBL_GCA_000011805-reform (MJM5028 and MJM5029) using bwa-mem V0.7.18. For both genomes, information for the 10 currently known sRNAs (VF_2577 csrB2, VF_2578 ryhB, VF_2579 spf, VF_2593 csrB1, VF_2597 qrr1, VF_2599 ffs, VF_2639 ssrA, VF_2651 ssrS, VF_2654 rnpB, VF_A1194 psrN) was manually appended.
Reads were assigned to gene features using htseq-count V0.6.1
Assembly: ENSEMBL_GCA_000011805
Supplementary files format and content: csv file with raw read counts for the sample

molecule: total RNA

organism: Aliivibrio fischeri

source_name: Vibrio fischeri ES114

growth_protocol: Vibrio fischeri cells were streaked onto LBS and grown overnight at 25 ˚C. Single colonies of each strain were inoculated into 3 mL LBS and grown for 16 hrs at 28 ˚C with shaking. Overnight cultures were diluted 1/100 into 20 mL fresh LBS and grown at 28 ˚C with shaking until OD600 ~1.8

extract_protocol:
1 mL samples of each strain were taken and centrifuged at 10,000 x g, for 1 min. Supernatants were discarded and each pellet was resuspended in 600 uL TriReagent (Zymo Research), and total RNA was purified using a Direct-Zol kit (Zymo Research).
RNA samples were prepared for sequencing using the Illumina Stranded Total RNA Prep Ligation Kit with Ribo-Zero Plus Microbiome (#20072063) with Illumina Unique Dual Indexes.

tag: cell type

value: Vibrio fischeri ES114

tag: genotype

value: WT attTn7::erm

tag: treatment

value: Liquid culture


title: MJM3381 replicate 2

description: Library name: Sample2


title: MJM3381 replicate 3

description: Library name: Sample3


title: snRNA-seq, visceral adipose tissue, 10x channel AD2 (donor DM_02)

city: Seongnam city

first: SungHee

last: Choi

address: Dolmaro 172, Bundang dist

department: Internal Medicine, Division of Endocrinology and Metabolism

country: South Korea

institute: Seoul National University Bundang Hospital

description:
Library name: AD2
Single-nucleus RNA-seq of visceral adipose tissue, 10x Genomics channel AD2, single donor DM_02. Metabolic group: obesity with type 2 diabetes. Sequenced across 4 lanes; all lane-level FASTQ files belong to this one library.
VAT_snRNA_matrix.mtx.gz
VAT_snRNA_barcodes.tsv.gz
VAT_snRNA_features.tsv.gz
VAT_snRNA_metadata.tsv

library_source: transcriptomic single cell

data_processing:
snRNA-seq: Raw reads were aligned to the human reference genome GRCh38 and gene-by-cell count matrices generated with CellRanger v7.0.1 using default parameters (11 channels, 21 donors).
snRNA-seq: Ambient RNA and empty droplets were removed with the remove-background function of CellBender v0.3.2. Per-cell QC metrics were computed with perCellQCMetrics (scuttle v1.4.0); nuclei with <2.5 log10 UMIs or >10% mitochondrial reads were excluded. Doublets were flagged with scDblFinder v1.8.0.
snRNA-seq: Donor identity in pooled channels was assigned with Souporcell v2.5, with the expected number of genotype clusters set to the number of pooled donors. Souporcell clusters were matched to donors by genotype concordance against donor-specific whole-exome sequencing (BWA-MEM2 v2.2.1 alignment, GATK v4.4.0.0 variant calling, exonic SNPs with QD >= 10, concordance computed with vcfR v1.14.0).
Bulk RNA-seq: Nextera adapter sequences and low-quality reads were removed with Trimmomatic v0.39. Reads were aligned to GRCh38 with HISAT2 v2.2.1, PCR and optical duplicates were removed with Picard v2.18.29, and reads were counted against the GRCh38 GTF annotation with HTSeq v0.11.2.
Assembly: GRCh38
Supplementary files format and content: VAT_Bulk_FPKM.txt: Tab-delimited text file containing the FPKM expression matrix for the 20 whole-tissue visceral adipose bulk RNA-seq samples (rows, 13,791 protein-coding genes identified by HGNC symbol; columns, samples labelled Lean_01-08, Ob_01-05 and DM_01-07). Values are FPKM computed from HTSeq gene counts.
Supplementary files format and content: VAT_Exvivo_mAb_Treated_RCM.csv: Comma-delimited text file containing the raw gene-level read count matrix for the 8 ex vivo explant libraries (rows, 61,541 genes identified by Ensembl gene ID; columns, 4 donors x 2 treatments, labelled AT_GS_01-04 with Naive or mAb suffix). Counts were generated with HTSeq v0.11.2 against the GRCh38 GTF annotation.
Supplementary files format and content: VAT_Exvivo_mAb_Treated_fpkm_combat.csv: Comma-delimited text file containing the batch-corrected FPKM expression matrix for the same 8 ex vivo explant libraries (rows, 19,424 protein-coding genes identified by HGNC symbol; columns as above). FPKM values were corrected for inter-donor variation with ComBat (sva package), treating each donor as a batch, and were used for the paired differential expression analysis reported in the manuscript.
Supplementary files format and content: Per-channel snRNA-seq matrices (AD1_barcodes.tsv.gz, AD1_features.tsv.gz, AD1_matrix.mtx.gz and the equivalent files for AD2-AD11): Gene-by-nucleus count matrix in 10x Genomics Market Exchange (MEX) format, provided as one set of three files per snRNA-seq channel. Matrices are the filtered_feature_bc_matrix output of CellRanger v7.0.1, before ambient-RNA removal and downstream filtering. Rows correspond to genes listed in the features file; columns correspond to nuclei listed in the barcodes file.
Supplementary files format and content: VAT_snRNA_matrix.mtx.gz, VAT_snRNA_barcodes.tsv.gz, VAT_snRNA_features.tsv.gz: Gene-by-nucleus count matrix in 10x Genomics Market Exchange (MEX) format, integrated across all 11 snRNA-seq channels after CellBender ambient-RNA removal, quality filtering, doublet removal and Souporcell donor demultiplexing. This is the matrix used for the analyses reported in the manuscript. Readable in R with Seurat::ReadMtx() or in Python with scanpy.read_10x_mtx().
Supplementary files format and content: VAT_snRNA_metadata.tsv: Tab-delimited per-nucleus metadata table for the integrated matrix, containing the 10x channel of origin, donor assignment, metabolic group, quality-control metrics, and the cell-type and subtype annotations reported in the manuscript. Row order matches the barcode order in VAT_snRNA_barcodes.tsv.gz.

molecule: nuclear RNA

organism: Homo sapiens

source_name: visceral adipose tissue

growth_protocol: Visceral adipose tissue was collected fresh at surgery and either snap-frozen in liquid nitrogen and stored at -80C, or processed immediately. For the ex vivo explant subset, tissue was minced and maintained in DMEM/F-12 supplemented with 10% FBS and 1% penicillin-streptomycin at 37C in 5% CO2, with medium replenished every 2 days.

extract_protocol:
snRNA-seq: Snap-frozen visceral adipose tissue was thawed in DMEM with 10% FBS at 37C for 10 min and washed twice in PBS, then minced into 2-4 mm pieces. Nuclei were released in TST buffer (10 mM Tris-HCl pH 8.0, 0.25% SDS, 1 mM EDTA, 150 mM NaCl, 1x protease inhibitor cocktail) for 20 min on ice with gentle shaking. The lysate was passed through 100 um, 70 um and 10 um strainers in sequence and pelleted at 500 x g for 5 min at 4C. Nuclei were resuspended in 10x Genomics Nuclei Buffer (PN-1000268) and counted on a hemocytometer. For multiplexed channels, nuclei from 2-3 donors of the same metabolic condition were pooled in equal proportions (approximately 10,000 nuclei per donor).  Bulk RNA-seq: Total RNA was extracted from whole visceral adipose tissue, or from ex vivo explant cultures, using TRIzol Reagent (15596018, Ambion) according to the manufacturer's protocol. RNA concentration and purity were assessed on a NanoDrop ND-1000 spectrophotometer.
snRNA-seq: Libraries were prepared with the Chromium Single Cell 3' Gene Expression Kit v3.1 (10x Genomics) following the manufacturer's instructions. For pooled channels, nuclei from 2-3 donors were combined in equal proportions before loading; no cell-labelling reagent was used, and donor identity was recovered computationally from natural genetic variation after sequencing. Libraries were sequenced on an Illumina NovaSeq 6000 by Genome Insight Inc. (Republic of Korea).  Bulk RNA-seq: Libraries were prepared with the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Plus (Illumina); ribosomal RNA was depleted to enrich for mRNA and non-coding RNA. Libraries were sequenced paired-end on an Illumina NovaSeq 6000.

treatment_protocol: Not applicable for the primary tissue samples. For the ex vivo explant subset, human visceral adipose tissue explants were treated for 5 days with an anti-THBS1 monoclonal antibody (clone A6-1, GTX21823, GeneTex; 1:100) or left untreated as the paired control from the same donor; treatment medium was replenished every 2 days.

tag: tissue

value: visceral adipose tissue

value: nucleus


title: MJM5028 replicate 1

description: Library name: Sample5

value: rscs* rtmR deletion attTn7::erm


title: Bulk RNA-seq, ex vivo visceral adipose tissue explant, donor DM13 (anti-THBS1 mAb)

description:
Library name: DM13_explant_aTHBS1
Ex vivo visceral adipose tissue explant culture, donor DM13, anti-THBS1 monoclonal antibody (clone A6-1), 5 days. Paired with the matched untreated explant from the same donor. Metabolic group: obesity with type 2 diabetes.
VAT_Exvivo_mAb_Treated_RCM.csv
VAT_Exvivo_mAb_Treated_fpkm_combat.csv
AT_GS_04_mAb


title: Bulk RNA-seq, ex vivo visceral adipose tissue explant, donor DM12 (anti-THBS1 mAb)

description:
Library name: DM12_explant_aTHBS1
Ex vivo visceral adipose tissue explant culture, donor DM12, anti-THBS1 monoclonal antibody (clone A6-1), 5 days. Paired with the matched untreated explant from the same donor. Metabolic group: obesity with type 2 diabetes.
VAT_Exvivo_mAb_Treated_RCM.csv
VAT_Exvivo_mAb_Treated_fpkm_combat.csv
AT_GS_03_mAb


title: Bulk RNA-seq, ex vivo visceral adipose tissue explant, donor DM12 (untreated)

description:
Library name: DM12_explant_ctrl
Ex vivo visceral adipose tissue explant culture, donor DM12, untreated control. Paired with the matched anti-THBS1-treated explant from the same donor. Metabolic group: obesity with type 2 diabetes.
VAT_Exvivo_mAb_Treated_RCM.csv
VAT_Exvivo_mAb_Treated_fpkm_combat.csv
AT_GS_03_Naive

value: untreated control


title: snRNA-seq, visceral adipose tissue, 10x channel AD9 (donors Lean_06, Lean_07, Lean_08)

description:
Library name: AD9
Single-nucleus RNA-seq of visceral adipose tissue, 10x Genomics channel AD9, pool of nuclei from donors Lean_06, Lean_07, Lean_08, combined in equal proportions before loading. Metabolic group: lean, normal glucose tolerance. No cell-labelling reagent was used; donor identity was assigned after sequencing by Souporcell genotype clustering from natural genetic variation, matched to donor-specific whole-exome sequencing. Sequenced across 1 lane; all lane-level FASTQ files belong to this one library.
VAT_snRNA_matrix.mtx.gz
VAT_snRNA_barcodes.tsv.gz
VAT_snRNA_features.tsv.gz
VAT_snRNA_metadata.tsv


title: snRNA-seq, visceral adipose tissue, 10x channel AD11 (donors DM_06, DM_07, DM_08)

description:
Library name: AD11
Single-nucleus RNA-seq of visceral adipose tissue, 10x Genomics channel AD11, pool of nuclei from donors DM_06, DM_07, DM_08, combined in equal proportions before loading. Metabolic group: obesity with type 2 diabetes. No cell-labelling reagent was used; donor identity was assigned after sequencing by Souporcell genotype clustering from natural genetic variation, matched to donor-specific whole-exome sequencing. Sequenced across 1 lane; all lane-level FASTQ files belong to this one library.
VAT_snRNA_matrix.mtx.gz
VAT_snRNA_barcodes.tsv.gz
VAT_snRNA_features.tsv.gz
VAT_snRNA_metadata.tsv


title: snRNA-seq, visceral adipose tissue, 10x channel AD8 (donors Ob_01, Ob_02, Ob_03)

description:
Library name: AD8
Single-nucleus RNA-seq of visceral adipose tissue, 10x Genomics channel AD8, pool of nuclei from donors Ob_01, Ob_02, Ob_03, combined in equal proportions before loading. Metabolic group: obesity. No cell-labelling reagent was used; donor identity was assigned after sequencing by Souporcell genotype clustering from natural genetic variation, matched to donor-specific whole-exome sequencing. Sequenced across 4 lanes; all lane-level FASTQ files belong to this one library. This channel is a technical re-processing replicate of channel AD6. Nuclei recovered from AD6 and AD8 were merged by biological donor identity after demultiplexing and were not counted as independent biological donors. Donor Ob_03 yielded too few nuclei in either channel to be retained in the downstream analysis.
VAT_snRNA_matrix.mtx.gz
VAT_snRNA_barcodes.tsv.gz
VAT_snRNA_features.tsv.gz
VAT_snRNA_metadata.tsv


title: Bulk RNA-seq, ex vivo visceral adipose tissue explant, donor DM10 (anti-THBS1 mAb)

description:
Library name: DM10_explant_aTHBS1
Ex vivo visceral adipose tissue explant culture, donor DM10, anti-THBS1 monoclonal antibody (clone A6-1), 5 days. Paired with the matched untreated explant from the same donor. Metabolic group: obesity with type 2 diabetes.
VAT_Exvivo_mAb_Treated_RCM.csv
VAT_Exvivo_mAb_Treated_fpkm_combat.csv
AT_GS_01_mAb


title: snRNA-seq, visceral adipose tissue, 10x channel AD10 (donors Ob_04, Ob_05)

description:
Library name: AD10
Single-nucleus RNA-seq of visceral adipose tissue, 10x Genomics channel AD10, pool of nuclei from donors Ob_04, Ob_05, combined in equal proportions before loading. Metabolic group: obesity. No cell-labelling reagent was used; donor identity was assigned after sequencing by Souporcell genotype clustering from natural genetic variation, matched to donor-specific whole-exome sequencing. Sequenced across 1 lane; all lane-level FASTQ files belong to this one library.
VAT_snRNA_matrix.mtx.gz
VAT_snRNA_barcodes.tsv.gz
VAT_snRNA_features.tsv.gz
VAT_snRNA_metadata.tsv


title: snRNA-seq, visceral adipose tissue, 10x channel AD3 (donor Lean_03)

description:
Library name: AD3
Single-nucleus RNA-seq of visceral adipose tissue, 10x Genomics channel AD3, single donor Lean_03. Metabolic group: lean, normal glucose tolerance. Sequenced across 4 lanes; all lane-level FASTQ files belong to this one library.
VAT_snRNA_matrix.mtx.gz
VAT_snRNA_barcodes.tsv.gz
VAT_snRNA_features.tsv.gz
VAT_snRNA_metadata.tsv


title: snRNA-seq, visceral adipose tissue, 10x channel AD7 (donors DM_03, DM_04, DM_05)

description:
Library name: AD7
Single-nucleus RNA-seq of visceral adipose tissue, 10x Genomics channel AD7, pool of nuclei from donors DM_03, DM_04, DM_05, combined in equal proportions before loading. Metabolic group: obesity with type 2 diabetes. No cell-labelling reagent was used; donor identity was assigned after sequencing by Souporcell genotype clustering from natural genetic variation, matched to donor-specific whole-exome sequencing. Sequenced across 4 lanes; all lane-level FASTQ files belong to this one library.
VAT_snRNA_matrix.mtx.gz
VAT_snRNA_barcodes.tsv.gz
VAT_snRNA_features.tsv.gz
VAT_snRNA_metadata.tsv


title: Bulk RNA-seq, whole visceral adipose tissue, donor DM_08

description:
Library name: DM_08_bulk
Whole visceral adipose tissue, donor DM_08. Metabolic group: obesity with type 2 diabetes. Ribosomal RNA-depleted total RNA-seq, paired-end.
VAT_Bulk_FPKM.txt


title: Bulk RNA-seq, whole visceral adipose tissue, donor DM_07

description:
Library name: DM_07_bulk
Whole visceral adipose tissue, donor DM_07. Metabolic group: obesity with type 2 diabetes. Ribosomal RNA-depleted total RNA-seq, paired-end.
VAT_Bulk_FPKM.txt


title: snRNA-seq, visceral adipose tissue, 10x channel AD1 (donor Lean_05)

description:
Library name: AD1
Single-nucleus RNA-seq of visceral adipose tissue, 10x Genomics channel AD1, single donor Lean_05. Metabolic group: lean, normal glucose tolerance. Sequenced across 4 lanes; all lane-level FASTQ files belong to this one library.
VAT_snRNA_matrix.mtx.gz
VAT_snRNA_barcodes.tsv.gz
VAT_snRNA_features.tsv.gz
VAT_snRNA_metadata.tsv


title: Bulk RNA-seq, whole visceral adipose tissue, donor DM_06

description:
Library name: DM_06_bulk
Whole visceral adipose tissue, donor DM_06. Metabolic group: obesity with type 2 diabetes. Ribosomal RNA-depleted total RNA-seq, paired-end.
VAT_Bulk_FPKM.txt


title: Bulk RNA-seq, whole visceral adipose tissue, donor DM_03

description:
Library name: DM_03_bulk
Whole visceral adipose tissue, donor DM_03. Metabolic group: obesity with type 2 diabetes. Ribosomal RNA-depleted total RNA-seq, paired-end.
VAT_Bulk_FPKM.txt


title: Bulk RNA-seq, ex vivo visceral adipose tissue explant, donor DM11 (anti-THBS1 mAb)

description:
Library name: DM11_explant_aTHBS1
Ex vivo visceral adipose tissue explant culture, donor DM11, anti-THBS1 monoclonal antibody (clone A6-1), 5 days. Paired with the matched untreated explant from the same donor. Metabolic group: obesity with type 2 diabetes.
VAT_Exvivo_mAb_Treated_RCM.csv
VAT_Exvivo_mAb_Treated_fpkm_combat.csv
AT_GS_02_mAb


title: Bulk RNA-seq, ex vivo visceral adipose tissue explant, donor DM13 (untreated)

description:
Library name: DM13_explant_ctrl
Ex vivo visceral adipose tissue explant culture, donor DM13, untreated control. Paired with the matched anti-THBS1-treated explant from the same donor. Metabolic group: obesity with type 2 diabetes.
VAT_Exvivo_mAb_Treated_RCM.csv
VAT_Exvivo_mAb_Treated_fpkm_combat.csv
AT_GS_04_Naive


title: Bulk RNA-seq, ex vivo visceral adipose tissue explant, donor DM10 (untreated)

description:
Library name: DM10_explant_ctrl
Ex vivo visceral adipose tissue explant culture, donor DM10, untreated control. Paired with the matched anti-THBS1-treated explant from the same donor. Metabolic group: obesity with type 2 diabetes.
VAT_Exvivo_mAb_Treated_RCM.csv
VAT_Exvivo_mAb_Treated_fpkm_combat.csv
AT_GS_01_Naive


title: Bulk RNA-seq, whole visceral adipose tissue, donor DM_05

description:
Library name: DM_05_bulk
Whole visceral adipose tissue, donor DM_05. Metabolic group: obesity with type 2 diabetes. Ribosomal RNA-depleted total RNA-seq, paired-end.
VAT_Bulk_FPKM.txt


title: snRNA-seq, visceral adipose tissue, 10x channel AD5 (donors Lean_01, Lean_02, Lean_04)

description:
Library name: AD5
Single-nucleus RNA-seq of visceral adipose tissue, 10x Genomics channel AD5, pool of nuclei from donors Lean_01, Lean_02, Lean_04, combined in equal proportions before loading. Metabolic group: lean, normal glucose tolerance. No cell-labelling reagent was used; donor identity was assigned after sequencing by Souporcell genotype clustering from natural genetic variation, matched to donor-specific whole-exome sequencing. Sequenced across 4 lanes; all lane-level FASTQ files belong to this one library.
VAT_snRNA_matrix.mtx.gz
VAT_snRNA_barcodes.tsv.gz
VAT_snRNA_features.tsv.gz
VAT_snRNA_metadata.tsv


title: Bulk RNA-seq, whole visceral adipose tissue, donor Ob_04

description:
Library name: Ob_04_bulk
Whole visceral adipose tissue, donor Ob_04. Metabolic group: obesity. Ribosomal RNA-depleted total RNA-seq, paired-end.
VAT_Bulk_FPKM.txt


title: Bulk RNA-seq, ex vivo visceral adipose tissue explant, donor DM11 (untreated)

description:
Library name: DM11_explant_ctrl
Ex vivo visceral adipose tissue explant culture, donor DM11, untreated control. Paired with the matched anti-THBS1-treated explant from the same donor. Metabolic group: obesity with type 2 diabetes.
VAT_Exvivo_mAb_Treated_RCM.csv
VAT_Exvivo_mAb_Treated_fpkm_combat.csv
AT_GS_02_Naive


title: Bulk RNA-seq, whole visceral adipose tissue, donor DM_02

description:
Library name: DM_02_bulk
Whole visceral adipose tissue, donor DM_02. Metabolic group: obesity with type 2 diabetes. Ribosomal RNA-depleted total RNA-seq, paired-end.
VAT_Bulk_FPKM.txt


title: Bulk RNA-seq, whole visceral adipose tissue, donor Ob_01

description:
Library name: Ob_01_bulk
Whole visceral adipose tissue, donor Ob_01. Metabolic group: obesity. Ribosomal RNA-depleted total RNA-seq, paired-end.
VAT_Bulk_FPKM.txt


title: Bulk RNA-seq, whole visceral adipose tissue, donor Lean_08

description:
Library name: Lean_08_bulk
Whole visceral adipose tissue, donor Lean_08. Metabolic group: lean, normal glucose tolerance. Ribosomal RNA-depleted total RNA-seq, paired-end.
VAT_Bulk_FPKM.txt


title: Bulk RNA-seq, whole visceral adipose tissue, donor Ob_02

description:
Library name: Ob_02_bulk
Whole visceral adipose tissue, donor Ob_02. Metabolic group: obesity. Ribosomal RNA-depleted total RNA-seq, paired-end.
VAT_Bulk_FPKM.txt


title: Bulk RNA-seq, whole visceral adipose tissue, donor Lean_07

description:
Library name: Lean_07_bulk
Whole visceral adipose tissue, donor Lean_07. Metabolic group: lean, normal glucose tolerance. Ribosomal RNA-depleted total RNA-seq, paired-end.
VAT_Bulk_FPKM.txt


title: Bulk RNA-seq, whole visceral adipose tissue, donor Ob_03

description:
Library name: Ob_03_bulk
Whole visceral adipose tissue, donor Ob_03. Metabolic group: obesity. Ribosomal RNA-depleted total RNA-seq, paired-end.
VAT_Bulk_FPKM.txt


title: Bulk RNA-seq, whole visceral adipose tissue, donor Ob_05

description:
Library name: Ob_05_bulk
Whole visceral adipose tissue, donor Ob_05. Metabolic group: obesity. Ribosomal RNA-depleted total RNA-seq, paired-end.
VAT_Bulk_FPKM.txt


title: Bulk RNA-seq, whole visceral adipose tissue, donor Lean_04

description:
Library name: Lean_04_bulk
Whole visceral adipose tissue, donor Lean_04. Metabolic group: lean, normal glucose tolerance. Ribosomal RNA-depleted total RNA-seq, paired-end.
VAT_Bulk_FPKM.txt


title: KLE cells, CuCl₂-treated, biological replicate 3

city: Nantong

first: Li

last: Ji

state: 江苏 / 江苏

address: No. 20 Xisi Street

country: China

institute: Nantong University

description:
Library name: KLE-cu-3
Bulk RNA-seq library from KLE human endometrial cancer cells; 200 µM CuCl₂ for 24 h; biological replicate 3.

data_processing:
Raw paired-end reads were filtered using fastp v0.18.0. Adapter-containing reads, reads with more than 10% unknown nucleotides, and reads with more than 50% bases having Q-values ＜=20 were removed.
Reads mapping to the ribosomal RNA database were identified using Bowtie2 v2.2.8 and removed before downstream analysis.
An index of the Homo sapiens GRCh38.p14 reference genome with Ensembl release 111 annotation was built, and paired-end clean reads were aligned to the reference genome using HISAT2 v2.1.0.
Transcript abundances were quantified as fragments per kilobase per million mapped reads (FPKM) using RSEM.
Differential expression analysis was performed using DESeq2, and genes with a fold change of at least 2 were identified as differentially expressed genes. Gene Ontology, KEGG, and WikiPathways enrichment analyses, sample correlation analysis, and principal component analysis were performed using R v4.2.2.
Assembly: GRCh38.p14
Supplementary files format and content: FPKM.txt
Supplementary files format and content: raw_counts.txt

source_name: endometrium

growth_protocol: Human Ishikawa and KLE endometrial cancer cell lines were obtained from the American Type Culture Collection and maintained in DMEM/F12 supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C in a humidified atmosphere containing 5% CO2. Cell lines were tested for mycoplasma and authenticated by short tandem repeat analysis before experiments.

extract_protocol:
Total RNA was extracted from cultured cells using TRIzol reagent (15596026; Invitrogen). RNA integrity was confirmed by RNase-free agarose gel electrophoresis and evaluated using an Agilent 2100 Bioanalyzer.
Transcriptome libraries were prepared using the Hieff NGS Ultima Dual-mode mRNA Library Prep Kit (12309ES; Yeasen). mRNA was enriched using Oligo(dT) beads, fragmented, and reverse-transcribed into cDNA. Double-stranded cDNA underwent end repair, A-tailing, and ligation to Illumina sequencing adapters. Ligation products were purified with AMPure XP Beads (1.0X), size-selected by agarose gel electrophoresis, amplified by PCR, and sequenced on an Illumina NovaSeq 6000 platform by Gene Denovo Biotechnology Co. (Guangzhou, China).

treatment_protocol: Cells were assigned to untreated control and high-copper-overload groups. Cells were cultured in parallel as untreated controls or exposed to 200 μM CuCl₂ for 24 h. Three independent biological replicates were prepared for each cell line and condition.

value: endometrium

tag: cell line

value: KLE

value: endometrial cancer cell

value: 200 µM CuCl₂ for 24 h


title: Bulk RNA-seq, whole visceral adipose tissue, donor Lean_05

description:
Library name: Lean_05_bulk
Whole visceral adipose tissue, donor Lean_05. Metabolic group: lean, normal glucose tolerance. Ribosomal RNA-depleted total RNA-seq, paired-end.
VAT_Bulk_FPKM.txt


title: Bulk RNA-seq, whole visceral adipose tissue, donor Lean_01

description:
Library name: Lean_01_bulk
Whole visceral adipose tissue, donor Lean_01. Metabolic group: lean, normal glucose tolerance. Ribosomal RNA-depleted total RNA-seq, paired-end.
VAT_Bulk_FPKM.txt


title: Bulk RNA-seq, whole visceral adipose tissue, donor Lean_03

description:
Library name: Lean_03_bulk
Whole visceral adipose tissue, donor Lean_03. Metabolic group: lean, normal glucose tolerance. Ribosomal RNA-depleted total RNA-seq, paired-end.
VAT_Bulk_FPKM.txt


title: Bulk RNA-seq, whole visceral adipose tissue, donor Lean_02

description:
Library name: Lean_02_bulk
Whole visceral adipose tissue, donor Lean_02. Metabolic group: lean, normal glucose tolerance. Ribosomal RNA-depleted total RNA-seq, paired-end.
VAT_Bulk_FPKM.txt


title: Ishikawa cells, CuCl₂-treated, biological replicate 3

description:
Library name: Ishikawa-cu-3
Bulk RNA-seq library from Ishikawa human endometrial cancer cells; 200 µM CuCl₂ for 24 h; biological replicate 3.

value: Ishikawa


title: KLE cells, CuCl₂-treated, biological replicate 1

description:
Library name: KLE-cu-1
Bulk RNA-seq library from KLE human endometrial cancer cells; 200 µM CuCl₂ for 24 h; biological replicate 1.


title: KLE cells, untreated control, biological replicate 3

description:
Library name: KLE-ctr-3
Bulk RNA-seq library from KLE human endometrial cancer cells; Untreated control (vehicle), 24 h; biological replicate 3.

value: Untreated control (vehicle), 24 h


title: Bulk RNA-seq, whole visceral adipose tissue, donor DM_01

description:
Library name: DM_01_bulk
Whole visceral adipose tissue, donor DM_01. Metabolic group: obesity with type 2 diabetes. Ribosomal RNA-depleted total RNA-seq, paired-end.
VAT_Bulk_FPKM.txt


title: Ishikawa cells, CuCl₂-treated, biological replicate 1

description:
Library name: Ishikawa-cu-1
Bulk RNA-seq library from Ishikawa human endometrial cancer cells; 200 µM CuCl₂ for 24 h; biological replicate 1.


title: Ishikawa cells, CuCl₂-treated, biological replicate 2

description:
Library name: Ishikawa-cu-2
Bulk RNA-seq library from Ishikawa human endometrial cancer cells; 200 µM CuCl₂ for 24 h; biological replicate 2.


title: KLE cells, CuCl₂-treated, biological replicate 2

description:
Library name: KLE-cu-2
Bulk RNA-seq library from KLE human endometrial cancer cells; 200 µM CuCl₂ for 24 h; biological replicate 2.


title: KLE cells, untreated control, biological replicate 1

description:
Library name: KLE-ctr-1
Bulk RNA-seq library from KLE human endometrial cancer cells; Untreated control (vehicle), 24 h; biological replicate 1.


title: Ishikawa cells, untreated control, biological replicate 3

description:
Library name: Ishikawa-ctr-3
Bulk RNA-seq library from Ishikawa human endometrial cancer cells; Untreated control (vehicle), 24 h; biological replicate 3.


title: Ishikawa cells, untreated control, biological replicate 2

description:
Library name: Ishikawa-ctr-2
Bulk RNA-seq library from Ishikawa human endometrial cancer cells; Untreated control (vehicle), 24 h; biological replicate 2.


title: iPSC-CM, PLXNA4 OE, Rep3

city: Cambridge

last: Chaffin

state: MA

address: 75 Ames Street

department: Cardiovascular Disease Initiative

institute: Broad Institute of MIT and Harvard

description: Library name: OE_plxna4_virus_3

data_processing:
mRNA libraries were aligned to a GENCODE v36 decoy-aware transcriptome using salmon v1.4.081 correcting for GC-bias (--gcBias). Differential expression was performed using the limma-voom framework after removing lowly detected genes using the edgeR function filterByExpr(). Normalization factors were calculated using DESeq2 normalization and contrasts were explicitly extracted for PLXNA4 knockdown versus control and PLXNA4 overexpression versus control. Two-sided p-values were estimated, and multiple testing correction was performed using the Benjamini-Hochberg correction.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file with raw counts for each sample

molecule: polyA RNA

growth_protocol: Cells were growing in a controlled normoxic gaseous environment with 10% CO2 at 37 °C. Differentiation occurred as follows. hiPSC-derived spheroids were pelleted and washed with DPBS containing 0.1% BSA, and then suspended in Basal Differentiation Media (DMEM/F12 with HEPES, 540 mg/L sodium bicarbonate, 1% non-essential amino acids (Thermo Fisher, 11140), 10 μg/mL holo-transferrin, 200 μM ascorbic acid, 63 ng/mL progesterone (Sigma, P8783), and 14 ng/mL sodium selenite). The media was supplemented with 50 ng/mL activin A, 10 ng/mL BMP4 (R&D Systems, 314-BP-050), 20 ng/mL bFGF (Shenandoah, 100-28-500UG), and 2 μM CHIR-99021 (Selleckchem, S2924). The following day (day 1), media was changed to Basal Differentiation Media without CHIR-99021. The next day, to initiate the transition into cardiac mesoderm, spheroids were treated with 10 μM XAV-939 (APExBio, A1877), 1 μM IWR1-Endo (APExBio, B2306), and 1 μM IWP-2 (APExBio, A3512). On day 3, cells were treated with 10 uM XAV-939. From days 6 to 17 spheroids were maintained in Basal Differentiation Media, supplemented with 4 μg/mL insulin. To enhance spontaneous beating and expedite maturation, 100 nM endothelin-1 (Alfa Aesar, J66977) was introduced from days 9 to 11. On day 17, spheroids were collected, washed, and dissociated  for one hour at 37°C using 1 mg/mL collagenase II (Thermo Fisher, 117010015) in Collagenase Digestion Buffer (5 mM sodium pyruvate (Thermo Fisher, 11360070), 20 mM glucose (Sigma, G8769), and 20 mM taurine (Sigma, T0625) in DPBS) and plated onto fibronectin-coated plates (Corning, 356008) at a density of 0.5 million cells per cm2. Non-cardiomyocytes were eliminated by culturing in Lactate Media for 4 days (DMEM without glucose (Thermo Fisher, 11966025), 540 mg/L sodium bicarbonate, 4 mM lactate (Sigma L6402), 200 μM ascorbic acid, and 14 ng/mL sodium selenite.). Cells were then maintained in Cardiomyocyte Maintenance Media (DMEM/F12, 10% FBS, and 1% Pen/Strep) until day 30, when cultures were enriched for cardiomyocytes using EasySep™ Human PSC-Derived Cardiomyocyte Enrichment Kit (StemCell Thechnology, 17965) and cells were phenotyped and plated for experiments. Cells were karotyped to confirm they were karotypically normal (Cell Line Genetics) and mycoplasma testing was conducted to confirm clean cultures (MP0035, Sigma).

extract_protocol:
Cells were lysed and RNA extracted using Zymo quickRNA microprep kit following manufacturers instructions (R1050, Zymo Research).
mRNA libraries were carried out on 1 ug of RNA following manufacturers protocols (Kapa RNA hyperprep kit with riboerase). Sample quality control was carried out using qPCR and a BioAnalyser and sequenced on Novaseq SP aiming for 25 million reads per sample.

treatment_protocol: After bead selection, cells were plated in maintenance media containing 10% FBS for RNA and protein experiments (1 million cells per well, 12 well plate) or imaging experiments (45,000 cells per well, 96 well plate). The day after plating, media was changed to maintenance media without FBS and cells were treated with either PLXNA4 siRNA (Thermofisher, silencer select Assay ID: 110470), scramble siRNA (Thermofisher, silencer select Assay ID: 4390843), PLXNA4 lentivirus or control lentivirus. Media was changed on all treatments. 72 h after treatment cells were harvested for total RNA extraction (RNeasy kit, Qiagen, 74106) following manufacturers protocols.

value: iPSC Cardiomyocyte

value: PLXNA4 overexpression lentivirus


title: KLE cells, untreated control, biological replicate 2

description:
Library name: KLE-ctr-2
Bulk RNA-seq library from KLE human endometrial cancer cells; Untreated control (vehicle), 24 h; biological replicate 2.


title: Ishikawa cells, untreated control, biological replicate 1

description:
Library name: Ishikawa-ctr-1
Bulk RNA-seq library from Ishikawa human endometrial cancer cells; Untreated control (vehicle), 24 h; biological replicate 1.


title: iPSC-CM, PLXNA4 OE, Rep2

description: Library name: OE_plxna4_virus_2


title: iPSC-CM, PLXNA4 OE, Rep1

description: Library name: OE_plxna4_virus_1


title: iPSC-CM, OE virus control, Rep2

description: Library name: OE_ctrl_virus_2

value: Lentivirus control


title: iPSC-CM, OE virus control, Rep3

description: Library name: OE_ctrl_virus_3


title: Bulk RNA-seq, whole visceral adipose tissue, donor Lean_06

description:
Library name: Lean_06_bulk
Whole visceral adipose tissue, donor Lean_06. Metabolic group: lean, normal glucose tolerance. Ribosomal RNA-depleted total RNA-seq, paired-end.
VAT_Bulk_FPKM.txt


title: iPSC-CM, PLXNA4 siRNA, Rep3

description: Library name: KD_plxna4_sirna_3

value: PLXNA4 siRNA


title: iPSC-CM, siRNA control, Rep2

description: Library name: KD_ctrl_scram_2

value: siRNA scramble control


title: iPSC-CM, siRNA control, Rep1

description: Library name: KD_ctrl_scram_1


title: iPSC-CM, PLXNA4 siRNA, Rep1

description: Library name: KD_plxna4_sirna_1


title: iPSC-CM, OE virus control, Rep1

description: Library name: OE_ctrl_virus_1


title: iPSC-CM, PLXNA4 siRNA, Rep2

description: Library name: KD_plxna4_sirna_2


title: iPSC-CM, siRNA control, Rep3

description: Library name: KD_ctrl_scram_3


title: TGF-beta-treated_3

city: Uppsala

first: Mohamad

middle: Moustafa

last: Ali

state: Uppsala län

address: husargatan 3, Biomedical Center

department: IMBIM

country: Sweden

institute: Uppsala University

description:
Library name: MDA-MB-231_Treatment3
Treatment-replicate 3

data_processing:
Raw sequencing reads were trimmed using Trimmomatic tool. Reads were aliged against the human reference genome using STAR aligner and counts were quantified sing the subread package.
Assembly: GRCH38
Supplementary files format and content: Quantified normalized reads generated using the subread package in txt format

source_name: Breast cancer

growth_protocol: MDA-MB-231 cells were cultured in DMEM medium supplemented with 10% FBS and 1% Pen-Strep antibiotics and maintained at 37C in a humified incubator with continuous supply of 5% CO2.

extract_protocol:
RNA was extracted using ReliaPrep™ RNA Cell Miniprep System following the manufacturer's protocol
Following RNA quality assessment, 500 ng of total RNA were subjected to library preparation using the TruSeq stranded total RNA Gold library preparation kit with RiboZero Gold treatment and unique dual indexes according to the manufacturer’s instructions (Protocol # 1000000040499, Illumina Inc., San Diego, CA, USA). Paired-end sequencing was carried out with v1.5 sequencing chemistry on a NovaSeq-6000 platform using S4 flow cells (Illumina Inc. USA).

treatment_protocol: Cells were treated with 5 ng/ml of recombinant TGF-beta1 for 48 hours and then collected by trypsin.

value: Breast cancer

value: Triple-negative

value: WT


title: Ctrl_3

description:
Library name: MDA-MB-231_WT3
Control-replicate3

value: Control


title: Patient 1748, RV, ARVC

description:
Library name: RV_1748_ARVC
10X Genomics 3' v3.1

data_processing:
snRNA-seq samples were processed with the 10x Genomics toolkit CellRanger, v4.0.0. Using cutadapt, we trimmed homopolymer repeats (A30, C30, G30, and T30), the template-switch oligo, and the template-switch oligo reverse complement. We aligned the trimmed reads to a GRCh38 pre-mRNA human reference (v2020-A) using cellranger count. Count output was further processed with CellBender v0.2 to identify non-empty droplets and correct ambient background RNA from count matrices.  Additionally, for each droplet in a sample, we calculated the proportion of reads mapping to exons, introns, or spanning both with the tool scR-Invex. Low quality nuclei were removed based on the following quality control metrics: 1. Percent of reads mapping to mitochondrial genes, 2. Proportion of reads mapping exclusively to exons, 3. Transcriptional entropy as calculated in the ndd v1.0.6 library, 4. Estimate of the likelihood that a droplet is a doublet as estimated using Scrublet v0.2.3, 5. Total number of UMI, 6. Total number of unique genes detected, and 7. log(nGenes)*entropy. High quality nuclei were represented in a UMAP embedding based on Harmony-aligned principal components (corrected for the donor identity) after regressing out the technical effect of %MT. Final Leiden clustering was applied at a resolution of 0.5.
Assembly: GRCh38
Supplementary files format and content: h5ad file containing processed, normalized and raw counts across high quality nuclei from all samples

source_name: Right Ventricle

extract_protocol:
Approximately 30 mg of tissue was sectioned in 100 um sections on a cryostat (Leica CM 1950). Sections were resuspended in 2 mL of NIM2 buffer (250 mM sucrose, 25 mM KCl, 0.05% IGEPAL-630, 3 mM MgCl2, 1 μM DTT, 10 mM Tris pH 8.0), mixed using a cut tip and moved into a 7 mL dounce. Samples were dounced 10 x using dounce A and 2 mL of NIM2 buffer was added. Samples were incubated for 2 min and then dounced 20 x using dounce B. Samples were carefully moved to a 15 mL tube and centrifuged at 40 x g for 2 min at 4 degrees. Avoiding the debris pellet, supernatants were filtered through stacked 40 um and 10 um filters and both washed with 4 mL of PBS wash buffer (0.01% BSA, 5 mM MgCl2, PBS), followed by 2 mL of wash buffer through the 10 um filter. Supernatants were centrifuged at 550 x g for 5 min to pellet nuclei, buffer was removed and 6 mL of PBS wash buffer gently added without disturbing the pellet. Samples were centrifuged at 550 x g for 5 mins at 4 degrees, supernatants removed and nuclei resuspended in 100 uL of NSB (PBS wash buffer + 0.4 U μl−1 murine RNAse inhibitor) buffer.
Nuclei were counted and 6,000 were loaded into the 10X Genomics 3’ v 3.1 kit. Protocol was carried out as written except for the following: GEMS were incubated at 4 °C for 15 min after emulsion generation to promote nuclei lysis, and the reverse transcription protocol was lengthened to be 42 °C for 20 min then 53 °C for 120 min. Libraries were quantified using qPCR and a BioAnalyser and sequenced on Novaseq S1 aiming for 15,000 reads per nucleus.

value: Right Ventricle

tag: disease state

value: ARVC

tag: Sex

value: Male


title: TGF-beta-treated_1

description:
Library name: MDA-MB-231_Treatment1
Treatment-replicate 1


title: Ctrl_2

description:
Library name: MDA-MB-231_WT2
Control-replicate2


title: Patient 1718, RV, Non-failing control

description:
Library name: RV_1718_NF
10X Genomics 3' v3.1

value: NF


title: Ctrl_1

description:
Library name: MDA-MB-231_WT1
Control-replicate1


title: Patient 1732, RV, Non-failing control

description:
Library name: RV_1732_NF
10X Genomics 3' v3.1

value: Female


title: TGF-beta-treated_2

description:
Library name: MDA-MB-231_Treatment2
Treatment-replicate 2


title: Patient 1746, RV, ARVC

description:
Library name: RV_1746_ARVC
10X Genomics 3' v3.1


title: Patient 1716, RV, Non-failing control

description:
Library name: RV_1716_NF
10X Genomics 3' v3.1


title: Patient 1712, RV, ARVC

description:
Library name: RV_1712_ARVC
10X Genomics 3' v3.1


title: Patient 1600, RV, Non-failing control

description:
Library name: RV_1600_NF
10X Genomics 3' v3.1


title: Patient 1723, RV, Non-failing control

description:
Library name: RV_1723_NF
10X Genomics 3' v3.1


title: Patient 1582, RV, Non-failing control

description:
Library name: RV_1582_NF
10X Genomics 3' v3.1


title: Patient 1705, RV, Non-failing control

description:
Library name: RV_1705_NF
10X Genomics 3' v3.1


title: Patient 1580, RV, Non-failing control

description:
Library name: RV_1580_NF
10X Genomics 3' v3.1


title: Patient 1638, RV, ARVC

description:
Library name: RV_1638_ARVC
10X Genomics 3' v3.1


title: Patient 1458, RV, ARVC

description:
Library name: RV_1458_ARVC
10X Genomics 3' v3.1


title: Patient 1584, RV, Non-failing control

description:
Library name: RV_1584_NF
10X Genomics 3' v3.1


title: Patient 1423, RV, ARVC

description:
Library name: RV_1423_ARVC
10X Genomics 3' v3.1


title: Patient 1496, RV, ARVC

description:
Library name: RV_1496_ARVC
10X Genomics 3' v3.1


title: Patient 1516, RV, Non-failing control

description:
Library name: RV_1516_NF
10X Genomics 3' v3.1


title: Transitional B cells, HC, VDJ, TY08

city: London

first: Claire

last: Beesley

address: Royal Free Hospital

country: United Kingdom

institute: UCL

description:
Library name: TY08_VDJ
filtered_contig_s8_igblast_db-pass.tsv

data_processing:
Raw sequencing data were processed using Cell Ranger (10x Genomics) for demultiplexing, barcode processing, and gene expression quantification.
Assembly: Homo sapiens (GRCh38)
Supplementary files format and content: Tab-seperated value files and matrix files

source_name: Peripheral blood

extract_protocol:
PBMCs were isolated from 40 mL blood using EDTA vacutainers and Ficoll-Paque PLUS. PBMCs were resuspended and frozen in 90% FBS plus 10% DMSO for overnight storage at -70°C in a MrFrosty container before transfer to liquid nitrogen. For cell sorting, PBMCs were thawed for two minutes in a 37C water bath before transfer to prewarmed RMPI medium containing 2% FBS. Staining was performed in MACs buffer (PBS with 2% FBS and 0.5 mM EDTA) for 30 minutes at 4C. Cells were sorted on a FACSAria cell sorter at 4C using a 130 um nozzle to optimise viability. Total CD19+CD24hiCD38hi transitional B cells were collected in 50% FBS plus PBS and transferred to UCL Genomics for single-cell processing.
Prior to loading, cells were counted on a LUNA-FL dual fluorescence cell counter to ensure high viability (>90%). For each sample, approximately 10,000 cells per lane were run on a Chromium 10X controller using 5’ chemistry (10X Genomics) with an expected recovery rate of >5,000 cells per lane. Libraries were generated according to the manufacturer’s instructions and run on an Illumina NovaSeq S1 at 50,000 reads per cell for the gene expression libraries and 5000 reads per cell for the V(D)J libraries.

value: Peripheral blood

value: PBMCs

tag: subject status

value: SSc patient

tag: batch


title: Transitional B cells, HC, GEX, TY08

description:
Library name: TY08_GEX
TY08_filtered_feature_bc_matrix.zip


title: Patient 1307, RV, Non-failing control

description:
Library name: RV_1307_NF
10X Genomics 3' v3.1


title: Patient 1409, RV, ARVC

description:
Library name: RV_1409_ARVC
10X Genomics 3' v3.1


title: Transitional B cells, SSc, GEX, TY05

description:
Library name: TY05_GEX
TY05_filtered_feature_bc_matrix.zip


title: Transitional B cells, SSc, VDJ, TY05

description:
Library name: TY05_VDJ
filtered_contig_s5_igblast_db-pass.tsv


title: Transitional B cells, SSc, VDJ, TY04, L002

description:
Library name: TY04_VDJ_L002
filtered_contig_s4_igblast_db-pass.tsv


title: Transitional B cells, SSc, GEX, TY07

description:
Library name: TY07_GEX
TY07_filtered_feature_bc_matrix.zip


title: Transitional B cells, SSc, GEX, TY06

description:
Library name: TY06_GEX
TY06_filtered_feature_bc_matrix.zip


title: Transitional B cells, SSc, GEX, TY04, L001

description:
Library name: TY04_GEX_L001
TY04_filtered_feature_bc_matrix.zip


title: Transitional B cells, SSc, VDJ, TY06

description:
Library name: TY06_VDJ
filtered_contig_s6_igblast_db-pass.tsv


title: Transitional B cells, HC, VDJ, TY03, L001

description:
Library name: TY03_VDJ_L001
filtered_contig_s3_igblast_db-pass.tsv

value: healthy control


title: Transitional B cells, SSc, VDJ, TY07

description:
Library name: TY07_VDJ
filtered_contig_s7_igblast_db-pass.tsv


title: Transitional B cells, SSc, VDJ, TY04, L001

description:
Library name: TY04_VDJ_L001
filtered_contig_s4_igblast_db-pass.tsv


title: Transitional B cells, SSc, GEX, TY04, L002

description:
Library name: TY04_GEX_L002
TY04_filtered_feature_bc_matrix.zip


title: Transitional B cells, HC, VDJ, TY03, L002

description:
Library name: TY03_VDJ_L002
filtered_contig_s3_igblast_db-pass.tsv


title: Transitional B cells, HC, GEX, TY03, L001

description:
Library name: TY03_GEX_L001
TY03_filtered_feature_bc_matrix.zip


title: Transitional B cells, HC, VDJ, TY02, L001

description:
Library name: TY02_VDJ_L001
filtered_contig_s2_igblast_db-pass.tsv


title: Transitional B cells, HC, GEX, TY02, L002

description:
Library name: TY02_GEX_L002
TY02_filtered_feature_bc_matrix.zip


title: Transitional B cells, HC, VDJ, TY02, L002

description:
Library name: TY02_VDJ_L002
filtered_contig_s2_igblast_db-pass.tsv


title: Transitional B cells, HC, GEX, TY03, L002

description:
Library name: TY03_GEX_L002
TY03_filtered_feature_bc_matrix.zip


title: Transitional B cells, HC, GEX, TY02, L001

description:
Library name: TY02_GEX_L001
TY02_filtered_feature_bc_matrix.zip


title: Transitional B cells, HC, GEX, TY01, L002

description:
Library name: TY01_GEX_L002
TY01_filtered_feature_bc_matrix.zip


title: Transitional B cells, HC, VDJ, TY01, L002

description:
Library name: TY01_VDJ_L002
filtered_contig_s1_igblast_db-pass.tsv


title: Transitional B cells, HC, GEX, TY01, L001

description:
Library name: TY01_GEX_L001
TY01_filtered_feature_bc_matrix.zip


title: lung_adjacent_male_20A041779

city: Shanghai

first: Leiqin

last: Liu

address: 320 Yueyang Road

institute: CAS Center for Excellence in Molecular Cell Science (CEMCS)

description: Library name: 20A041779

library_source: genomic

data_processing:
Sequence adapters were trimmed by trim_galore (version 0.6.2) in paired-end mode with default parameters.
Trimmed sequences were aligned to the human genome version hg19 using BSMAP, with options “-q 20 -f 5 -r 0 -v 0.05 -s 16 -S 1”.
Duplicate reads were marked by Sambamba (version 0.7.1).
Mean CpG methylation levels were extracted using MethylDackel (https://github.com/dpryan79/MethylDackel) (version 0.5.0).
Assembly: hg19
Supplementary files format and content: The bedGraph contains the following 6 columns: 1) The chromosome. 2) The start coordinate. 3) The end coordinate. 4) The methylation percentage rounded to an integer. 5) The number of alignments/pairs reporting methylated bases. 6) The number of alignments/pairs reporting unmethylated bases.

molecule: genomic DNA

source_name: lung

extract_protocol:
Genomic DNA was isolated using the DNeasy Blood & Tissue Kit (QIAGEN, Cat. No. 69504; Hilden, Germany) per the manufacturer’s instructions. Then, 200 ng of purified genomic DNA were sheared to 100-500 bp using a Covaris S2 (Covaris; Woburn, MA, USA) sonicator. Next, we treated the fragmented DNA using the EpiTect Fast Bisulfite Conversion Kit (QIAGEN, Cat. No. 59824; Hilden, Germany) with a modified protocol--two cycles of 98°C for 5 min and 60°C for 25 min, followed by a hold at 25°.
The bisulfite-converted DNA was subjected to WGBS construction using the Accel-NGS Methyl-seq DNA Library Kit (Swift Biosciences, Cat. No. 51002025P; Ann Arbor, MI, USA) as recommended by the manufacturer. WGBS libraries were sequenced for 2x150 cycles in an Illumina NovaSeq 6000 sequencer.

value: lung

tag: clinical prognosis

value: normal

tag: gender

value: male

tag: age


title: Transitional B cells, HC, VDJ, TY01, L001

description:
Library name: TY01_VDJ_L001
filtered_contig_s1_igblast_db-pass.tsv


title: colon_adjacent_female_20A041720

description: Library name: 20A041720

source_name: colon

value: colon

value: female


title: colon_adjacent_male_20A041719

description: Library name: 20A041719


title: lung_adjacent_male_20A041778

description: Library name: 20A041778


title: stomach_adjacent_male_20A041701

description: Library name: 20A041701

source_name: stomach

value: stomach


title: intestine_adjacent_male_20A041715

description: Library name: 20A041715

source_name: intestine

value: intestine


title: lung_adjacent_female_20A041496

description: Library name: 20A041496


title: stomach_adjacent_male_20A041700

description: Library name: 20A041700


title: LUAD_male_20A042624

description: Library name: 20A042624

value: LUAD


title: LUAD_female_20A042220_2

description: Library name: 20A042220_2


title: LUSC_male_20A042605

description: Library name: 20A042605

value: LUSC


title: LUAD_female_20A042618

description: Library name: 20A042618


title: breast_adjacent_female_20A041494

description: Library name: 20A041494

source_name: breast

value: breast


title: intestine_adjacent_female_20A041716

description: Library name: 20A041716


title: breast_adjacent_female_20A041493

description: Library name: 20A041493


title: breast_adjacent_female_20A041492

description: Library name: 20A041492


title: LUSC_male_20A042558

description: Library name: 20A042558


title: LUAD_male_20A042516

description: Library name: 20A042516


title: LUAD_female_20A042529

description: Library name: 20A042529


title: LUAD_male_20A042501

description: Library name: 20A042501


title: LUAD_female_20A042271

description: Library name: 20A042271


title: LUSC_male_20A042240

description: Library name: 20A042240


title: stomach_adjacent_female_20A041699

description: Library name: 20A041699


title: LUSC_male_20A042226

description: Library name: 20A042226


title: LUSC_male_20A042223

description: Library name: 20A042223


title: LUSC_male_20A042474

description: Library name: 20A042474


title: LUAD_female_20A042220

description: Library name: 20A042220


title: LUAD_female_20A042202

description: Library name: 20A042202


title: LUSC_male_20A042440

description: Library name: 20A042440


title: LUAD_female_20A042186

description: Library name: 20A042186


title: LUAD_male_20A042161

description: Library name: 20A042161


title: LUAD_male_20A042187

description: Library name: 20A042187


title: LUAD_male_20A042143

description: Library name: 20A042143


title: LUSC_male_20A042194

description: Library name: 20A042194


title: LUSC_male_20A042138

description: Library name: 20A042138


title: LUAD_female_20A042163

description: Library name: 20A042163


title: HeLa cells, shDKC1, replicate2

city: Beijing

first: Xiaoyang

address: 5th Yiheyuan road

institute: Peking University

description: Library name: HeLa_sh4_rep2

data_processing:
For the processing of raw sequencing data, Cutadapt (v4.4) is first used to remove adapter sequences. Subsequently, Bowtie2 (v2.5.1) is employed to align the data to the rRNA reference sequences with default parameters, so as to filter out rRNA - related reads, retaining only the unaligned sequences. Next, STAR (v2.7.10b) is utilized to map the rRNA - depleted data to the human reference genome and transcriptome (hg38, GENCODE v42), with reads having a mismatch count ≤ 10 retained. To ensure data reliability, FastQC (v0.12.1) is used for quality assessment both before and after adapter removal. The quality control results are integrated and visualized using MultiQC (v1.14).
Assembly: hg38
Supplementary files format and content: txt files include RPKM values for each Sample

source_name: HeLa

extract_protocol:
Total RNA was isolated using TRIzol reagents (Invitrogen) in accordance with standard manufacturer’s protocols. Two rounds of polyA (+) selection were performed using DynabeadsTM Oligo(dT)25 (Invitrogen) to obtain mRNA.
Library preparation was performed by using VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina NR605 (Vazyme) according to the manufacturer’s protocols. Sequencing was performed on an Illumina NovaSeq 6000 S4 machine in pair-end mode with 150 bp per read.

value: HeLa

value: Human Cervical Carcinoma Cells

value: DKC1 knockdown


title: LUSC_male_20A042159

description: Library name: 20A042159


title: LUAD_male_20A042185

description: Library name: 20A042185


title: LUSC_male_20A042176

description: Library name: 20A042176


title: LUSC_male_20A042160

description: Library name: 20A042160


title: HeLa_shDKC1.2_input_rep2

description: Library name: HeLa_shDKC1.2_input_rep2

data_processing:
The adapter sequences are removed using cutadapt (v4.4), and clean reads are obtained (retaining only reads with a length of at least 18 bp). These clean reads are then aligned to the rRNA reference sequence using bowtie2 (v2.5.1), and unmapped reads are retained for further analysis. Reads that map to rRNA are realigned using the realignGap program; successfully realigned reads are used for quality control, while those that fail realignment are converted to FASTQ format for subsequent analysis. The sequencing data after rRNA removal, along with reads that mapped to rRNA but failed realignment, are aligned to the reference genome and transcriptome (hg38 Gencode v42) using STAR (v2.7.10b), retaining only reads with no more than 10 mismatches.
Assembly: hg38
Supplementary files format and content: identified Ψ sites information

extract_protocol:
caRNA from chromosome-associated fraction was isolated using TRIzol reagents (Invitrogen) in accordance with standard manufacturer’s protocols.  Non-ribosomal RNA was extracted from the total RNA using the RiboMinus transcriptome isolation kit (Invitrogen) according to the manufacturer’s protocols, followed by purification and small RNA depletion using RNA Clean & Concentrator™-5 (Zymo Research).
PRAISE was performed as previously described but with several substitutions2. Briefly, the DNase I treated non-ribosomal mRNA or caRNA was fragmented to ~150nt by 2 × Frag/Prime Buffer (Vazyme) for 5min at 94 °C and purified by RNA Clean & Concentrator™-5 (Zymo Research). Elute RNA with 11 μL RNase-free water to get 10 μL RNA elution. Save 1.5 μL RNA elution as “input” sample and keep on ice. After bisulfite treatment and desulphonation, the purified RNA was used as “treated” sample. Then library construction was performed by SMARTer Stranded Total RNA-Seq Kit v3—Pico Input Mammalian (Takara Bio, 634485)2 according to PRAISE’s optimization. After MGI Easy Circularization Kit to add sequencing adapters compatible with the MGI high-throughput sequencer.,library sequencing was performed on Ilumina NovaSeq 6000 S4.

value: PRAISE-seq of HeLa DKC1 KD cell line2, without bisulfite treatment, replicate2


title: HeLa cells, shControl, replicate2

description: Library name: HeLa_Ctrl_rep2

value: WT


title: HeLa cells, shDKC1, replicate1

description: Library name: HeLa_sh4_rep1


title: HeLa_shDKC1.2_BS_rep2

description: Library name: HeLa_shDKC1.2_BS_rep2

value: PRAISE-seq of HeLa DKC1 KD cell line2, with bisulfite treatment, replicate2


title: HeLa_shDKC1.2_input_rep1

description: Library name: HeLa_shDKC1.2_input_rep1

value: PRAISE-seq of HeLa DKC1 KD cell line2, without bisulfite treatment, replicate1


title: HeLa_shDKC1.1_input_rep1

description: Library name: HeLa_shDKC1.1_input_rep1

value: PRAISE-seq of HeLa DKC1 KD cell line1, without bisulfite treatment, replicate1


title: HeLa cells, shControl, replicate1

description: Library name: HeLa_Ctrl_rep1


title: HeLa_Ctrl_input_rep2

description: Library name: HeLa_Ctrl_input_rep2

value: PRAISE-seq of HeLa control cells without bisulfite treatment, replicate2


title: HeLa_shDKC1.1_input_rep2

description: Library name: HeLa_shDKC1.1_input_rep2

value: PRAISE-seq of HeLa DKC1 KD cell line1, without bisulfite treatment, replicate2


title: HeLa_Ctrl_BS_rep2

description: Library name: HeLa_Ctrl_BS_rep2

value: PRAISE-seq of HeLa control cells with bisulfite treatment, replicate2


title: HeLa_Ctrl_BS_rep1

description: Library name: HeLa_Ctrl_BS_rep1

value: PRAISE-seq of HeLa control cells with bisulfite treatment, replicate1


title: Pilot 5 CD4+CD8- and CD4-CD8- cells, HTO

city: La Jolla

first: Kendall

last: Kearns

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

description:
Library name: HIPC_Pilot_Hu_5_8D_HTO
10X Genomics

library_source: other

data_processing:
Sequencing reads were aligned to the GRCh38 human reference genome and gene counting was performed using the multi pipeline in CellRanger (v5.0.0).
Downstream analyses were performed using Seurat (v4.4.0).
CD4-CD8- T cells were isolated by lack of expression of the CD4 ADT marker.
Seurat's HastagDemux was used for hashtag demultiplexing and singlet assignment. Donors TT0105 and TS0012 were remvoved from analyses.
Assembly: GRCh38
Supplementary files format and content: tab-separated values files and matrix files
Library strategy: CITE-seq

molecule: protein

source_name: PBMC

extract_protocol:
Freshly thawed PBMCs were incubated for 10 minutes with Zombie UV Fixable Viability Kit (BioLegend) following the manufacturer’s protocol. To neutralize and block unbound viability dye, 10% fetal bovine serum (FBS) in 1X PBS was added to the cells followed by a centrifugation step. FcR blocking reagent (BioLegend) at a 1:50 dilution from the stock reagent solution was added to the cells. Samples were further incubated for 10 minutes at room temperature. For oligonucleotide-conjugated antibody staining, 2 µL of each TotalSeqTM-C antibody was added per sample in a final staining volume not exceeding 100 µL in 1X PBS and cells were incubated at room temperature for 15 minutes. TotalSeqTM-C antibodies that were used included anti-HLA-DR (clone L243, barcode 0159) and anti-CD4 (clone SK3, barcode 0045), as well as several anti-CD45 or anti-CD298 plus anti-beta2-microglobulin antibodies to identify each sample in downstream analyses. Samples were spun down and excess unbound antibody was removed before proceeding to the next step. A cocktail of fluorochrome-conjugated antibodies, 10 µL BD HorizonTM Brilliant Stain Buffer Plus (BD Biosciences), and 1X PBS were added to a final volume of 100 µL. The antibodies included in the cocktail were anti-CCR7 BB515 (BD Biosciences, clone 2-L1-A), anti-CD11c BV785 (BioLegend, clone 3.9), anti-CD123 PerCP-Cy5.5 (BioLegend, clone 6H6), anti-CD14 BV480 (BD Biosciences, clone M5E2), anti-CD16 BUV737 (BD Biosciences, clone 3G8), anti-CD19 BV605 (BioLegend, clone HIB19), anti-CD1c BV650 (BioLegend, clone L161), anti-CD20 BUV563 (BD Biosciences, clone 2H7), anti-CD3 BUV805 (BD Biosciences, clone UCHT1), anti-CD38 PE-Dazzle594 (BioLegend, clone HIT2), anti-CD4 APC-eF780 (eBiosciences, clone RPA-T4), anti-CD45 BUV395 (BD Biosciences, clone HI30), anti-CD45RA BV570 (BioLegend, clone HI100), anti-CD56 APC (BioLegend, clone 5.1H11), anti-CD71 PE-Cy5 (BD Biosciences, clone M-A712), anti-CD8 BUV495 (BD Biosciences, clone RPA-T8), anti-HLA-DR PE-Cy7 (BioLegend, clone LN3), anti-IgD BV750 (BD Biosciences, clone IA6-2), and anti-TCRγδ BV421 (BD Biosciences, clone 11F2). Cells were incubated for 15 minutes in the dark at room temperature. Cells were washed once in 10 mL of 1X PBS to remove all unbound antibody and stored at 4˚C protected from light for up to 4 hours until flow cytometry acquisition. Live singlets CD3+CD19-CD14-CD8- cells (including CD4+ and CD4-) were sorted using a BD Symphony S6 sorter and sequenced using droplet-based 10x Genomics.
Single-cell suspensions were then immediately loaded on the 10x Genomics Chromium Controller with a loading target of 30,000-60,000 cells. Libraries were generated using the Chromium Next GEM Single Cell 5’ Reagent Kit v2 (Dual Index) per the manufacturer’s instructions. Additional steps were included for the amplification of HTO barcodes and V(D)J libraries (10x Genomics). Libraries were sequenced on an Illumina NovaSeq with a target of 30,000 reads per cell RNA library, 5,000 reads per cell HTO barcode library, and 5,000 reads per cell for V(D)J libraries. As the V(D)J libraries utilized the default TCRαβ primers, the data was not used in this work but were analyzed further in another study (Series GSE293807).

value: PBMC


title: MTB20L CD4+CD8- and CD4-CD8- cells, CITE

description:
Library name: MTB20L_Hu_CD3_CITE
10X Genomics


title: MTB20L CD4+CD8- and CD4-CD8- cells, HTO

description:
Library name: MTB20L_Hu_CD3_HTO
10X Genomics


title: Pilot 5 CD4+CD8- and CD4-CD8- cells, CITE

description:
Library name: HIPC_Pilot_Hu_5_8D_CITE
10X Genomics


title: MTB20L CD4+CD8- and CD4-CD8- cells, GEX

description:
Library name: MTB20L_Hu_CD3_Gex
10X Genomics

data_processing:
Sequencing reads were aligned to the GRCh38 human reference genome and gene counting was performed using the multi pipeline in CellRanger (v5.0.0).
Downstream analyses were performed using Seurat (v4.4.0).
CD4-CD8- T cells were isolated by lack of expression of the CD4 ADT marker.
Seurat's HastagDemux was used for hashtag demultiplexing and singlet assignment. Donors TT0105 and TS0012 were remvoved from analyses.
Assembly: GRCh38
Supplementary files format and content: tab-separated values files and matrix files


title: HeLa_shDKC1.1_BS_rep1

description: Library name: HeLa_shDKC1.1_BS_rep1

value: PRAISE-seq of HeLa DKC1 KD cell line1, with bisulfite treatment, replicate1


title: HeLa_shDKC1.2_BS_rep1

description: Library name: HeLa_shDKC1.2_BS_rep1

value: PRAISE-seq of HeLa DKC1 KD cell line2, with bisulfite treatment, replicate1


title: HeLa_Ctrl_input_rep1

description: Library name: HeLa_Ctrl_input_rep1

value: PRAISE-seq of HeLa control cells without bisulfite treatment, replicate1


title: MTB20I CD4+CD8- and CD4-CD8- cells, HTO

description:
Library name: MTB20I_Hu_CD3_HTO
10X Genomics


title: MTB20J CD4+CD8- and CD4-CD8- cells, CITE

description:
Library name: MTB20J_Hu_CD3_CITE
10X Genomics


title: MTB20J CD4+CD8- and CD4-CD8- cells, HTO

description:
Library name: MTB20J_Hu_CD3_HTO
10X Genomics


title: MTB20I CD4+CD8- and CD4-CD8- cells, CITE

description:
Library name: MTB20I_Hu_CD3_CITE
10X Genomics


title: MTB20J CD4+CD8- and CD4-CD8- cells, GEX

description:
Library name: MTB20J_Hu_CD3_Gex
10X Genomics


title: HeLa_shDKC1.1_BS_rep2

description: Library name: HeLa_shDKC1.1_BS_rep2

value: PRAISE-seq of HeLa DKC1 KD cell line1, with bisulfite treatment, replicate2


title: Pilot 5 CD4+CD8- and CD4-CD8- cells, GEX

description:
Library name: HIPC_Pilot_Hu_5_8D_Gex
10X Genomics


title: MTB20H CD4+CD8- and CD4-CD8- cells, CITE

description:
Library name: MTB20H_Hu_CD3_CITE
10X Genomics


title: MTB20G CD4+CD8- and CD4-CD8- cells, HTO

description:
Library name: MTB20G_Hu_CD3_HTO
10X Genomics


title: MTB20G CD4+CD8- and CD4-CD8- cells, CITE

description:
Library name: MTB20G_Hu_CD3_CITE
10X Genomics


title: MTB20H CD4+CD8- and CD4-CD8- cells, GEX

description:
Library name: MTB20H_Hu_CD3_Gex
10X Genomics


title: MTB20H CD4+CD8- and CD4-CD8- cells, HTO

description:
Library name: MTB20H_Hu_CD3_HTO
10X Genomics


title: MTB20E CD4+CD8- and CD4-CD8- cells, CITE

description:
Library name: Mtb20E_Hu_CD3_CITE
10X Genomics


title: MTB20I CD4+CD8- and CD4-CD8- cells, GEX

description:
Library name: MTB20I_Hu_CD3_Gex
10X Genomics


title: MTB20C CD4+CD8- and CD4-CD8- cells, HTO

description:
Library name: MTB20C_Hu_CD3_HTO
10X Genomics


title: MTB20D CD4+CD8- and CD4-CD8- cells, GEX

description:
Library name: MTB20D_Hu_CD3_Gex
10X Genomics


title: MTB20D CD4+CD8- and CD4-CD8- cells, HTO

description:
Library name: MTB20D_Hu_CD3_HTO
10X Genomics


title: MTB20D CD4+CD8- and CD4-CD8- cells, CITE

description:
Library name: MTB20D_Hu_CD3_CITE
10X Genomics


title: MTB20E CD4+CD8- and CD4-CD8- cells, HTO

description:
Library name: Mtb20E_Hu_CD3_HTO
10X Genomics


title: MTB20C CD4+CD8- and CD4-CD8- cells, GEX

description:
Library name: MTB20C_Hu_CD3_Gex
10X Genomics


title: MTB20E CD4+CD8- and CD4-CD8- cells, GEX

description:
Library name: Mtb20E_Hu_CD3_Gex
10X Genomics


title: MTB20B CD4+CD8- and CD4-CD8- cells, GEX

description:
Library name: MTB20B_Hu_CD3_Gex
10X Genomics


title: MTB20C CD4+CD8- and CD4-CD8- cells, CITE

description:
Library name: MTB20C_Hu_CD3_CITE
10X Genomics


title: MTB20B CD4+CD8- and CD4-CD8- cells, CITE

description:
Library name: MTB20B_Hu_CD3_CITE
10X Genomics


title: MTB20B CD4+CD8- and CD4-CD8- cells, HTO

description:
Library name: MTB20B_Hu_CD3_HTO
10X Genomics


title: MTB20A CD4+CD8- and CD4-CD8- cells, GEX

description:
Library name: MTB20A_Hu_CD3_Gex
10X Genomics


title: MTB20G CD4+CD8- and CD4-CD8- cells, GEX

description:
Library name: MTB20G_Hu_CD3_Gex
10X Genomics


title: MTB20A CD4+CD8- and CD4-CD8- cells, HTO

description:
Library name: MTB20A_Hu_CD3_HTO
10X Genomics


title: BlisterFluid87, SCAR, rep1

city: Perth

first: Andrew

last: Gibson

state: Western Australia

address: Building 390, Discovery Way, Murdoch University

country: Australia

institute: Murdoch University

data_processing:
Single-cell sequencing data were processed using CellRanger v6.1.2 to demultiplex individual cell barcodes, remove PCR duplicates, and align reads to the reference GRCh38 human transcriptome. The individual hashes within each 10x run were further demultiplexed using Souporcell to cluster samples based on SNPs in the RNA-seq reads. The hashtag negatives or doublets, as well as cells with >50% mitochondrial content were removed to filter low quality, dead, or dying populations for initial QC, with a second pass filter excluding apoptotic populations characterized by a low percentage of ribosomal genes and a high percentage of mitochondrial genes, using a defined mitochondrial-ribosomal RNA ratio of >0.47. A standardized mitochondrial DNA threshold of 10% is recommended for human tissue, which was met by 98% of ‘live’ cells identified. The remaining 2% of cells were excluded. Downstream transcriptome-based graph clustering and PCA with cell phenotype calling were performed using R Seurat v4.1.1 package, without input of TCR, BCR, mitochondrial, ribosomal, or sex-linked genes to avoid bias due to known expression variability. Batch correction for 10x run, sample type (skin or blister fluid), and cell cycle phase were performed using harmony. Experimental doublets were identified and removed using a majority consensus benchmark of three independent bioinformatic algorithms (DoubletFinder, scDBLfinder, scDS).
Assembly: GRCh38
Supplementary files format and content: Normalized_Counts.csv : This is the normalized count matrix derived from Seurat's normalize method for all the single-cells included in the project.
Supplementary files format and content: Metadata_CITESeq+TCR.tsv : This tab-delimited text file contains for each cell barcode - sample meta-data  (such as age, sex, etc.) , CITESeq antibody counts and TCR alpha/beta chains.

source_name: Blister fluid

extract_protocol:
Cryopreserved skin biopsies were thawed and digested using published methods optimized for lymphoid cell recovery and single-cell sequencing (RPMI 1640 medium with 10% FBS, 1mg/ml collagenase P and 40ug/ml DNAase I with agitation for 90 minutes). Tissue lysates were washed and passed through a 70µm Flowmi™ Cell Strainer. Single-cell suspensions of enzymatically-digested skin or thawed unprocessed blister fluid were then subject to surface antibody staining for a panel of up to 137 functional and surface lineage markers in the TotalSeq™-C Human Universal Cocktail, V1.0 (Biolegend) as per manufacturer’s protocol. 1µl of the appropriate hashtag antibody was also added, with subsequent incubation for 30mins at 4°C. Each cell-antibody cocktail was then resuspended in 3.5ml cell staining buffer and washed three times in PBS before cells were passed through a 70µm Flowmi™ Cell Strainer. Cell count and viability were recorded and cells were diluted as per the manufacturer’s instruction for loading onto the 10X Chromium Next GEM chip K.
Cells were loaded onto the chromium Next GEM chip K chip at the manufacturer (10x Genomics) recommended concentration and single-cell libraries made using a chromium controller and Chromium Next GEM Single Cell 5' Reagent Kit, Version 2.0 (10x Genomics) as per manufacturer instruction (https://www.10xgenomics.com/support/single-cell-immune-profiling/documentation/steps/library-prep/chromium-single-cell-5-reagent-kits-user-guide-v-2-chemistry-dual-index-with-feature-barcoding-technology-for-cell-surface-protein-and- immune-receptor-mapping), with a target of 1,000-20,000 cells. 5’ libraries were then sequenced using the Illumina NovaSeq 6000 platform.

value: Blister fluid

value: female


title: BlisterFluid86, SCAR, rep1


title: MTB20A CD4+CD8- and CD4-CD8- cells, CITE

description:
Library name: MTB20A_Hu_CD3_CITE
10X Genomics


title: BlisterFluid88, SCAR, rep1


title: BlisterFluid91, BURN, rep1


title: Skin17, SCAR, rep1

source_name: Skin biopsy Affected

value: Skin biopsy Affected

value: Male


title: BlisterFluid80, SCAR, rep1

value: Female


title: M55 line with Dox-inducible ACTG1 transgene, Dox_1000ng/mL, P12, Rep1

status: Public on Aug 15 2026

city: Boston

first: Alex

last: Plesa

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description:
Library name: A1
Donor age 55, Passage 12

data_processing:
To minimize variability arising from differences in sequencing depth, FASTQ files for all libraries (except LIB058979, LIB092645, and LIB083102) were downsampled to 20 million reads using Seqtk-1.3.
Raw RNA-seq reads were aligned to the GRCh38/GRCm39 reference genome using STAR v2.5.2b and checked for quality control using FastQC v0.11.5
Alignment files were indexed using SAMtools v1.3.154 and gene-level counts were obtained using featureCounts from the Subread v2.0.1 package
Assembly: GRCh38, GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: NHDFs were maintained in low-glucose DMEM supplemented with 15% fetal bovine serum (FBS) and 1% Pen-strep (P/S) in humidified atmosphere with 5% CO2 and 5% O2, at 37C. iPSCs were maintained in mTESR+supplement in humidified atmosphre with 5% CO2 at 37C.

extract_protocol:
Cells were lysed using the Monarch DNA/RNA Protection Reagent (NEB T2011) and stored at -80°C until RNA extraction. Total RNA was extrqacted using the Monarch Total RNA Miniprep kit (NEB T2010). Mouse tissues were processed by Novogene.
Libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina using the polyA mRNA workflow according to manufacturer's instructions. LIB058979 was genereated using the Tecan MagicPrepRevelo mRNA-seq kit acoording to manufacturare's instructions. LIB083102 was generated by Novogene using a directional mRNA library preparation method.

treatment_protocol: Transgene was induced using doxycycline at the specified concentration for the specified amount of time. Similarly, rapamycin was added to the media at the 100nM for the specified amount of time.

value: Fibroblast

value: Dox_1000ng/mL, 3days


title: Skin18, SCAR, rep1


title: BlisterFluid90, BURN, rep1


title: BlisterFluid89, BURN, rep1


title: BlisterFluid75, SCAR, rep1


title: BlisterFluid73, SCAR, rep1


title: Skin19, SCAR, rep1

source_name: Skin biopsy Unaffected

value: Skin biopsy Unaffected


title: Skin13, SCAR, rep1


title: BlisterFluid72, BURN, rep1


title: BlisterFluid81, SCAR, rep1


title: Skin14, SCAR, rep1


title: Skin15, SCAR, rep1

source_name: Skin biopsy

value: Skin biopsy


title: BlisterFluid71, BURN, rep1


title: BlisterFluid68, SCAR, rep1


title: BlisterFluid67, SCAR, rep1


title: Skin16, SCAR, rep1


title: Skin10, SCAR, rep1


title: Skin11, SCAR, rep1


title: Skin, Healthy Donor, rep1


title: Skin7, SCAR, rep1


title: Skin8, SCAR, rep1


title: BlisterFluid60, SCAR, rep1

source_name: Hash 1_SCAR patient 3, blister fluid / Hash 2_SCAR patient 3, blister fluid


title: Skin9, SCAR, rep1


title: BlisterFluid58, SCAR, rep1

value: Hash 1_SCAR patient 3, blister fluid / Hash 2_SCAR patient 3, blister fluid


title: BlisterFluid59, SCAR, rep1


title: Skin29, SCAR, rep1


title: BlisterFluid55, SCAR, rep1


title: BlisterFluid70, BURN, rep1


title: BlisterFluid74, SCAR, rep1


title: BlisterFluid51, SCAR, rep1


title: BlisterFluid69, SCAR, rep1


title: BlisterFluid53, SCAR, rep1


title: TH_4

city: shanghai

first: Yiqi

last: Ma

address: Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No.197, Ruijin 2nd Road, Shanghai, China.

institute: Ruijin hospital, shanghai jiaotong university school of medicine

description:
Library name: sample 10
FPKM.TH_4

data_processing:
Raw paired-end reads were filtered using Cutadapt version 1.9. Reads containing adapter sequences, poly(A) or poly(G) sequences, more than 5% unknown nucleotides, or more than 20% low-quality bases with Q values less than or equal to 20 were removed. The remaining high-quality reads were retained as clean reads for downstream analysis.
The quality of the clean reads was assessed using FastQC version 0.11.9. Sequencing quality metrics, including Q20, Q30, and GC content, were calculated and evaluated.
Clean paired-end reads were aligned to the Mus musculus reference genome using HISAT2 version 2.2.1. HISAT2 allowed up to 20 alignments per read by default and a maximum of two mismatches during read mapping. Potential splice junctions were identified and incorporated into the alignment process.
Mapped reads from each sample were assembled using StringTie version 2.1.6 with default parameters. Transcript assemblies from all samples were merged using gffcompare version 0.9.8 to generate a comprehensive transcriptome. StringTie and Ballgown were then used to estimate transcript and mRNA expression abundance. Expression levels were normalized and reported as fragments per kilobase of transcript per million mapped reads (FPKM).
Differential gene expression analysis between the TGF-β1 plus hemin group and the TGF-β1 group was performed using DESeq2. Genes with a false discovery rate below 0.05 and an absolute fold change greater than or equal to 2 were considered differentially expressed. Differentially expressed genes were subsequently subjected to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text matrix containing FPKM-normalized expression values for all annotated mRNAs across all samples. Rows represent annotated genes and columns represent individual RNA-seq libraries. Gene identifiers and gene symbols are included.

organism: Mus musculus

source_name: bone marrow

extract_protocol:
Total RNA was extracted from bone marrow-derived macrophages using TRIzol reagent (Thermo Fisher Scientific, catalog no. 15596018) according to the manufacturer's instructions. RNA quantity, purity, and integrity were evaluated using an Agilent 2100 Bioanalyzer and the RNA 6000 Nano LabChip Kit (Agilent Technologies, catalog no. 5067-1511). High-quality RNA samples with an RNA integrity number (RIN) greater than 7.0 were used for library construction.
Approximately 5 μg of total RNA was used for library construction. Polyadenylated mRNA was purified from total RNA through two rounds of selection using Dynabeads Oligo (dT) beads. The purified mRNA was fragmented using divalent cations at 94°C for 5–7 minutes with the Magnesium RNA Fragmentation Module (NEB, catalog no. e6150). The fragmented RNA was reverse-transcribed using SuperScript II Reverse Transcriptase to generate first-strand cDNA. U-labeled second-strand cDNA was synthesized using E. coli DNA polymerase I, RNase H, and dUTP.

value: bone marrow

value: bone marrow-derived macrophage


title: BlisterFluid57, SCAR, rep1


title: BlisterFluid54, SCAR, rep1


title: BlisterFluid56, SCAR, rep1


title: BlisterFluid49, SCAR, rep1


title: TH_6

description:
Library name: sample 12
FPKM.TH_6


title: BlisterFluid48, SCAR, rep1


title: BlisterFluid47, SCAR, rep1


title: BlisterFluid52, SCAR, rep1


title: Skin12, SCAR, rep1


title: BlisterFluid50, SCAR, rep1


title: TH_5

description:
Library name: sample 11
FPKM.TH_5


title: TH_3

description:
Library name: sample 9
FPKM.TH_3


title: T_3

description:
Library name: sample 3
FPKM.T_3


title: BlisterFluid44, SCAR, rep1

source_name: Hash 3_SCAR patient 14, blister fluid / Hash 4_SCAR patient 14, blister fluid


title: BlisterFluid45, SCAR, rep1

value: Hash 3_SCAR patient 14, blister fluid / Hash 4_SCAR patient 14, blister fluid


title: BlisterFluid43, SCAR, rep1


title: T_1

description:
Library name: sample 1
FPKM.T_1


title: BlisterFluid41, SCAR, rep1

source_name: Hash 1_SCAR patient 18, blister fluid / Hash 2_SCAR patient 18, blister fluid


title: A1328_LP PIC_5

city: Lyon

first: Pierre-Olivier

last: Vidalain

address: 21 Avenue Tony Garnier

country: France

institute: CIRI

description: Library name: 5-LP PIC

data_processing:
BCL Convert software (version 4.3.6) was used for demultiplexing and trimming of Illumina adapter residuals (no further refinement or selection). Read quality was assessed using FastQC version 0.11.1. Reads with average quality score <24, containing uncalled "N" bases, or shorter than 25 bases after trimming were filtered using BBTools version 38.86
Reads were mapped using STAR version 2.7.11b to the Illumina iGenomes reference genome
Gene counts were generated using htseq-count (HTSeq version 0.13.5; uniquely mapped reads to annotated genes)
Normalization and differential expression analysis were performed using the DESeq2 R package version 1.44.0
KEGG pathway and Gene Ontology (GO) gene set enrichment analyses were performed using the GAGE R package version 2.36.0.
Assembly: GRCm38
Supplementary files format and content: Text files (.counts) containing gene counts (raw values)

source_name: BMDM

growth_protocol: BMDM cells were cultured at 37°C and 5% CO2 in DMEM with Glutamax, 30% L929 cell-line derived conditioned medium (enriched in CSF-1), 20% FBS and 100 U/mL of Penicillin/Streptomycin

extract_protocol:
Cells were washed with PBS and total RNA were extracted with NucleoSpin RNA (Macherey-Nagel, Germany) kit
Libraries were prepared from total RNA using the Illumina Stranded RNA Library Prep Kit with poly(A) enrichment, following the manufacturer's instructions.

treatment_protocol: Cells were treated for 48h with the different formulations

tag: mouse id

value: BMDM

value: LP PIC


title: T_5

description:
Library name: sample 5
FPKM.T_5


title: BlisterFluid46, SCAR, rep1


title: T_4

description:
Library name: sample 4
FPKM.T_4


title: A1328_LP 3M PIC_5

description: Library name: 5-LP 3M PIC

value: LP 3M PIC


title: BlisterFluid40, SCAR, rep1

value: Hash 1_SCAR patient 18, blister fluid / Hash 2_SCAR patient 18, blister fluid


title: T_6

description:
Library name: sample 6
FPKM.T_6


title: TH_2

description:
Library name: sample 8
FPKM.TH_2


title: A1328_LP 3M_5

description: Library name: 5-LP 3M

value: LP 3M


title: 68591_LP_4

description: Library name: 4-LP

value: LP


title: 68591_LP PIC_4

description: Library name: 4-LP PIC


title: BlisterFluid42, SCAR, rep1


title: BlisterFluid37, SCAR, rep1

value: Blister fluid


title: BlisterFluid35, SCAR, rep1

source_name: Hash 1_SCAR patient 18, blister fluid / Hash 2_SCAR patient 23, blister fluid


title: 68591_LP 3M PIC_4

description: Library name: 4-LP 3M PIC


title: A1328_LP_5

description: Library name: 5-LP


title: BlisterFluid39, SCAR, rep1


title: T_2

description:
Library name: sample 2
FPKM.T_2


title: 68589_LP 3M PIC_3

description: Library name: 3-LP 3M PIC


title: BlisterFluid31, SCAR, rep1

source_name: Hash 1_SCAR patient 10, blister fluid / Hash 2_SCAR patient 12, blister fluid

value: Pooled Male and Female


title: BlisterFluid30, SCAR, rep1

source_name: Hash 1_SCAR patient 2, blister fluid / Hash 2_SCAR patient 17, blister fluid

value: Female


title: 68589_LP 3M_3

description: Library name: 3-LP 3M


title: BlisterFluid38, SCAR, rep1


title: A7127_LP_2

description: Library name: 2-LP


title: BlisterFluid34, SCAR, rep1

value: Hash 1_SCAR patient 18, blister fluid / Hash 2_SCAR patient 23, blister fluid


title: BlisterFluid32, SCAR, rep1

value: Hash 1_SCAR patient 10, blister fluid / Hash 2_SCAR patient 12, blister fluid


title: BlisterFluid36, SCAR, rep1


title: 68589_LP_3

description: Library name: 3-LP


title: BlisterFluid33, SCAR, rep1


title: BlisterFluid27, SCAR, rep1

source_name: Hash 1_SCAR patient 24, blister fluid / Hash 2_SCAR patient 25, blister fluid


title: A7124_LP_1

description: Library name: 1-LP


title: 68589_LP PIC_3

description: Library name: 3-LP PIC


title: BlisterFluid25, SCAR, rep1

value: Hash 1_SCAR patient 24, blister fluid / Hash 2_SCAR patient 25, blister fluid


title: 68591_LP 3M_4

description: Library name: 4-LP 3M


title: Skin6, SCAR, rep1

source_name: Hash 1_SCAR patient 26, skin biopsy / Hash 2_SCAR patient 26, skin biopsy


title: A7124_LP PIC_1

description: Library name: 1-LP PIC


title: Skin5, SCAR, rep1

value: Hash 1_SCAR patient 26, skin biopsy / Hash 2_SCAR patient 26, skin biopsy


title: A7124_LP 3M_1

description: Library name: 1-LP 3M


title: BlisterFluid29, SCAR, rep1

value: Hash 1_SCAR patient 2, blister fluid / Hash 2_SCAR patient 17, blister fluid


title: A7127_LP PIC_2

description: Library name: 2-LP PIC


title: Skin4, SCAR, rep1


title: APCs, AKD_2

city: GUANGZHOU

first: ZHU

last: TIANXIN

address: 107 Yanjiang West Road

institute: Sun Yat-sen Memorial Hospital

description: Library name: AKD_2

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Homo sapiens reference genome using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by DESeq2 software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: GRCm38
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: adipose

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

value: adipose

value: Adipocyte Precursor Cells

value: circRNA BRAKE knock down

value: adipogenic differentiation


title: APCs, AKD_3

description: Library name: AKD_3


title: Skin2, SCAR, rep1

source_name: Hash 1_SCAR patient 26, skin biopsy / Hash 2_SCAR patient 26, PBMC


title: BlisterFluid28, SCAR, rep1


title: A7127_LP 3M PIC_2

description: Library name: 2-LP 3M PIC

value: BMDM


title: A7127_LP 3M_2

description: Library name: 2-LP 3M


title: BlisterFluid18, SCAR, rep1

source_name: Hash 1_SCAR patient 4, blister fluid / Hash 2_SCAR patient 18, blister fluid / Hash 3_SCAR patient 8, blister fluid / Hash 4_SCAR patient 3; blister fluid


title: Skin3, SCAR, rep1

value: Hash 1_SCAR patient 26, skin biopsy / Hash 2_SCAR patient 26, PBMC


title: APCs, WT_1

description: Library name: WT_1

value: WT


title: APCs, WT_3

description: Library name: WT_3


title: A7124_LP 3M PIC_1

description: Library name: 1-LP 3M PIC

value: LP 3M PIC


title: APCs, WT_2

description: Library name: WT_2


title: BlisterFluid14, SCAR, rep1

source_name: Hash 2_SCAR patient 15, blister fluid / Hash 3_SCAR patient 2, blister fluid / Hash 4_SCAR patient 14, blister fluid / Hash 5_SCAR patient 27; blister fluid


title: BlisterFluid16, SCAR, rep1

value: Hash 1_SCAR patient 4, blister fluid / Hash 2_SCAR patient 18, blister fluid / Hash 3_SCAR patient 8, blister fluid / Hash 4_SCAR patient 3; blister fluid


title: BlisterFluid26, SCAR, rep1


title: Ileum, IEC-Ppara homozygous, Rep4

city: Cincinnati

first: Kelli

middle: L

last: VanDussen

state: OH

address: 3333 Burnet Ave, MLC 2010

institute: Cincinnati Children's Hospital Medical Center

description:
Library name: Sample 16
Column name in all.gene_CPM.tsv and all.gene_moderated_log2cpm.tsv: sample.doub_chow_4

data_processing:
Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.23.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.04.
Assembly: Ensembl release 101 primary assembly, GRCm38 (mm10)
Supplementary files format and content: gene_counts.txt files contain raw counts for each sample in tab-delimited format
Supplementary files format and content: all.gene_CPM.tsv contains counts per million for all samples in tab-delimited format
Supplementary files format and content: all.gene_moderated_log2cpm.tsv contains moderated log2 counts per million for all samples in tab-delimited format

source_name: Ileum

growth_protocol: Mice were maintained in a specific pathogen-free barrier facility with a 14-hr light cycle, temperature of (22.2°C), and humidity (30%-70%) with ad libitum access to water and chow (Teklad #2919; 3.3 kcal/g with 23% calories from protein, 22% calories from fat, and 55% calories from carbohydrate).

extract_protocol:
Total RNA from whole-thickness ileal tissue was extracted and DNase-treated using a Nucleospin RNA kit (Takara). Total RNA concentration and purity was obtained from an absorbance ratio at 260nm and 280nm. Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation.
Library preparation was performed with 5 to 10ug of total RNA with a Bioanalyzer RIN score greater than 8.0. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

treatment_protocol: To induce Cre-mediated genetic recombination, male and female mice (8-13 weeks of age) were administered tamoxifen (100 mg/kg) via intraperitoneal injection daily for 3 consecutive days. Ileal tissues were collected for RNA isolation 2 weeks after the final tamoxifen injection.

value: Ileum

value: IEC-Ppara homozygous

value: Male


title: Ileum, IEC-Ppara homozygous, Rep3

description:
Library name: Sample 15
Column name in all.gene_CPM.tsv and all.gene_moderated_log2cpm.tsv: sample.doub_chow_3


title: Ileum, IEC-Ppara homozygous, Rep5

description:
Library name: Sample 17
Column name in all.gene_CPM.tsv and all.gene_moderated_log2cpm.tsv: sample.doub_chow_5

value: Female


title: Skin1, SCAR, rep1


title: BlisterFluid13, SCAR, rep1

value: Hash 2_SCAR patient 15, blister fluid / Hash 3_SCAR patient 2, blister fluid / Hash 4_SCAR patient 14, blister fluid / Hash 5_SCAR patient 27; blister fluid

value: Pooled Male and Female


title: APCs, AKD_1

description: Library name: AKD_1


title: BlisterFluid15, SCAR, rep1


title: Ileum, IEC-Ppara homozygous, Rep2

description:
Library name: Sample 14
Column name in all.gene_CPM.tsv and all.gene_moderated_log2cpm.tsv: sample.doub_chow_2


title: BlisterFluid12, SCAR, rep1

source_name: Hash 1_SCAR patient 5, blister fluid / Hash 2_SCAR patient 1, blister fluid / Hash 3_SCAR patient 9, blister fluid / Hash 4_SCAR patient 16; blister fluid


title: Ileum, IEC-Ppara homozygous, Rep6

description:
Library name: Sample 18
Column name in all.gene_CPM.tsv and all.gene_moderated_log2cpm.tsv: sample.doub_chow_6


title: BlisterFluid17, SCAR, rep1


title: Ileum, IEC-Ppara homoozygous, Rep1

description:
Library name: Sample 13
Column name in all.gene_CPM.tsv and all.gene_moderated_log2cpm.tsv: sample.doub_chow_1


title: BlisterFluid11, SCAR, rep1

value: Hash 1_SCAR patient 5, blister fluid / Hash 2_SCAR patient 1, blister fluid / Hash 3_SCAR patient 9, blister fluid / Hash 4_SCAR patient 16; blister fluid


title: BlisterFluid10, SCAR, rep1


title: BlisterFluid9, SCAR, rep1

source_name: Hash 1_SCAR patient 5, blister fluid / Hash 2_SCAR patient 28, skin biopsy / Hash 3_SCAR patient 9, blister fluid / Hash 4_SCAR patient 16, blister fluid


title: Ileum, IEC-Ppara heterozygous, Rep5

description:
Library name: Sample 11
Column name in all.gene_CPM.tsv and all.gene_moderated_log2cpm.tsv: sample.het_chow_5

value: IEC-Ppara heterozygous


title: BlisterFluid8, SCAR, rep1

value: Hash 1_SCAR patient 5, blister fluid / Hash 2_SCAR patient 28, skin biopsy / Hash 3_SCAR patient 9, blister fluid / Hash 4_SCAR patient 16, blister fluid


title: Ileum, IEC-Ppara heterozygous, Rep4

description:
Library name: Sample 10
Column name in all.gene_CPM.tsv and all.gene_moderated_log2cpm.tsv: sample.het_chow_4


title: BlisterFluid6, SCAR, rep1

source_name: Hash 1_SCAR patient 29, skin biopsy / Hash 2_SCAR patient 9, skin biopsy / Hash 3_SCAR patient 7, blister fluid


title: BlisterFluid4, SCAR, rep1

value: Hash 1_SCAR patient 29, skin biopsy / Hash 2_SCAR patient 9, skin biopsy / Hash 3_SCAR patient 7, blister fluid


title: BlisterFluid7, SCAR, rep1


title: Ileum, IEC-Ppara heterozygous, Rep1

description:
Library name: Sample 7
Column name in all.gene_CPM.tsv and all.gene_moderated_log2cpm.tsv: sample.het_chow_1


title: BlisterFluid2, SCAR, rep1

source_name: Hash 1_SCAR patient 30, blister fluid / Hash 2_SCAR patient 31, skin biopsy / Hash 3_SCAR patient 27, blister fluid / Hash 4_SCAR patient 32; skin biopsy


title: Ileum, IEC-Ppara heterozygous, Rep2

description:
Library name: Sample 8
Column name in all.gene_CPM.tsv and all.gene_moderated_log2cpm.tsv: sample.het_chow_2


title: BlisterFluid5, SCAR, rep1


title: Ileum, IEC-Ppara heterozygous, Rep3

description:
Library name: Sample 9
Column name in all.gene_CPM.tsv and all.gene_moderated_log2cpm.tsv: sample.het_chow_3


title: Ileum, Control, Rep6

description:
Library name: Sample 6
Column name in all.gene_CPM.tsv and all.gene_moderated_log2cpm.tsv: sample.wt_chow_6

value: Control


title: Ileum, Control, Rep5

description:
Library name: Sample 5
Column name in all.gene_CPM.tsv and all.gene_moderated_log2cpm.tsv: sample.wt_chow_5


title: Ileum, IEC-Ppara heterozygous, Rep6

description:
Library name: Sample 12
Column name in all.gene_CPM.tsv and all.gene_moderated_log2cpm.tsv: sample.het_chow_6


title: BlisterFluid3, SCAR, rep1

value: Hash 1_SCAR patient 30, blister fluid / Hash 2_SCAR patient 31, skin biopsy / Hash 3_SCAR patient 27, blister fluid / Hash 4_SCAR patient 32; skin biopsy


title: Ileum, Control, Rep4

description:
Library name: Sample 4
Column name in all.gene_CPM.tsv and all.gene_moderated_log2cpm.tsv: sample.wt_chow_4


title: P7 cortex-layer 2-repeat#3

city: Baltimore

middle: L.

last: Kolodkin

state: MD

address: 600 N. Wolfe St.

department: Neuroscience

institute: Johns Hopkins School of Medicine

description: Library name: VNec-P7_15_3

data_processing:
HISAT2 index
.sam to .bam conversion, sorting and indexing of .bam files
stringtie & featurecounts
Assembly: GRCm39
Supplementary files format and content: .txt, TPMs for each gene

source_name: cerebral cortex

extract_protocol:
Rneasy mini kit
SMART-Seq mRNA LP kit

value: cerebral cortex

value: layer 2 CPN

value: wt

value: postnatal day 7


title: P7 cortex-layer 2-repeat#2

description: Library name: VNec-P7_15_2


title: Ileum, Control, Rep3

description:
Library name: Sample 3
Column name in all.gene_CPM.tsv and all.gene_moderated_log2cpm.tsv: sample.wt_chow_3


title: BlisterFluid1, SCAR, rep1


title: Ileum, Control, Rep2

description:
Library name: Sample 2
Column name in all.gene_CPM.tsv and all.gene_moderated_log2cpm.tsv: sample.wt_chow_2


title: SZ_16

city: Philadelphia

first: Benjamin

middle: C.

last: Reiner

state: PA

address: 125 S 31st St

institute: University of Pennsylvania

description:
nuclear mRNA
snRNAseq

data_processing:
10x Genomics Cell Ranger v3.1.
Genome_build: hg38 pre-mRNA transcriptome supplied with Cell Ranger v3.1.
Supplementary_files_format_and_content: Cell Ranger raw feature barcode matrix.

source_name: frozen postmortem dorsolateral prefrontal cortex brain

extract_protocol:
Nuclei were captured with the 10x Genomics Chromium controller for 3' gene expression assay (v3.1) according to manufacturer protocols.
Libraries were prepared according to 10x Genomics manufacturer protocols.

value: dorsolateral prefrontal cortex

tag: diagnosis

value: Schizophrenia

tag: ethnicity

value: European


title: P7 cortex-layer 3-repeat#3

description: Library name: VNec-P7_14_3

value: layer 3 CPN


title: P7 cortex-layer 3-repeat#2

description: Library name: VNec-P7_14_2


title: Ileum, Control, Rep1

description:
Library name: Sample 1
Column name in all.gene_CPM.tsv and all.gene_moderated_log2cpm.tsv: sample.wt_chow_1

value: Ileum

value: Female


title: SZ_15

description:
nuclear mRNA
snRNAseq

value: Male


title: P7 cortex-layer 2-repeat#1

description: Library name: VNec-P7_15_1


title: SZ_14

description:
nuclear mRNA
snRNAseq


title: P7 cortex-layer 3-repeat#1

description: Library name: VNec-P7_14_1


title: SZ_13

description:
nuclear mRNA
snRNAseq


title: P3 cortex-layer 2-repeat#2

description: Library name: VNec-P3_15_2

value: postnatal day 3


title: P3 cortex-layer 3-repeat#3

description: Library name: VNec-P3_14_3