title: Huh7 cells/ PB56874852 treatment/4uM/Rep1

description:
Library name: C4_1
C4_1


title: wsberry, rep 2

status: Public on Dec 16 2025

type: SRA

city: Cambridge

first: Erin

middle: E

last: Reynolds

state: MA

address: 455 Main St

country: USA

institute: Whitehead Institute

description: Library name: wsberry_2

library_source: transcriptomic

data_processing:
RNA-seq read alignment to the W. somnifera genome was performed using STAR (v 2.7.1a) 2-pass mapping, starting with a genome index generated with gene models and the option "--sjdbOverhang 100" and then re-mapping with a genome index using splice junctions from the initial mapping and the option "--limitOutSJcollapsed 2000000".
Gene counts were generated by featureCounts (v 2.0.1) with the options "-p -s 2 -M --fraction".
Assembly: unpublished
Supplementary files format and content: tab-delimited text file including raw counts for each sample

molecule: polyA RNA

organism: Withania somnifera

source_name: berry

growth_protocol: W. somnifera seeds were acquired from “All good things organic seeds” on Amazon.com in March 2017. Seeds were sown on potting mix with added vermiculite and vernalized for three to five days at 4 °C under a humidified lid. They were then grown on in-door growth shelves installed with full-spectrum LED growth lights (80–120 μmol photons m−2 s−1) under a 16 h light/8 h dark photoperiod at 22 °C. RNA was extracted from four different tissue types of W. somnifera (young leaves, old leaves, berry, and root) with three biological replicates per tissue. Young leaves were defined as leaves smaller than 2 cm and were plucked from the top of the plant, near the budding region. Young leaves, old leaves, and root tissue were harvested from ~6-week-old plants and berry tissue was harvested from ~6-month-old plants.

extract_protocol:
100 mg wet weight of old leaf and berry tissue was harvested, 30 mg wet weight young leaf tissue, and 150-200 mg wet weight of root tissue was harvested. Harvested tissues were flash frozen in liquid nitrogen and ground to a fine powder in liquid nitrogen using a mortar and pestle. RNA was extracted using the Qiagen RNeasy Plant Mini Kit. Extracted RNA samples were flash frozen in liquid nitrogen and submitted to the Genome Technology Core at Whitehead Institute for Illumina paired-end RNA sequencing.
Libraries were prepared for RNA-Seq using IDT’s Swift Rapid RNA Library Prep Kit, according to manufacturer’s directions.

tag: tissue

value: berry


title: Huh7 cells/ PB56874852 treatment/10uM/Rep3

city: Grand Rapids

first: Bin

last: Chen

state: Michigan

address: 400 Monroe Ave NW

department: Department of Pediatrics and Human Development

institute: MICHIGAN STATE UNIVERSITY

description:
Library name: C10_3
C10_3

data_processing:
RNA-Seq reads were mapped on hg38 transcriptome using the ENSEMBL GRCh38 annotation with the STAR aligner and further processed using RSEM.
Supplementary files format and content: comma-separated file includes Human ensembl_gene_id as rows and log2 transformed TPM and raw read count values for each sample as columns.
Assembly: Assembly: hg38
Supplementary files format and content: The processed data files are comma-separated files including Human ensembl_gene_id as rows and log2 transformed TPM and raw gene count values for each sample as columns.

molecule: total RNA

organism: Homo sapiens

source_name: Huh7 xenograft

growth_protocol: Subcutaneous Huh7 xenograft mouse model was constructed in 6 to 10 weeks old male NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mice (Strain #:005557, RRID:IMSR_JAX:005557).

extract_protocol:
The tumor tissues were resected. Total RNA was extracted from tumor tissues using RNeasy Plus Mini Kit (cat# 74136, Qiagen).
RNA libraries for RNA-seq were prepared using by the Genomics Core at the Van Andel Institute using total RNA

treatment_protocol: 1 ug compound  PB56874852 (dissolved in DMSO, 20ug/ml) was administrated via intratumor injection every 3 days for two weeks.

value: Huh7 xenograft

tag: disease

value: HCC

tag: treatment

value: Compound PB56874852

tag: dose

tag: batch


title: Huh7 cells/ PB56874852 treatment/10uM/Rep2

description:
Library name: C10_2
C10_2


title: Huh7 cells/ DMSO treatment/control/Rep3

description:
Library name: Ctr3
Ctr3

value: DMSO


title: Zebrafish Tail Fin, Taz Crispant Injured, biol rep 1

city: Edinburgh

first: Carsten

middle: Gram

last: Hansen

address: 4-5 Little France Dr

department: Centre for Inflammation Research

country: United Kingdom

institute: University of Edinburgh

description:
Library name: Sample 17
TazIn1

data_processing:
Trim Galore was used to remove adapters (Illumina and GCT AAT CAT TGC AAG CAG TGG TAT CAA CGC AGA GTA CAT).
Burrows-Wheeler Aligner-MEM was used to align trimmed fastq files, creating sam files.
SAMtools was used to convert files to bam files and sort by coordinates.
HTSeq was used via anaconda to generate count tables for downstream analysis.
Assembly: GRCz11
Supplementary files format and content: CSV files include raw counts for each Sample

organism: Danio rerio

source_name: Zebrafish Tail Fin

extract_protocol:
Both uninjured and injured tail fins were removed caudal to the end of the dorsal vein (at the beginning of the pigment gap). Tissue was collected in chilled PBS and kept on ice for a maximum of one hour before extraction. RNA extraction was performed using the Qiagen RNeasy micro kit and initial quality check and sample concentration determined by NanoDrop.
Libraries were prepared by the Genetics Core, Wellcome Trust Clinical Research Facility Edinburgh, using the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina according to the provided protocol.

treatment_protocol: For injured samples, fish were injured at 3dpf using the severe tail fin injury paradigm, then left to recover for 24 hours in 0.3X Danieau’s solution.

value: Zebrafish Tail Fin

tag: genotype

value: Taz Crispant

value: 24h post tail fin injury

tag: strain

value: WIK

tag: age


title: Zebrafish Tail Fin, Taz Crispant Uninjured, biol rep 2

description:
Library name: Sample 15
TazUn2

value: Uninjured


title: Zebrafish Tail Fin, Taz Crispant Injured, biol rep 3

description:
Library name: Sample 19
TazIn3


title: Zebrafish Tail Fin, Taz Crispant Uninjured, biol rep 3

description:
Library name: Sample 16
TazUn3


title: Zebrafish Tail Fin, Yap Crispant Injured, biol rep 4

description:
Library name: Sample 13
YapIn4

value: Yap Crispant


title: wsyoungleaf, rep 2

description: Library name: wsyoungleaf_2

source_name: young leaf

value: young leaf


title: Zebrafish Tail Fin, Taz Crispant Injured, biol rep 2

description:
Library name: Sample 18
TazIn2


title: Zebrafish Tail Fin, Taz Crispant Uninjured, biol rep 1

description:
Library name: Sample 14
TazUn1


title: WCM1078 organoids, active compound, 24h, rep1, eRNA

city: Bern

first: Andrej

last: Benjak

address: Murtenstrasse 24-28

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

description: Library name: WCM078_A947_Rep.1

data_processing:
RNA-seq: Sequencing reads were aligned against the human genome hg38 with STAR v.2.7.3a. Gene counts were generated with RSEM v.1.3.2, whose index was generated using the GENCODE v33 primary assembly annotation.
ChIP-seq: Fastq files were aligned on the hg38 human genome reference using Bowtie2  (v2.2.6) followed by alignment sorting (samtools v1.7) of resulting bam files with filtering out of unmapped  reads and keeping reads with mapping quality higher than 30. Duplicates were removed with Picard’s MarkDuplicates  (v1.126) function, followed by indexation of resulting bam files with samtools. For each bam file, genome coverage was computed with bedtools (v2.26.0), followed by the generation of bigwig  (wigToBigWig v377) files. Peaks were called with macs2 (v2.2.4) for each treatment sample using a pooled input alignment (.bam file) as control. Downstream analyses were performed with DiffBind v3.11.1 with default parameters, except for summits=250 in dba.count(). dba.contrast() and dba.analyzed() were used to  compute significant differential peaks with DESeq2.
ATAC-seq: ATAC-seq reads were analyzed using the ENCODE ATAC-seq pipeline (version 1). Reads were trimmed of adapters using cutadapt (version 1.9.1) and mapped to hg38 using Bowtie 2 (version 2.2.6). Bam files were converted to tagAlign format, which was then adjusted for Tn5 by shifting +4 bp for positive strands and −5 bp for negative strands. TagAlign files were used to call peaks using MACS2 (version 2.1.0), and those peaks with P < 1 × 10−6 were retained for differential analysis with DiffBind (version 3.0.13) or the bamCount function of the R package bamsignals (version 1.24.0). Differential accessibility analysis was performed using either the R package DiffBind (version 3.0.13) or DESeq2 (version 1.32.0). The genomic distribution of differential peaks was annotated with ChIPpeakAnno (version 3.24.1). Bigwigs corresponding to a fold change against the background control were generated by MACS2 and used to generate heatmaps with the heatmap function of deepTools (version 3.5.0).
scRNA: Harvested cells were stained with 100ng/ml DAPI to stain dead cells. Using a cell sorter (conducted by Flow Cytometry Core, DBMR, Bern) and the recommended settings (Single Cell Discoveries B.V.), DAPI-negative cells were sorted as single cells in 376 wells of four 384-well plates containing immersion oil per condition. Resulting in a theoretical cell number of 1504 cells per condition. All post-harvesting steps were performed at 4°C. Plates were snap-frozen on dry ice for 15 minutes and sent out for sequencing at Single Cell Discoveries B.V. Data were analyzed using the Seurat package v.4.3.0. Cell QC filtering was done using the following thresholds: nCount > 4000, nFeature > 1000, percent.mito < 25, log10GenesPerUMI > 0.85. Cell phase was regressed out using the Seurat function ScaleData(seur.filt, vars.to.regress = c("S.Score", "G2M.Score")).
PRO-cap: Sequencing data was trimmed with fastp version 0.22.0 and then aligned to the human genome (hg38) concatenated with EBV and human rDNA sequences (GenBank U13369.1) using STAR V2.7.10b. Raw alignments were filtered with samtools version 1.18 and deduplicated using umi_tools version 1.1.2. Alignments were converted to bigwig files using bedtools version 2.30.0 and kentUtils bedGraphToBigWig V2.8. Peaks were called using PINTS version 1.1.6. Divergent peaks not overlapping with TSS +/-500 bp (GENCODE V37) were regarded as candidate enhancer RNAs.
Assembly: hg38
Supplementary files format and content: RNA-seq: Tables of gene counts. Tab-delimited text files.
Supplementary files format and content: ChIP-seq: BigWig files. Peak regions text files. Sample metadata text file.
Supplementary files format and content: ATAC-seq: BigWig files. Peak regions text files. Sample metadata text file.
Supplementary files format and content: scRNA: Raw cell counts and filtered cell counts as RDS files containing Seurat objects.
Supplementary files format and content: PRO-cap: BigWig files. Peak bed files.

molecule: nuclear RNA

source_name: organoid

growth_protocol: Metastatic prostate cancer biopsy pieces were minced and digested in 5 ml of 5 mg/ml collagenase type II (Invitrogen) in Advanced DMEM/F12 (ADMEM/F12) and digested for 0.5–2 hr at 37°C with gently shaking. Dissociated cells were washed and seeded in growth factor reduced Matrigel (BD biosciences).

extract_protocol:
RNA-seq: RNA was extracted using the RNeasy Kit (Qiagen)
Standard Illumina library
scRNA: 1x10e6 cells were harvested in PBS. SORT-seq was performed using Single Cell Discoveries (SCD) service.
ATAC-seq: Performed from 50’000 cryo-preserved cells per condition.
PRO-cap: Approximately 30 million cells were processed per sample. Library preparations for two biological replicates were performed separately. Cells were permeabilized, and run-on reactions were performed. After RNA isolation, two adaptor ligations and reverse transcription were performed with custom adaptors. Between adaptor ligations, cap state selection reactions were carried out using a series of enzymatic steps. RNA washes, phenol:chloroform extractions and ethanol precipitations were conducted between reactions. All steps were performed under RNase-free conditions.

treatment_protocol: organoids were treated with A858 or A947 (1µM)

value: organoid

tag: cell type

value: prostate tumor

value: SMARCA2/SMARCA4 targeting PROTAC


title: WCM1078 organoids, inactive compound, 24h, rep1, eRNA

description: Library name: WCM078_A858_Rep.1

value: inactive compound


title: WCM1078 organoids, active compound, 24h, rep2, eRNA

description: Library name: WCM078_A947_Rep.2


title: WCM1078 organoids, active compound, 48h, rep3, mRNA

description:
Library name: WCM1078-A947-48h-REP3_mRNA
Column name in RSEM results: 1078-947-48h-REP3


title: WCM1078 organoids, active compound, 48h, rep2, mRNA

description:
Library name: WCM1078-A947-48h-REP2_mRNA
Column name in RSEM results: 1078-947-48h-REP2


title: Zebrafish Tail Fin, Yap Crispant Injured, biol rep 3

description:
Library name: Sample 12
YapIn3


title: Zebrafish Tail Fin, Yap Crispant Injured, biol rep 2

description:
Library name: Sample 11
YapIn2


title: wsleaf, rep 1

description: Library name: wsleaf_1

source_name: leaf

value: leaf


title: Zebrafish Tail Fin, Yap Crispant Uninjured, biol rep 3

description:
Library name: Sample 9
YapUn3


title: WCM1078 organoids, active compound, 48h, rep1, mRNA

description:
Library name: WCM1078-A947-48h-REP1_mRNA
Column name in RSEM results: 1078-947-48h-REP1


title: WCM1078 organoids, active compound, 24h, rep3, mRNA

description:
Library name: WCM1078-A947-24h-REP3_mRNA
Column name in RSEM results: 1078-947-24h-REP3


title: Zebrafish Tail Fin, Yap Crispant Uninjured, biol rep 1

description:
Library name: Sample 7
YapUn1


title: Huh7 cells/ PB56874852 treatment/10uM/Rep1

description:
Library name: C10_1
C10_1


title: WCM1078 organoids, active compound, 24h, rep2, mRNA

description:
Library name: WCM1078-A947-24h-REP2_mRNA
Column name in RSEM results: 1078-947-24h-REP2


title: WCM1078 organoids, inactive compound, 24h, rep2, eRNA

description: Library name: WCM078_A858_Rep.2


title: Zebrafish Tail Fin, Yap Crispant Injured, biol rep 1

description:
Library name: Sample 10
YapIn1


title: Zebrafish Tail Fin, WT Injured, biol rep 3

description:
Library name: Sample 6
WtIn3

value: Wild type


title: WCM1078 organoids, inactive compound, 48h, rep3, mRNA

description:
Library name: WCM1078-A858-48h-REP3_mRNA
Column name in RSEM results: 1078-858-48h-REP3


title: Zebrafish Tail Fin, WT Injured, biol rep 2

description:
Library name: Sample 5
WtIn2


title: Zebrafish Tail Fin, WT Injured, biol rep 1

description:
Library name: Sample 4
WtIn1


title: WCM1078 organoids, inactive compound, 48h, rep1, mRNA

description:
Library name: WCM1078-A858-48h-REP1_mRNA
Column name in RSEM results: 1078-858-48h-REP1


title: Zebrafish Tail Fin, WT Uninjured, biol rep 3

description:
Library name: Sample 3
WtUn3


title: WCM1078 organoids, inactive compound, 24h, rep3, mRNA

description:
Library name: WCM1078-A858-24h-REP3_mRNA
Column name in RSEM results: 1078-858-24h-REP3


title: WCM1078 organoids, inactive compound, 24h, rep1, mRNA

description:
Library name: WCM1078-A858-24h-REP1_mRNA
Column name in RSEM results: 1078-858-24h-REP1


title: WCM1078 organoids, inactive compound, 48h, rep2, mRNA

description:
Library name: WCM1078-A858-48h-REP2_mRNA
Column name in RSEM results: 1078-858-48h-REP2


title: Zebrafish Tail Fin, WT Uninjured, biol rep 2

description:
Library name: Sample 2
WtUn2


title: WCM1078 organoids, inactive compound, 24h, rep2, mRNA

description:
Library name: WCM1078-A858-24h-REP2_mRNA
Column name in RSEM results: 1078-858-24h-REP2


title: Patient 78, female, 56 years old, healthy, plasma

city: Lodz

first: Urszula

last: Smyczynska

address: 15, Mazowiecka Street

department: Department of Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Lodz

description: Library name: 31230-243

data_processing:
FASTQ files were generated using Illumina bcl2fastq. Sequencing reads were mapped to miRBase in version 22.1 using nf-core/smrnaseq in version 2.3.0. Contamination filtration was switched on with minor modification added to allow for detailed quantification of contaminants. Computational resources were limited to available server capacity, while other parameters were left at default values.
Assembly: miRBase version 22.1
Supplementary files format and content: Processed data are stored in two Excel (xlsx) files. First contains raw counts for all samples as generated by nf-core/smrnaseq pipeline. The second file stores filtered, normalized, and log-transformed counts. miRNAs present in at least 10 counts per million (CPM) in at least 50% of samples in either plasma or serum were kept. After removal of low-expression miRNAs, raw counts of remaining miRNAs were normalized to CPM with respect to sum of their counts and log2-transformed (after adding 0.5 to each value to avoid logarithms of 0), yielding log2(CPM) used in further analysis.

source_name: plasma

extract_protocol:
Total RNA was extracted from serum or plasma.
Libraries were prepared with QIAseq miRNA Library Kit (QIAGEN).

value: plasma

tag: Sex

value: female

value: 56 years old

value: healthy


title: Zebrafish Tail Fin, WT Uninjured, biol rep 1

description:
Library name: Sample 1
WtUn1

value: Zebrafish Tail Fin


title: Patient 77, female, 43 years old, healthy, plasma

description: Library name: 31230-242

value: 43 years old


title: Patient 76, female, 57 years old, healthy, plasma

description: Library name: 31230-241

value: 57 years old


title: Patient 75, female, 60 years old, healthy, plasma

description: Library name: 31230-237

value: 60 years old


title: Zebrafish Tail Fin, Yap Crispant Uninjured, biol rep 2

description:
Library name: Sample 8
YapUn2

value: Uninjured

value: WIK


title: WCM1078 organoids, active compound, 24h, rep1, mRNA

description:
Library name: WCM1078-A947-24h-REP1_mRNA
Column name in RSEM results: 1078-947-24h-REP1


title: RD cells-TAK1 shRNA-1

city: Houston

first: Ashok

last: Kumar

state: Texas

address: 4349 Martin Luther King Blvd.

department: Pharmacological and Pharmaceutical Sciences

institute: University of Houston

description:
Library name: Sample 4
Column name in Raw_counts_All_samples.csv: RD-TAK1_shRNA-1

data_processing:
Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data/Raw Reads) by CASAVA base recognition (Base Calling). To obtain clean reads, the sequencing raw reads were filtered to remove adaptor contamination, constitution of uncertain nucleotides (N>10%), and reads containing more than 50% of low quality nucleotides (base quality<5). STAR software was used to accomplish the mapping and alignment, which precisely and effectively performs positioning junction reads for RNA sequencing data analysis.
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: Raw_counts_All_samples.csv

source_name: RD cells

extract_protocol:
Total RNA was extracted from RD cells using TRIzol reagent (Thermo Fisher Scientific) and RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s protocols.
Library construction was performed using an mRNA-seq pipeline implemented by Novogene Co., Ltd.

tag: cell line

value: RD cells

value: ERMS

value: Transduced with lentiviral particles containing TAK1 shRNA


title: RD cells-TAK1 shRNA-3

description:
Library name: Sample 6
Column name in Raw_counts_All_samples.csv: RD-TAK1_shRNA-3


title: RD cells-TAK1 shRNA-2

description:
Library name: Sample 5
Column name in Raw_counts_All_samples.csv: RD-TAK1_shRNA-2


title: RD cells-Scrambled shRNA-3

description:
Library name: Sample 3
Column name in Raw_counts_All_samples.csv: RD-Scrambled_shRNA-3

value: Transduced with lentiviral particles containing scrambled shRNA


title: Patient 73, female, 39 years old, healthy, plasma

description: Library name: 31230-235

value: 39 years old


title: Patient 72, female, 50 years old, healthy, plasma

description: Library name: 31230-231

value: 50 years old


title: RD cells-Scrambled shRNA-2

description:
Library name: Sample 2
Column name in Raw_counts_All_samples.csv: RD-Scrambled_shRNA-2


title: sh2_2

city: qingdao

first: Wenjie

last: Wei

address: 16 Jiangsu Road, Shinan District

department: Department of Urology

country: China

institute: The Affiliated Hospital of Qingdao University

description:
Library name: sample 8
CALD1_sh2 group, replicate biosample 2

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to DM 1-3 516 R44 (v6.1)  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes TPM for each sample

source_name: cisplatin-resistant xenograft model of human bladder cancer

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


title: Patient 70, female, 45 years old, healthy, plasma

description: Library name: 31230-225

value: 45 years old


title: sh2_1

description:
Library name: sample 7
CALD1_sh2 group, replicate biosample 1

value: cisplatin-resistant xenograft model of human bladder cancer


title: sh1_3

description:
Library name: sample 6
CALD1_sh1 group, replicate biosample 3


title: Patient 68, female, 54 years old, healthy, plasma

description: Library name: 31230-223

value: plasma

value: female

value: 54 years old


title: Patient 66, female, 58 years old, healthy, plasma

description: Library name: 31230-221

value: 58 years old

value: healthy


title: RD cells-Scrambled shRNA-1

description:
Library name: Sample 1
Column name in Raw_counts_All_samples.csv: RD-Scrambled_shRNA-1


title: Patient 67, female, 60 years old, healthy, plasma

description: Library name: 31230-222


title: sh2_3

description:
Library name: sample 9
CALD1_sh2 group, replicate biosample 3


title: scramble_3

description:
Library name: sample 3
CALD1_scramble group, replicate biosample 3


title: sh1_2

description:
Library name: sample 5
CALD1_sh1 group, replicate biosample 2


title: Patient 69, female, 32 years old, healthy, plasma

description: Library name: 31230-224

value: 32 years old


title: Patient 65, female, 28 years old, healthy, plasma

description: Library name: 31230-220

value: 28 years old


title: scramble_2

description:
Library name: sample 2
CALD1_scramble group, replicate biosample 2


title: Patient 64, female, 43 years old, healthy, plasma

description: Library name: 31230-219

value: 43 years old


title: Patient 63, female, 61 years old, healthy, plasma

description: Library name: 31230-217

value: 61 years old


title: scramble_1

description:
Library name: sample 1
CALD1_scramble group, replicate biosample 1


title: BBN9266, AD with infection

city: Exeter

first: Giulia

last: Pegoraro

address: Barrack Road

institute: University of Exeter

description: Library name: BBN9266

data_processing:
The FASTQ files containing the sequenced data underwent QC analysis using FastQC. Subsequently, FastQ Screen was utilized to assess typical contaminants, and fastp was employed for trimming adapters and removing low-quality reads.
The genes in the count matrix underwent expression level filtration using the filterByExpr function in EdgeR, with a minimum count set to 10 and the minimum proportion of samples where a gene needs to be expressed set to 80%. Data were normalized by taking the log2 of the values obtained from the counts per million (CPM) method. Normalization factors were computed based on library sizes using the trimmed mean of the M-values method (TMM) with the calcNormFactors function.
Assembly: GrCh38
Supplementary files format and content: csv file containing raw counts
Supplementary files format and content: csv file containing log2 CPM normalized counts

source_name: Prefrontal cortex

extract_protocol:
Qiagen AllPrep DNA/RNA/miRNA Universal kit
The library preparation was performed using Illumina Stranded Total RNA Prep protocol using 9ng total RNA with samples organised across plates by RIN score, whilst randomising for other variables.

value: Prefrontal cortex

tag: gender

value: M

tag: ad

tag: infection

tag: sequencing plate_number

tag: library size

tag: extraction batch

tag: sample group

value: AD with infection


title: Patient 62, female, 62 years old, healthy, plasma

description: Library name: 31230-216

tag: tissue

value: 62 years old

tag: disease


title: BBN9409, AD no infection

description: Library name: BBN9409

value: F

value: AD no infection


title: Patient 74, female, 50 years old, healthy, plasma

description: Library name: 31230-236

value: 50 years old


title: Patient 61, female, 52 years old, healthy, plasma

description: Library name: 31230-214

value: 52 years old


title: B16F10, Adam12pCKO, endothelial, R3

city: Beijing

first: Qile

last: Guo

state: Beijing

address: Yiheyuan Road

department: BIOPIC

institute: Peking University

data_processing:
Quality control and preprocessing of fastq files were conducted with fastp (v 0.23.4) using default parameters. Reads were mapped to the mouse genome mm10 using STAR aligner (v.2.7.10a) with default settings. FeatureCounts (v. 2.0.6) was then applied to count reads overlapping genes.
Assembly: mm10
Supplementary files format and content: Tab-separated counts file (gzipped format)

organism: Mus musculus

source_name: Lung

extract_protocol:
Lung tissues containing metastases were excised and isolated for dissociation. Tissues were dissociated using gentleMACS C tubes with an enzymatic digestion solution composed of collagenase A (Sigma Aldrich), dispase II (Sigma Aldrich), and DNase I (Roche) in RPMI 1640. The obtained single cells suspensions were filtered on 100-µm cell strainers, incubated with RBC lysis buffer for 10 minutes on ice and resuspended in the appropriate buffer for cell counting and down-stream application. Endothelial cells were enriched as CD45-CD326-CD24-CD31+ live cells via FACS. Fibroblasts were enriched as CD45-CD326-CD24-CD31- via FACS. Total RNA was extracted from the isolated cells using the RNA isolation Total RNA Extraction Reagent (Vazyme). 100 ng of total RNA was used for the construction of sequencing libraries.
RNA sequencing libraries were prepared using TruePrep RNA Library Prep Kit for Illumina (Vazyme)

value: Lung

value: Adam12flox/flox ,PdgfraCreERT2

value: endothelial cell

tag: time

value: Day 18


title: BBN19603, CTR with infection

description: Library name: BBN19603

value: CTR with infection


title: Patient 71, female, 30 years old, healthy, plasma

description: Library name: 31230-228

value: plasma

value: female

value: 30 years old

value: healthy


title: Patient 60, female, 72 years old, healthy, plasma

description: Library name: 31230-213

value: 72 years old


title: Patient 59, female, 56 years old, healthy, plasma

description: Library name: 31230-212

value: 56 years old


title: sh1_1

description:
Library name: sample 4
CALD1_sh1 group, replicate biosample 1

value: cisplatin-resistant xenograft model of human bladder cancer


title: BBN9296, AD no infection

description: Library name: BBN9296

value: Prefrontal cortex


title: Patient 57, female, 54 years old, healthy, plasma

description: Library name: 31230-209

value: 54 years old


title: BBN00126493, CTR with infection

description: Library name: BBN00126493

value: M


title: BBN25058, CTR no infection

description: Library name: BBN25058

value: F

value: CTR no infection


title: BBN24337, CTR with infection

description: Library name: BBN24337


title: Patient 56, female, 33 years old, healthy, plasma

description: Library name: 31230-208

value: 33 years old


title: Patient 58, female, 31 years old, healthy, plasma

description: Library name: 31230-210

value: 31 years old


title: BBN8910, AD with infection

description: Library name: BBN8910

value: AD with infection


title: Patient 55, female, 44 years old, healthy, plasma

description: Library name: 31230-204

value: 44 years old


title: BBN00530812, CTR with infection

description: Library name: BBN00530812

value: CTR with infection


title: BBN5761, CTR with infection

description: Library name: BBN5761


title: Patient 52, female, 50 years old, healthy, plasma

description: Library name: 31230-171

value: plasma

value: 50 years old


title: Patient 53, female, 56 years old, healthy, plasma

description: Library name: 31230-181

value: female


title: Patient 51, female, 32 years old, healthy, plasma

description: Library name: 31230-166

value: 32 years old

value: healthy


title: BBN9329, CTR with infection

description: Library name: BBN9329


title: BBN00332243, CTR with infection

description: Library name: BBN00332243


title: BBN9346, AD with infection

description: Library name: BBN9346


title: Patient 50, female, 53 years old, healthy, plasma

description: Library name: 31230-158

value: 53 years old


title: Patient 48, female, 32 years old, healthy, plasma

description: Library name: 31230-150


title: BBN7413, AD with infection

description: Library name: BBN7413


title: Patient 49, female, 60 years old, healthy, plasma

description: Library name: 31230-156

value: 60 years old


title: Patient 47, female, 56 years old, healthy, plasma

description: Library name: 31230-131

value: 56 years old


title: DOGMAseq, ATAC, Sample 68

city: Philadelphia

first: Vincent

last: Wu

state: PA

address: 402 Johnson Pavilion

department: Microbiology

institute: University of Pennsylvania

description:
Library name: 68___ATAC
ATAC library

library_source: genomic single cell

data_processing:
Raw BCL files from sequencing for ADT/HTO modalities were demultiplexed using bcl2fastq2 (Illumina) or cellranger-arc (10X Genomics) mkfastq. ATAC fastq files were filtered for index hopping using index-hopping-filter (10X Genomics). ATAC and GEX fastq files were then aligned to a chimeric hg38-HIV (HXB2 sequence) genome and count matrices were generated using cellranger-arc count. ADT and HTO fastq files were aligned to the TotalSeqA cocktail catalog using kallisto and bustools which includes barcode correction and counting to create cell by feature matrices. A Snakemake pipeline for kallisto and bustools is found here: https://github.com/betts-lab/scc-proc.
Assembly: hg38 + HXB2
Supplementary files format and content: For ATAC files, standard cellranger-arc count output files for fragments with cell barcodes. For GEX files, standard cellranger-arc count output files for filtered matrix output. For ADT/HTO, matrix/feature/cell files that are outputted from kallisto bustools.

molecule: genomic DNA

source_name: lymph node

extract_protocol:
Buffer and cell preparation were performed as previously published (Mimitou et al.) following the LLL permeabilization protocol. All subsequent cell preparation and antibody staining steps, including centrifugation, were performed at 10°C or on ice unless specified. 5 x 105 - 1 x 106 sorted CD3+, CD8- non-naive T cells were pelleted at 500g for 5 minutes. Cell pellet was resuspended in 22.5uL of Staining Buffer (PBS, 1% BSA, 0.2U/uL RNAse Inhibitor (Roche)) and incubated with 2.5uL of TruStain FcX (Biolegend) for 10 minutes. One vial of TotalSeq-A Human Universal Cocktail, v1.0 (Biolegend) was resuspended according to the Biolegend protocol with Staining Buffer. 25uL of prepared antibody cocktail was added to the cells and incubated for 30 minutes. Cells were washed three times with 1 mL of Staining Buffer at 400g for 5 minutes. After the final wash cells were resuspended in 450uL of PBS.  Following the LLL permeabilization protocol cells were fixed with 0.1% paraformaldehyde for 10 minutes at room temperature and quenched with 0.125M final glycine solution. Fixed cells were washed two times with Staining Buffer at 400g for 5 minutes. Cells were lysed with 100uL of LLL lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 1% BSA, 1 mM DTT, 2 U/μl RNAse inhibitor) for 3 minutes. Cells were washed with 1mL of cold LLL wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 1% BSA, 1 mM DTT, 1 U/μl RNAse inhibitor) and the tube inverted before pelleting the cells at 500g for 5 minutes. Cell pellet was resuspended with 10X Genomics Multiome 1x Nuclei Buffer, and complete cell permeabilization was confirmed using Trypan blue staining. If aggregates were detected in the cell count, cells were filtered using a 40um FlowMi strainer (Sigma) and re-counted. Cells were diluted as needed according to the 10X Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (Version CG000338 RevF).  Samples were processed using the Chromium X platform (10X Genomics).
Single-cell sequencing library preparations for the ATAC and GEX libraries were made following the 10X Genomics User Guide Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (Version CG000338 RevF), with the following modifications as previously published and outlined below. Step 4.1, during the preamplification PCR spike in 1 μL of 0.2 μM ADT/HTO additive primer (ADT additive primer sequence: 5’CCTTGGCACCCGAGAATT*C*C, HTOv2 additive primer sequence:5’GTGACTGGAGTTCAGACGTGTGCTCTTCCGAT*C*T) was added to each individual sample preparation. Step 4.3k, during the SPRI clean-up, elute the pre-amplification sample in 100uL of EB buffer. Use 25uL of pre-amplification sample +15uL of EB (Qiagen) as input for the ATAC library indexing, and use 35uL of pre-amplification sample as input for the cDNA amplification reaction. Use 5uL of pre-amplification sample as input for the ADT and HTO libraries.  ADT/HTO dual index single-cell sequencing library preparation followed the antibody manufacturer’s protocol (BioLegend). Briefly, 5uL of the pre-amplification sample was mixed with 40uL of H20. The antibody-derived oligomers were amplified and indexed with 50 μL of KAPA HiFi HotStart ReadyMix (KAPA Biosystems) and 5 μL of forward/reverse indexing primers.  Post-amplification, ADT/HTO libraries were purified with 120 μL SPRIselect (Beckman) cleanup and eluted with 30 μL of EB buffer. All final libraries were quantified using a Qubit dsDNA HS Assay Kit (Invitrogen) and analyzed using a High Sensitivity D1000 DNA tape (Agilent) on a TapeStation D4200 (Agilent).

value: lymph node

value: sorted cd3+ cd8- non-naive cells

tag: disease state

value: ART-treated


title: DOGMAseq, ATAC, Sample 69

description:
Library name: 69___ATAC
ATAC library


title: Patient 46, female, 49 years old, healthy, plasma

description: Library name: 31230-125

value: 49 years old


title: DOGMAseq, ATAC, Sample 67

description:
Library name: 67___ATAC
ATAC library


title: Patient 54, female, 37 years old, healthy, plasma

description: Library name: 31230-183

value: 37 years old


title: BBN3378, CTR no infection

description: Library name: BBN3378

value: Prefrontal cortex

value: F

value: CTR no infection


title: Patient 45, female, 57 years old, breast cancer, plasma

description: Library name: 31230-124

value: 57 years old

value: breast cancer


title: DOGMAseq, ATAC, Sample 66

description:
Library name: 66___ATAC
ATAC library


title: Patient 43, female, 62 years old, healthy, plasma

description: Library name: 31230-120

value: plasma

value: 62 years old


title: Patient 42, female, 66 years old, ovarian cancer, plasma

description: Library name: 31230-111

value: female

value: 66 years old

value: ovarian cancer


title: DOGMAseq, ATAC, Sample 64

description:
Library name: 64___ATAC
ATAC library


title: DOGMAseq, ATAC, Sample 63

description:
Library name: 63___ATAC
ATAC library


title: Patient 41, female, 63 years old, ovarian cancer, plasma

description: Library name: 31230-109

value: 63 years old


title: DOGMAseq, ATAC, Sample 65

description:
Library name: 65___ATAC
ATAC library


title: DOGMAseq, ATAC, Sample 62

description:
Library name: 62___ATAC
ATAC library


title: DOGMAseq, ATAC, Sample 61

description:
Library name: 61___ATAC
ATAC library


title: DOGMAseq, ATAC, Sample 60

description:
Library name: 60___ATAC
ATAC library


title: Patient 38, female, 36 years old, healthy, plasma

description: Library name: 31230-092

value: 36 years old

value: healthy


title: DOGMAseq, ATAC, Sample 59

description:
Library name: 59___ATAC
ATAC library

value: lymph node

value: sorted cd3+ cd8- non-naive cells


title: DOGMAseq, ATAC, Sample 58

description:
Library name: 58___ATAC
ATAC library

value: ART-treated


title: Patient 36, female, 76 years old, healthy, plasma

description: Library name: 31230-090

value: 76 years old


title: Patient 35, female, 62 years old, healthy, plasma

description: Library name: 31230-088


title: DOGMAseq, ATAC, Sample 57

description:
Library name: 57___ATAC
ATAC library


title: Patient 34, female, 55 years old, healthy, plasma

description: Library name: 31230-084

value: 55 years old


title: DOGMAseq, ATAC, Sample 55

description:
Library name: 55___ATAC
ATAC library


title: Patient 33, female, 66 years old, healthy, plasma

description: Library name: 31230-081


title: DOGMAseq, ATAC, Sample 54

description:
Library name: 54___ATAC
ATAC library


title: Patient 44, female, 76 years old, healthy, plasma

description: Library name: 31230-123


title: Patient 32, female, 50 years old, healthy, plasma

description: Library name: 31230-079

value: 50 years old


title: DOGMAseq, ATAC, Sample 80

description:
Library name: 80___ATAC
ATAC library


title: DOGMAseq, ATAC, Sample 53

description:
Library name: 53___ATAC
ATAC library


title: Patient 31, female, 73 years old, healthy, plasma

description: Library name: 31230-078

value: 73 years old


title: DOGMAseq, ATAC, Sample 52

description:
Library name: 52___ATAC
ATAC library


title: Patient 30, female, 63 years old, healthy, plasma

description: Library name: 31230-077


title: DOGMAseq, ATAC, Sample 51

description:
Library name: 51___ATAC
ATAC library


title: DOGMAseq, ATAC, Sample 50

description:
Library name: 50___ATAC
ATAC library


title: Patient 28, female, 81 years old, healthy, plasma

description: Library name: 31230-074

value: 81 years old


title: Patient 40, female, 37 years old, ovarian cancer, plasma

description: Library name: 31230-107

value: 37 years old


title: Patient 27, female, 73 years old, healthy, plasma

description: Library name: 31230-073

value: plasma


title: DOGMAseq, ATAC, Sample 49

description:
Library name: 49___ATAC
ATAC library


title: Patient 39, female, 43 years old, healthy, plasma

description: Library name: 31230-105

value: 43 years old


title: Patient 26, female, 50 years old, healthy, plasma

description: Library name: 31230-070

value: female


title: Patient 25, female, 43 years old, healthy, plasma

description: Library name: 31230-069


title: DOGMAseq, ATAC, Sample 47

description:
Library name: 47___ATAC
ATAC library


title: Patient 37, female, 52 years old, healthy, plasma

description: Library name: 31230-091

value: 52 years old


title: DOGMAseq, ATAC, Sample 46

description:
Library name: 46___ATAC
ATAC library


title: Patient 24, female, 42 years old, healthy, plasma

description: Library name: 31230-068

value: 42 years old


title: DOGMAseq, ATAC, Sample 56

description:
Library name: 56___ATAC
ATAC library


title: DOGMAseq, ATAC, Sample 45

description:
Library name: 45___ATAC
ATAC library


title: PBMCs, 3 timepoint samples, Adenovirus infection, BCR

city: La Jolla

first: Gio

state: CA

address: 3147 Biomedical Sciences Wy

institute: University of California San Diego

description:
Library name: RIM01_BCR
BD Rhapsody TCR

library_source: transcriptomic single cell

data_processing:
WTA fastq files were trimmed using the Cutadapt app v1.18 trim function. Parameters were set as follows: -e 0.1 -n 5 -O 20, --quality base=33, the adapter file for argument -a was set to a fasta file with 10 repeating base pairs of each nucleotide, R1 and R2 reads were trimmed separately --length 51 and --length 71 respectively in order to mimic the BD recommended run configuration.
Sample tag, TCR/BCR, and trimmed WTA fastq files were input to the app BD Rhapsody™ Sequence Analysis Pipeline v2.2.1. The reference input was set to the manufacturer-provided file RhapRef_Human_WTA_2023-02.tar.gz made from hg38 and GENCODE v43. App settings were as follows: basic cell calling, Sample Tags Version set to “Single-Cell Multiplex Kit – Human", VDJ set to "Human VDJ - BCR and TCR".
Assembly: hg38 and GENCODE v43
Supplementary files format and content: Seurat object RDS file and H5MU file
Supplementary files format and content: Tab and comma-separated values and matrix files

source_name: PBMC

extract_protocol:
PBMC isolation from fresh whole blood using SepMate™ tubes and STEMCELL Technologies Lymphoprep™ protocol. PBMCs were washed twice using PBS with 2% FBS then counted Eosin stain for viability. Cells were then centrifuged at 400 g for 5 minutes and resuspended in FBS with 10% DMSO for cryopreservation. For BD Rhapsody proccessing, cryopreserved PBMCs from the three timepoints were thawed simultaneously for loading onto a single-lane BD Rhapsody Cartridge and cell capture using Enhanced Cell Capture Beads V1 (BD Biosciences, cat# 664887). Cells were thawed in a 37°C water bath, washed in DMEM with 2% FBS Cell preparation, loading, lysis, and Capture Bead retreival were conducted as per manufacturer’s protocol. All centrifugation steps were conducted at 400 x g for 5 minutes at 4°C.
Library preparation was performed in accordance with BD Rhapsody Human TCR/BCR + WTA + Sample Tag Library Preparation Protocol. AMPure® XP magnetic beads were used for all PCR cleanups (Beckman Coulter, cat# A63880) and libraries were dual indexed with Illumina TruSeq and Nextera primers. Quality check of the dual indexed libraries was done using the Invitrogen Qubit™ dsDNA HS Kit and the Agilent High Sensitivity D5000 Tapestation kit. Libraries were pooled and sequenced on the Illumina NovaSeq X 25B flow cell with run configuration paired end 150 bp reads and loading concentration 100mM

value: 10 years old

value: PBMC

value: Adenovirus infection and reactive infectious mucocutaneous eruptions, 3 timepoints:active infection, post treatment, recovered state

tag: treatment

value: corticosteroids, IVIg, Etanercept


title: Patient 23, female, 79 years old, healthy, plasma

description: Library name: 31230-067

value: 79 years old

value: healthy


title: DOGMAseq, ATAC, Sample 44

description:
Library name: 44___ATAC
ATAC library

value: lymph node

value: sorted cd3+ cd8- non-naive cells

value: ART-treated


title: PBMCs, 3 timepoint samples, Adenovirus infection,TCR

description:
Library name: RIM01_TCR
BD Rhapsody TCR


title: Patient 22, female, 66 years old, healthy, plasma

description: Library name: 31230-066

value: 66 years old


title: PAX5-2

city: hangzhou

first: ailing

last: wu

address: yuhangtang street

institute: hangzhou normal university

description: Library name: Sample4

library_source: genomic

data_processing:
bigWig files were generated by deepTools.ChIP-seq tracks were visualized in IGV.
Assembly: GRCh38
Supplementary files format and content: bigWig

extract_protocol:
Genomic DNA was isolated using KIT (TIANGEN) according to the manufacturer’s instructions.
The ChIP-Seq library preparation was proceeded as follows: (1) The DNA fragments were end-repaired and A-tailed. (2) The DNA fragments with A tail were ligated with sequencing adaptors. (3) The final DNA library was obtained after size selection and PCR amplification. Libraries were analyzed for size distribution by Agilent 5400 system（Agilent, USA）and quantified by QPCR (1.5 nM). The qualified libraries were pooled and sequenced on Illumina platforms with PE150, according to the effective library concentration and data amount required.

value: human small cell lung cancer cell

value: WT


title: PBMCs, 3 timepoint samples, Adenovirus infection, sample multiplex

description:
Library name: RIM01_ST
BD Rhapsody SMK

library_source: other

molecule: protein


title: PBMCs, 3 timepoint samples, Adenovirus infection, RNA whole transcriptome

description:
Library name: RIM01_WTA
BD Rhapsody WTA


title: PAX5-1

description: Library name: Sample3


title: DOGMAseq, ATAC, Sample 43

description:
Library name: 43___ATAC
ATAC library


title: Patient 21, female, 39 years old, healthy, plasma

description: Library name: 31230-065

value: plasma

value: 39 years old


title: DOGMAseq, ATAC, Sample 42

description:
Library name: 42___ATAC
ATAC library


title: Input-2

description: Library name: Sample2


title: Patient 20, female, 55 years old, healthy, plasma

description: Library name: 31230-062

value: female

value: 55 years old


title: Patient 29, female, 35 years old, healthy, plasma

description: Library name: 31230-076

value: 35 years old


title: DOGMAseq, ATAC, Sample 48

description:
Library name: 48___ATAC
ATAC library


title: VEGF2

description: Library name: Sample4

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Reference genome and gene model annotation files were downloaded from genome website. Use HISAT2 (2.2.1) to build the index of the reference genome, and use HISAT2 to align paired-end clean reads to3 the reference genome.
featureCounts (2.0.6) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
For DESeq2 with biological replicates: Differential expression analysis for two conditions/groups was performed using the DESeq2 R package(1.42.0).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

extract_protocol:
Total RNA was isolated using TRIzol (TIANGEN) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using Fast RNA-seq Lib Prep Kit V2 following manufacturer's protocols.

value: human lung adenocarcinoma cell

tag: genotype

value: VEGF treatment


title: Patient 19, female, 28 years old, healthy, plasma

description: Library name: 31230-061

tag: age

value: 28 years old


title: VEGF1

description: Library name: Sample3

tag: cell type


title: Input-1

description: Library name: Sample1


title: DOGMAseq, ATAC, Sample 40

description:
Library name: 40___ATAC
ATAC library


title: DOGMAseq, ATAC, Sample 39

description:
Library name: 39___ATAC
ATAC library


title: CT1

description: Library name: Sample1

value: vehicle control


title: Patient 18, female, 53 years old, healthy, plasma

description: Library name: 31230-060

tag: Sex

value: 53 years old


title: DOGMAseq, ATAC, Sample 38

description:
Library name: 38___ATAC
ATAC library


title: Patient 17, female, 68 years old, healthy, plasma

description: Library name: 31230-056

value: 68 years old

value: healthy


title: Patient 16, female, 49 years old, healthy, plasma

description: Library name: 31230-028

value: 49 years old


title: Eye chart array messenger library for 2D reconstruction

city: Seattle

first: Sanjay

last: Srivatsan

state: WA

address: 1100 Fairview Ave N. Mailstop A2-119

institute: Fred Hutchinson Cancer Center

description: Library name: eye_chart_messengers

data_processing:
custom processing pipeline
Supplementary files format and content: csv files of sparse interaction matrices, as well as the index to barcode string mapping dictionaries.

molecule: other

organism: synthetic construct

source_name: none (synthetic)

growth_protocol: synthetic hydrogel barcoded beads

extract_protocol:
SCOPE reactions were performed on a 2D bead array or 3D bead-embedded gel matrix. Molecules with barcode-barcode associations were collected, PCR amplified, and indexed for sequencing.
SCOPE libraries are indexed with TruseqP5 and TruseqP7.

tag: cell line

value: none (synthetic)


title: Bead-embedded gel star messenger library for 3D reconstruction

description: Library name: 3D_star


title: DOGMAseq, ATAC, Sample 37

description:
Library name: 37___ATAC
ATAC library

value: lymph node

value: sorted cd3+ cd8- non-naive cells

value: ART-treated


title: Bead-embedded gel letter E messenger library for 3D reconstruction

description: Library name: 3D_letter_E


title: Bead-embedded gel butterfly messenger library for 3D reconstruction

description: Library name: 3D_butterfly


title: Bead-embedded gel teddy bear messenger library for 3D reconstruction

description: Library name: 3D_bear


title: DOGMAseq, ATAC, Sample 36

description:
Library name: 36___ATAC
ATAC library


title: Eye chart array decoder library of the printed image

description: Library name: eye_chart_decoders


title: Patient 15, female, 52 years old, healthy, plasma

description: Library name: 31230-027

value: plasma

value: 52 years old


title: Patient 14, female, 60 years old, healthy, plasma

description: Library name: 31230-026

value: female

value: 60 years old


title: DOGMAseq, ATAC, Sample 35

description:
Library name: 35___ATAC
ATAC library


title: Asymmetric bead array messenger library for 2D reconstruction

description: Library name: asymmetric_messengers


title: DOGMAseq, ATAC, Sample 41

description:
Library name: 41___ATAC
ATAC library


title: Circular bead array messenger library for 2D reconstruction

description: Library name: circular_messengers


title: DOGMAseq, ATAC, Sample 34

description:
Library name: 34___ATAC
ATAC library


title: Patient 12, female, 60 years old, healthy, plasma

description: Library name: 31230-023


title: CT2

description: Library name: Sample2

value: WT


title: Patient 13, female, 52 years old, healthy, plasma

description: Library name: 31230-025


title: Circular bead array messenger library for 2D reconstruction (more deeply sequenced)

description: Library name: circular_messengers_2


title: SILP SPF isotype M rep1

city: San Diego

first: Eduardo

last: Ansaldo

address: 15550 Torrey Pines Rd

department: IMM

institute: Scripps Research

description: Library name: SILP_SPF_isotype_M_rep1

data_processing:
The initial processing of the expression data involved generating fastq files and count matrices using Cell Ranger v7.1.0 [@zheng2017] (10X Genomics, Pleasanton, CA) that was run with the “Include introns=True” option and the mm10-2020-A transcriptome reference. The TCR data was processed with Cell Ranger v7.1.0 using a VDJ reference based on the IGMT database: The IGMT reference was generated with Cell Ranger v7.1.0 using the 'fetch-imgt' and 'cellranger mkvdjref' functions. Processing of the expression data was performed with the 'cellranger multi' and 'cellranger aggr' functions. After processing and aggregation, the estimated number of cells and mean reads per cell for each library were as follows: 56451 estimated number of cells, 24386 mean reads per cell (from 4 GEX libraries), 609 Median hashtag UMIs per Cell (across 4 HTO libraries), 43091 cells with a productive TRA and/or TRB V-J spanning sequence, 34070 of which contain both a productive V-J spanning TRA and TRB pair (from 4 VDJ libraries). The overall sequencing quality was high in the 4 mRNA libraries: \>95% of bases in the barcode and UMI regions had Q30 (99.99% inferred base call accuracy) quality score or above, whereas \>94% of bases in the RNA reads had Q30 or above. Furthermore, across the 4 GEX libraries the median gene count per cell range was 1835-2018, the sequencing saturation ranged between 68-78%, and 73-76% of the reads mapped confidently to the transcriptome. Across the 4 TCR libraries, the mean used reads per cell was 1107-5279 (average 3201). Across the 4 hashtag (HTO) libraries the mean antibody reads usable per cell was 1165-1486 (average 1319).
The downstream analysis of the expression data was performed in R 4.4.2, the Cell Ranger aggregation output (filtered_feature_bc_matrix directory) was loaded into Seurat version 5.1.0 [@hao2021] using the CreateSeuratObject function with min.cells=3. For filtering out low-quality cells, we established maximum thresholds for gene and UMI counts (nCount_RNA \> 100, nFeature_RNA \> 500), and a maximum threshold for percentage mitochondrial content (percent.mt \< 5) based on visual inspection of the corresponding metric distributions across all cells. Log-normalization (LogNormalize) of the RNA count data and centered log-ratio transformation (CLR) of the HTO count data were carried out using the NormalizeData function. For HTO demultiplexing cells into individual mice and removing any doublets, HTODemux was run with a positive quantile = 0.99 and only cells identified as Singlets were kept. The top 2000 variable features were determined with the VariableFeatures function, expression data was scaled with ScaleData, and dimensionality reduction was performed with the RunPCA function on the variable features, followed by determining the dimensionality of the dataset on an elbow plot (ElbowPlot function), which was determined to be 70. Subsequently, FindNeighbors, FindClusters, and RunUMAP were run on 70 dimensions and a range of resolutions to determine the optimal resolution that captures biological diversity in the dataset, which was determined to be 0.5, resulting in 26 clusters. The clusters identified by the FindClusters function of Seurat (default Louvain clustering setting and 0.5 resolution) were annotated using cell type specific markers, cluster specific differentially expressed genes, and with the aid of SingleR [@aran2019], using the ImmGen database reference. Contaminating clusters comprised of B cells and epithelial cells were removed. On the second iteration of clustering and removal of contaminating cell types, Tregs were removed so that only CD4^+^T-bet^+^Foxp3^-^ T cells remained. On the remaining cells FindVariableFeatures (nFeatures=2000) was run, data was scaled with ScaleData, RunPCA was run (npcs=100) and the top 45 dimensions were used to run FindNeighbors, FindClusters (with a range of resolutions and a final chosen resolution of 0.15), and RunUMAP.
Assembly: mm10
Supplementary files format and content: The filtered_feature_bc_matrix.h5 file contains the gene and HTO expression output of the cellranger (10x Genomics) multi and aggr commands. Please see the supplementary files for the HTO - sample correspondence and aggregation parameters.
Supplementary files format and content: The filtered_contig_annotations.csv file contains the gene and HTO expression output of the cellranger (10x Genomics) multi and aggr commands. Please see the supplementary files for the HTO - sample correspondence and aggregation parameters.
Supplementary files format and content: The .rds file contains the final Seurat object, product of the analysis described in the processing step section.

source_name: Small Intestine Lamina Propria

extract_protocol:
Serum-free media was prepared with RPMI containing 20 mM HEPES,  L-Glutamine, 100U/mL Penicillin, 100ug/mL Streptomycin sulfate, 50 µM β-mercaptoethanol, 1mM sodium pyruvate, 1mM non-essential amino acids.3% media was prepared with RPMI containing 3% FBS, 20 mM HEPES,  L-Glutamine, 100U/mL Penicillin, 100ug/mL Streptomycin sulfate, 50 µM β-mercaptoethanol, 1mM sodium pyruvate, 1mM non-essential amino acids. Mice were sacrificed by CO2 inhalation. For cell extraction from small intestinal lamina propria, Peyer’s patches and mesenteric adipose tissue were removed. For each intestine, tissues were cut open longitudinally, washed several times in cold PBS to remove feces, and further cut into 1- to 2-cm segments before being placed in 50 ml beakers with a stir bar. Tissue pieces were incubated in 10 ml per intestine of 3% RPMI with 5 mM EDTA, and 0.145 mg/ml DTT for 20 min at 37° C with stirring ~400 rpm. To separate the lamina propria (LP) and intestinal epithelial lymphocyte (IEL) layer, each beaker’s contents were strained through a sterile fine-meshed stainless-steel sieve into a corresponding 500 ml beaker containing 10 ml of 3% RPMI media held on ice. After straining, tissue pieces from each intestine were transferred to a 50 ml conical tube containing 10 ml of serum-free RPMI with 2 mM EDTA. Each tube was shaken vigorously for 30 seconds and then strained through the respective sieve into the corresponding beaker. The shake and strain processes were repeated two more times. To isolate the IEL compartment, strained contents were filtered through 70 µm cell strainers atop 50 ml conical tubes on ice. Cell suspensions were centrifuged for 5 minutes at 450 g, 4° C. After gently discarding the supernatant, cell pellets were resuspended in 4 ml of a 30% Percoll gradient and centrifuged for 5 minutes at 1800 rpm, 4° C. After removing the supernatant with a pipette, cells were resuspended in 1 ml of 3% RPMI media. To isolate the LP compartment, small intestine pieces recovered from the shake and strain steps were placed into a 50 ml beaker and finely minced with scissors. Tissues were then incubated with 10 ml of serum-free media with 0.1 mg/ml Liberase TL and 5 mg/ml DNAse I for 25 min at 37° C with stirring ~400 rpm. After the incubation, 5 ml of 3% RPMI was added to each beaker. The contents of each beaker were pipetted through 70 µm cell strainers atop 50 ml conical tubes on ice. Each beaker and strainer was rinsed with an additional 10 ml of 3% RPMI. Cell suspensions were centrifuged for 5 minutes at 450 g, 4° C. After gently discarding the supernatant, cell pellets were resuspended in 4 ml of a 30% Percoll gradient and centrifuged for 5 minutes at 1800 rpm, 4° C. After removing the supernatant with a pipette, cells were resuspended in 1 ml of 3% RPMI media.
SILP CD4^+^T-bet^+^ T cells (Live, CD45+CD90.2+, TCRb+, CD4+, T-bet-ZsGreen+) from GF T-bet-ZsGreen mice raised on casein, amino acid, or regular chow diet were sorted from samples labeled with TotalSeqC hashtags antibodies (Biolegend) using a Sony MA900 sorter. Sorted cells were pooled during sorting and 40000 cells per lane (total of 4 lanes) were loaded on a Chromium Single Cell Controller (10X Genomics) to encapsulate the cells into droplets. The gene expression (GEX), hashtag oligonucleotide (HTO) and VDJ (TCR) sequencing libraries were prepared using Chromium Single Cell 5’ v2 reagent kits following the manufacturer’s instructions, and sequenced on an Illumina Nextseq1000 platform (NextSeq 1000/2000 P2 reagents)

value: Small Intestine Lamina Propria

value: T-bet-ZsGreen

value: isotype


title: SILP SPF isotype M rep3

description: Library name: SILP_SPF_isotype_M_rep3


title: DOGMAseq, ATAC, Sample 33

description:
Library name: 33___ATAC
ATAC library


title: SILP SPF isotype F rep3

description: Library name: SILP_SPF_isotype_F_rep3


title: SILP SPF isotype M rep2

description: Library name: SILP_SPF_isotype_M_rep2


title: Patient 11, female, 53 years old, healthy, plasma

description: Library name: 31230-022


title: DOGMAseq, ATAC, Sample 32

description:
Library name: 32___ATAC
ATAC library


title: SILP SPF isotype F rep1

description: Library name: SILP_SPF_isotype_F_rep1


title: Patient 10, female, 42 years old, healthy, plasma

description: Library name: 31230-021

value: 42 years old


title: SILP SPF aCD3 M rep3

description: Library name: SILP_SPF_aCD3_M_rep3


title: DOGMAseq, ATAC, Sample 31

description:
Library name: 31___ATAC
ATAC library


title: SILP SPF aCD3 M rep2

description: Library name: SILP_SPF_aCD3_M_rep2


title: Patient 9, female, 27 years old, healthy, plasma

description: Library name: 31230-020

value: 27 years old


title: SILP SPF aCD3 M rep1

description: Library name: SILP_SPF_aCD3_M_rep1


title: DOGMAseq, ATAC, Sample 30

description:
Library name: 30___ATAC
ATAC library


title: SILP SPF aCD3 F rep3

description: Library name: SILP_SPF_aCD3_F_rep3


title: Patient 8, female, 65 years old, healthy, plasma

description: Library name: 31230-019

value: 65 years old


title: SILP SPF aCD3 F rep2

description: Library name: SILP_SPF_aCD3_F_rep2


title: SILP SPF aCD3 F rep1

description: Library name: SILP_SPF_aCD3_F_rep1


title: SILP GF isotype M rep5

description: Library name: SILP_GF_isotype_M_rep5


title: Patient 7, female, 42 years old, healthy, plasma

description: Library name: 31230-018

value: healthy


title: DOGMAseq, ATAC, Sample 28

description:
Library name: 28___ATAC
ATAC library


title: SILP GF isotype M rep4

description: Library name: SILP_GF_isotype_M_rep4


title: Patient 6, female, 63 years old, healthy, plasma

description: Library name: 31230-017

value: 63 years old


title: SILP GF isotype M rep2

description: Library name: SILP_GF_isotype_M_rep2


title: DOGMAseq, ATAC, Sample 27

description:
Library name: 27___ATAC
ATAC library


title: SILP GF isotype M rep1

description: Library name: SILP_GF_isotype_M_rep1


title: SILP GF isotype F rep5

description: Library name: SILP_GF_isotype_F_rep5


title: Patient 5, female, 42 years old, healthy, plasma

description: Library name: 31230-016


title: Patient 4, female, 57 years old, healthy, plasma

description: Library name: 31230-014

value: 57 years old


title: SILP GF isotype M rep3

description: Library name: SILP_GF_isotype_M_rep3


title: SILP SPF isotype F rep2

description: Library name: SILP_SPF_isotype_F_rep2


title: DOGMAseq, ATAC, Sample 26

description:
Library name: 26___ATAC
ATAC library

value: lymph node


title: SILP GF isotype F rep4

description: Library name: SILP_GF_isotype_F_rep4


title: DOGMAseq, ATAC, Sample 25

description:
Library name: 25___ATAC
ATAC library

value: sorted cd3+ cd8- non-naive cells


title: Patient 3, female, 61 years old, healthy, plasma

description: Library name: 31230-004

value: 61 years old


title: SILP GF isotype F rep3

description: Library name: SILP_GF_isotype_F_rep3


title: SILP GF isotype F rep2

description: Library name: SILP_GF_isotype_F_rep2


title: DOGMAseq, ATAC, Sample 24

description:
Library name: 24___ATAC
ATAC library

value: viremic


title: SILP GF isotype F rep1

description: Library name: SILP_GF_isotype_F_rep1


title: Patient 2, female, 64 years old, healthy, plasma

description: Library name: 31230-002

value: plasma

value: 64 years old


title: DOGMAseq, ATAC, Sample 23

description:
Library name: 23___ATAC
ATAC library


title: SILP GF aCD3 M rep4

description: Library name: SILP_GF_aCD3_M_rep4


title: SILP GF aCD3 M rep5

description: Library name: SILP_GF_aCD3_M_rep5


title: DOGMAseq, ATAC, Sample 29

description:
Library name: 29___ATAC
ATAC library

value: ART-treated


title: Patient 1, female, 69 years old, healthy, plasma

description: Library name: 31230-001

value: female

value: 69 years old


title: SILP GF aCD3 M rep3

description: Library name: SILP_GF_aCD3_M_rep3

value: Small Intestine Lamina Propria

value: T-bet-ZsGreen


title: Patient 94, healthy, female, 50 years old

description: Library name: 31179-200

data_processing:
FASTQ files were generated using Illumina bcl2fastq. Sequencing reads were mapped to miRBase in version 22.1 using nf-core/smrnaseq in version 2.2.4. Computational resources were limited to available server capacity, while other parameters were left at default values.
Assembly: miRBase version 22.1
Supplementary files format and content: Processed data are stored in two Excel (xlsx) files. First contains raw counts for all samples as generated by nf-core/smrnaseq pipeline. The second file stores filtered, normalized, and log-transformed counts. miRNAs present in at least 10 counts per million (CPM) in at least 50% of samples in either plasma or serum were kept. After removal of low-expression miRNAs, raw counts of remaining miRNAs were normalized to CPM with respect to sum of their counts and log2-transformed (after adding 0.5 to each value to avoid logarithms of 0), yielding log2(CPM) used in further analysis.

source_name: Serum

value: Serum

value: BRCA wild-type


title: SILP GF aCD3 M rep2

description: Library name: SILP_GF_aCD3_M_rep2


title: SILP GF aCD3 M rep1

description: Library name: SILP_GF_aCD3_M_rep1


title: SILP GF aCD3 F rep1

description: Library name: SILP_GF_aCD3_F_rep1


title: DOGMAseq, ATAC, Sample 21

description:
Library name: 21___ATAC
ATAC library


title: Patient 93, healthy, female, 41 years old

description: Library name: 31179-195

value: BRCA mutated


title: scRNAseq VDJ 10x Lane 3

description:
Library name: VDJ 10x Lane 3
10x Genomics lane, biological replicates hashtagged and pooled.


title: DOGMAseq, ATAC, Sample 20

description:
Library name: 20___ATAC
ATAC library


title: scRNAseq VDJ 10x Lane 2

description:
Library name: VDJ 10x Lane 2
10x Genomics lane, biological replicates hashtagged and pooled.


title: DOGMAseq, ATAC, Sample 22

description:
Library name: 22___ATAC
ATAC library


title: DOGMAseq, ATAC, Sample 19

description:
Library name: 19___ATAC
ATAC library


title: Patient 91, healthy, female, 39 years old

description: Library name: 31179-192


title: Patient 92, healthy, female, 45 years old

description: Library name: 31179-194


title: scRNAseq HTO 10x Lane 4

description:
Library name: HTO 10x Lane 4
10x Genomics lane, biological replicates hashtagged and pooled.


title: DOGMAseq, ATAC, Sample 18

description:
Library name: 18___ATAC
ATAC library


title: scRNAseq HTO 10x Lane 3

description:
Library name: HTO 10x Lane 3
10x Genomics lane, biological replicates hashtagged and pooled.


title: scRNAseq HTO 10x Lane 1

description:
Library name: HTO 10x Lane 1
10x Genomics lane, biological replicates hashtagged and pooled.


title: DOGMAseq, ATAC, Sample 17

description:
Library name: 17___ATAC
ATAC library


title: scRNAseq VDJ 10x Lane 1

description:
Library name: VDJ 10x Lane 1
10x Genomics lane, biological replicates hashtagged and pooled.


title: scRNAseq HTO 10x Lane 2

description:
Library name: HTO 10x Lane 2
10x Genomics lane, biological replicates hashtagged and pooled.


title: Patient 89, healthy, female, 45 years old

description: Library name: 31179-189


title: DOGMAseq, ATAC, Sample 16

description:
Library name: 16___ATAC
ATAC library


title: scRNAseq GEX 10x Lane 3

description:
Library name: GEX 10x Lane 3
10x Genomics lane, biological replicates hashtagged and pooled.


title: Patient 88, healthy, female, 49 years old

description: Library name: 31179-187


title: scRNAseq GEX 10x Lane 4

description:
Library name: GEX 10x Lane 4
10x Genomics lane, biological replicates hashtagged and pooled.


title: scRNAseq GEX 10x Lane 2

description:
Library name: GEX 10x Lane 2
10x Genomics lane, biological replicates hashtagged and pooled.


title: scRNAseq GEX 10x Lane 1

description:
Library name: GEX 10x Lane 1
10x Genomics lane, biological replicates hashtagged and pooled.


title: DOGMAseq, ATAC, Sample 15

description:
Library name: 15___ATAC
ATAC library


title: scRNAseq VDJ 10x Lane 4

description:
Library name: VDJ 10x Lane 4
10x Genomics lane, biological replicates hashtagged and pooled.


title: scRNAseq VDJ 10x Lane 4

data_processing:
The initial processing of the expression data involved generating fastq files and count matrices using Cell Ranger v7.1.0 [@zheng2017] (10X Genomics, Pleasanton, CA) that was run with the “Include introns=True” option and the mm10-2020-A transcriptome reference. The TCR data was processed with Cell Ranger v7.1.0 using a VDJ reference based on the IGMT database: The IGMT reference was generated with Cell Ranger v7.1.0 using the 'fetch-imgt' and 'cellranger mkvdjref' functions. Processing of the expression data was performed with the 'cellranger multi' and 'cellranger aggr' functions. After processing and aggregation, the estimated number of cells and mean reads per cell for each library were as follows: 74799 estimated number of cells, 20476 mean reads per cell (from 4 GEX libraries), 1261 Median hashtag UMIs per Cell (across 4 HTO libraries), 48717 cells with a productive TRA and/or TRB V-J spanning sequence, 38824 of which contain both a productive V-J spanning TRA and TRB pair (from 4 VDJ libraries). The overall sequencing quality was high in the 4 mRNA libraries: 68-97% of bases in the barcode and UMI regions had Q30 (99.99% inferred base call accuracy, average 92%) quality score or above, whereas 68-95% (average 90) of bases in the RNA reads had Q30 or above. Furthermore, across the 4 GEX libraries the median gene count per cell range was 1774-1963, the sequencing saturation ranged between 48-53%, and 76-79% of the reads mapped confidently to the transcriptome. Across the 4 TCR libraries, the mean used reads per cell was 1306-4043 (average 2112). Across the 4 hashtag (HTO) libraries the mean antibody reads usable per cell was 2532-3912 (average 2960).
The downstream analysis of the expression data was performed in R 4.4.2, the Cell Ranger aggregation output (filtered_feature_bc_matrix directory) was loaded into Seurat version 5.1.0 [@hao2021] using the CreateSeuratObject function with min.cells=3. For filtering out low-quality cells, we established maximum thresholds for gene and UMI counts (nCount_RNA \> 1200, nFeature_RNA \> 500), and a maximum threshold for percentage mitochondrial content (percent.mt \< 5) based on visual inspection of the corresponding metric distributions across all cells. Log-normalization (LogNormalize) of the RNA count data and centered log-ratio transformation (CLR) of the HTO count data were carried out using the NormalizeData function. For HTO demultiplexing cells into individual mice and removing any doublets, HTODemux was run with a positive quantile = 0.99 and only cells identified as Singlets were kept. The top 2000 variable features were determined with the VariableFeatures function, expression data was scaled with ScaleData, and dimensionality reduction was performed with the RunPCA function on the variable features, followed by determining the dimensionality of the dataset on an elbow plot (ElbowPlot function), which was determined to be 45. Subsequently, FindNeighbors, FindClusters, and RunUMAP were run on 45 dimensions and a range of resolutions to determine the optimal resolution that captures biological diversity in the dataset, which was determined to be 0.25, resulting in 26 clusters. The clusters identified by the FindClusters function of Seurat (default Louvain clustering setting and 0.25 resolution) were annotated using cell type specific markers, cluster specific differentially expressed genes, and with the aid of SingleR [@aran2019], using the ImmGen database reference. Contaminating clusters comprised of B cells, fibroblasts, and epithelial cells were removed. On the remaining cells FindVariableFeatures (nFeatures=2000) was run, data was scaled with ScaleData, RunPCA was run (npcs=100) and the top 40 dimensions were used to run FindNeighbors, FindClusters (with a range of resolutions and a final chosen resolution of 0.4), and RunUMAP. The resulting 19 clusters were annotated using cell type specific markers, cluster specific differentially expressed genes, and with the aid of SingleR [@aran2019], using the ImmGen database reference.
Assembly: mm10
Supplementary files format and content: The filtered_feature_bc_matrix.h5 file contains the gene and HTO expression output of the cellranger (10x Genomics) multi and aggr commands. Please see the supplementary files for the HTO - sample correspondence and aggregation parameters.
Supplementary files format and content: The filtered_contig_annotations.csv file contains the gene and HTO expression output of the cellranger (10x Genomics) multi and aggr commands. Please see the supplementary files for the HTO - sample correspondence and aggregation parameters.
Supplementary files format and content: The .rds file contains the final Seurat object, product of the analysis described in the processing step section.

extract_protocol:
Serum-free media was prepared with RPMI containing 20 mM HEPES,  L-Glutamine, 100U/mL Penicillin, 100ug/mL Streptomycin sulfate, 50 µM β-mercaptoethanol, 1mM sodium pyruvate, 1mM non-essential amino acids.3% media was prepared with RPMI containing 3% FBS, 20 mM HEPES,  L-Glutamine, 100U/mL Penicillin, 100ug/mL Streptomycin sulfate, 50 µM β-mercaptoethanol, 1mM sodium pyruvate, 1mM non-essential amino acids. Mice were sacrificed by CO2 inhalation. For cell extraction from small intestinal lamina propria, Peyer’s patches and mesenteric adipose tissue were removed. For each intestine, tissues were cut open longitudinally, washed several times in cold PBS to remove feces, and further cut into 1- to 2-cm segments before being placed in 50 ml beakers with a stir bar. Tissue pieces were incubated in 10 ml per intestine of 3% RPMI with 5 mM EDTA, and 0.145 mg/ml DTT for 20 min at 37° C with stirring ~400 rpm. To separate the lamina propria (LP) and intestinal epithelial lymphocyte (IEL) layer, each beaker’s contents were strained through a sterile fine-meshed stainless-steel sieve into a corresponding 500 ml beaker containing 10 ml of 3% RPMI media held on ice. After straining, tissue pieces from each intestine were transferred to a 50 ml conical tube containing 10 ml of serum-free RPMI with 2 mM EDTA. Each tube was shaken vigorously for 30 seconds and then strained through the respective sieve into the corresponding beaker. The shake and strain processes were repeated two more times. To isolate the IEL compartment, strained contents were filtered through 70 µm cell strainers atop 50 ml conical tubes on ice. Cell suspensions were centrifuged for 5 minutes at 450 g, 4° C. After gently discarding the supernatant, cell pellets were resuspended in 4 ml of a 30% Percoll gradient and centrifuged for 5 minutes at 1800 rpm, 4° C. After removing the supernatant with a pipette, cells were resuspended in 1 ml of 3% RPMI media. To isolate the LP compartment, small intestine pieces recovered from the shake and strain steps were placed into a 50 ml beaker and finely minced with scissors. Tissues were then incubated with 10 ml of serum-free media with 0.1 mg/ml Liberase TL and 5 mg/ml DNAse I for 25 min at 37° C with stirring ~400 rpm. After the incubation, 5 ml of 3% RPMI was added to each beaker. The contents of each beaker were pipetted through 70 µm cell strainers atop 50 ml conical tubes on ice. Each beaker and strainer was rinsed with an additional 10 ml of 3% RPMI. Cell suspensions were centrifuged for 5 minutes at 450 g, 4° C. After gently discarding the supernatant, cell pellets were resuspended in 4 ml of a 30% Percoll gradient and centrifuged for 5 minutes at 1800 rpm, 4° C. After removing the supernatant with a pipette, cells were resuspended in 1 ml of 3% RPMI media.
SILP CD4^+^ T cells (Live, CD45+CD90.2+, TCRb+, CD4+) from SPF or GF T-bet-ZsGreen mice that received aCD3 or isotype as described in the corresponding methods section were sorted from samples labeled with TotalSeqC hashtags antibodies (Biolegend) using a Sony MA900 sorter. Sorted cells were pooled during sorting and 40000 cells per lane (total of 4 lanes) were loaded on a Chromium Single Cell Controller (10X Genomics) to encapsulate the cells into droplets. The gene expression (GEX), hashtag oligonucleotide (HTO) and VDJ (TCR) sequencing libraries were prepared using Chromium Single Cell 5’ v2 reagent kits following the manufacturer’s instructions, and sequenced on an Illumina Nextseq1000 platform (NextSeq 1000/2000 P2 reagents).


title: Patient 86, healthy, female, 63 years old

description: Library name: 31179-184


title: scRNAseq VDJ 10x Lane 2


title: scRNAseq VDJ 10x Lane 3


title: DOGMAseq, ATAC, Sample 14

description:
Library name: 14___ATAC
ATAC library


title: Patient 87, healthy, female, 53 years old

description: Library name: 31179-185


title: scRNAseq VDJ 10x Lane 1


title: Patient 85, healthy, female, 39 years old

description: Library name: 31179-181


title: Patient 90, healthy, female, 44 years old

description: Library name: 31179-191


title: DOGMAseq, ATAC, Sample 11

description:
Library name: 11___ATAC
ATAC library


title: DOGMAseq, ATAC, Sample 12

description:
Library name: 12___ATAC
ATAC library


title: scRNAseq HTO 10x Lane 4


title: scRNAseq HTO 10x Lane 3


title: Patient 84, healthy, female, 42 years old

description: Library name: 31179-178


title: scRNAseq HTO 10x Lane 2


title: scRNAseq HTO 10x Lane 1


title: scRNAseq GEX 10x Lane 4


title: DOGMAseq, ATAC, Sample 10

description:
Library name: 10___ATAC
ATAC library


title: scRNAseq GEX 10x Lane 3


title: Patient 81, healthy, female, 49 years old

description: Library name: 31179-173


title: scRNAseq GEX 10x Lane 2


title: DOGMAseq, ATAC, Sample 8

description:
Library name: 8___ATAC
ATAC library


title: DOGMAseq, ATAC, Sample 9

description:
Library name: 9___ATAC
ATAC library


title: scRNAseq GEX 10x Lane 1

tag: batch

value: w


title: scRNAseq VDJ 10x Lane 8

description:
Library name: VDJ 10x Lane 8
10x Genomics lane, 8 Samples (4 SPF mice, 4 GF mice) hashtagged and pooled.

data_processing:
The initial processing of the expression data involved generating fastq files and count matrices using Cell Ranger v7.1.0 [@zheng2017] (10X Genomics, Pleasanton, CA) that was run with the “Include introns=True” option and the mm10-2020-A transcriptome reference. The TCR data was processed with Cell Ranger v7.1.0 using a VDJ reference based on the IGMT database: The IGMT reference was generated with Cell Ranger v7.1.0 using the 'fetch-imgt' and 'cellranger mkvdjref' functions. Processing of the expression data was performed with the 'cellranger multi' and 'cellranger aggr' functions. After processing and aggregation, the estimated number of cells and mean reads per cell for each library were as follows: 89077 estimated number of cells, 19550 mean reads per cell (from eight GEX libraries), 1208 Median hashtag UMIs per Cell (across eight HTO libraries), 56835 lls with a productive TRA and/or TRB V-J spanning sequence, 38232 of which contain both a productive V-J spanning TRA and TRB pair (from eight VDJ libraries). The overall sequencing quality was medium to high in the eight mRNA libraries: \>82.7% of bases in the barcode and UMI regions had Q30 (99.99% inferred base call accuracy, mean 94%) quality score or above, whereas \>75.4% of bases in the RNA reads had Q30 or above (mean 85.6%). Furthermore, across the eight GEX libraries the median gene count per cell range was 974-1332, the sequencing saturation ranged between 69-76%, and 39-54% of the reads mapped confidently to the transcriptome. Across the eight TCR libraries, the mean used reads per cell was 1771-4034 (average 2755). Across the eight hashtag (HTO) libraries the mean antibody reads usable per cell was 1956-6321 (average 3015).
In the downstream analysis of the expression data, the Cell Ranger aggregation output (filtered_feature_bc_matrix directory) was loaded into Seurat version 4.4.1 (58) using the CreateSeuratObject function with min.cells=3. For filtering out low-quality cells, we established minimum thresholds for gene (nCount_RNA > 1000) and UMI counts (nFeature_RNA > 300), and a maximum threshold for percentage mitochondrial content (percent.mt < 6) based on visual inspection of the corresponding metric distributions across all cells. Log-normalization (LogNormalize function) of the RNA count data and centered log-ratio transformation (CLR) of the HTO count data were carried out using the NormalizeData function. For HTO demultiplexing cells into the individual mice within nulliparous/pregnant/lactation groups and removing any doublets, HTODemux was run with a positive quantile = 0.99. The top 2000 variable features were determined with the VariableFeatures function, expression data was scaled with ScaleData, and dimensionality reduction was performed with the RunPCA  function on the variable features, followed by determining the dimensionality of the dataset on an elbow plot (ElbowPlot function), which was determined to be 60. Subsequently, FindNeighbors, FindClusters, and RunUMAP were run on 60 dimensions and a range of resolutions to determine the optimal resolution that captures biological diversity in the dataset, which was determined to be 0.25, resulting in 16 clusters. The clusters identified by the FindClusters function of Seurat (default Louvain clustering setting and 0.25 resolution) were further annotated using cell type-specific markers.
Assembly: mm10
Supplementary files format and content: The filtered_feature_bc_matrix.h5 file contains the gene and HTO expression output of the cellranger (10x Genomics) multi and aggr commands. Please see the supplementary files for the HTO - sample correspondence and aggregation parameters.
Supplementary files format and content: The filtered_contig_annotations.csv file contains the gene and HTO expression output of the cellranger (10x Genomics) multi and aggr commands. Please see the supplementary files for the HTO - sample correspondence and aggregation parameters.
Supplementary files format and content: The .rds file contains the final Seurat object, product of the analysis described in the processing step section.

extract_protocol:
Serum-free media was prepared with RPMI containing 20 mM HEPES,  L-Glutamine, 100U/mL Penicillin, 100ug/mL Streptomycin sulfate, 50 µM β-mercaptoethanol, 1mM sodium pyruvate, 1mM non-essential amino acids.3% media was prepared with RPMI containing 3% FBS, 20 mM HEPES,  L-Glutamine, 100U/mL Penicillin, 100ug/mL Streptomycin sulfate, 50 µM β-mercaptoethanol, 1mM sodium pyruvate, 1mM non-essential amino acids. Mice were sacrificed by CO2 inhalation. For cell extraction from small intestinal lamina propria, Peyer’s patches and mesenteric adipose tissue were removed. For each intestine, tissues were cut open longitudinally, washed several times in cold PBS to remove feces, and further cut into 1- to 2-cm segments before being placed in 50 ml beakers with a stir bar. Tissue pieces were incubated in 10 ml per intestine of 3% RPMI with 5 mM EDTA, and 0.145 mg/ml DTT for 20 min at 37° C with stirring ~400 rpm. To separate the lamina propria (LP) and intestinal epithelial lymphocyte (IEL) layer, each beaker’s contents were strained through a sterile fine-meshed stainless-steel sieve into a corresponding 500 ml beaker containing 10 ml of 3% RPMI media held on ice. After straining, tissue pieces from each intestine were transferred to a 50 ml conical tube containing 10 ml of serum-free RPMI with 2 mM EDTA. Each tube was shaken vigorously for 30 seconds and then strained through the respective sieve into the corresponding beaker. The shake and strain processes were repeated two more times. To isolate the IEL compartment, strained contents were filtered through 70 µm cell strainers atop 50 ml conical tubes on ice. Cell suspensions were centrifuged for 5 minutes at 450 g, 4° C. After gently discarding the supernatant, cell pellets were resuspended in 4 ml of a 30% Percoll gradient and centrifuged for 5 minutes at 1800 rpm, 4° C. After removing the supernatant with a pipette, cells were resuspended in 1 ml of 3% RPMI media. To isolate the LP compartment, small intestine pieces recovered from the shake and strain steps were placed into a 50 ml beaker and finely minced with scissors. Tissues were then incubated with 10 ml of serum-free media with 0.1 mg/ml Liberase TL and 5 mg/ml DNAse I for 25 min at 37° C with stirring ~400 rpm. After the incubation, 5 ml of 3% RPMI was added to each beaker. The contents of each beaker were pipetted through 70 µm cell strainers atop 50 ml conical tubes on ice. Each beaker and strainer was rinsed with an additional 10 ml of 3% RPMI. Cell suspensions were centrifuged for 5 minutes at 450 g, 4° C. After gently discarding the supernatant, cell pellets were resuspended in 4 ml of a 30% Percoll gradient and centrifuged for 5 minutes at 1800 rpm, 4° C. After removing the supernatant with a pipette, cells were resuspended in 1 ml of 3% RPMI media.
SILP CD4 T cells (Live, CD45+CD90.2+, TCRb+, CD4+) from 4 SPF and 4 GF T-bet-ZsGreen mice were sorted from samples labeled with TotalSeqC hashtags antibodies (Biolegend) using a Sony MA900 sorter. Sorted cells were pooled during sorting and 32000 cells per lane (total of 8 lanes) were loaded on a Chromium Single Cell Controller (10X Genomics) to encapsulate the cells into droplets. The gene expression (GEX), hashtag oligonucleotide (HTO) and VDJ (TCR) sequencing libraries were prepared using Chromium Single Cell 5’ v2 reagent kits following the manufacturer’s instructions, and sequenced on an Illumina Nextseq2000 platform (NextSeq 1000/2000 P2 reagents)


title: Patient 80, healthy, female, 47 years old

description: Library name: 31179-171


title: DOGMAseq, ATAC, Sample 13

description:
Library name: 13___ATAC
ATAC library


title: scRNAseq VDJ 10x Lane 7

description:
Library name: VDJ 10x Lane 7
10x Genomics lane, 8 Samples (4 SPF mice, 4 GF mice) hashtagged and pooled.


title: scRNAseq VDJ 10x Lane 5

description:
Library name: VDJ 10x Lane 5
10x Genomics lane, 8 Samples (4 SPF mice, 4 GF mice) hashtagged and pooled.


title: DOGMAseq, ATAC, Sample 7

description:
Library name: 7___ATAC
ATAC library


title: scRNAseq VDJ 10x Lane 4

description:
Library name: VDJ 10x Lane 4
10x Genomics lane, 8 Samples (4 SPF mice, 4 GF mice) hashtagged and pooled.


title: Patient 83, healthy, female, 40 years old

description: Library name: 31179-176


title: DOGMAseq, ATAC, Sample 6

description:
Library name: 6___ATAC
ATAC library


title: scRNAseq VDJ 10x Lane 3

description:
Library name: VDJ 10x Lane 3
10x Genomics lane, 8 Samples (4 SPF mice, 4 GF mice) hashtagged and pooled.


title: scRNAseq VDJ 10x Lane 2

description:
Library name: VDJ 10x Lane 2
10x Genomics lane, 8 Samples (4 SPF mice, 4 GF mice) hashtagged and pooled.


title: DOGMAseq, ATAC, Sample 5

description:
Library name: 5___ATAC
ATAC library


title: Patient 79, healthy, female, 62 years old

description: Library name: 31179-170


title: scRNAseq HTO 10x Lane 8

description:
Library name: HTO 10x Lane 8
10x Genomics lane, 8 Samples (4 SPF mice, 4 GF mice) hashtagged and pooled.


title: scRNAseq VDJ 10x Lane 1

description:
Library name: VDJ 10x Lane 1
10x Genomics lane, 8 Samples (4 SPF mice, 4 GF mice) hashtagged and pooled.


title: Patient 77, healthy, female, 40 years old

description: Library name: 31179-167


title: Patient 78, healthy, female, 49 years old

description: Library name: 31179-169


title: scRNAseq HTO 10x Lane 7

description:
Library name: HTO 10x Lane 7
10x Genomics lane, 8 Samples (4 SPF mice, 4 GF mice) hashtagged and pooled.


title: Patient 82, healthy, female, 47 years old

description: Library name: 31179-175


title: scRNAseq HTO 10x Lane 5

description:
Library name: HTO 10x Lane 5
10x Genomics lane, 8 Samples (4 SPF mice, 4 GF mice) hashtagged and pooled.


title: Patient 75, healthy, female, 70 years old

description: Library name: 31179-161


title: scRNAseq HTO 10x Lane 4

description:
Library name: HTO 10x Lane 4
10x Genomics lane, 8 Samples (4 SPF mice, 4 GF mice) hashtagged and pooled.


title: DOGMAseq, ATAC, Sample 2

description:
Library name: 2___ATAC
ATAC library


title: scRNAseq HTO 10x Lane 3

description:
Library name: HTO 10x Lane 3
10x Genomics lane, 8 Samples (4 SPF mice, 4 GF mice) hashtagged and pooled.


title: scRNAseq VDJ 10x Lane 6

description:
Library name: VDJ 10x Lane 6
10x Genomics lane, 8 Samples (4 SPF mice, 4 GF mice) hashtagged and pooled.


title: Patient 74, healthy, female, 45 years old

description: Library name: 31179-160


title: scRNAseq HTO 10x Lane 2

description:
Library name: HTO 10x Lane 2
10x Genomics lane, 8 Samples (4 SPF mice, 4 GF mice) hashtagged and pooled.


title: DOGMAseq, ATAC, Sample 1

description:
Library name: 1___ATAC
ATAC library


title: scRNAseq HTO 10x Lane 1

description:
Library name: HTO 10x Lane 1
10x Genomics lane, 8 Samples (4 SPF mice, 4 GF mice) hashtagged and pooled.


title: scRNAseq GEX 10x Lane 8

description:
Library name: GEX 10x Lane 8
10x Genomics lane, 8 Samples (4 SPF mice, 4 GF mice) hashtagged and pooled.


title: Patient 76, healthy, female, 53 years old

description: Library name: 31179-162


title: scRNAseq GEX 10x Lane 7

description:
Library name: GEX 10x Lane 7
10x Genomics lane, 8 Samples (4 SPF mice, 4 GF mice) hashtagged and pooled.


title: DOGMAseq, ATAC, Sample 4

description:
Library name: 4___ATAC
ATAC library


title: Leukocytes_Ficoll_P47

city: Liege

first: Gregory

last: Ehx

address: Avenue de l'Hopital, 11

department: GIGA Institute

country: Belgium

institute: University of Liege

description:
Library name: P47Ficoll
P47Ficoll

data_processing:
Raw reads were counted with kallisto 0.51.1 (reverse-forward mode) using a transcriptome index built on human genome GRCh38 and Ensembl 113 annotations.
Assembly: GRCh38
Supplementary files format and content: The expression file is tab delimited with column 1 being Ensembl transcript identifiers and subsequent columns being the estimated counts of indicated samples in the first row.

source_name: Blood

growth_protocol: None of the samples were expanded

extract_protocol:
RNA was extracted using the RNeasy mini kit of Qiagen.
RNA libraries were prepared with the TruSeq mRNA stranded kit of Illumina

treatment_protocol: No treatment applied

value: Blood

value: Total leukocytes

value: WT

tag: isolation method

value: Ficoll


title: scRNAseq GEX 10x Lane 6

description:
Library name: GEX 10x Lane 6
10x Genomics lane, 8 Samples (4 SPF mice, 4 GF mice) hashtagged and pooled.


title: Patient 71, healthy, female, 66 years old

description: Library name: 31179-149


title: scRNAseq GEX 10x Lane 5

description:
Library name: GEX 10x Lane 5
10x Genomics lane, 8 Samples (4 SPF mice, 4 GF mice) hashtagged and pooled.


title: scRNAseq GEX 10x Lane 2

description:
Library name: GEX 10x Lane 2
10x Genomics lane, 8 Samples (4 SPF mice, 4 GF mice) hashtagged and pooled.


title: Leukocytes_Lysis_P45

description:
Library name: P45Lysis
P45Lysis

value: Red blood cell lysis


title: scRNAseq HTO 10x Lane 6

description:
Library name: HTO 10x Lane 6
10x Genomics lane, 8 Samples (4 SPF mice, 4 GF mice) hashtagged and pooled.


title: Leukocytes_Lysis_P47

description:
Library name: P47Lysis
P47Lysis


title: Leukocytes_Ficoll_P45

description:
Library name: P45Ficoll
P45Ficoll


title: DOGMAseq, ATAC, Sample 3

description:
Library name: 3___ATAC
ATAC library

value: lymph node

value: sorted cd3+ cd8- non-naive cells

value: viremic


title: Patient 70, healthy, female, 49 years old

description: Library name: 31179-147


title: scRNAseq GEX 10x Lane 1

description:
Library name: GEX 10x Lane 1
10x Genomics lane, 8 Samples (4 SPF mice, 4 GF mice) hashtagged and pooled.


title: Leukocytes_Ficoll_P44

description:
Library name: P44Ficoll
P44Ficoll


title: scRNAseq GEX 10x Lane 3

description:
Library name: GEX 10x Lane 3
10x Genomics lane, 8 Samples (4 SPF mice, 4 GF mice) hashtagged and pooled.


title: Patient 68, healthy, female, 63 years old

description: Library name: 31179-142


title: Patient 72, healthy, female, 43 years old

description: Library name: 31179-151


title: WCM1078 organoids, active compound, 4h, rep3, ATAC

description:
Library name: WCM1078-A947_Rep.3_4h_SAM24473278_ATAC
Column name in ATAC_metadata.tsv: SAM24473278

value: organoid

value: prostate tumor

value: SMARCA2/SMARCA4 targeting PROTAC


title: WCM1078 organoids, active compound, 4h, rep1, ATAC

description:
Library name: WCM1078-A947_Rep.1_4h_SAM24473276_ATAC
Column name in ATAC_metadata.tsv: SAM24473276


title: WCM1078 organoids, active compound, 4h, rep2, ATAC

description:
Library name: WCM1078-A947_Rep.2_4h_SAM24473277_ATAC
Column name in ATAC_metadata.tsv: SAM24473277


title: Patient 67, healthy, female, 40 years old

description: Library name: 31179-141


title: WCM1078 organoids, inactive compound, 4h, rep3, ATAC

description:
Library name: WCM1078-A858_Rep.3_4h_SAM24473275_ATAC
Column name in ATAC_metadata.tsv: SAM24473275

value: inactive compound


title: WCM1078 organoids, inactive compound, 4h, rep2, ATAC

description:
Library name: WCM1078-A858_Rep.2_4h_SAM24473274_ATAC
Column name in ATAC_metadata.tsv: SAM24473274


title: Leukocytes_Ficoll_P42

description:
Library name: P42Ficoll
P42Ficoll


title: scRNAseq GEX 10x Lane 4

description:
Library name: GEX 10x Lane 4
10x Genomics lane, 8 Samples (4 SPF mice, 4 GF mice) hashtagged and pooled.

value: Small Intestine Lamina Propria

value: T-bet-ZsGreen


title: Patient 66, healthy, female, 38 years old

description: Library name: 31179-137

value: Serum


title: WCM1078 organoids, inactive compound, 4h, rep1, ATAC

description:
Library name: WCM1078-A858_Rep.1_4h_SAM24473273_ATAC
Column name in ATAC_metadata.tsv: SAM24473273


title: Patient 73, healthy, female, 60 years old

description: Library name: 31179-155

value: BRCA wild-type


title: Leukocytes_Lysis_P42

description:
Library name: P42Lysis
P42Lysis


title: WCM1078 organoids, active compound, 4h, rep2, ChIP

description:
Library name: WCM1078-A947_Rep.2_4h_SAM24473284_ChIP
Column name in ChIP_metadata.tsv: SAM24473284

tag: chip antibody

value: TCF7L2 (Cell Signalling, #2569)


title: WCM1078 organoids, active compound, 4h, rep1, ChIP

description:
Library name: WCM1078-A947_Rep.1_4h_SAM24473283_ChIP
Column name in ChIP_metadata.tsv: SAM24473283


title: Leukocytes_Ficoll_P41

description:
Library name: P41Ficoll
P41Ficoll

value: Blood


title: Patient 69, healthy, female, 49 years old

description: Library name: 31179-145


title: Patient 65, healthy, female, 45 years old

description: Library name: 31179-136

value: BRCA mutated


title: WCM1078 organoids, active compound, 4h, input, ChIP

description:
Library name: WCM1078-A947_input_4h_SAM24473282_ChIP
Column name in ChIP_metadata.tsv: SAM24473282


title: Patient 64, healthy, female, 41 years old

description: Library name: 31179-130


title: WCM1078 organoids, inactive compound, 4h, rep2, ChIP

description:
Library name: WCM1078-A858_Rep.2_4h_SAM24473281_ChIP
Column name in ChIP_metadata.tsv: SAM24473281


title: WCM1078 organoids, inactive compound, 4h, rep1, ChIP

description:
Library name: WCM1078-A858_Rep.1_4h_SAM24473280_ChIP
Column name in ChIP_metadata.tsv: SAM24473280


title: Leukocytes_Lysis_P41

description:
Library name: P41Lysis
P41Lysis

value: Total leukocytes

value: WT


title: WCM1078 organoids, inactive compound, 4h, input, ChIP

description:
Library name: WCM1078-A858_input_4h_SAM24473279_ChIP
Column name in ChIP_metadata.tsv: SAM24473279


title: Patient 61, healthy, female, 43 years old

description: Library name: 31179-126