title: P347Lho_3w_3

city: Shanghai

first: Chenyue

last: Hang

address: 100 Haining Road, Shanghai 200080, China

institute: Shanghai general hospital

description:
Library name: P347Lho_3w_3
gene_count.xls

data_processing:
After library quality control, different libraries were pooled based on theeffective concentration and targeted data amount, then subjected toIllumina sequencing. The basic principle of sequencing is "Sequencing bySynthesis", where fluorescently labeled dNTPs, DNA polymerase, andadapter primers are added to the sequencing flow cell for amplification.As each sequencing cluster extends its complementary strand, theaddition of each fluorescently labeled dNTP releases a correspondingfluorescence signal. The sequencer captures these fluorescence signalsand converts them into sequencing peaks through computer software,thereby obtaining the sequence information of the target fragment.
Raw data (raw reads) of fastq format were firstly processed through fastpsoftware. In this step, clean data (clean reads) were obtained byremoving reads containing adapter, reads containing ploy-N and lowquality reads from raw data. At the same time, Q20, Q30 and GC contentthe clean data were calculated. All the downstream analyses were basedon the clean data with high quality.
Reference genome and gene model annotation files were downloadedfrom genome website. Use HISAT2 (2.2.1) to build the index of thereference genome, and use HISAT2 to align paired-end clean reads to the reference genome. HISAT2 can use the gene model annotation file tocreate splice-aware alignments, providing better alignment accuracycompared to other non-splice alignment tools.
Assembly: GRCm39
Supplementary files format and content: gene_fpkm.xls

source_name: retina

extract_protocol:
Retinas of 3-week-old C57BL/6J, hRHOL125R/L125R and hRHOP347L/P347L mice (n=3 mice per genotype) were quickly separated and immediately homogenized in TRIzol reagent (Invitrogen 15596018CN).
RNAseq library was prepared by Novogene (Beijing, China). Non strand specific libraryMessenger RNA was purified from total RNA using poly-T oligo-attachedmagnetic beads. After fragmentation, the first strand cDNA wassynthesized using random hexamer primers followed by the secondstrand cDNA synthesis. The library was ready after end repair, A-tailing,adapter ligation, size selection, amplification, and purification. Thelibrary was checked with Qubit and real-time PCR for quantification andbioanalyzer for size distribution detection.Strand specific libraryMessenger RNA was purified from total RNA using poly-T oligo-attachedmagnetic beads. After fragmentation, the first strand cDNA wassynthesized using random hexamer primers. Then the second strandcDNA was synthesized using dUTP, instead of dTTP. The directionallibrary was ready after end repair, A-tailing, adapter ligation, sizeselection, USER enzyme digestion, amplification, and purification. Thelibrary was checked with Qubit and real-time PCR for quantification andbioanalyzer for size distribution detection.

value: retina

value: retinal cells

value: hRHO P347L/P347L insertion


title: FeCon9

status: Public on Jul 22 2026

type: SRA

city: Zhengzhou

first: Shuai

last: Cheng

address: No.1, East Jian She Road

country: China

institute: The First Affiliated Hospital of Zhengzhou University

description:
Library name: Sample 30
Column name in raw_counts.txt:FeCon9

library_source: transcriptomic

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 0.1%, afterwards clean reads were obtained and stored in FASTQ format.
Bowtie2 was applied to align the clean reads to the gene set. Expression level of gene was calculated by RSEM (v1.3.1).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample.

molecule: total RNA

organism: Mus musculus

source_name: Thoracic aorta

growth_protocol: All animals were housed under specific pathogen-free conditions with controlled temperature, 12-h light/dark cycles, and stable humidity.

extract_protocol:
Total RNA was extracted from tissues using RNeasy Micro Kit（QIAGEN，Germany）according to manual instruction. Subsequently, total RNA was qualified and quantified using an Agilent 2100 Bioanalyzer (Agilent, CA, USA).
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China) according to manual instruction.

treatment_protocol: Male and female 3-week-old C57BL/6J mice (GemPharmatech) were maintained under specific pathogen-free (SPF) conditions. To establish the aortic dissection (AD) model, mice in the experimental groups had ad libitum access to drinking water containing 0.4% β-aminopropionitrile (BAPN) for 28 consecutive days. Sex-matched control mice received normal drinking water. At the end of the 28-day induction period, the mice were euthanized. The thoracic aortas were carefully harvested, snap-frozen in liquid nitrogen, and subjected to strand-specific bulk RNA sequencing.

tag: tissue

value: Thoracic aorta

tag: Sex

value: Female

tag: genotype

value: WT

tag: treatment

value: Normal drinking water control


title: 253949419110_S01_GE1_107_Sep09_2_1

type: RNA

city: Augsburg

first: Victoria

middle: Elisabeth

last: Fincke

address: Stenglinstraße 2

country: Germany

institute: Childens Cancer Center - University hospital Augsburg

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing: NOT PROVIDED; REQUESTED

organism: Homo sapiens

source_name: aortic tissue

label_protocol: standard protocol

extract_protocol: RNA was extracted from cryoconserved aortic tissue on the QIAsymphony SP platform. Samples were processed by homogenizing ~10mg of tissue in 400µl RLT and QIAgen buffer. The 400µl homogenate was filtered with QIAsymphony. Following extraction and elution (50 µl), the samples were quantified and 260/280 ratio determined on Nanodrop 8000. Quality control and sample validation was performed on the Agilent 2100 Bioanalyzer.

value: male

tag: main diagnosis

value: CoA

value: aortic tissue


title: NPS_8801_CD_5

city: Amsterdam

first: Lisa

last: Willemsen

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC - locatie AMC

description:
Library name: NPS_8801_CD_5
RNA-Seq of CHIM NPS

data_processing:
Paired-end reads that passed Illumina quality filters were further screened to remove sequences aligning to tRNA, rRNA, adapter sequences, and spike-in controls. The remaining reads were aligned to the GRCh38 human reference genome with Gencode v27 annotations using STAR (v2.6.1) [PMID: 23104886]. Read complexity was assessed with PRINSEQ Lite (v0.20.3) [PMID: 21278185], and low-complexity reads (DUST score > 4) were excluded from the BAM files. The alignment results were parsed via the SAMtools [PMID: 19505943] to generate SAM files. Gene-level counts were then obtained using featureCounts (v1.6.5) [PMID: 24227677] using the default option along with a minimum quality cut-off (Phred > 10), and transcripts per million (TPM) reads values were calculated. T cell receptor (TCR) transcripts were aggregated into four groups: TCR-α, TCR-β, TCR-γ, and TCR-δ. B cell receptor (BCR) transcripts were aggregated into light chains (IGK and IGL) and heavy chains (IGH-), with isotype transcripts (IGHG1-4, IGHM, IGHD, IGHE, IGHA1-2) analyzed separately. Transcripts were filtered using EdgeR’s filterByExpr function (v4.2.2) [PMID: 39844453] with “participants + timepoint” as the design. For each participant, baseline TPMs were averaged and raw counts were summed. Differential expression was assessed using the DESeq2 package (v1.44.0) [PMID: 25516281] for NPS and EdgeR for PBMCs in an R (v4.4.0) environment, with gene expression called differential with an FDR<0.05. Gene set enrichment analysis (GSEA) was performed using Metascape [PMID: 30944313] and GSEA (v4.4.0) [PMID: 16199517], both with the Gene Ontology (GO) gene sets [PMID: 36866529].
Assembly: GRCh38
Supplementary files format and content: "PBMC_counts.tsv" contains raw count values per sample and gene of PBMC.
Supplementary files format and content: "PBMC_tpm.tsv" contains TPM values per sample and gene of PBMC.
Supplementary files format and content: "PBMC_tpm_baseline_means_BCR_TCR_aggr.csv" contains TPM values per sample and gene in which TCR and BCR genes were aggregated and baseline PBMC samples per participant were averaged.
Supplementary files format and content: "PBMC_counts_baseline_sums_BCR_TCR_aggr.csv" contains counts per sample and gene in which TCR and BCR genes were aggregated and baseline PBMC samples per participant were summed.
Supplementary files format and content: "NPS_counts.csv" contains raw count values per sample and gene of NPS.
Supplementary files format and content: "NPS_tpm.csv" contains TPM values per sample and gene of NPS.
Supplementary files format and content: "NPS_tpm_baseline_means_TCR_BCR_aggr.csv" contains TPM values per sample and gene in which TCR and BCR genes were aggregated and baseline NPS samples per participant were averaged.
Supplementary files format and content: NPS_counts_baseline_sums_BCR.TCR.aggr.csv" contains counts per sample and gene in which TCR and BCR genes were aggregated and baseline NPS samples per participant were summed.
Supplementary files format and content: "participant_metadata_filtered.csv" contains metadata per participant.

molecule: polyA RNA

source_name: Nose

extract_protocol:
NPS: RNA was extracted with on-column DNase treatment using the miRNeasy Mini Kit (Qiagen) following the manufacturer's instructions. RNA was quantified by qPCR using the housekeeping gene B2M.
PBMC: 500K cells were stored in 750 μL TRIzol at -80°C. RNA until further processing. RNA was extracted with on-column DNase treatment using the miRNeasy Mini Kit (Qiagen) following the manufacturer's instructions.
NPS: For cDNA synthesis, 10 ng of RNA was reverse-transcribed and pre-amplified (14 cycles) according to the Smart-Seq2 protocol. cDNA was purified with AMPure XP beads (Beckman Coulter), and 0.5 ng was used for Nextera XT sequencing library preparation with 8-bp Unique Dual Index (UDI) barcodes (IDT, Illumina) and the Nextera XT DNA Library Preparation Kit (Illumina). To minimize inter-assay variability, all purification steps were performed using an EpMotion 5075 (Eppendorf), and sequencing libraries were prepared in a 96-well format using a Mantis microfluidics liquid dispenser (Formulamatrix). Quality control included assessment of total RNA quality and quantity, optimization of pre-amplification cycle numbers, and fragment size analysis by capillary electrophoresis (5300 Fragment Analyzer, Agilent). cDNA and final libraries were quantified with the Quant-iT PicoGreen assay (Thermo Fisher Scientific). All samples passed quality thresholds, with >70% of fragments ranging from 300–700 bp and <5% primer dimers. Libraries were quantified by qPCR using the KAPA Library Quantification Kit (Roche), normalized to equimolar concentrations, and loaded onto a NovaSeq X Plus sequencing platform (Illumina) with a 25B flow cell. Paired-end sequencing (150 bp) yielded 4.2 billion total reads, corresponding to an average depth of ~15 million reads per sample.
PBMC: Quantabio Sparq mRNA-Seq kit was used to prepare stranded libraries using 8 ng of high-quality total RNA as input, except in 10 samples where the yield was below 8 ng. Libraries underwent 16-18 PCR amplification cycles and libraries were indexed with xGen 10 nt Unique Dual Indexes (UDIs). Paired-end (50x50) sequencing was performed on a NovaSeq 6000 targeting 40 million reads per library.

value: Nose

tag: age

tag: cell type

value: NPS

tag: days post_challenge


title: P347Lho_3w_2

description:
Library name: P347Lho_3w_2
gene_count.xls

tag: cell line

tag: batch


title: FeCon8

description:
Library name: Sample 29
Column name in raw_counts.txt:FeCon8


title: CD8+ T Cells, DiSBey, Chronic Stimulation, Day 14, chr1, batch1, biol_rep 1

city: Minneapolis

first: Nuri

middle: Alpay

last: Temiz

state: MN

address: 2231 6th St SE

department: Masonic Cancer Center

country: USA

institute: University of Minnesota

description: Library name: QE1D14_1

library_source: genomic

data_processing:
Adapter and primer sequences were removed with cutadapt
Sequences were aligned to ensembl GRcm39 with BWA MEM
Sequences were deduplicated using UMI Tools
Insertion locations were extracted from the bam file using R
Assembly: Mus musculus GRcm39
Supplementary files format and content: esTAG_counts.txt - tab-delimited text file including raw transposon counts and direction for each sample

molecule: genomic DNA

source_name: Spleen

growth_protocol: Spleens were collected and passed through 70 µm strainers. Red blood cells were then lysed with 1X RBC Lysis Buffer (diluted from Invitrogen 00-4300-54) for 5 minutes before washing with FACS buffer (2% FBS, 2 mM EDTA in PBS). Naïve CD8+ T cells were isolated using Naive CD8a+ T Cell Isolation Kit (Miltenyi 130-096-543), and resuspended at 1×106 cells per ml in mouse T cell media, which consisted with 10% FBS, 1% sodium pyruvate (MP Biomedicals 091682049), 1% Non-essential amino-acids (Gibco 11140050), 100U Pen/Strep (Corning 30002CI), 50 nM of β-mercaptoethanol (Millipore Sigma M3148) in RPMI and supplemented with 10 ng/mL of mouse IL-2 (R&D Systems 402-ML-020/CF). Naive CD8+ T cells were then activated by anti-CD3/anti-CD28 Dynabeads (Gibco 11456D). 2 days later, magnetic Dynabeads were removed, and CD8+ T cells were expanded in TCM for experiments. Fluorescent mKate2 positivity from DiSBey CD8+ T cells was routinely checked with flow cytometry when applicable.

extract_protocol:
Simultaneous genomic DNA and RNA of murine CD8+ T cell samples (Figure 2A) were isolated using Quick-DNA/RNA MagBead (Zymo R2130).
For esTAG-seq, genomic DNA was tagmented with UMI-loaded Tn5 transposase (seqWell 301230). For insertion site enrichment with PCR, primers targeting SB inverted regions were paired with the p5 forward primer in sequential nested PCR reactions. PCR products were purified with SPRI Beads and sequenced with Element Aviti 2x150 bp with a 20 nt i5 index read (to sequence the Tagify 10 nt i5 index and 10 nt UMI sequences)

treatment_protocol: Adapted from Belk et al.13. After anti-CD3/anti-CD28 activation, CD8+ T cells were seeded in cultured plates coated with (for chronic stimulation) or without (for acute stimulation) 5 µg/ml anti-CD3ε (BioLegend 100359). Afterwards, 75% of TCM in each well was changed every odd day, and T cells were counted with Cellaca MX (AO/PI staining) and replated at 106 cells per ml every even day until day 18.

value: Spleen

value: CD8+ T Cells

value: DiSBey

value: Chronic Stimulation

tag: day

tag: launch chr

tag: biol rep


title: 253949419110_S01_GE1_107_Sep09_2_2


title: 253949419206_S01_GE1_107_Sep09_1_2


title: NPS_8799_CD_5

description:
Library name: NPS_8799_CD_5
RNA-Seq of CHIM NPS

value: female


title: FeCon7

description:
Library name: Sample 28
Column name in raw_counts.txt:FeCon7


title: P347Lho_3w_1

description:
Library name: P347Lho_3w_1
gene_count.xls

value: retina


title: NPS_8797_CD_4

description:
Library name: NPS_8797_CD_4
RNA-Seq of CHIM NPS


title: FeCon6

description:
Library name: Sample 27
Column name in raw_counts.txt:FeCon6


title: NPS_8779_CD_4

description:
Library name: NPS_8779_CD_4
RNA-Seq of CHIM NPS


title: L125Rho_3w_3

description:
Library name: L125Rho_3w_3
gene_count.xls

value: retinal cells

value: hRHO L125R/L125R insertion


title: 253949419207_S01_GE1_107_Sep09_2_1

value: D-TGA


title: NPS_8796_CD_6

description:
Library name: NPS_8796_CD_6
RNA-Seq of CHIM NPS


title: CD8+ T Cells, DiSBey, Acute Stimulation, Day 18, chr1, batch1, biol_rep 1

description: Library name: QI-1-D18_1

value: Acute Stimulation


title: L125Rho_3w_2

description:
Library name: L125Rho_3w_2
gene_count.xls


title: FeCon5

description:
Library name: Sample 26
Column name in raw_counts.txt:FeCon5

value: Thoracic aorta

value: Female

value: WT


title: FeNonAD6

description:
Library name: Sample 37
Column name in raw_counts.txt:FeNonAD6

value: Continuous β-aminopropionitrile (0.4%) administration in drinking water


title: 253949419110_S01_GE1_107_Sep09_1_2

value: male

value: aortic tissue


title: NPS_8793_CD_5

description:
Library name: NPS_8793_CD_5
RNA-Seq of CHIM NPS

value: Nose

value: NPS


title: L125Rho_3w_1

description:
Library name: L125Rho_3w_1
gene_count.xls


title: 253949419207_S01_GE1_107_Sep09_1_3

value: PS sub


title: NPS_8790_CD_4

description:
Library name: NPS_8790_CD_4
RNA-Seq of CHIM NPS


title: FeCon4

description:
Library name: Sample 25
Column name in raw_counts.txt:FeCon4

value: Normal drinking water control


title: FeCon3

description:
Library name: Sample 24
Column name in raw_counts.txt:FeCon3


title: WT_3w_3

description:
Library name: WT_3w_3
gene_count.xls


title: 253949419205_S01_GE1_107_Sep09_2_1


title: NPS_8789_CD_4

description:
Library name: NPS_8789_CD_4
RNA-Seq of CHIM NPS


title: WT_3w_2

description:
Library name: WT_3w_2
gene_count.xls


title: FeNonAD3

description:
Library name: Sample 34
Column name in raw_counts.txt:FeNonAD3


title: 253949419206_S01_GE1_107_Sep09_2_3

value: PA+VSD+MAPCA


title: NPS_8784_CD_3

description:
Library name: NPS_8784_CD_3
RNA-Seq of CHIM NPS


title: WT_3w_1

description:
Library name: WT_3w_1
gene_count.xls


title: FeCon2

description:
Library name: Sample 23
Column name in raw_counts.txt:FeCon2


title: FeCon1

description:
Library name: Sample 22
Column name in raw_counts.txt:FeCon1


title: NPS_8783_CD_3

description:
Library name: NPS_8783_CD_3
RNA-Seq of CHIM NPS


title: 253949419206_S01_GE1_107_Sep09_2_1

value: TGA


title: exa1-3-39

city: Weifang

first: Yingtang

last: Ma

address: No. 699 Binhu Road, Xiashan Ecological Economic Development Zone

institute: Peking University Institute of Advanced Agricultural Sciences

description: Library name: sample 24

data_processing:
Clean mRNA-seq reads were aligned to the Arabidopsis thaliana reference genome (TARI10) using HISAT2 (v2.0.4) with default parameters.
Gene-level read counts were calculated with HTseq (v0.6.1p1) with the union mode.
Assembly: TAIR 10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: seedlings grown on 1/2 MS mediate with 1% sucrose

extract_protocol:
Total RNA was extracted from about 50 mg samples of 9-day-old seedlings using RNAprep pure Plant Kit (TIANGEN Biotech, Cat. # DP432).
mRNA-Seq (Strand-Specific)  libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1/2 MS, 200 mM NaCl, 23℃,or 39℃ 60min

value: whole seedlings

value: exa1-1 mutant

value: 39℃ 60 min


title: MaAAD7

description:
Library name: Sample 21
Column name in raw_counts.txt:MaAAD7

value: Male


title: MD+GPPD

city: College Station

first: Aditya

middle: D

last: Joshi

state: Texas

address: 560 Raymond Stotzer Pkwy

institute: Texas A&M University

description: Library name: Sample 3

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggreggation was performed using Cell Ranger Software
Assembly: GRCm39 vM35
Supplementary files format and content: Features, and matrix files

source_name: Liver

extract_protocol:
Single nuclei suspensions were prepared by detergent-based lysis, filtration, and wash steps according to the manufacturer’s protocol (10x Genomics, Chromium Single Cell 3’ Reagent Kits v3).
Nuclei were counted on a hemocytometer, diluted to 700–1,200 nuclei/µL, and loaded into the Chromium Controller for partitioning into Gel Bead-in-Emulsions (GEMs). Each GEM contained a gel bead with oligonucleotides consisting of a 16-bp cell barcode, a 10-bp Unique Molecular Identifier (UMI), and a poly-dT sequence for capturing polyadenylated RNA transcripts. Reverse transcription was carried out inside the GEMs to generate barcoded full-length cDNA, followed by recovery and amplification. cDNA was enzymatically fragmented, end-repaired, A-tailed, and ligated with Illumina-compatible sequencing adapters. Libraries were indexed, quantified by Qubit dsDNA High Sensitivity Assay (ThermoFisher), and sized using AATI Fragment Analyzer. Final libraries were normalized and pooled.

treatment_protocol: Mice in the MD + GPPD cohort received 10 mg/kg (body weight) GPPD three times a week on Mondays, Wednesdays, and Fridays via intraperitoneal (i.p.) injection. Mice in the CD and MD groups were treated with vehicle (0.2% DMSO + 99.8% saline) via i.p. three days a week (Mondays, Wednesdays, and Fridays) for 30 weeks.

value: Liver

value: MD+GPPD


title: exa1-2-39

description: Library name: sample 23


title: NPS_8782_CD_4

description:
Library name: NPS_8782_CD_4
RNA-Seq of CHIM NPS

value: female


title: MaAAD6

description:
Library name: Sample 20
Column name in raw_counts.txt:MaAAD6

value: Thoracic aorta

value: WT


title: exa1-1-39

description: Library name: sample 22


title: MD

description: Library name: Sample 2

value: MD


title: NPS_8781_CD_4

description:
Library name: NPS_8781_CD_4
RNA-Seq of CHIM NPS

value: male


title: MaAAD5

description:
Library name: Sample 19
Column name in raw_counts.txt:MaAAD5

value: Continuous β-aminopropionitrile (0.4%) administration in drinking water


title: CD

description: Library name: Sample 1

value: CD


title: exa1-3-23

description: Library name: sample 21

value: 23℃ 60 min


title: NPS_8780_CD_3

description:
Library name: NPS_8780_CD_3
RNA-Seq of CHIM NPS

value: Nose

value: NPS


title: MaAAD4

description:
Library name: Sample 18
Column name in raw_counts.txt:MaAAD4


city: Daejeon

first: Mi-Young

last: Son

address: 111 Gwahangno, Yuseong-gu

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

description:
Library name: EtOH+DS1073
Gene exression of GES-1 cells pretreated with DS1073 CFS before EtOH exposure

data_processing:
Sequence reads were assessed for quality using FastQC (v0.11.9)
Sequence reads were trimmed for adapter sequences and low-quality bases using cutadapt (v4.9)
Trimmed sequence reads were mapped to GRCh38 using HISAT2(v2.2.1)(default parameters)
Transcript assembly and expression quantification were performed using StringTie(v2.1.1) with the reference annotation.
Assembly: GRCh38(Genome Reference Consortium Human Build 38)
Supplementary files format and content: tab-delimited text file includes FPKM for each Sample

extract_protocol:
Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific), and the samples were subsequently treated with DNase to remove genomic DNA contamination.
RNA libraries for RNA-Seq were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina) following the manufacturer's protocols.

value: Gastric epithelial cell lines


title: exa1-2-23

description: Library name: sample 20

value: whole seedlings


title: NPS_8779_CD_3

description:
Library name: NPS_8779_CD_3
RNA-Seq of CHIM NPS


description:
Library name: EtOH+MRS
Gene exression of GES-1 cells pretreated with MRS before EtOH exposure


title: MaAAD3

description:
Library name: Sample 17
Column name in raw_counts.txt:MaAAD3


title: exa1-1-23

description: Library name: sample 19

value: exa1-1 mutant


title: NPS_8778_CD_4

description:
Library name: NPS_8778_CD_4
RNA-Seq of CHIM NPS


title: GES-1 cells treated with MRS only

description:
Library name: MRS
Gene exression of GES-1 cells treated with MRS only

value: MRS treated


title: WT-3-39

description: Library name: sample 18

value: wild type

value: 39℃ 60 min


title: MaAAD2

description:
Library name: Sample 16
Column name in raw_counts.txt:MaAAD2

value: Male


title: WT-2-39

description: Library name: sample 17


title: GES-1 cells, untreated (control)

description:
Library name: NT
Gene exression of GES-1 cells, untreated (control)

value: untreated


title: MaAAD1

description:
Library name: Sample 15
Column name in raw_counts.txt:MaAAD1

value: Thoracic aorta


title: NPS_8879_CD_1

description:
Library name: NPS_8879_CD_1
RNA-Seq of CHIM NPS


title: NPS_8784_CD_2

description:
Library name: NPS_8784_CD_2
RNA-Seq of CHIM NPS


title: NPS_8878_CD_2

description:
Library name: NPS_8878_CD_2
RNA-Seq of CHIM NPS


title: WT-1-39

description: Library name: sample 16


title: MaNonAD4

description:
Library name: Sample 14
Column name in raw_counts.txt:MaNonAD4

value: WT


title: CD8+ T Cells, Wild Type, Acute Stimulation, Day 6, chr1, batch2, biol_rep 3

description: Library name: WI3D6_1

data_processing:
Quality and adapter trimming via Trimmomatic
Mapping via RNAStar to ensembl annotation GRcm39
T2/Onc2 Fusions called and quantified using Arriba
Removal of Chimeric (T2/Onc2 fusion reads) and realignment to ensembl annotation GRcm39 using Hisat2
Gene Count Quantification via subread
Assembly: Mus musculus GRcm39
Supplementary files format and content: RNA_seq_counts.txt - tab-delimited text file including raw counts for each sample
Supplementary files format and content: SB_counts.txt - tab-delimited text file containing all T2/Onc2 Fusion locations for each sample

extract_protocol:
Simultaneous genomic DNA and RNA of murine CD8+ T cell samples (Figure 2A) were isolated using Quick-DNA/RNA MagBead (Zymo R2130).
Libraries differ by batch: Batch 1 and 2 were prepared using the DNBSEQ Eukaryotic Strand-specific Transcriptome Resequencing kit by following the manufacturers instructions. Batch 3 was prepared using Illumina Truseq Stranded Total RNA with PolyA selection for mRNA species for rRNA removal

value: Spleen

value: CD8+ T Cells

value: Wild Type

value: Acute Stimulation


title: WT-3-23

description: Library name: sample 15

value: 23℃ 60 min


title: MaNonAD3

description:
Library name: Sample 13
Column name in raw_counts.txt:MaNonAD3

value: Continuous β-aminopropionitrile (0.4%) administration in drinking water


title: CD8+ T Cells, Wild Type, Acute Stimulation, Day 14, chr1, batch2, biol_rep 3

description: Library name: WI3D14_1


title: NPS_8877_CD_1

description:
Library name: NPS_8877_CD_1
RNA-Seq of CHIM NPS

value: Nose

value: NPS

value: male


title: CD8+ T Cells, Wild Type, Acute Stimulation, Day 10, chr1, batch2, biol_rep 3

description: Library name: WI3D10_1


title: MaNonAD2

description:
Library name: Sample 12
Column name in raw_counts.txt:MaNonAD2


title: NPS_8876_CD_2

description:
Library name: NPS_8876_CD_2
RNA-Seq of CHIM NPS

value: female


title: MaNonAD1

description:
Library name: Sample 11
Column name in raw_counts.txt:MaNonAD1


title: WT-2-23

description: Library name: sample 14

value: whole seedlings


title: CD8+ T Cells, Wild Type, Acute Stimulation, Day 6, chr1, batch2, biol_rep 2

description: Library name: WI2D6_1


title: WT-1-23

description: Library name: sample 13

value: wild type


title: CD8+ T Cells, Wild Type, Acute Stimulation, Day 14, chr1, batch2, biol_rep 2

description: Library name: WI2D14_1


title: NPS_8803_CD_2

description:
Library name: NPS_8803_CD_2
RNA-Seq of CHIM NPS


title: MaCon10

description:
Library name: Sample 10
Column name in raw_counts.txt:MaCon10

value: Normal drinking water control


title: exa1-3-Na

description: Library name: sample 12

value: exa1-1 mutant

value: 200 mM NaCl 60 min


title: NPS_8802_CD_3

description:
Library name: NPS_8802_CD_3
RNA-Seq of CHIM NPS


title: CD8+ T Cells, Wild Type, Acute Stimulation, Day 10, chr1, batch2, biol_rep 2

description: Library name: WI2D10_1


title: MaCon9

description:
Library name: Sample 9
Column name in raw_counts.txt:MaCon9

value: Thoracic aorta

value: Male


title: exa1-2-Na

description: Library name: sample 11


title: NPS_8801_CD_3

description:
Library name: NPS_8801_CD_3
RNA-Seq of CHIM NPS


title: CD8+ T Cells, Wild Type, Acute Stimulation, Day 6, chr1, batch2, biol_rep 1

description: Library name: WI1D6_1

value: Spleen


title: MaCon8

description:
Library name: Sample 8
Column name in raw_counts.txt:MaCon8

value: WT


title: exa1-1-Na

description: Library name: sample 10


title: NPS_8799_CD_3

description:
Library name: NPS_8799_CD_3
RNA-Seq of CHIM NPS


title: MaCon7

description:
Library name: Sample 7
Column name in raw_counts.txt:MaCon7


title: NPS_8797_CD_3

description:
Library name: NPS_8797_CD_3
RNA-Seq of CHIM NPS


title: CD8+ T Cells, Wild Type, Acute Stimulation, Day 14, chr1, batch2, biol_rep 1

description: Library name: WI1D14_1

value: CD8+ T Cells

value: Wild Type


title: exa1-3-MS

description: Library name: sample 9

value: 1/2 MS 60min


title: CD8+ T Cells, Wild Type, Acute Stimulation, Day 10, chr1, batch2, biol_rep 1

description: Library name: WI1D10_1

value: Acute Stimulation


title: exa1-2-MS

description: Library name: sample 8


title: MaCon6

description:
Library name: Sample 6
Column name in raw_counts.txt:MaCon6


title: NPS_8796_CD_4

description:
Library name: NPS_8796_CD_4
RNA-Seq of CHIM NPS

value: Nose


title: CD8+ T Cells, Wild Type, Chronic Stimulation, Day 6, chr1, batch2, biol_rep 3

description: Library name: WE3D6_1

value: Chronic Stimulation


title: MaCon5

description:
Library name: Sample 5
Column name in raw_counts.txt:MaCon5


title: exa1-1-MS

description: Library name: sample 7


title: NPS_8793_CD_3

description:
Library name: NPS_8793_CD_3
RNA-Seq of CHIM NPS

value: NPS


title: CD8+ T Cells, Wild Type, Chronic Stimulation, Day 14, chr1, batch2, biol_rep 3

description: Library name: WE3D14_1


title: MaCon4

description:
Library name: Sample 4
Column name in raw_counts.txt:MaCon4


title: WT-3-Na

description: Library name: sample 6


title: NPS_8789_CD_2

description:
Library name: NPS_8789_CD_2
RNA-Seq of CHIM NPS

value: male


title: WT-2-Na

description: Library name: sample 5

value: whole seedlings


title: MaCon3

description:
Library name: Sample 3
Column name in raw_counts.txt:MaCon3


title: CD8+ T Cells, Wild Type, Chronic Stimulation, Day 10, chr1, batch2, biol_rep 3

description: Library name: WE3D10_1


title: CD8+ T Cells, Wild Type, Chronic Stimulation, Day 6, chr1, batch2, biol_rep 2

description: Library name: WE2D6_1


title: NPS_8783_CD_2

description:
Library name: NPS_8783_CD_2
RNA-Seq of CHIM NPS


title: MaCon2

description:
Library name: Sample 2
Column name in raw_counts.txt:MaCon2


title: NPS_8782_CD_2

description:
Library name: NPS_8782_CD_2
RNA-Seq of CHIM NPS

value: female


title: WT-1-Na

description: Library name: sample 4

value: wild type


title: CD8+ T Cells, Wild Type, Chronic Stimulation, Day 14, chr1, batch2, biol_rep 2

description: Library name: WE2D14_1


title: MaCon1

description:
Library name: Sample 1
Column name in raw_counts.txt:MaCon1

value: Normal drinking water control


title: WT-3-MS

description: Library name: sample 3


title: NPS_8781_CD_2

description:
Library name: NPS_8781_CD_2
RNA-Seq of CHIM NPS


title: CD8+ T Cells, Wild Type, Chronic Stimulation, Day 10, chr1, batch2, biol_rep 2

description: Library name: WE2D10_1


title: WT-2-MS

description: Library name: sample 2


title: Old serum-exos

city: Nanjing

first: yunlu

last: Sheng

address: 300 Guangzhou Road

institute: the First Affiliated Hospital of Nanjing Medical University

description: Library name: Sample4

data_processing:
Raw reads were trimmed and filtered using SOAPnuke and then aligned to reference using Bowtie2 (v2.2.9). The small RNA expression level was calculated by counting absolute numbers of molecules using unique molecular identifiers.
Assembly: GRCm38.
Supplementary files format and content: core_table.txt

source_name: serum

growth_protocol: Male C57BL/6J aged 3 months and 18 months were maintained on a 12-h light/dark cycle and fed ad libitum with standard laboratory chow.

extract_protocol:
Exosomes obtained from young and aged small intestinal epithelium and serum were isolated by ultracentrifugation. A total of 4 RNA samples representing 4 individual groups were isolated using the miRNeasy Serum/Plasma Kit according to the manufacturer’s instructions.
MGI Easy Small RNA Library Prep Kit (940-000196-00, MGI), and quality and quantity were assessed at all steps by capillary electrophoresis (Agilent Bioanalyzer). Libraries were sequenced on a DNBSEQ-G400 with cPAS chemistry (DNBSEQ-G400RS High-throughput Sequencing Set, FCL SE50, 1000016941, MGI).

treatment_protocol: At the end of the study, the mice were sacrificed, small intestines were isolated and blood was withdrawn by cardiac puncture.

value: serum

tag: strain

value: 18 months old

value: cell-free (purified EVs)


title: NPS_8779_CD_2

description:
Library name: NPS_8779_CD_2
RNA-Seq of CHIM NPS


title: WT-1-MS

description: Library name: sample 1


title: Young serum-exos

description: Library name: Sample3

value: 3 months old


title: CD8+ T Cells, Wild Type, Chronic Stimulation, Day 6, chr1, batch2, biol_rep 1

description: Library name: WE1D6_1

value: Spleen


title: NPS_8778_CD_2

description:
Library name: NPS_8778_CD_2
RNA-Seq of CHIM NPS


title: CD8+ T Cells, Wild Type, Chronic Stimulation, Day 14, chr1, batch2, biol_rep 1

description: Library name: WE1D14_1

value: CD8+ T Cells


title: NPS_8877_CD_8

description:
Library name: NPS_8877_CD_8
RNA-Seq of CHIM NPS


title: Pexa1-3-39

description: Library name: sample 24

extract_protocol:
Polysome-bound mRNA RNA was extracted from about 200 mg samples of 9-day-old seedlings using RNAprep pure Plant Kit (TIANGEN Biotech, Cat. # DP432).
mRNA-Seq (Strand-Specific)  libraries were prepared for sequencing using standard Illumina protocols

value: exa1-1 mutant

value: 39℃ 60 min


title: CD8+ T Cells, Wild Type, Chronic Stimulation, Day 10, chr1, batch2, biol_rep 1

description: Library name: WE1D10_1

value: Wild Type


title: Young SI epithelium-exos

description: Library name: Sample1

source_name: small intestinal epithelium

value: small intestinal epithelium


title: Old SI epithelium-exos

description: Library name: Sample2


title: Pexa1-2-39

description: Library name: sample 23


title: CD8+ T Cells, Wild Type, Input, Day 2, chr1, batch2, biol_rep 1

description: Library name: WAD2_1

value: Input


title: NPS_8803_CD_1

description:
Library name: NPS_8803_CD_1
RNA-Seq of CHIM NPS

value: Nose

value: NPS


title: 70mtDD

city: Ramat-Gan

first: Hiba

last: Waldman Ben-Asher

address: Ramat-Gan

department: Life-Sciences

country: Israel

institute: Bar-Ilan University

data_processing:
Sequenced reads were mapped to the Arabidobsis reference genome sequences  (TAIR10) using STAR.
The aligned reads were quantitated by Htseq. The normalization and differentially expressed genes test were implemented by DESeq2.
Assembly: TAIR10
Supplementary files format and content: Excel file with all normalised counts for each sample

source_name: Leaf

growth_protocol: Col-0 and rtnlb16-1 plants where grown in pots containing soil under CLL conditions or under 16:8 dark:light conditions for four weeks.

extract_protocol: RNA extracted using Trisol reagent

treatment_protocol: CLL conditions :light intensity ~50 µmol/sec/m2. 16:8 dark:light conditions: light intensity ~80 µmol/sec/m2

value: Leaf

value: Four weeks old mature leaves

value: rtnlb16-1 mutant (Salk_122275)

value: CLL


title: Pexa1-1-39

description: Library name: sample 22

value: whole seedlings


title: CD8+ T Cells, DiSBey, Acute Stimulation, Day 6, chr1, batch2, biol_rep 3

description: Library name: QI3D6_1

value: DiSBey

value: Acute Stimulation


title: NPS_8802_CD_1

description:
Library name: NPS_8802_CD_1
RNA-Seq of CHIM NPS

value: male


title: Pexa1-3-23

description: Library name: sample 21

value: 23℃ 60 min


title: 69mtDD


title: NPS_8801_CD_1

description:
Library name: NPS_8801_CD_1
RNA-Seq of CHIM NPS


title: CD8+ T Cells, DiSBey, Acute Stimulation, Day 14, chr1, batch2, biol_rep 3

description: Library name: QI3D14_1

value: Spleen

value: CD8+ T Cells


title: 68mtDD


title: Pexa1-2-23

description: Library name: sample 20

value: exa1-1 mutant


title: NPS_8799_CD_1

description:
Library name: NPS_8799_CD_1
RNA-Seq of CHIM NPS

value: female


title: CD8+ T Cells, DiSBey, Acute Stimulation, Day 10, chr1, batch2, biol_rep 3

description: Library name: QI3D10_1


title: 67wtDD

value: Wild type (Col-0)


title: NPS_8797_CD_1

description:
Library name: NPS_8797_CD_1
RNA-Seq of CHIM NPS


title: Pexa1-1-23

description: Library name: sample 19


title: 66wtDD


title: CD8+ T Cells, DiSBey, Acute Stimulation, Day 6, chr1, batch2, biol_rep 2

description: Library name: QI2D6_1


title: PWT-3-39

description: Library name: sample 18

value: wild type

value: 39℃ 60 min


title: NPS_8796_CD_1

description:
Library name: NPS_8796_CD_1
RNA-Seq of CHIM NPS

value: Nose

value: NPS


title: CD8+ T Cells, DiSBey, Acute Stimulation, Day 14, chr1, batch2, biol_rep 2

description: Library name: QI2D14_1


title: PWT-2-39

description: Library name: sample 17


title: 65wtDD

value: Leaf

value: Four weeks old mature leaves


title: CD8+ T Cells, DiSBey, Acute Stimulation, Day 10, chr1, batch2, biol_rep 2

description: Library name: QI2D10_1


title: 52mtDN

value: rtnlb16-1 mutant (Salk_122275)

value: 16:8 (light:Dark)


title: NPS_8793_CD_1

description:
Library name: NPS_8793_CD_1
RNA-Seq of CHIM NPS


title: PWT-1-39

description: Library name: sample 16

value: whole seedlings


title: NPS_8789_CD_1

description:
Library name: NPS_8789_CD_1
RNA-Seq of CHIM NPS


title: CD8+ T Cells, DiSBey, Acute Stimulation, Day 6, chr1, batch2, biol_rep 1

description: Library name: QI1D6_1

value: DiSBey

value: Acute Stimulation


title: 51mtDN


title: CD8+ T Cells, DiSBey, Acute Stimulation, Day 14, chr1, batch2, biol_rep 1

description: Library name: QI1D14_1


title: 50mtDN


title: PWT-2-23

description: Library name: sample 14

value: 23℃ 60 min


title: NPS_8784_CD_1

description:
Library name: NPS_8784_CD_1
RNA-Seq of CHIM NPS

value: male


title: NPS_8783_CD_1

description:
Library name: NPS_8783_CD_1
RNA-Seq of CHIM NPS


title: CD8+ T Cells, DiSBey, Acute Stimulation, Day 10, chr1, batch2, biol_rep 1

description: Library name: QI1D10_1

value: Spleen

value: CD8+ T Cells


title: 49wtDN


title: NPS_8782_CD_1

description:
Library name: NPS_8782_CD_1
RNA-Seq of CHIM NPS

value: female


title: CD8+ T Cells, DiSBey, Chronic Stimulation, Day 6, chr1, batch2, biol_rep 2

description: Library name: QE2D6_1

value: Chronic Stimulation


title: Pexa1-3-Na

description: Library name: sample 12

value: exa1-1 mutant

value: 200 mM NaCl 60 min


title: PWT-1-23

description: Library name: sample 13

value: wild type


title: 48wtDN

value: Wild type (Col-0)


title: NPS_8781_CD_1

description:
Library name: NPS_8781_CD_1
RNA-Seq of CHIM NPS

value: Nose

value: NPS


title: CD8+ T Cells, DiSBey, Chronic Stimulation, Day 14, chr1, batch2, biol_rep 2

description: Library name: QE2D14_1


title: 47wtDN

value: Leaf

value: Four weeks old mature leaves


title: Pexa1-2-Na

description: Library name: sample 11

value: whole seedlings


title: NPS_8780_CD_1

description:
Library name: NPS_8780_CD_1
RNA-Seq of CHIM NPS


title: CD8+ T Cells, DiSBey, Chronic Stimulation, Day 10, chr1, batch2, biol_rep 2

description: Library name: QE2D10_1

value: DiSBey


title: PaTu8902 Cells, MHC-I high sort

city: Stanford

first: Anthony

last: Venida

state: CA

address: 240 Pasteur Drive

institute: Stanford University

description: Library name: Sample 2

data_processing:
Data was analyzed using publicly available code (https://github.com/mhorlbeck/ScreenProcessing). Sequences were aligned to the CRISPRi-V2 sgRNA library, individual sgRNAs with less than 10 reads in both the high and low sort bins were filtered out, and remaining sgRNAs used to calculate phenotype scores and p-values based on relative sgRNA abundances as outlined in the pipeline documentation. Volcano plots were generated in R (v4.3.1) using the ggplot2 package (v3.4.2). Custom code can be made available upon request.
Supplementary files format and content: .txt file containing raw counts
Library strategy: CRISPR Screen

growth_protocol: PaTu8902 cells were obtained from ATCC and cultured in DMEM (11995073, Gibco) supplemented with 10% FBS (Corning), 1% penicillin/streptomycin (15140122, Gibco), and 15 mM HEPES (15630080, Gibco). All cell lines were maintained at 37°C and 5% CO2. Cells were regularly tested and verified to be mycoplasma negative via PCR

extract_protocol:
Genomic DNA was isolated from frozen cell pellets (Zymo D3067).
sgRNA cassettes were amplified by PCR using Q5 Ultra II polymerase (NEB M0544) using 10 µg of genomic DNA, and primers containing sample-specific indexes and Illumina sequencing adapters; PCR amplicons were purified by double-sided 0.65-1X SPRI selection (Beckman B23317); and pooled equimolarly. Subsequently, sgRNA amplicon pools were sequenced on a HiSeq4000 (Illumina) with single-end 50 reads achieving >140M reads/sample.

value: Human pancreatic adenocarcinoma

value: WT


title: Pexa1-1-Na

description: Library name: sample 10


title: NPS_8779_CD_1

description:
Library name: NPS_8779_CD_1
RNA-Seq of CHIM NPS


title: CD8+ T Cells, DiSBey, Chronic Stimulation, Day 6, chr1, batch2, biol_rep 1

description: Library name: QE1D6_1


title: PaTu8902 Cells, MHC-I low sort

description: Library name: Sample 1


title: Pexa1-3-MS

description: Library name: sample 9

value: 1/2 MS 60min


title: NPS_8778_CD_1

description:
Library name: NPS_8778_CD_1
RNA-Seq of CHIM NPS


title: CD8+ T Cells, DiSBey, Chronic Stimulation, Day 14, chr1, batch2, biol_rep 1

description: Library name: QE1D14_1

value: Spleen


title: MCF7 aZAL 72 hours rep 3

city: Piscataway

first: Cassandra

last: Winz

state: NJ

address: 160 Frelinghuysen Rd

institute: Rutgers University

description: Library name: z401

data_processing:
Data processing was completed by Novogene.
Assembly: GRCh38
Supplementary files format and content: Raw counts for each sample in a csv file

source_name: breast cancer

growth_protocol: MCF-7 cells were maintained in DMEM F12 media supplemented with FBS 10% in a humidified atmosphere at 37˚C 5% CO2.

extract_protocol:
Total RNA was extracted with trizol 12 or 72 hours after treatment.
Library construction was completed by Novogene.

treatment_protocol: Cells were washed and treated with RPMI media supplemented with charcoal stripped FBS 5% one day after seeding

value: breast cancer

value: ER+ transformed breast cancer

value: aZAL 1 uM


title: Pexa1-2-MS

description: Library name: sample 8

value: exa1-1 mutant


title: CD8+ T Cells, DiSBey, Chronic Stimulation, Day 10, chr1, batch2, biol_rep 1

description: Library name: QE1D10_1

value: CD8+ T Cells

value: Chronic Stimulation


title: NPS_8876_CD_9

description:
Library name: NPS_8876_CD_9
RNA-Seq of CHIM NPS

value: female


title: Pexa1-1-MS

description: Library name: sample 7


title: MCF7 aZAL 12 hours rep 3

description: Library name: z393


title: PWT-3-23

description: Library name: sample 15

value: wild type

value: 23℃ 60 min


title: NPS_8878_CD_8

description:
Library name: NPS_8878_CD_8
RNA-Seq of CHIM NPS

value: Nose

value: NPS

value: male


title: CD8+ T Cells, DiSBey, Input, Day 2, chr1, batch2, biol_rep 1

description: Library name: QAD2_1

value: DiSBey

value: Input


title: PWT-3-Na

description: Library name: sample 6

value: whole seedlings

value: 200 mM NaCl 60 min


title: CD8+ T Cells, Wild Type, Acute Stimulation, Day 18, chr1, batch1, biol_rep 3

description: Library name: WI-3-D18_1

value: Spleen

value: Wild Type

value: Acute Stimulation


title: MCF7 aZAL 72 hours rep 2

description: Library name: z341

value: breast cancer

value: ER+ transformed breast cancer

value: WT

value: aZAL 1 uM


title: PIP-seq, postnatal day 14, replicate 2

city: Chapel Hill

first: LI

last: QIAN

address: 111 Mason Farm Road, MBRB

department: Department of pathology

institute: UNC

description: Library name: PIP-seq library 2

data_processing:
To map sequencing read to the mouse transcriptome and our sgRNA sequence, a customized csv file was generated containing the probe sequences of the whole mouse transcriptome and sgRNAs. Cellranger aggr function was used to generate the count matrix.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz
Supplementary files format and content: features.tsv.gz
Supplementary files format and content: matrix.mtx.gz

molecule: nuclear RNA

source_name: Heart

extract_protocol:
Hearts were harvested on postnatal day 14. Hearts were perfused with KCl and PBS before harvesting. After removing the heart from the chest, the ventricles of the harvested heart were minced into pieces on a glass petri dish on ice using a razor blade. A cut/bore tip was used to transfer tissue pieces from the glass petri dish to a 15ml falcon tube. The tube was then topped with fixation buffer (4% formaldehyde, 1X Fix & Perm Buffer) to reach a 25 mg tissue to 1ml fixation ratio. The tissue pieces were then incubated in the fixation buffer for 20 hours at 4°C without rotation. The incubation time should be consistent between samples for the same batch of experiments. After incubation, tissue pieces were centrifuged at 850 g for 5 min at room temperature. The supernatant was removed without disturbing the tissue pellet. Then the tissue pieces were washed again with 2 ml chilled PBS and resuspended in tissue homogenization buffer for nuclei isolation. The nuclei isolation for fixed heart tissue is almost the same as previously described for snRNA-seq. One notable difference is instead of performing 30 strokes with tight pestles, 50 strokes were performed for each heart. After nuclei isolation, flow cytometry was performed to enrich the GFP+/DRAQ+ population.
Then, fixed RNA single-nucleus libraries were generated with the GFP+/DRAQ5+ population by strictly following the manufacturer’s manual (Chromium Fixed RNA Profiling Reagent Kits for Singleplexed Samples, CG000691). During the spike in step of the custom probes, the left hand side probes were spiked at 20nM/probe instead of default 2nM/probe, and the right hand side probes were spiked at 10nM/probe instead of 2nM/probe as default.

value: Heart


title: Dark SkO

city: Boston

first: Karl

middle: Russell

last: Koehler

state: MA

address: 3 Blackfan Circle

department: Otolaryngology-Head and Neck Surgery

institute: Boston Children's Hospital-Harvard Medical School

description:
Library name: 6-D-GEX
10x Genomics

data_processing:
The alignment, barcoded processing, gene counting and aggregation were made using the Cell Ranger v7.1.0.
Ambient RNA was removed using SoupX v1.6.2.
Multiplets were identified using the scds v1.14.0 and excluded.
Cells exhibiting extremely low or high library sizes and number of gene features, falling outside the 95% confidence interval, as well as those displaying greater than 10% mitochondrial content were excluded.
Assembly: GRCh38
Supplementary files format and content: HDF5 (.h5) format, containing filtered gene expression matrix produced from CellRanger

source_name: Organoid

growth_protocol: hPSC lines and maintenance. Human PS lines–iPS-FH202-sev1, iPS-FHT243-sev1, iPS-FHT299-sev2, and iPS-FH310-sev3 hiPSC lines (passages 19–26)–were obtained from the Wistar institute. Cells were cultured on vitronectin-coated (0.5 µg/cm2; Gibco) 6-well plates in either Essential 8 Flex (hereafter, E8; Gibco) media. Medium was replenished every 1-2 days depending on confluency. Upon reaching ~80% confluency (typically every 4–5 days), cells were passaged: Cells were dissociated into small clusters (5-8 cells per cluster) using Accutase (Gibco) for cultures in E8 or 0.5 mM EDTA (Invitrogen) for cultures in mTeSR. Following dissociation, cells were replated in their respective media (E8 or mTeSR) supplemented with 10 µM Y27632 (hereafter, Y; a ROCK inhibitor that inhibits apoptosis; ReproCELL). After 24 hrs, medium was replaced with E8 or mTeSR without Y. All cell lines were assessed for karyotypic stability and routinely tested for mycoplasma contamination (Invivogen).

extract_protocol:
Skin organoid dissociation for scRNA-seq. Day-130 organoids (n = 1 per group) were incubated in 10% Dispase (Corning) containing the CEPT cocktail (hereafter, CEPT; final concentrations: 50 nM Chroman 1 (MedChem Express), 5 µM Emricasan (Selleck Chemicals), 1x Polyamine Supplement (Sigma-Aldrich), and 0.7 µM Trans-ISRIB (Tocris)) for 30 min at 37°C. During incubation, samples were gently pipetted every 10 minutes–initially using wide-orifice p1000 or p200 tips (Rainin), followed by standard p200 tips to enhance dissociation. Residual aggregate clumps were briefly centrifuged into pellets, and the dissociated cell suspensions were retained and kept on ice. The pellets were then resuspended in TrypLE™ (Gibco) supplemented with CEPT and further incubated until fully dissociated (typically an additional 30 min at 37°C with 10 min interval pipetting). Dispase and TrypLE™ fractions were pooled and gently mixed. Enzymatic activity was neutralized by adding 3% cold BSA (Invitrogen) in CEPT-supplemented medium at a 2:1 ratio volume ratio (medium:cell suspension). Cells were centrifuged into pellets (230 rcf, 5 min 30 sec, room temperature (RT)) and washed twice with a neutralizing buffer. The final suspension was filtered through a 40 µm Flowmi™ strainer (Bel-Art™). Cell viability and concentration (target: ~1,000 cells/µL; >90% viable) were determined using Trypan Blue and a Countess™ III FL Automated Cell Counter.
Single-cell cDNA library construction and sequencing. Day-130 light- and dark-SkO samples were processed for single-cell transcriptomic profiling using the Chromium Single Cell 3’ system (10x Genomics) and sequenced on NovaSeq 6000 platform. Approximately 17,000 cells per sample (targeting recovery of ~10,000 cells) were resuspended in the reverse transcription (RT) master mix from the Chromium Single Cell 3’ Reagent Kit v3.1 (10x Genomics). Cell suspensions were then combined with barcoded gel beads and partitioning oil in a Single Cell A Chip and loaded into the Chromium Controller for generation of Gel Beads-in-Emulsion (GEMs). RT, cDNA amplification, and library preparation were performed according to the manufacturer’s protocol (CG000183, Rev C). The quality of amplified cDNA and final libraries was assessed using a Bioanalyzer (Agilent). Sequencing was conducted with paired-end read lengths for the NovaSeq 6000–to achieve a read depth of >30,000 reads per cell.

treatment_protocol: Skin organoid differentiation. Skin organoid differentiation was performed as previously described (Lee et al., Nat. Protoc. 2022) [REF] with minor refinements. To initiate differentiation, hPSCs were dissociated into single cells using Accutase and resuspended in E8  with 10 µM Y (hereafter, E8-10Y). Viable cells were counted via Trypan Blue (invitrogen) exclusion using the Countess™ III FL Automated Cell Counter (Invitrogen) Cells were diluted in E8 with 20 µM Y (hereafter, E8-20Y) to 3,500 cells/100 µL and seeded in 96-well U-bottom low-attachment plates (Thermo Scientific). Following centrifugation (110 rcf, 6 min), aggregates were incubated at 37°C with 5% CO2; this time point was designated as day -2. On day -1, 100 µL of E8 was added per well. Matrigel (Corning) was thawed overnight (O/N) at 4°C in preparation for day 0 differentiation. On day 0, aggregates were washed 3 times with Essential 6 medium (hereafter, E6; Gibco) and transferred into new 96-well U-bottom low-attachment plates in 100 µL of E6 containing 2% Matrigel, 10 µM SB431542 (ReproCELL), 4 ng/mL basic-FGF (hereafter, bFGF; PeproTech), 2.5-7.5 ng/mL BMP-4 (PeproTech), and 100 µg/mL Normocin (Invivogen). In this study, BMP4 concentration was optimized to 5 ng/mL based on titration (see Supplementary Fig. 2 for representative images). On day 3, 25 µL of E6 containing 1 µM LDN193189 (hereafter, LDN; ReproCELL) and 250 ng/mL bFGF was added to each well to yield final concentrations of 200 nM LDN and 50 ng/mL bFGF in a total volume of 125 µL. On day 6, 75 µL of E6 was added per well (final volume: 200 µL). On day 9, 100 µL (half the well volume) of medium was replaced with fresh E6. On day 12, aggregates were washed in Advanced DMEM/F12 (Gibco) and transferred to individual wells of 24-well low-attachment plates (Thermo Scientific) in 500 µL of organoid maturation medium (OMM) with 1% Matrigel. OMM was composed of Advanced DMEM/F12 and Neurobasal media (1:1; Gibco), supplemented with 1x GlutaMAX™ (Gibco), 0.5x B-27 minus vitamin A (Gibco), 0.5x N2 (Gibco), 0.1 mM 2-mercaptoethanol (Gibco), and 100 µg/mL Normocin. Organoids were maintained on an orbital shaker (65 rpm, 37°C, 5% CO2). On day 15, 250 µL (half the well volume) of OMM was replaced with fresh OMM containing 1% Matrigel. From day 18 onward, organoids were maintained in OMM without Matrigel. Between days 18–45, organoides underwent weekly full-medium changes and 2-3 day half-medium changes. After day 45, the medium was fully changed (500 µL) every 2-3 days. As organoids grew, OMM volume per well was increased to 1 mL around day 80. Detailed protocols are available in Lee et al., Nat. Protoc. 2022.

value: Organoid

tag: tissue type

value: dark-pigmented skin organoids (SkO)

value: day 130


title: MCF7 aZAL 12 hours rep 2

description: Library name: z333


title: Light SkO

description:
Library name: 4-L-GEX
10x Genomics

value: light-pigmented skin organoids (SkO)


title: CD8+ T Cells, Wild Type, Acute Stimulation, Day 18, chr1, batch1, biol_rep 2

description: Library name: WI-2-D18_1

value: CD8+ T Cells


title: MCF7 aZAL 72 hours rep 1

description: Library name: z20


title: PWT-2-Na

description: Library name: sample 5

value: wild type


title: PWT-1-Na

description: Library name: sample 4


title: 16PlexMs_FLEX_Cells_GEX

city: Pittsburgh

first: Sudhagar

last: Babu

address: 200 Lothrop Street

institute: University of Pittsburgh School of Medicine

description:
Library name: Cambi_051724_16PlexMs_FLEX_Cells_GEX
The library contains 16 multiplexed biological samples that were demultiplexed using Cell Ranger multi. Sample-specific probe barcode assignments and multiplexing information are provided in the **cellranger_multi_config.csv** file.

library_source: other

data_processing:
Raw FASTQ sequencing files were demultiplexed and aligned to the Chromium Mouse Transcriptome Probe Set v1.0.1 (mm10-2020A) from 10x Genomics using the Cell Ranger multi pipeline (version 8.0.1).
Assembly: mm10
Supplementary files format and content: .h5

molecule: other

source_name: Hippocampus

extract_protocol:
Mice were deeply anesthetized and perfused intracardially with ice cold PBS, brains were removed, and hippocampi were quickly dissected on ice. We collected hippocampi from 2 brains/sample. The cell suspensions were prepared using the Adult Brain Dissociation Kit (Miltenyi Biotec 130-107-677) according to the manufacturer’s instructions with the following modifications that increased cell yield. The tissues were chopped into small pieces on ice prior to adding to the Enzyme 1 mix, after enzymatic and mechanical dissociation, the mixtures were triturated with P1000 5-10 times to dissociate undigested pieces of tissue, red blood cell removal step was omitted since brains were thoroughly perfused with PBS. Cell counts and viability were measured with AO/PI staining in an automated cell count system (Cellometer Cell Viability Counter, Nexcelom).
Cells were immediately fixed using 10X FLEX reagents and 10x Genomics protocol, counted post-fixation and stored at -80 C according to 10X Genomics protocol. 4 biological replicates per genotype (M:F ratio was 40:60), each replicate containing hippocampi from two brains, were submitted to the Single Cell Transcriptomics Core at the University of Pittsburgh. Each sample contained ∼300,000 cells and the viability was >80%. Libraries were prepared using the Chromium Fixed RNA Profiling Reagents Kit for Multiplexed Samples (10x Genomics) according to the manufacturer’s protocol. Libraries sequencing performed by the Health Sciences Sequencing Core at the University of Pittsburgh generated 1.8 billion reads which covers more than 10,000 reads per cell.

value: Hippocampus

value: AppNL-G-F, AppNL-G-F/ Fusfl/fl/Cnpcre/+, Fusfl/fl/Cnpcre/+, Fusfl/fl


title: MCF7 aZAL 12 hours rep 1

description: Library name: z12


title: CD8+ T Cells, Wild Type, Acute Stimulation, Day 18, chr1, batch1, biol_rep 1

description: Library name: WI-1-D18_1


title: PWT-3-MS

description: Library name: sample 3

value: whole seedlings

value: 1/2 MS 60min


title: PWT-2-MS

description: Library name: sample 2


title: RNAseq of AAV9-sgNT injected postnatal heart at day 35, rep 3

description: Library name: sgNT_day35_rep3

data_processing:
Bulk RNA-seq reads (paired-end) were aligned to the mouse mm10 reference genome using HISAT2 (version 2.2.1). For each sample, raw FASTQ files were aligned with hisat2 default parameter and then directly sorted to BAM using samtools (version 1.23) sort, followed by BAM indexing with samtools index. Gene-level quantification was performed with Subread (version 2.1.1) featureCounts using the mm10 GTF annotation file. Reads were summarized with featureCounts in paired-end mode (-p), assigning features by gene_id (-g gene_id) and counting reads overlapping transcript features (-t transcript), producing a count matrix. Gene-level count matrices generated by featureCounts were imported into R (4.3.0) and used for differential expression analysis with DESeq2 (version 1.42.1). Briefly, the featureCounts output table was read in and non-count annotation columns were removed prior to downstream analysis. Samples were assigned to two conditions (sgNT and sgRreb1; n=3 each), and a DESeq2 object was constructed using the design formula ~ condition. Lowly expressed genes were prefiltered by retaining genes with a total raw count >10 across all samples. Size-factor normalization and dispersion estimation were performed using DESeq2’s negative binomial model, and differential expression was tested using Wald statistics. Pairwise differential expression contrasts were computed for sgRreb1 vs sgNT. Differential expression between experimental groups was assessed using the Wald test, and p-values were adjusted for multiple testing using the Benjamini–Hochberg method to control the false discovery rate (FDR).
Assembly: mm10
Supplementary files format and content: txt file of TPM value for each sample

extract_protocol:
Hearts were perfused with KCl and PBS before harvesting. After removing the heart from the chest, the ventricles of the harvested heart were minced into pieces on a glass petri dish on ice using a razor blade.  Minced heart tissue was then transferred to a 15 ml falcon tube for tissue homogenization with 1 ml of homogenization buffer (0.32M sucrose, 1mM Tris-HCl PH8.0, 3mM Magnesium Acetate, 0.1mM EDTA, 5mM Calcium Chloride, 0.1% Triton, 1x cOmplete Protease Inhibitor Cocktail, 200 U/ml RNase OUT, 1mM DTT). The tissue homogenization was performed on ice with two cycles of 30 second on and 60 sec off. After the tissue was completely homogenized, the tissue lysate was then transferred to a 7 ml tissue grinder. 1 ml of tissue homogenization buffer was used to wash the falcon tube before adding it to the tissue grinder. Eight strokes were performed with a loose pestle (A) on ice. 50 strokes were performed with a tight pestle (B) on ice. Then the tissue lysate was passed through a 70 μm and followed with a 40 μm cell strainer.  Wash off any left-over tissue lysate from the 40 μm cell strainer with 1 ml of the homogenization buffer. Then the nuclei were pelleted by centrifuging at 500 g for 5 min at 4°C. Wash the pellet twice with resuspension buffer (PBS/1%BSA, 200 U/ml RNase OUT, 1 mM DTT). After nuclei isolation, flow cytometry was performed to enrich the GFP+/DRAQ+ population.
Total RNA was extracted using RNeasy Micro Kit (Qiagen) with genome DNA removed through on-column DNase I digestion. RNA-seq libraries were constructed using kapa mRNA Stranded library Kit and were on a Nextseq 2000 (Illumina) with 100 base-pair pair-end reads.

value: Cardiomyocyte


title: CD8+ T Cells, Wild Type, Chronic Stimulation, Day 18, chr1, batch1, biol_rep 3

description: Library name: WE-3-D18_1

value: Spleen

value: Wild Type

value: Chronic Stimulation


title: RNAseq of AAV9-sgNT injected postnatal heart at day 35, rep 2

description: Library name: sgNT_day35_rep2


title: MCF7 BPA 72 hours rep 3

description: Library name: b400

value: breast cancer

value: ER+ transformed breast cancer

value: WT

value: BPA 1 uM


title: PWT-1-MS

description: Library name: sample 1


title: CD8+ T Cells, Wild Type, Chronic Stimulation, Day 18, chr1, batch1, biol_rep 2

description: Library name: WE-2-D18_1


title: MCF7 BPA 12 hours rep 3

description: Library name: b392


title: CD8+ T Cells, Wild Type, Chronic Stimulation, Day 18, chr1, batch1, biol_rep 1

description: Library name: WE-1-D18_1


title: RNAseq of AAV9-sgNT injected postnatal heart at day 35, rep 1

description: Library name: sgNT_day35_rep1

value: Heart


title: e1-39-3

description: Library name: sample 24

treatment_protocol: no treatment

value: exa1-1 mutant

value: 39℃ 60 min


title: RNAseq of AAV9-sgRreb1 injected postnatal heart at day 35, rep 3

description: Library name: sgRreb1_day35_rep3


title: MCF7 BPA 72 hours rep 2

description: Library name: b340


title: CD8+ T Cells, Wild Type, Input, Day 2, chr1, batch1, biol_rep 1

description: Library name: WA_1

value: CD8+ T Cells

value: Input


title: MCF7 BPA 12 hours rep 2

description: Library name: b332


title: e1-39-2

description: Library name: sample 23


title: CD8+ T Cells, DiSBey, Acute Stimulation, Day 18, chr1, batch1, biol_rep 3

description: Library name: QI-3-D18_1

value: DiSBey

value: Acute Stimulation


title: RNAseq of AAV9-sgRreb1 injected postnatal heart at day 35, rep 2

description: Library name: sgRreb1_day35_rep2


title: MCF7 BPA 72 hours rep 1

description: Library name: b19


title: e1-39-1

description: Library name: sample 22

value: whole seedlings


title: CD8+ T Cells, DiSBey, Acute Stimulation, Day 18, chr1, batch1, biol_rep 2

description: Library name: QI-2-D18_1


title: RNAseq of AAV9-sgRreb1 injected postnatal heart at day 35, rep 1

description: Library name: sgRreb1_day35_rep1


title: MCF7 BPA 12 hours rep 1

description: Library name: b11


title: e1-23-3

description: Library name: sample 21

value: 23℃ 60 min


title: Mouse Cardiac Myofibroblast, Normoxia, Control, Rep 3

city: Edmonton

first: Zamaneh

last: Kassiri

state: Alberta

address: 474 HMRC

department: Physiology

country: Canada

institute: University of Alberta

description: Library name: MNC3

data_processing:
Kallisto (v0.44.0)
Assembly: Mus_musculus.GRCm39.cdna.all.fa,
Supplementary files format and content: abundance.tsv, abundance.h5, run_info.json

growth_protocol: DMEM-F12 with 2% FBS

extract_protocol:
RNeasy Plus Universal Mini Kit (QIAGEN, 73404)
Completed by SBME UBC (https://bme.ubc.ca/home/sequencing-facility/)

treatment_protocol: Normoxia (21% Oxygen) / Hypoxia (1% Oxygen)

value: Cardiac Myofibroblast

tag: passage

value: Passage 1

value: Wild type

value: pooled male and female

value: Control siRNA, Normoxia


title: e1-23-2

description: Library name: sample 20


title: MCF7 E2 72 hours rep 3

description: Library name: e399

value: breast cancer

value: ER+ transformed breast cancer


title: CD8+ T Cells, DiSBey, Acute Stimulation, Day 18, chr1, batch1, biol_rep 1

description: Library name: QI-1-D18_1

value: Spleen


title: Mouse Cardiac Myofibroblast, Normoxia, Control, Rep 2

description: Library name: MNC2

value: Heart


title: CD8+ T Cells, DiSBey, Chronic Stimulation, Day 18, chr1, batch1, biol_rep 2

description: Library name: QE-2-D18_1

value: Chronic Stimulation


title: MCF7 E2 12 hours rep 3

description: Library name: e391

value: WT


title: e1-23-1

description: Library name: sample 19

value: exa1-1 mutant


title: CD8+ T Cells, DiSBey, Chronic Stimulation, Day 18, chr1, batch1, biol_rep 1

description: Library name: QE-1-D18_1

value: CD8+ T Cells


title: Mouse Cardiac Myofibroblast, Normoxia, Control, Rep 1

description: Library name: MNC1


title: MCF7 E2 72 hours rep 2

description: Library name: e339


title: WT-39-3

description: Library name: sample 18

value: wild type

value: 39℃ 60 min


title: Mouse Cardiac Myofibroblast, Normoxia, Adam17 siRNA, Rep 3

description: Library name: MNA3

value: Adam17siRNA, Normoxia


title: CD8+ T Cells, DiSBey, Input, Day 2, chr1, batch1, biol_rep 1

description: Library name: QA_1

value: DiSBey

value: Input


title: WT-39-2

description: Library name: sample 17

value: whole seedlings


title: MCF7 E2 12 hours rep 2

description: Library name: e331


title: siF3

city: Rancagua

first: Nicolas

last: Santander

address: Libertador Bernardo O'Higgins 611

country: Chile

institute: Universidad de O´Higgins

description:
Library name: siF3
counts_table_siFLVCR2.txt

data_processing:
Align to hg38  with Rsubread
Quantification with FeatureCounts
Normalization and diffierential expression with DESeq2
Assembly: ARS-UCD1.2
Supplementary files format and content: tab delimited file with raw counts for each sample

organism: Bos taurus

source_name: Retina

extract_protocol:
Rneasy Plus micro kit Qiagen
NEBNext Ultra II RNA Library Prep Kit

value: Retina

value: Endothelial cell


title: Mouse Cardiac Myofibroblast, Normoxia, Adam17 siRNA, Rep 2

description: Library name: MNA2

value: Cardiac Myofibroblast

value: Passage 1

value: Wild type

value: pooled male and female


title: MCF7 E2 72 hours rep 1

description: Library name: e18

value: breast cancer

value: ER+ transformed breast cancer


title: WT-39-1

description: Library name: sample 16


title: Mouse Cardiac Myofibroblast, Normoxia, Adam17 siRNA, Rep 1

description: Library name: MNA1

value: Heart


title: siF2

description:
Library name: siF2
counts_table_siFLVCR2.txt


title: MCF7 E2 12 hours rep 1

description: Library name: e10

value: WT


title: WT-23-3

description: Library name: sample 15

value: 23℃ 60 min


title: Mouse Cardiac Myofibroblast, Hypoxia, Control, Rep 4

description: Library name: MHC4

value: Control siRNA, Hypoxia


title: siF1

description:
Library name: siF1
counts_table_siFLVCR2.txt


title: MCF7 control 72 hours rep 3

description: Library name: c398


title: WT-23-2

description: Library name: sample 14

value: wild type


title: Mouse Cardiac Myofibroblast, Hypoxia, Control, Rep 3

description: Library name: MHC3


title: Scr4

description:
Library name: Scr4
counts_table_siFLVCR2.txt

value: scr


title: MCF7 control 12 hours rep 3

description: Library name: c390


title: WT-23-1

description: Library name: sample 13


title: Mouse Cardiac Myofibroblast, Hypoxia, Control, Rep 2

description: Library name: MHC2


title: MCF7 control 72 hours rep 2

description: Library name: c338


title: Scr3

description:
Library name: Scr3
counts_table_siFLVCR2.txt


title: e1-N-3

description: Library name: sample 12

value: exa1-1 mutant

value: 200 mM NaCl 60 min


title: MCF7 control 12 hours rep 2

description: Library name: c330


title: Scr2

description:
Library name: Scr2
counts_table_siFLVCR2.txt


title: e1-N-2

description: Library name: sample 11

value: whole seedlings


title: Mouse Cardiac Myofibroblast, Hypoxia, Control, Rep 1

description: Library name: MHC1


title: Mouse Cardiac Myofibroblast, Hypoxia, Adam17 siRNA, Rep 4

description: Library name: MHA4

value: Adam17siRNA, Hypoxia


title: MCF7 control 72 hours rep 1

description: Library name: c17


title: Mouse Cardiac Myofibroblast, Hypoxia, Adam17 siRNA, Rep 3

description: Library name: MHA3


title: e1-N-1

description: Library name: sample 10


title: e1-MS-3

description: Library name: sample 9

value: 1/2 MS 60min


title: SA3

description:
Library name: SA3
counts_table_SA.txt

value: Retina

value: Endothelial cell

value: SA


title: e1-MS-2

description: Library name: sample 8


title: R147-H-008

city: CARDIFF

first: Neil

last: Rodrigues

address: Maindy Road

department: The European Cancer Stem Cell Research Institute

country: United Kingdom

institute: Cardiff University

description:
Library name: Gata2; Mx1-Cre Heterozygote -4
Gata2 heterozygote HSC 4 (LSK CD48- CD150+)

data_processing:
Trimming to remove adapter sequencer and poor quality ends of reads was performed by Trim Galore ( a wrapper to cutadapt). Trimming was performed using default parameters in paired-end mode.
Trimmed paired-end reads were aligned to the GRCm38 reference using STAR (v2.5.1b), an ultrafast universal RNA-seq aligner, following the 2-pass method.  STAR mapping was carried out using the MultimapNMax=1 flag, whereby reads that map to more than one genomic location are treated as being unmapped so as to excluded them from downstream analysis.
Transcript level counts were calculated using Subread featureCounts Version 1.5.1. Transcript and locations used in the analysis derive from the GENCODE GRCm38 v17 gene annotation.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files containing: ensemble transcript ID, chromosome, start and end locations, strand, transcripts length and counts in STAR mapped bam file.

source_name: bone marrow

extract_protocol:
HSC cells were resuspended in RLT buffer (Qiagen) and stored at -80 degrees. RNA extraction was carried out using a RNAeasy Plus micro kit (Qiagen) following the manufacturers instructions. Total RNA quality and quantity was assessed using Agilent 2100 Bioanalyser and a RNA Nano 6000 kit (Agilent Technologies). 30-260ng of Total RNA with a RIN value >8 was depleted of ribosomal RNA using the NEBNext® rRNA Depletion Kit (Human/Mouse/Rat), (New England BioLabs, NEB).
Sequencing libraries were prepared using the NEB® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB). The steps included RNA fragmentation and priming, 1st strand cDNA synthesis, 2nd strand cDNA synthesis, adenylation of 3’ ends, adapter ligation, PCR amplification (11-cycles) and validation. The manufacturer’s instructions were followed. The libraries were validated using the Agilent 2100 Bioanalyser and a high-sensitivity kit (Agilent Technologies) to ascertain the insert size, and the Qubit® (Life Technologies) was used to perform the fluorometric quantitation. Following validation, the libraries were normalized to 10nM, pooled together and clustered on the cBot™2 following the manufacturer’s recommendations. The pool was then sequenced using a 75-base paired-end (2x75bp PE) dual index read format on the Illumina® HiSeq4000 according to the manufacturer’s instructions.

value: bone marrow

value: HSCs

value: Gata2 heterozygote


title: Mouse Cardiac Myofibroblast, Hypoxia, Adam17 siRNA, Rep 1

description: Library name: MHA1

value: Heart

value: Cardiac Myofibroblast

value: Passage 1

value: Wild type

value: pooled male and female


title: SA2

description:
Library name: SA2
counts_table_SA.txt


title: e1-MS-1

description: Library name: sample 7


title: Mouse Cardiac Fibroblast, Normoxia, Control, Rep 3

description: Library name: FNC3

value: Cardiac Fibroblast

value: Control siRNA, Normoxia


title: R147-H-006

description:
Library name: Gata2; Mx1-Cre Heterozygote -2
Gata2 heterozygote HSC 2 (LSK CD48- CD150+)


title: SA1

description:
Library name: SA1
counts_table_SA.txt


title: WT-N-3

description: Library name: sample 6

value: wild type

value: 200 mM NaCl 60 min


title: Con4

description:
Library name: Con4
counts_table_SA.txt

value: con


title: WT-N-2

description: Library name: sample 5

value: whole seedlings


title: R147-H-004

description:
Library name: Gata2 WT-4
Wild Type HSC 4 (LSK CD48- CD150+)

value: Gata2 WT


title: Con3

description:
Library name: Con3
counts_table_SA.txt

value: Retina

value: Endothelial cell


title: WT-N-1

description: Library name: sample 4


title: Mouse Cardiac Fibroblast, Normoxia, Adam17 siRNA, Rep 3

description: Library name: FNA3

value: Adam17siRNA, Normoxia


title: Con2

description:
Library name: Con2
counts_table_SA.txt


title: WT-MS-3

description: Library name: sample 3

value: 1/2 MS 60min


title: R147-H-003

description:
Library name: Gata2 WT-3
Wild Type HSC 3 (LSK CD48- CD150+)

value: bone marrow

value: HSCs


title: Con1

description:
Library name: Con1
counts_table_SA.txt


title: WT-MS-2

description: Library name: sample 2


title: R147-H-002

description:
Library name: Gata2 WT-2
Wild Type HSC 2 (LSK CD48- CD150+)


title: Mouse Cardiac Fibroblast, Normoxia, Adam17 siRNA, Rep 1

description: Library name: FNA1

value: Heart


title: Subject 33 BAL

city: Denver

first: Elizabeth

last: Wynn

state: CO

address: 1400 Jackson St.

institute: National Jewish Health

description: Library name: Subject 33 BAL

data_processing:
PBMC RNA-seq: Reads were adapter-trimmed and quality-controlled, then aligned to the human genome using STAR. Transcript abundance was quantified with Salmon and summarized to gene-level counts using tximeta.  BAL AmpliSeq: Ion Torrent AmpliSeq RNA plugin was used to generate count tables.
Assembly: GRCh38
Supplementary files format and content: comma separated (.csv) matrix of raw counts. Rows are features and columns are cells.

source_name: BAL

extract_protocol:
Aspirated alveolar fluid and blood were collected in parallel from patients in cell preparation tubes (CPT) and immediately processed. Cells were cryopreserved and later thawed for RNA isolation. Total RNA was extracted from BAL cells and PBMCs using standard column-based RNA extraction methods according to manufacturer instructions.
BAL (AmpliSeq): Targeted RNA libraries were prepared using the Ion AmpliSeq Human Transcriptome Panel. Sixteen nanograms of total RNA was reverse transcribed, amplified, barcoded, purified with magnetic beads, and PCR-amplified per manufacturer protocol. Libraries were quantified, pooled, templated on an Ion Chef Instrument, and sequenced on an Ion Torrent S5 Prime.  PBMC (RNA-seq): Libraries were prepared using the KAPA mRNA HyperPrep kit. Poly(A)+ mRNA was isolated from 50 ng total RNA, fragmented, converted to cDNA, adapter-ligated with dual indices, PCR amplified, pooled, and sequenced on an Illumina NovaSeq 6000 (paired-end).

value: BAL

tag: gender

value: Male


title: R147-H-001

description:
Library name: Gata2 WT-1
Wild Type HSC 1 (LSK CD48- CD150+)

tag: tissue


title: WT-MS-1

description: Library name: sample 1

extract_protocol:
Total RNA was extracted from about 50 mg samples of 9-day-old seedlings using RNAprep pure Plant Kit (TIANGEN Biotech, Cat. # DP432).
mRNA-Seq (Strand-Specific)  libraries were prepared for sequencing using standard Illumina protocols


title: Mouse Cardiac Fibroblast, Hypoxia, Control, Rep 4

description: Library name: FHC4

value: Passage 1

value: Wild type

tag: Sex

value: pooled male and female

value: Control siRNA, Hypoxia


title: Subject 32 BAL

description: Library name: Subject 32 BAL


title: S3KO_CD8_D661Y_rep2

city: Maimi

first: Alejandro

last: Villarino

state: Florida

address: 1600 NW 10th Ave, Rosenstiel Medical Science Building (RMSB), Room 3152A

institute: University of Miami

description:
Library name: Villarino-26343-045_RNAseq
Hennighausen_STAT3_D661_CD8_GEO_RNAseq_gene_counts.txt

data_processing:
bulk RNA-seq: FASTQ alignment with Tophat2
bulk RNA-seq: transcript assembly with cufflinks
bulk RNA-seq: Gene level read count data generated using htseq-count
Assembly: bulk RNA-seq: mm10
Supplementary files format and content: bulk RNA-seq: Tab delimited text of RNA-seq gene-level expression count data

source_name: pooled LN and spleen

growth_protocol: 20-100K viable, GFP+ cells were sorted and cultured, then lysed and stored in Trizol

extract_protocol:
Total RNA isolated from TRIzol by phenol/chloroform extraction, then mRNA enriched with NEBNext Poly(A) mRNA Magnetic Isolation Module
For bulk RNA-seq, sequencing libraries were generated with NEBNext Ultra II Library Prep Kit for Illumina (E7645L, New England Biolabs).

treatment_protocol: 20-100K viable cells were sorted and cultured with IL-27, then lysed and stored in Trizol

value: pooled LN and spleen

value: CD8+ T cell

value: Viable CD8+ GFP+ RV tranduced

tag: genotype


title: Mouse Cardiac Fibroblast, Hypoxia, Control, Rep 3

description: Library name: FHC3

value: Cardiac Fibroblast

tag: treatment


title: 24 month HSC CITEseq

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

institute: Weatheral Institute of Molecular Medicine

description:
Library name: HSC_24mon_ADT
ADT library

data_processing:
ATAC and GEX FASTQ files were demultiplexed using CellRanger-arc v2.0.2
CITEseq data were demultiplexed using CITE-seq-Count v1.4.5
Assembly: mm10
Supplementary files format and content: h5 - contains feature count result matrices of ATAC and GEX libraries
Supplementary files format and content: csv - contains CellRanger-arc produced per barcode quality control information or CITEseq featruecount result matrix
Supplementary files format and content: tsv - the fragment file of the ATAC modality
Library strategy: CITE-seq

molecule: protein

source_name: Bone Marrow

extract_protocol:
Bone marrow cells were c-Kit enriched, antibody stained and cell populations were FACS isolated. Cells were processed with the 10x Chromium platform.
ATAC and GEX libraries were prepared following the 10X Genomics protocol (CG000338 Rev F), with modifications described in the DOGMA-seq protocol (https://static-content.springer.com/esm/art%3A10.1038%2Fs41587-021-00927-2/MediaObjects/41587_2021_927_MOESM1_ESM.pdf) to enable ADT library generation.

value: Bone Marrow

value: Females, 24 month old

value: Long-term HSC

value: Wild-type


title: Scr1

description:
Library name: Scr1
counts_table_siFLVCR2.txt

value: Retina

value: Endothelial cell

value: scr


title: Subject 31 BAL

description: Library name: Subject 31 BAL

value: BAL


title: SA4

description:
Library name: SA4
counts_table_SA.txt

value: SA


title: 24 month HSC gene expression

description:
Library name: HSC_24mon_GEX
GEX 3' mRNA library

data_processing:
ATAC and GEX FASTQ files were demultiplexed using CellRanger-arc v2.0.2
CITEseq data were demultiplexed using CITE-seq-Count v1.4.5
Assembly: mm10
Supplementary files format and content: h5 - contains feature count result matrices of ATAC and GEX libraries
Supplementary files format and content: csv - contains CellRanger-arc produced per barcode quality control information or CITEseq featruecount result matrix
Supplementary files format and content: tsv - the fragment file of the ATAC modality


title: S3KO_CD8_D661Y_rep1

description:
Library name: Villarino-26343-013_RNAseq
Hennighausen_STAT3_D661_CD8_GEO_RNAseq_gene_counts.txt


title: MCF7 control 12 hours rep 1

description: Library name: c9

value: breast cancer

value: ER+ transformed breast cancer

value: WT


title: Mouse Cardiac Myofibroblast, Hypoxia, Adam17 siRNA, Rep 2

description: Library name: MHA2

value: Heart

value: Cardiac Myofibroblast

value: Passage 1

value: Wild type

value: pooled male and female

value: Adam17siRNA, Hypoxia


title: R147-H-007

description:
Library name: Gata2; Mx1-Cre Heterozygote -3
Gata2 heterozygote HSC 3 (LSK CD48- CD150+)

value: bone marrow

value: HSCs

value: Gata2 heterozygote


title: 24 month HSC ATAC

description:
Library name: HSC_24mon_ATAC
Tn5 transposed DNA library

value: Bone Marrow

value: Females, 24 month old

value: Long-term HSC

value: Wild-type


title: Subject 30 BAL

description: Library name: Subject 30 BAL

value: BAL

value: Female


title: S3KO_CD8_D661V_rep2

description:
Library name: Villarino-26343-043_RNAseq
Hennighausen_STAT3_D661_CD8_GEO_RNAseq_gene_counts.txt

value: pooled LN and spleen

value: CD8+ T cell

value: Viable CD8+ GFP+ RV tranduced


title: Mouse Cardiac Fibroblast, Hypoxia, Control, Rep 2

description: Library name: FHC2

value: Heart

value: Cardiac Fibroblast

value: Control siRNA, Hypoxia


title: Mouse Cardiac Fibroblast, Hypoxia, Control, Rep 1

description: Library name: FHC1

value: Passage 1

value: Wild type

value: pooled male and female


title: Citeseq, HSC, ADT

description:
Library name: HSC_8wk_ADT
Antibody-derived oligonucleotide tag

data_processing:
ATAC and GEX data were demultiplexed using CellRanger-arc
CITEseq data were demultiplexed using CITE-seq-Count
Assembly: mm10
Supplementary files format and content: CellRanger-arc output files: per_barcode_metrics.csv, filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz
Supplementary files format and content: CITE-seq-Count output file: cite_umi_matrix.mtx.gz
Library strategy: CITE-seq

source_name: Bone marrow

extract_protocol:
Bone marrow was isolated from the sternum, femur, tibia, and pelvis by crushing the bones in FACS buffer (PBS 5% FCS 2 mM EDTA) and filtering through a 50 µm strainer. WBC counts were measured using a haematology analyser. Cells were enriched for c-Kit expression using magnetic beads. After centrifugation, cells were resuspended at 1 million WBCs/µl, incubated with beads on ice, washed, and passed through a LS column. c-Kit+ cells were eluted for downstream processing. Cells were blocked, stained with a 2× antibody cocktail (FACS + CITE-seq), and resuspended in FACS buffer containing 7AAD. Long-term HSCs (LSK CD48− CD150+ CD34−) were FACS-sorted and processed following the DOGMA-seq protocol:: https://static-content.springer.com/esm/art%3A10.1038%2Fs41587-021-00927-2/MediaObjects/41587_2021_927_MOESM1_ESM.pdf
ATAC and GEX libraries were prepared following the 10X Genomics protocol (CG000338 Rev F), with modifications based on the DOGMA-seq protocol to enable ADT library generation.

value: Bone marrow

value: Long-term haematopoietic stem cell

tag: library type

value: ADT

tag: adt

value: Mix of Totalseq and in-house conjugated ADTs, tag information in the supplementary files


title: Subject 29 BAL

description: Library name: Subject 29 BAL

tag: age


title: Mouse Cardiac Fibroblast, Normoxia, Control, Rep 2

description: Library name: FNC2

tag: cell type

value: Control siRNA, Normoxia


title: S3KO_CD8_D661V_rep1

description:
Library name: Villarino-26343-011_RNAseq
Hennighausen_STAT3_D661_CD8_GEO_RNAseq_gene_counts.txt

tag: cell line


title: Subject 28 BAL

description: Library name: Subject 28 BAL

value: Male


title: Mouse Cardiac Fibroblast, Hypoxia, Adam17 siRNA, Rep 4

description: Library name: FHA4

value: Adam17siRNA, Hypoxia

tag: batch


title: R147-H-005

description:
Library name: Gata2; Mx1-Cre Heterozygote -1
Gata2 heterozygote HSC 1 (LSK CD48- CD150+)

value: bone marrow

value: HSCs

value: Gata2 heterozygote


title: Mouse Cardiac Fibroblast, Normoxia, Control, Rep 1

description: Library name: FNC1


title: S3KO_CD8_STAT3.203_rep2

description:
Library name: Villarino-26343-042_RNAseq
Hennighausen_STAT3_D661_CD8_GEO_RNAseq_gene_counts.txt

value: pooled LN and spleen

value: CD8+ T cell

value: Viable CD8+ GFP+ RV tranduced


title: Multiome, HSC, GEX

description:
Library name: HSC_8wk_GEX
PolyA RNA

data_processing:
ATAC and GEX data were demultiplexed using CellRanger-arc
CITEseq data were demultiplexed using CITE-seq-Count
Assembly: mm10
Supplementary files format and content: CellRanger-arc output files: per_barcode_metrics.csv, filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz
Supplementary files format and content: CITE-seq-Count output file: cite_umi_matrix.mtx.gz

value: Wild-type

value: mRNA


title: Mouse Cardiac Fibroblast, Hypoxia, Adam17 siRNA, Rep 3

description: Library name: FHA3

value: Heart

value: Cardiac Fibroblast

value: Passage 1

value: Wild type


title: Subject 27 BAL

description: Library name: Subject 27 BAL

value: BAL


title: Multiome, HSC, ATAC

description:
Library name: HSC_8wk_ATAC
Transposed DNA

library_source: genomic single cell

value: Bone marrow

value: Long-term haematopoietic stem cell

value: ATAC


title: S3KO_CD8_STAT3.203_rep1

description:
Library name: Villarino-26343-010_RNAseq
Hennighausen_STAT3_D661_CD8_GEO_RNAseq_gene_counts.txt


title: Mouse Cardiac Fibroblast, Hypoxia, Adam17 siRNA, Rep 2

description: Library name: FHA2

value: pooled male and female

value: Adam17siRNA, Hypoxia


title: S3KO_CD8_MigR1_rep2

description:
Library name: Villarino-26343-073_RNAseq
Hennighausen_STAT3_D661_CD8_GEO_RNAseq_gene_counts.txt


title: Subject 26 BAL

description: Library name: Subject 26 BAL

value: Male


title: MeRIP-Seq M3

city: Taiyuanshi

first: Zhaoya

last: Jin

address: Zhongdu Campus of Shanxi Medical University in Jinzhong City, Shanxi Province

institute: Shanxi Medical University

description: Library name: Sample6

data_processing:
Raw data processing: Trimmomatic filtering (sliding window=4, avg quality=15) to remove adapters, poly-N and low-quality reads. rRNA removal with SortMeRNA. HISAT2 alignment to BosGru3.0 genome (default parameters). Quality assessed via Guitar and deeptools.
m6A peak analysis: MeTDiff peak calling (FRAGMENT_LENGTH=200, PEAK_CUTOFF_PVALUE=0.01, PEAK_CUTOFF_FDR=0.05) with input controls. Differential peak identification using MeTDiff (FDR=0.05).
Genomic annotation: Peak annotation with ChIPseeker. Visualization using Integrative Genomics Viewer (IGV).
Expression analysis: Differential gene expression (DEGs) with DESeq.
Assembly: GRCm39
Supplementary files format and content: bigWig,narrowPeak
Library strategy: MeRIP-Seq

source_name: hippocampal neurons

extract_protocol:
Fragmented RNA enrichment: 25 μg total RNA dissolved in 50 μL ultrapure water + 250 μL fragmentation buffer. Fragmented at 94°C for 5 min, stopped with stop buffer and cooled on ice. Enriched with 150 μL m6A-Dynabeads (1h rotation, 7 rpm). Washed and eluted with pre-heated buffer. Extracted with acid phenol-chloroform, purified with RNase-free chloroform, precipitated and resuspended in ultrapure water.
RIP library prep: Constructed with 100 ng RNA (input & post-IP) using Illumina TruSeq Stranded mRNA Library Prep Kit. Libraries prepared without fragmentation step. Paired-end sequenced (2×150 bp) on Illumina HiSeq 4000 platform (OE Biotech Co., Ltd.).

value: hippocampal neurons

value: HT22 cells

value: immortalized mouse hippocampal neuronal cell line


title: Mouse Cardiac Fibroblast, Hypoxia, Adam17 siRNA, Rep 1

description: Library name: FHA1


title: Subject 25 BAL

description: Library name: Subject 25 BAL

value: Female


title: MeRIP-Seq M2

description: Library name: Sample5


title: CD8+ T Cells, Wild Type, Acute Stimulation, Day 18, chr4, batch3, biol_rep 4

city: Minneapolis

first: Nuri

last: Temiz

address: 2231 6th St SE

institute: University of Minnesota

description: Library name: WI4_001

data_processing:
Quality and adapter trimming via Trimmomatic
Mapping via RNAStar to ensembl annotation GRcm39
T2/Onc2 Fusions called and quantified using Arriba
Removal of Chimeric (T2/Onc2 fusion reads) and realignment to ensembl annotation GRcm39 using Hisat2
Gene Count Quantification via subread
Assembly: Mus musculus GRcm39
Supplementary files format and content: RNA_seq_counts.txt - tab-delimited text file including raw counts for each sample
Supplementary files format and content: SB_counts.txt - tab-delimited text file containing all T2/Onc2 Fusion locations for each sample

source_name: Spleen

extract_protocol:
Simultaneous genomic DNA and RNA of murine CD8+ T cell samples (Figure 2A) were isolated using Quick-DNA/RNA MagBead (Zymo R2130).
Libraries differ by batch: Batch 1 and 2 were prepared using the DNBSEQ Eukaryotic Strand-specific Transcriptome Resequencing kit by following the manufacturers instructions. Batch 3 was prepared using Illumina Truseq Stranded Total RNA with PolyA selection for mRNA species for rRNA removal

value: Spleen

value: CD8+ T Cells

value: Wild Type

value: Acute Stimulation

tag: day


title: Subject 24 BAL

description: Library name: Subject 24 BAL


title: MeRIP-Seq M1

description: Library name: Sample4


title: S3KO_CD8_MigR1_rep1

description:
Library name: Villarino-26343-041_RNAseq
Hennighausen_STAT3_D661_CD8_GEO_RNAseq_gene_counts.txt

value: pooled LN and spleen

value: CD8+ T cell

value: Viable CD8+ GFP+ RV tranduced


title: CD8+ T Cells, Wild Type, Acute Stimulation, Day 18, chr4, batch3, biol_rep 3

description: Library name: WI3_001

tag: launch chr


title: Mouse Cardiac Fibroblast, Normoxia, Adam17 siRNA, Rep 2

description: Library name: FNA2

value: Heart

value: Cardiac Fibroblast

value: Passage 1

value: Wild type

value: Adam17siRNA, Normoxia


title: S3KO_CD4_D661H_rep2

description:
Library name: Villarino-14055-030_RNAseq
Hennighausen_STAT3_D661_CD4_GEO_RNAseq_gene_counts.txt

value: CD4+ T cell

value: Viable CD4+ GFP+ RV tranduced


title: Subject 23 BAL

description: Library name: Subject 23 BAL

value: BAL

value: Male


title: MeRIP-Seq C3

description: Library name: Sample3

value: hippocampal neurons

value: HT22 cells

value: immortalized mouse hippocampal neuronal cell line


title: S3KO_CD4_D661N_rep2

description:
Library name: Villarino-14055-029_RNAseq
Hennighausen_STAT3_D661_CD4_GEO_RNAseq_gene_counts.txt


title: Subject 22 BAL

description: Library name: Subject 22 BAL


title: CD8+ T Cells, Wild Type, Acute Stimulation, Day 18, chr4, batch3, biol_rep 2

description: Library name: WI2_001

value: Spleen

value: CD8+ T Cells

value: Wild Type

tag: biol rep


title: S3KO_CD4_D661Y_rep2

description:
Library name: Villarino-14055-028_RNAseq
Hennighausen_STAT3_D661_CD4_GEO_RNAseq_gene_counts.txt

value: pooled LN and spleen


title: MeRIP-Seq C2

description: Library name: Sample2


title: Subject 21 BAL

description: Library name: Subject 21 BAL


title: MeRIP-Seq C1

description: Library name: Sample1


title: CD8+ T Cells, Wild Type, Acute Stimulation, Day 18, chr4, batch3, biol_rep 1

description: Library name: WI1_001

value: Acute Stimulation


title: Subject 20 BAL

description: Library name: Subject 20 BAL


title: S3KO_CD4_STAT3.203_rep2

description:
Library name: Villarino-14055-026_RNAseq
Hennighausen_STAT3_D661_CD4_GEO_RNAseq_gene_counts.txt


title: M3

description:
Library name: Sample6
M3_input

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-coun
Assembly: GRCm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.


title: CD8+ T Cells, Wild Type, Chronic Stimulation, Day 18, chr4, batch3, biol_rep 4

description: Library name: WE4_001

value: Chronic Stimulation


title: S3KO_CD4_D661V_rep2

description:
Library name: Villarino-14055-027_RNAseq
Hennighausen_STAT3_D661_CD4_GEO_RNAseq_gene_counts.txt


title: CD8+ T Cells, Wild Type, Chronic Stimulation, Day 18, chr4, batch3, biol_rep 3

description: Library name: WE3_001


title: Subject 19 BAL

description: Library name: Subject 19 BAL

value: Female


title: S3KO_CD4_D661H_rep1

description:
Library name: Villarino-14055-023_RNAseq
Hennighausen_STAT3_D661_CD4_GEO_RNAseq_gene_counts.txt


title: M2

description:
Library name: Sample5
M2_input


title: CD8+ T Cells, Wild Type, Chronic Stimulation, Day 18, chr4, batch3, biol_rep 2

description: Library name: WE2_001


title: Subject 18 BAL

description: Library name: Subject 18 BAL


title: M1

description:
Library name: Sample4
M1_input


title: S3KO_CD4_D661N_rep1

description:
Library name: Villarino-14055-022_RNAseq
Hennighausen_STAT3_D661_CD4_GEO_RNAseq_gene_counts.txt


title: CD8+ T Cells, Wild Type, Chronic Stimulation, Day 18, chr4, batch3, biol_rep 1

description: Library name: WE1_001


title: Subject 17 BAL

description: Library name: Subject 17 BAL


title: C3

description:
Library name: Sample3
C3_input


title: S3KO_CD4_D661Y_rep1

description:
Library name: Villarino-14055-021_RNAseq
Hennighausen_STAT3_D661_CD4_GEO_RNAseq_gene_counts.txt


title: Subject 16 BAL

description: Library name: Subject 16 BAL


title: CD8+ T Cells, Wild Type, Input, Day 2, chr4, batch3, biol_rep 1

description: Library name: WA_001

value: Input


title: S3KO_CD4_D661V_rep1

description:
Library name: Villarino-14055-020_RNAseq
Hennighausen_STAT3_D661_CD4_GEO_RNAseq_gene_counts.txt


title: C2

description:
Library name: Sample2
C2_input


title: CD8+ T Cells, DiSBey, Acute Stimulation, Day 18, chr4, batch3, biol_rep 4

description: Library name: QI4_001

value: DiSBey


title: Subject 15 BAL

description: Library name: Subject 15 BAL


title: C1

description:
Library name: Sample1
C1_input


title: S3KO_CD4_STAT3.203_rep1

description:
Library name: Villarino-14055-019_RNAseq
Hennighausen_STAT3_D661_CD4_GEO_RNAseq_gene_counts.txt


title: CD8+ T Cells, DiSBey, Acute Stimulation, Day 18, chr4, batch3, biol_rep 3

description: Library name: QI3_001


title: Subject 14 BAL

description: Library name: Subject 14 BAL


title: CD8+ T Cells, DiSBey, Acute Stimulation, Day 18, chr4, batch3, biol_rep 2

description: Library name: QI2_001


title: control 3

city: Los Angeles

first: Anja

last: Karlstaedt

state: California

address: 127 San Vincente Blvd

department: Cardiology

institute: Cedars Sinai Medical Center

data_processing:
Sequence reads were trimmed for adaptor sequences and low quality reads using FastQC.
Raw reads were aligned to reference genome using tophat2
Gene expression was assembled from aligned reads using samtools and HTSeq.
Differential gene expression analysis was conducted using Rstudio and DeSeq2.
Assembly: mm10
Supplementary files format and content: tab-deliminated text file includes raw counts for each sample

source_name: heart

extract_protocol:
The quality of each RNA sample was checked using an Agilent 4200 Tape Station with Agilent High Sensitivity RNA ScreenTape according to the manufacturer’s instructions. Poly-A RNA was purified from mRNA using oligo-dT magnetic beads for library preparation. mRNA was fragmented, and cDNA was synthesized. A-tailing was conducted to enable subsequent ligation of paired-end sequencing adapters. Library quality was determined using an Agilent 4200 Tape Station with Agilent High Sensitivity D5000 DNA ScreenTape to ensure correct fragment sizes between 250 and 300 bp.
RNA-sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Sample Preparation Kit

value: heart

value: cardiomyocyte

value: wildtype

value: perfusion


title: Retina_Sham-injected_S4

first: Milica

last: Margeta

address: 20 Staniford Street

department: Ophthalmology

institute: Mass Eye and Ear

description:
Library name: AMf45
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
CD45+ cells from retina and optic nerve were collected by FACS sorting.
Library was performed according to the manufacturer’s instructions (Chromium Next GEM Single Cell 3ʹ v3.1(Dual Index), 10x Genomics).

value: Retina

value: CD45+ cells

value: Sham-injected


title: Subject 13 BAL

description: Library name: Subject 13 BAL

value: BAL


title: control 2


title: Retina_MB-injected_S3

description:
Library name: AMf41
10x Genomics

value: MB-injected


title: CD8+ T Cells, DiSBey, Acute Stimulation, Day 18, chr4, batch3, biol_rep 1

description: Library name: QI1_001

value: Spleen

value: CD8+ T Cells


title: control 1


title: Subject 12 BAL

description: Library name: Subject 12 BAL

value: Male


title: Retina_Sham-injected_S3

description:
Library name: AMf40
10x Genomics


title: CD8+ T Cells, DiSBey, Chronic Stimulation, Day 18, chr4, batch3, biol_rep 4

description: Library name: QE4_001


title: Subject 11 BAL

description: Library name: Subject 11 BAL


title: Acly-KD 3

value: Acly-KD


title: Optic nerve_MB-injected_S3

description:
Library name: AMf37
10x Genomics

source_name: Optic Nerve

value: Optic Nerve


title: CD8+ T Cells, DiSBey, Chronic Stimulation, Day 18, chr4, batch3, biol_rep 3

description: Library name: QE3_001

value: Chronic Stimulation


title: Subject 10 BAL

description: Library name: Subject 10 BAL

value: Female


title: Optic nerve_Sham-injected_S3

description:
Library name: AMf36
10x Genomics


title: Acly-KD 2


title: Subject 9 BAL

description: Library name: Subject 9 BAL


title: CD8+ T Cells, DiSBey, Chronic Stimulation, Day 18, chr4, batch3, biol_rep 2

description: Library name: QE2_001

value: DiSBey


title: Acly-KD 1

value: heart


title: Optic nerve_Sham-injected_S2

description:
Library name: AMf35
10x Genomics


title: CD8+ T Cells, DiSBey, Chronic Stimulation, Day 18, chr4, batch3, biol_rep 1

description: Library name: QE1_001


title: Subject 8 BAL

description: Library name: Subject 8 BAL


title: CD8+ T Cells, DiSBey, Input, Day 2, chr4, batch3, biol_rep 1

description: Library name: QA_001

value: Input