title: 6mo,SCD,rep4,ADT

library_source: other

data_processing:
ScRNA-Seq FASTQ files were aligned to the mouse genome (GRC m39 with GENCODE annotation M33) and quantified with the STAR aligner’s (v2.7.11) STARsolo workflow (parameters for read trimming and filtering and cell filtering: “--clipAdapterType CellRanger4 --outFilterScoreMin 30 --soloCellFilter EmptyDrops_CR 3000 0.99 10 45000 90000 500 0.01 20000 0.01”). Cell surface protein tag data was counted with CITE-seq-Count (v.1.4.4, https://github.com/Hoohm/CITE-seq-Count) using the tag sequences provided by Biolegend.
Read counts for both assays were first read into R and assembled into one Seurat object per sample (Seurat v5). Gene expression was normalized with SCTransform v2, with each sample processed separately and merged post-normalization. Antibody-derived tag data was normalized with ADTnorm. Cells found in both gene and cell surface protein assays, having fewer than 10% mitochondria-derived reads, and with expression of at least 500 genes were taken forward.
Putative doublets/multiplets (more than one cell captured in a single droplet) were removed through an ensemble approach based on gene expression including: (1) cells that were outliers for total read counts or total expressed genes (> 3 MAD for either), (2) cells that were outliers for total read counts or total expressed genes and having a score from scDblFinder > 0.9, and (3) cells having both scDblFinder score > 0.9 and called as a doublet by DoubletFinder.  Genes expressed in 50 or fewer cells across the filtered dataset were removed.
An ensemble approach was also implemented to filter cells out extreme outliers based on ADT expression level, which could represent empty droplets (much lower than most values) or multiplets (multiple times higher than most values). Briefly, cells were removed if they met any three of four criteria: (1) > 10 MAD on the right tail for any antibody, (2) ≥ limit determined by histogram-based outlier detection in the R package “bigutilsr” with a maximum outlier detection fraction of 0.01 and 100 bootstrap iterations, (3) called as an outlier by the “adjusted outlyingness” method as implemented in the R package “univOutl”, and (4) called as an outlier by the Robust Kernel-based Outlier Factor with bootstrap cutoff determination as implemented in the R package “OutlierDetection”
Assembly: GRC m39 with GENCODE annotation M33
Supplementary files format and content: For GEX: 10x-style sparse matrix output consisting of a barcodes.tsv, genes.tsv, and matrix.mtx file, along with a cell_metadata.txt file. There are two sets of files, each in a separate folder- one has the original counts, and the other has SCTransform v2-normalized log scale expression. The cell_metadata.txt file is tab-delimited and includes the annotated cell type, inferred cell cycle state, and the 2D UMAP embeddings.
Supplementary files format and content: For ADT: Cell x Antibody count matrix (cells in rows), and Cell x Antibody matrix of normalized ADT data using ADTnorm (cells in rows)
Library strategy: CITE-Seq

molecule: protein

extract_protocol:
RNA extraction was performed as part of the 10x single-cell prep workflow.
Labeled cells were processed for single cell RNA sequencing using the Chromium Single Cell 3’ Reagent Kit v3 with a Chromium Controller (10x Genomics) and libraries were prepared for sequencing according to the manufacturer’s instructions, yielding libraries for both gene expression and antibody-derived tags (ADTs).

treatment_protocol: SCD and non-SCD mouse bone marrow samples from two and six-month old animals (n =4/group) were enriched for c-Kit+ cells (i.e. total HSPCs) via magnetic enrichment using anti-CD117 microbeads and an autoMACs magnetic cell separator (Miltenyi Biotec, Carlsbad, CA) per manufacturer’s instructions. c-Kit-enriched samples were prepared for CITE-seq by staining with a panel of Biolegend TotalSeq-A antibodies (Ly-6A, CD150, CD48, CD16/CD32, CD105, CD41, and CD71). Towards this, samples were incubated at 4°C for 30 minutes in 50 µL of Cell Staining buffer (Biolegend, Catalog# 42020) containing TotalSeq-A antibodies (0.02 µg/mL per antibody), and then washed and resuspended in 2%FBS (1.5x106/mL). Two-month old animals were processed for CITE-Seq and 10x cell capture in one batch, while six-month animals were processed in another, due to limited lanes on the 10x microfluidic chip.

value: cKit-enriched

value: SCD

value: AA

tag: library type

value: ADT


title: lymph node, CD8+ Tfc, rep1

status: Public on Jul 22 2026

type: SRA

city: Córdoba

first: Yamila

middle: Natali

last: Gazzoni

state: Córdoba

address: Avenida Haya de La Torre y Medina Allende

country: Argentina

institute: CIBICI-Facultad de Ciencias Químicas-UNC

description: Library name: LN-Tfc1

library_source: transcriptomic

data_processing:
Adapter sequences and low-quality bases were removed using Trimmomatic v0.36.
Trimmed reads were aligned to the Mus musculus reference genome (GRCm38, Ensembl) using STAR aligner v2.5.2b.
gene-level counts were obtained from aligned reads
Count matrices were imported into DESeq2 for normalization and differential expression analysis.
Differential expression between predefined sample groups was calculated using the Wald test. Genes with adjusted p-value < 0.05 and |log2 fold change| > 1 were considered differentially expressed.
Assembly: Mus musculus reference genome GRCm38 (Ensembl release)
Supplementary files format and content: CSV file containing raw gene-level counts for all samples
Supplementary files format and content: Tab-delimited tables containing DESeq2 differential expression results including gene identifiers, log2 fold change, p-values, and adjusted p-values for all comparisons.

molecule: total RNA

organism: Mus musculus

source_name: inguinal lymph nodes

extract_protocol:
Total RNA was extracted from sorted CD8? T cell subsets using the Arcturus PicoPure RNA Isolation Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions.
Poly(A)+ mRNA was enriched by polyA selection for rRNA depletion. Libraries were prepared using an ultra-low input RNA-seq library preparation protocol by GENEWIZ (Azenta Life Sciences, NJ, USA) following standard manufacturer procedures.

tag: tissue

value: inguinal lymph nodes

tag: cell type

value: CD8 T lymphocytes

tag: genotype


title: lymph node, CD8+ Tfc, rep2

description: Library name: Ln-Tfc2


title: PBMC_8590_CD_1

city: Amsterdam

first: Lisa

last: Willemsen

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC - locatie AMC

description:
Library name: PBMC_8590_CD_1
RNA-Seq of CHIM PBMC

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

organism: Homo sapiens

source_name: Blood

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: Blood

tag: age

value: PBMC

tag: days post_challenge

tag: Sex

value: male


title: NC_5

city: Beijing

first: Zishanbai

last: Zhang

address: No.1 Dongjiaominxiang, Dongcheng District

country: China

institute: Beijing Tongren Hospital

description:
Library name: FIN2
FPKM.FIN2

data_processing:
Quality control: The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through fastp software. Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). Quantification of gene expression level: featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: human reference genome (hg38)
Supplementary files format and content: siBACH1gene expression.xlsx: D3, siIL1B gene expression.xlsx: FPKM.FIN1

source_name: FaDu

growth_protocol: FaDu cells were maintained in Minimum Essential Medium (MEM) supplemented with 10% fetal bovine serum (FBS) and 1% non-essential amino acids (NEAA). Cells were maintained in a humidified incubator equilibrated with 5% CO2 at 37 ºC.

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

treatment_protocol: Cells were infected and drug screende in FaDu cells with NC or siBACH1 or siIL1B.

tag: cell line

value: FaDu

value: Human medulloblastoma cell

value: NC


title: 6mo,SCD,rep3,ADT

city: Memphis

first: Shannon

last: McKinney-Freeman

state: TN

address: 262 Danny Thomas Pl

department: Experimental Hematology

country: USA

institute: St. Jude Children's Research Hospital

source_name: bone marrow

value: bone marrow

tag: condition

value: 6 months

value: M


title: H2.35 cells, Uninfected Control, Set 3

city: Singapore

first: Solomonraj

last: Wilson

address: 8A Biomedical Grove

country: Singapore

institute: SIgN

description:
Library name: R13501
Row name in Raw counts_All Samples.txt: R13501_36

data_processing:
Partek™ Flow™ software, v 12.9.1
Sequence reads were trimmed for bases with a minimum quality score of 35 from the 3-prime end
Trimmed sequenced reads were mapped to GRCm39/mm39 using STAR.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include raw counts for each sample

growth_protocol: H2.35 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37 degrees celsius.

extract_protocol:
RNA was extacted with mirVanaTM miRNA isolation kit according to manufacturer's instructions.
SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1. Addition of 20 µM TSO; 2. Use of 200 pg cDNA with 1/5 reaction of Illumina Nextera XT kit.

treatment_protocol: Cells were infected with 0.1 MOI of MHV for one hour. Excess viral inoculum was removed and respective drug treatments diluted in DMEM supplemented with 2% FBS and 0.5% DMSO. Cultures were maintained for 24 hours before harvesting with a cell scraper.

value: Hepatocyte

value: WT

tag: treatment

value: No treatment


title: Subject 3 PBMC

city: Denver

first: Elizabeth

last: Wynn

state: CO

address: 1400 Jackson St.

institute: National Jewish Health

description: Library name: Subject 3 PBMC

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: PBMC

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).

tag: gender

value: Male


title: CD8+ T cells, Control, co-cultured with CMT93-OVA cells, replicate2

first: Zhidong

last: Gao

address: No.11 Xizhimen South Street

institute: Peking University People’s Hospital

description:
Library name: sg-Int+sg-Int treat 2
cII2

data_processing:
We applied the RNA-Seq immune analysis pipeline (RIMA) to analyze bulk RNA-Seq data. In brief, sequencing reads were aligned to the mouse reference genome (GRCm38/mm10) using STAR v2.6.1d. Salmon v0.13.1 was utilized to map transcripts to genes and generate a gene count matrix.
Differentially expressed genes were identified using DESeq2 v1.34.0, with an adjusted P-value (FDR) threshold of <0.05 for determining significance. The replicates of RNA-Seq from each condition were considered as a covariate in DESeq2.
Assembly: mm10
Supplementary files format and content: txt file includes raw counts for each sample

source_name: CD8+ T cells

growth_protocol: Arid3b/Runx3-dKO, Runx3-KO, Arid3b-KO or Control OT1 CD8+ T cells were cultured in complete RPMI-1640 medium (containing 10% fetal bovine serum, 1% penicillin/streptomycin, 1% non-essential amino acids, 20 mM HEPES, 1 mM sodium pyruvate, and 0.05 mM 2-mercaptoethanol) supplemented with 20 ng/mL IL-2.

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA kit following manufacturer’s instructions.

treatment_protocol: Arid3b/Runx3-dKO, Runx3-KO, Arid3b-KO or Control OT1 CD8+ T cells were co-cultured with or without CMT93-OVA cells for 4 hours.

value: CD8+ T cells

value: intergenic sequence knockout

value: CD8+ T cells were co-cultured with CMT93-OVA cells for 4 hours.

tag: time

value: 4 hours


title: Subject 2 PBMC

description: Library name: Subject 2 PBMC

value: Female


title: PBMC_8589_CD_1

description:
Library name: PBMC_8589_CD_1
RNA-Seq of CHIM PBMC

value: Blood

value: PBMC

value: female


title: NC_4

description:
Library name: FIN1
FPKM.FIN1

value: FaDu

value: Human medulloblastoma cell


title: PIP-seq, postnatal day 14, replicate 3

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 3

library_source: transcriptomic single cell

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: H2.35 cells, MHV Infected 6um Ivermectin, Set 3

description:
Library name: R13500
Row name in Raw counts_All Samples.txt: R13500_35

value: MHV Infection with 6um Ivermectin treatment


title: BACH_3

description:
Library name: D3
fpkm_D3

value: BACH1 knockdown


title: 6mo,SCD,rep2,ADT

value: bone marrow

value: cKit-enriched

value: SCD

value: AA

value: 6 months

value: M

value: ADT


title: PBMC_8336_CD_1

description:
Library name: PBMC_8336_CD_1
RNA-Seq of CHIM PBMC


title: 6mo,SCD,rep1,ADT

value: F


title: H2.35 cells, MHV Infected 0.3um Remdesivir, Set 3

description:
Library name: R13499
Row name in Raw counts_All Samples.txt: R13499_34

value: Hepatocyte

value: WT

value: MHV Infection with 0.3um Remdesivir treatment


title: BACH_2

description:
Library name: D2
fpkm_D2


title: PBMC_8334_CD_1

description:
Library name: PBMC_8334_CD_1
RNA-Seq of CHIM PBMC

value: Blood

value: PBMC

value: male


title: H2.35 cells, MHV Infected 10um Remdesivir, Set 3

description:
Library name: R13498
Row name in Raw counts_All Samples.txt: R13498_33

value: MHV Infection with 10um Remdesivir treatment


title: 6mo,nonSCD,rep4,ADT

value: non-SCD


title: PBMC_8325_CD_1

description:
Library name: PBMC_8325_CD_1
RNA-Seq of CHIM PBMC


title: BACH_1

description:
Library name: D1
fpkm_D1

value: FaDu

value: Human medulloblastoma cell

value: BACH1 knockdown


title: 6mo,nonSCD,rep3,ADT

value: bone marrow

value: cKit-enriched


title: NC_3

description:
Library name: A3
fpkm_A3

value: NC


title: NPS_8879_CD_7

description:
Library name: NPS_8879_CD_7
RNA-Seq of CHIM NPS

source_name: Nose

value: Nose

value: NPS


title: H2.35 cells, MHV Infected Control, Set 3

description:
Library name: R13496
Row name in Raw counts_All Samples.txt: R13496_31

value: MHV Infection


title: NC_2

description:
Library name: A2
fpkm_A2


title: 6mo,nonSCD,rep2,ADT

value: AA

value: 6 months

value: F

value: ADT


title: 6mo,nonSCD,rep1,ADT

value: M


title: H2.35 cells, Uninfected Control, Set 2

description:
Library name: R13495
Row name in Raw counts_All Samples.txt: R13495_36 0124

value: Hepatocyte

value: WT

value: No treatment


title: NPS_8876_CD_8

description:
Library name: NPS_8876_CD_8
RNA-Seq of CHIM NPS

value: female


title: 2mo,SCD,rep4,ADT

value: SCD

value: SS

value: 2 months


title: H2.35 cells, MHV Infected 6um Ivermectin, Set 2

description:
Library name: R13494
Row name in Raw counts_All Samples.txt: R13494_35 0124

value: MHV Infection with 6um Ivermectin treatment


title: NPS_8803_CD_8

description:
Library name: NPS_8803_CD_8
RNA-Seq of CHIM NPS

value: male


title: sg-CSDE3#1 Ishikaw cell

city: Shanghai

first: Li

last: Cheng

state: Shanghai

address: 500 Quxi Road, Shanghai 200011

department: Department of Rehabilitation Medicine

institute: The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine

description: Library name: K3

data_processing:
The raw paired-end fastq reads underwent filtering by fastp to eliminate adapters and low-quality bases.
The resulting clean reads were then aligned to the genome using HISAT2, followed by reference-guided transcriptome assembly and gene expression quantification utilizing StringTie.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include gene_count values, gene_tpm value for each Sample

source_name: endometrium

extract_protocol:
Total RNA was isolated using a TRIzol total RNA extraction kit (TIANGEN,Cat.No.DP424)
High-quality RNA samples were used to construct a sequencing library.

value: endometrium

value: HEC

value: CSDE1 KO

value: CRISPR/Cas9-mediated genome editing


title: 2mo,SCD,rep3,ADT

value: bone marrow

value: cKit-enriched


title: sg-CSDE2#1 Ishikaw cell

description: Library name: K2


title: NPS_8801_CD_9

description:
Library name: NPS_8801_CD_9
RNA-Seq of CHIM NPS

value: Nose

value: NPS


title: H2.35 cells, MHV Infected 10um Remdesivir, Set 2

description:
Library name: R13492
Row name in Raw counts_All Samples.txt: R13492_33 0124

value: Hepatocyte

value: MHV Infection with 10um Remdesivir treatment


title: 2mo,SCD,rep2,ADT

value: M

value: ADT


title: sg-CSDE1#1 Ishikaw cell

description: Library name: K1


title: NPS_8799_CD_9

description:
Library name: NPS_8799_CD_9
RNA-Seq of CHIM NPS

value: female


title: 2mo,SCD,rep1,ADT

value: SCD

value: SS


title: H2.35 cells, MHV Infected Combination (0.3um Remdesivir, 6um Ivermectin), Set 2

description:
Library name: R13491
Row name in Raw counts_All Samples.txt: R13491_32 0124

value: WT

value: MHV Infection with 0.3um Remdesivir, 6um Ivermectin treatment


title: H2.35 cells, MHV Infected Control, Set 2

description:
Library name: R13490
Row name in Raw counts_All Samples.txt: R13490_31 0124

value: MHV Infection


title: NPS_8797_CD_8

description:
Library name: NPS_8797_CD_8
RNA-Seq of CHIM NPS


title: Ishikaw cell WT 2

description: Library name: WT2

value: endometrium

value: HEC

value: no treated


title: H2.35 cells, Uninfected Control, Set 1

description:
Library name: R13489
Row name in Raw counts_All Samples.txt: R13489_26 0124

value: No treatment


title: 2mo,nonSCD,rep3,ADT

value: bone marrow

value: cKit-enriched

value: non-SCD

value: AA

value: 2 months


title: Ishikawa cell WT 1

description: Library name: WT1


title: H2.35 cells, MHV Infected 6um Ivermectin, Set 1

description:
Library name: R13488
Row name in Raw counts_All Samples.txt: R13488_25 0124

value: Hepatocyte

value: MHV Infection with 6um Ivermectin treatment


title: 2mo,nonSCD,rep2,ADT

value: F

value: ADT


title: NPS_8790_CD_8

description:
Library name: NPS_8790_CD_8
RNA-Seq of CHIM NPS

value: Nose

value: NPS

value: female


title: NPS_8784_CD_7

description:
Library name: NPS_8784_CD_7
RNA-Seq of CHIM NPS

value: male


title: DPSCs, BSN, 24hrs, Biol rep4

city: Sakaka

first: Saeed

last: Alqahtani

country: Saudi Arabia

institute: Jouf University-College of Dentistry

description:
Library name: Sample16
column name in raw_counts_all_samples.txt: BSN_24h4

data_processing:
Bioinformatic analysis was performed by Novogene using in-house Perl scripts (Novogene Co., LTD, Cambridge, UK).
Assembly: Human Genome Assembly GRCh38.p14
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Primary human dental pulp stem cells (DPSCs)

growth_protocol: DPSCs were maintained in Knock-out DMEM supplemented with 10 % Foetal bovine serum, 1 % L-Glutamine, and 1 % Penicillin-Streptomycin in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen). 2.65 μg of total RNA was used for the construction of sequencing libraries.
RNA library preparation by polyA capture using the NEB Next® Ultra™ RNA Library Prep Kit.

treatment_protocol: Treated DPSCs were stimulated with 1:1 BSN for 4 and 24 h. Untreated DPSCs were maintained in normal culture media.

value: Dental pulp

value: Mesenchymal stem cell

value: BSN treated


title: 2mo,nonSCD,rep1,ADT

value: M


title: DPSCs, BSN, 24hrs, Biol rep3

description:
Library name: Sample15
column name in raw_counts_all_samples.txt: BSN_24h3


title: NPS_8783_CD_7

description:
Library name: NPS_8783_CD_7
RNA-Seq of CHIM NPS


title: 6mo,SCD,rep4,GEX

value: bone marrow

value: SCD

value: SS

value: 6 months

value: mRNA


title: H2.35 cells, MHV Infected 10um Remdesivir, Set 1

description:
Library name: R13486
Row name in Raw counts_All Samples.txt: R13486_23 0124

value: Hepatocyte

value: WT

value: MHV Infection with 10um Remdesivir treatment


title: DPSCs, BSN, 24hrs, Biol rep2

description:
Library name: Sample14
column name in raw_counts_all_samples.txt: BSN_24h2


title: NPS_8782_CD_8

description:
Library name: NPS_8782_CD_8
RNA-Seq of CHIM NPS


title: 6mo,SCD,rep3,GEX

value: cKit-enriched


title: H2.35 cells, MHV Infected Combination (0.3um Remdesivir, 6um Ivermectin), Set 1

description:
Library name: R13485
Row name in Raw counts_All Samples.txt: R13485_22 0124

value: MHV Infection with 0.3um Remdesivir, 6um Ivermectin treatment


title: DPSCs, BSN, 24hrs, Biol rep1

description:
Library name: Sample13
column name in raw_counts_all_samples.txt: BSN_24h1


title: H2.35 cells, MHV Infected Control, Set 1

description:
Library name: R13484
Row name in Raw counts_All Samples.txt: R13484_21 0124

value: MHV Infection


title: 6mo,SCD,rep2,GEX


title: DPSCs, BSN, 4hrs, Biol rep4

description:
Library name: Sample12
column name in raw_counts_all_samples.txt: BSN_4h4


title: 6mo,SCD,rep1,GEX

value: F


title: NPS_8779_CD_7

description:
Library name: NPS_8779_CD_7
RNA-Seq of CHIM NPS

value: Nose

value: NPS

value: female


title: Mpfad3fad7_wound_3

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

description: Library name: Mpfad3fad7_wound_3

data_processing:
Adaptors were trimmed and low quality reads were filtered with Trim Galore
Alignment to genome sequence with HISAT2
Summarization of reads was performed with HTSeq-count program
Normalization and differential expression analysis with EdgeR
Assembly: MpTak1_v5.1
Supplementary files format and content: Matrix containing raw counts per gene. One column per sample named as in Library Name

organism: Marchantia polymorpha

source_name: Leaflets

growth_protocol: Marchantia polymorpha accession Takaragaike-1 (Tak-1; male) and double mutant Mpdes6fad5 were used in this work. Plants were subcultivated on 0.5 Gamborg’s B5 medium containing 1% agar for 3 weeks. Apical fragments of the plants, excluding gemma cups, were ground in liquid nitrogen prior RNA extraction. Every independent biological replicate contained 6-8 plants.

extract_protocol:
Total RNA from Marchantia was extracted with Favorgen Plant RNA Extraction and DNase on-column digestion (Qiagen) was performed to remove genomic DNA contamination.
The RNA-seq library was prepared by Novogene, using standard Illumina protocols.

treatment_protocol: Leaflets were wounded with tweezers and frozen 2 h after treatment

value: Leaflets

value: Wound, 2 hours


title: DPSCs, BSN, 4hrs, Biol rep3

description:
Library name: Sample11
column name in raw_counts_all_samples.txt: BSN_4h3

value: Dental pulp

value: Mesenchymal stem cell

value: BSN treated


title: NPS_8778_CD_8

description:
Library name: NPS_8778_CD_8
RNA-Seq of CHIM NPS


title: 6mo,nonSCD,rep4,GEX

value: bone marrow

value: non-SCD

value: AA

value: 6 months


title: Mpfad3fad7_wound_2

description: Library name: Mpfad3fad7_wound_2


title: DPSCs, BSN, 4hrs, Biol rep2

description:
Library name: Sample10
column name in raw_counts_all_samples.txt: BSN_4h2


title: NPS_8879_CD_6

description:
Library name: NPS_8879_CD_6
RNA-Seq of CHIM NPS

value: male


title: 6mo,nonSCD,rep3,GEX

value: cKit-enriched

value: mRNA


title: Mpfad3fad7_wound_1

description: Library name: Mpfad3fad7_wound_1


title: NPS_8878_CD_7

description:
Library name: NPS_8878_CD_7
RNA-Seq of CHIM NPS


title: 6mo,nonSCD,rep2,GEX


title: Mpfad3fad7_mock_3

description: Library name: Mpfad3fad7_mock_3

value: mock, 2 hours


title: DPSCs, control, 24hrs, Biol rep4

description:
Library name: Sample8
column name in raw_counts_all_samples.txt: Ctrl_24h4

value: untreated


title: NPS_8877_CD_6

description:
Library name: NPS_8877_CD_6
RNA-Seq of CHIM NPS

value: Nose


title: 6mo,nonSCD,rep1,GEX

value: M


title: DPSCs, control, 24hrs, Biol rep3

description:
Library name: Sample7
column name in raw_counts_all_samples.txt: Ctrl_24h3


title: Mpfad3fad7_mock_2

description: Library name: Mpfad3fad7_mock_2


title: 2mo,SCD,rep4,GEX

value: SCD

value: SS

value: 2 months

value: F


title: DPSCs, control, 24hrs, Biol rep2

description:
Library name: Sample6
column name in raw_counts_all_samples.txt: Ctrl_24h2

value: Dental pulp

value: Mesenchymal stem cell


title: 2mo,SCD,rep3,GEX

value: bone marrow


title: Tak1_wound_3

description: Library name: Tak1_wound_3

value: Leaflets

value: Wound, 2 hours


title: NPS_8802_CD_8

description:
Library name: NPS_8802_CD_8
RNA-Seq of CHIM NPS

value: NPS


title: 2mo,SCD,rep2,GEX


title: Tak1_wound_2

description: Library name: Tak1_wound_2


title: DPSCs, control, 4hrs, Biol rep4

description:
Library name: Sample4
column name in raw_counts_all_samples.txt: Ctrl_4h4


title: DPSCs, BSN, 4hrs, Biol rep1

description:
Library name: Sample9
column name in raw_counts_all_samples.txt: BSN_4h1

value: BSN treated


title: NPS_8801_CD_8

description:
Library name: NPS_8801_CD_8
RNA-Seq of CHIM NPS

value: male


title: 2mo,SCD,rep1,GEX

value: cKit-enriched

value: mRNA


title: Tak1_wound_1

description: Library name: Tak1_wound_1


title: NPS_8876_CD_7

description:
Library name: NPS_8876_CD_7
RNA-Seq of CHIM NPS

value: female


title: DPSCs, control, 4hrs, Biol rep3

description:
Library name: Sample3
column name in raw_counts_all_samples.txt: Ctrl_4h3

value: untreated


title: Mpfad3fad7_mock_1

description: Library name: Mpfad3fad7_mock_1

value: mock, 2 hours


title: NPS_8799_CD_8

description:
Library name: NPS_8799_CD_8
RNA-Seq of CHIM NPS

value: Nose


title: 2mo,nonSCD,rep4,GEX

value: non-SCD

value: AA


title: NPS_8803_CD_7

description:
Library name: NPS_8803_CD_7
RNA-Seq of CHIM NPS


title: Tak1_mock_3

description: Library name: Tak1_mock_3


title: DPSCs, control, 4hrs, Biol rep2

description:
Library name: Sample2
column name in raw_counts_all_samples.txt: Ctrl_4h2


title: NPS_8797_CD_7

description:
Library name: NPS_8797_CD_7
RNA-Seq of CHIM NPS


title: 2mo,nonSCD,rep3,GEX

value: 2 months

value: M


title: DPSCs, control, 24hrs, Biol rep1

description:
Library name: Sample5
column name in raw_counts_all_samples.txt: Ctrl_24h1

value: Dental pulp

value: Mesenchymal stem cell


title: Tak1_mock_2

description: Library name: Tak1_mock_2

value: Leaflets


title: DPSCs, control, 4hrs, Biol rep1

description:
Library name: Sample1
column name in raw_counts_all_samples.txt: Ctrl_4h1


title: NPS_8793_CD_8

description:
Library name: NPS_8793_CD_8
RNA-Seq of CHIM NPS


title: H2.35 cells, MHV Infected Combination (0.3um Remdesivir, 6um Ivermectin), Set 3

description:
Library name: R13497
Row name in Raw counts_All Samples.txt: R13497_32

value: Hepatocyte

value: WT

value: MHV Infection with 0.3um Remdesivir, 6um Ivermectin treatment


title: Tak1_mock_1

description: Library name: Tak1_mock_1


title: 2mo,nonSCD,rep2,GEX

value: bone marrow

value: F


title: 116_AS_Ex_Vivo

city: Basel

first: Francis

last: Jacob

address: Hebelstrasse 20

department: Department of Biomedicine (DBM)

country: Switzerland

institute: University Hospital Basel and University of Basel

description: Library name: 116_AS_Ex_Vivo

data_processing:
Raw reads were mapped to the GRCh38 reference genome using 10x Genomics Cell Ranger Multi v 7.1.0 to infer read counts per gene per cell
Assembly: GRCh38
Supplementary files format and content: .rds file with raw counts and metadata

source_name: Ascites

extract_protocol:
Frozen ascites samples were resuspended in 1 mL of pre-warmed (37°C) Ovarian TumorMACS growth medium (Miltenyi Biotec) directly in the cryotube. The suspension was transferred to a 15 mL conical tube, and an additional 2 mL of Ovarian TumorMACS growth medium was added to reach a total volume of 3 mL. Cells were pelleted by centrifugation at 300 × g for 4 min, and the pellet was resuspended in 2 mL of 50% Accutase (diluted 1:1 in DMEM supplemented with 10% FBS and 1% antibiotic–antimycotic solution) and incubated for 10 minutes at 37°C. This was followed by treatment with 1 mL of trypsin for 5 min at 37 °C. Cells were centrifuged again at 300 × g for 4 min, resuspended in RNase-free PBS (1×) containing 0.04% BSA (Thermo Fisher Scientific), passed through a 70 µm cell strainer, and counted using an automated cell counter to assess total cell number and viability. For samples with viability below 75%, the Dead Cell Removal MicroBeads kit (Miltenyi Biotec) was applied according to the manufacturer’s instructions. A minimum of 2 × 10⁶ cells was required for downstream processing. Cells were divided into two conditions: (i) original control and (ii) seeded into 3D Petri dish micro-molds (Sigma-Aldrich) at 250,000 cells per chip, four chips per patient, and cultured for 48 h as ex vivo controls. Samples, including the original control immediately after thawing and short dissociation, as well as the ex vivo control after 72 hours of culture, were collected, centrifuged, resuspended in 1 mL of chilled PBS containing 0.04% RNase-free BSA, and washed once in the same buffer before downstream processing. Cells were fixed using Fixation & Permeabilization Buffer (10x Genomics PN-2000517) supplemented with formaldehyde (Sigma-Aldrich) for 1 h at room temperature, then stored at 4°C for 24 h. After incubation, samples were centrifuged, and 1 mL of Quenching Buffer (10x Genomics PN-2000516) was added, followed by 100 µL of pre-warmed (65 °C) Enhancer (10x Genomics PN-2000482) and 275 µL of 50% glycerol, followed by storage  at −80 °C until further use. Fixed cell samples  were transferred to the Genomics Facility Basel for further processing and data generation. Samples  were processed with Chromium Fixed RNA Kit, Human Transcriptome (10x Genomics), according to the user guide CG00527 Rev B (10x Genomics), multiplexing 16 samples, and starting with step “Post-Storage Processing” in demonstrated protocol CG000478 Rev C (10x Genomics). Probes were hybridised for 18 hours. Cells, stained with AOPI, were counted with Nexcelom Cellometer K2.  Quality control of sequencing libraries was performed with the Fragment Analyzer 12 Capillary system and HS NGS Fragment Kit, DNA-474-1000 (Agilent Technologies) and concentrations measured with Qubit Fluorometer and dsDNA HS Assay kit (Thermo Fisher Scientific)
10x Genomics Chromium platform using the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit, 16 rxns PN-1000414 on 10x Genomics Chromium Single Cell Controller

value: Ascites

value: advanced stage ovarian cancer

value: ex vivo cultured

tag: batch


title: NPS_8790_CD_7

description:
Library name: NPS_8790_CD_7
RNA-Seq of CHIM NPS

value: NPS

value: female


title: NPS_8877_CD_7

description:
Library name: NPS_8877_CD_7
RNA-Seq of CHIM NPS

value: Nose

value: male


title: 2mo,nonSCD,rep1,GEX

value: cKit-enriched

value: non-SCD

value: AA

value: 2 months

value: mRNA


title: NC_1

description:
Library name: A1
fpkm_A1

value: FaDu

value: Human medulloblastoma cell

value: NC


title: H2.35 cells, MHV Infected 0.3um Remdesivir, Set 2

description:
Library name: R13493
Row name in Raw counts_All Samples.txt: R13493_34 0124

value: Hepatocyte

value: WT

value: MHV Infection with 0.3um Remdesivir treatment


title: 116_AS_Original

description: Library name: 116_AS_Original

value: Ascites

value: advanced stage ovarian cancer

value: tissue


title: NPS_8789_CD_7

description:
Library name: NPS_8789_CD_7
RNA-Seq of CHIM NPS

value: NPS


title: Mouse brain tissue, Radiation+ND1, replicate 3

city: Guangzhou

first: Yamei

last: Tang

state: Guangdong

address: 107 Yan Jiang West Road

department: Department of Neurology

institute: Sun Yat-Sen Memorial Hospital

data_processing:
Clean data were filtered from the reads obtained from the sequencing machines with fastp (version 0.18.0) using the following parameters: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides(N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
The clean reads were quality controlled with FastQC and aligned to the mouse genome GRCm39 with HISAT (version 2.2.4) using the default parameters.
After the alignment, the reads were quantified to gene level with RSEM (version 1.2.19) using the Ensembl annotation (GRCm39).
The read counts of genes were used for further analysis.
Assembly: GRCm39
Supplementary files format and content: comma-delimited text files include feature counts for each Sample

source_name: Thalamus

growth_protocol: The male C57BL/6J mice (8-10 weeks old) were purchased from Beijing Vital River Laboratory Animal Technology Co. Ltd. and were housed in a specific-pathogen-free (SPF) environment with a maximum of five mice per cage, a temperature range of 21-26°C, relative humidity range of 40%-60%, and a light cycle of 8:00-20:00. All animals were allowed to ad libitum access to food and water.

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB#E7530, New England Biolabs, Ipswich, MA, USA). following the manufacturer's protocol.

treatment_protocol: Two weeks after the establishment of the thalamic radiation brain injury model, the mice were randomly divided into two groups: the control virus group and the ND1-treated group. 2 μL of virus was injected into the thalamic region at coordinates AP: -1.46 mm, ML: 1.25 mm, DV: -3.5 mm. The ND1-treated mice were injected with AAV9 GFAP104::mND1-tdTomato (5320, PackGene Biotech) at a virus concentration of 5.0E+11 GC/mL, while the control virus mice were injected with AAV9 GFAP104::tdTomato (10061, PackGene Biotech) at a virus concentration of 5.0E+11 GC/mL.

value: Thalamus

value: Whole tissue

tag: strain

value: Radiation+AAV9 GFAP104::mND1-tdTomato


title: 112_AS_Ex_Vivo

description: Library name: 112_AS_Ex_Vivo

value: ex vivo cultured


title: MuSC RNA-seq III BMP6+DAPT 3h biol rep 3

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

country: Germany

institute: Charite

description:
Library name: Cultured adult mouse MuSC, serum starved, BMP6-stimulated + DAPT-treated for 3h, biological replicate 3
TPM_joined.tab: TPM_wt3BMP6DAPT3h
FPKM_joined.tab: FPKM_wt3BMP6DAPT3h

data_processing:
After removing the sequencing adapters, the resulting FASTQ files were filtered for the desired length of 150 bp and for quality scores of Phred+33. FASTQ files were aligned to the mouse genome (GENCODE GRCm39) using STAR v2.7.11a with the following settings: --runThreadN 80 --outReadsUnmapped Fastx --outFilterScoreMinOverLread 0.66 --outFilterMatchNminOverLread 0.66 --seedSearchStartLmax 75 --outFilterMatchNmin 250 --alignSoftClipAtReferenceEnds No --outSAMattrIHstart 0 --alignEndsType EndToEnd --twopassMode Basic. The resulting *.bam file was sorted and indexed using samtools v1.17.
The sorted *.bam file was passed to StringTie v2.2.1 with the following settings: -u -p 80 -e. The resulting *.gtf files were merged using stringtie merge and normalized read counts (TPM and FPKM) were generated using stringtie ballgown. The read counts of all experimental samples were then concatenated into two tables: output.tpm.csv and output.fpkm.csv.
Assembly: GENCODE M32 (GRCm39)
Supplementary files format and content: Stringtie ballgown output files: *.cov.refs.ballgown.gtf => contains details of the transcripts that StringTie assembles from RNA-seq data in the GTF format; *.gene_abund.ballgown.tab => contains gene abundance counts as normalized FPKM and TPM values as a table; *.out.ballgown.gtf => This is a file listing all the transcripts in the reference annotation that are fully covered, end to end, by reads. The output format is a GTF file as described above. Each line of the GTF is corresponds to a gene or transcript in the reference annotation.
Supplementary files format and content: FPKM_joined.tab, FPKM_joined.xlsx, TPM_joined.tab, TPM_joined.xlsx => fused tables with all the samples of the experiment in TAB and XLSX format provided as TPM and FPKM values, gene_count.csv => fused tables with the fragment counts for all the samples of the experiment

source_name: skeletal muscle

growth_protocol: Muscle stem cells were isolated from forelimb, hindlimb, dorsal, and breast muscles of female 8-week-old mice by autoMACS and cultured in DMEM (Gibco, 41966029), 15% FBS (Gibco), 2.5 ng/mL basic FGF (Sigma, F3133), 10 ng/mL leukemia inhibitory factor (Sigma, ESG1106), and 1% Pen/Strep (Gibco) in Matrigel® (Corning, 356231)-coated dishes at 3% O2 and 5% CO2 at 37 °C for 48 hours. After the first 24 hours, 1x B27 without vitamin A (Gibco, 12587010) was added. In order to eliminate the effect of BMPs in the culture medium (e.g. from serum supplements), cells were then cultured in serum-free medium containing soluble BMP receptor (recombinant mouse BMPR-1A-Fc Chimera, R&D Systems, 437-MR) at a concentration of 200 ng/mL for 6 h.

extract_protocol:
Cells were washed, trypsinized, centrifuged, and frozen at -80 °C for later RNA extraction. RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel, 740955). RNA quantity and quality were assessed using a NanoDrop® 2000c spectrophotometer (Thermo Fisher Scientific)
The construction of the eukaryotic strand-specific transcriptome library was performed according to the "DNBSEQ Eukaryotic Strand-specific Transcriptome Resequencing" protocol of the  Beijing Genetics Institute (BGI). Briefly, 500 ng total RNA was enriched for poly(A)-carrying molecules using oligo-dT beads. The RNA was then fragmented and the first cDNA strand was synthesized using random primers. Second strand cDNA was synthesized using dUTP instead of dTTP and the synthesized cDNA was subjected to end repair and 3' adenylation. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments, which were then amplified by PCR. After quality control, the library was circularized and amplified to produce DNA nanoballs (DNBs).

treatment_protocol: Depending on the condition, cells were optionally pretreated with 20 µM DAPT or 10 µM cycloheximide for 10 minutes and subsequently stimulated with 100 ng/mL BMP6 or treated with vehicle (4 mM HCl containing 0.1% BSA) for 1 or 3 hours.

value: skeletal muscle

value: muscle stem cells

value: biol rep 3


title: MuSC RNA-seq III BMP6+CHX 3h biol rep 3

description:
Library name: Cultured adult mouse MuSC, serum starved, BMP6-stimulated + cycloheximide-treated for 3h, biological replicate 3
TPM_joined.tab: TPM_wt3BMP6CXD3h
FPKM_joined.tab: FPKM_wt3BMP6CXD3h


title: NPS_8784_CD_6

description:
Library name: NPS_8784_CD_6
RNA-Seq of CHIM NPS

value: Nose

value: male


title: Mouse brain tissue, Radiation+ND1, replicate 2


title: 112_AS_Original

description: Library name: 112_AS_Original


title: MuSC RNA-seq III BMP6 3h biol rep 3

description:
Library name: Cultured adult mouse MuSC, serum starved, BMP6-stimulated for 3h, biological replicate 3
TPM_joined.tab: TPM_wt3BMP63h
FPKM_joined.tab: FPKM_wt3BMP63h


title: Ishikaw  cell WT 3

description: Library name: WT3

value: endometrium

value: HEC

value: no treated


title: 2mo,nonSCD,rep4,ADT

value: bone marrow

value: cKit-enriched

value: non-SCD

value: AA

value: 2 months

value: F

value: ADT


title: NPS_8783_CD_6

description:
Library name: NPS_8783_CD_6
RNA-Seq of CHIM NPS

value: NPS


title: Mouse brain tissue, Radiation+ND1, replicate 1

value: Thalamus

value: Whole tissue

value: WT

value: Radiation+AAV9 GFAP104::mND1-tdTomato


title: 102_AS_Ex_Vivo

description: Library name: 102_AS_Ex_Vivo

value: Ascites

value: advanced stage ovarian cancer

value: ex vivo cultured


title: MuSC RNA-seq III control 3h biol rep 3

description:
Library name: Cultured adult mouse MuSC, serum starved, control-treated for 3h, biological replicate 3
TPM_joined.tab: TPM_wt3control3h
FPKM_joined.tab: FPKM_wt3control3h

value: skeletal muscle

value: muscle stem cells

value: control

value: biol rep 3


title: NPS_8793_CD_9

description:
Library name: NPS_8793_CD_9
RNA-Seq of CHIM NPS

value: Nose

value: female


title: Mouse brain tissue, Radiation+Control virus, replicate 3

value: Radiation+AAV9 GFAP104::tdTomato


title: NPS_8782_CD_7

description:
Library name: NPS_8782_CD_7
RNA-Seq of CHIM NPS


title: MuSC RNA-seq III BMP6+CHX 3h biol rep 2

description:
Library name: Cultured adult mouse MuSC, serum starved, BMP6-stimulated + cycloheximide-treated for 3h, biological replicate 2
TPM_joined.tab: TPM_wt2BMP6CXD3h
FPKM_joined.tab: FPKM_wt2BMP6CXD3h

value: biol rep 2


title: 102_AS_Original

description: Library name: 102_AS_Original

value: tissue


title: NPS_8781_7

description:
Library name: NPS_8781_7
RNA-Seq of CHIM NPS

value: NPS

value: male


title: Mouse brain tissue, Radiation+Control virus, replicate 2

value: Thalamus

value: Whole tissue


title: MuSC RNA-seq III BMP6+DAPT 3h biol rep 2

description:
Library name: Cultured adult mouse MuSC, serum starved, BMP6-stimulated + DAPT-treated for 3h, biological replicate 2
TPM_joined.tab: TPM_wt2BMP6DAPT3h
FPKM_joined.tab: FPKM_wt2BMP6DAPT3h


title: SN50ug_9days_SelB

city: Camperdown

first: G.

middle: Greg

last: Neely

state: NSW

address: Charles Perkins Centre, D17.

country: Australia

institute: University of Sydney

description:
Library name: SN50ug_9days_SelB
Amplified sgRNA region to identify genes that sensitise or protect againt venom compared to diversity controls, 9 days

library_source: genomic

data_processing:
Data was analyzed using the MAGeCK (v05.9.2) pipeline
Assembly: GRCh37.p13
Supplementary files format and content: .txt file containing robust rank aggregation of genes
Supplementary files format and content: .txt file containing robust rank aggregation of inidividual sgRNAs
Library strategy: CRISPR Screen

molecule: genomic DNA

extract_protocol:
Genomic DNA was extracted from cell pellets with the ISOLATE II Genomic DNA Kit (Bioline). Samples of gDNA (25 μg for controls and 5 μg for selected samples) were added to NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs) along with the following primers to amplify the integrated sgRNA-containing sequence: NGSCRISPRv2F1 5’-GGACAGCAGAGATCCAGTTTGGT-3’; NGSCRISPRv2R1 5’-GAGCCAATTCCCACTCCTTTCAA-3’. A second PCR reaction with a staggered primer mix of P5 and P7 indexing primers unique to each sample was prepared. Reactions were isolated by gel electrophoresis.
Samples were sequenced with Novogene

value: 50 ug/mL of Chrysaora quinquecirrha venom over 9 days, Replicate B


title: NPS_8780_CD_6

description:
Library name: NPS_8780_CD_6
RNA-Seq of CHIM NPS


title: SN50ug_9days_SelA

description:
Library name: SN50ug_9days_SelA
Amplified sgRNA region to identify genes that sensitise or protect againt venom compared to diversity controls, 9 days

value: 50 ug/mL of Chrysaora quinquecirrha venom over 9 days, Replicate A


title: Mouse brain tissue, Radiation+Control virus, replicate 1

value: WT


title: MuSC RNA-seq III BMP6 3h biol rep 2

description:
Library name: Cultured adult mouse MuSC, serum starved, BMP6-stimulated for 3h, biological replicate 2
TPM_joined.tab: TPM_wt2BMP63h
FPKM_joined.tab: FPKM_wt2BMP63h


title: NPS_8779_CD_6

description:
Library name: NPS_8779_CD_6
RNA-Seq of CHIM NPS


title: H2.35 cells, MHV Infected 0.3um Remdesivir, Set 1

description:
Library name: R13487
Row name in Raw counts_All Samples.txt: R13487_24 0124

value: Hepatocyte

value: MHV Infection with 0.3um Remdesivir treatment


title: SN50ug_9days_CTLB

description:
Library name: SN50ug_9days_CTLB
Diversity control, 9 days

value: Untreated, 9 days Replicate B


title: RNA-Seq of Phyllotreta striolata:pupal whole-body-Rep1

city: Hangzhou

first: Yanyan

last: Zhou

address: Xueyuan street 258

institute: China Jiliang University

description: Library name: PSP_1

data_processing:
Raw reads were quality-filtered by fastp. Clean reads were aligned to the reference genome using HISAT2. Gene expression levels were quantified as raw counts using featureCounts.
Assembly: ncbi_phyllotreta_striolata_gca_918026865_1_pgi_phyevi_v3
Supplementary files format and content: "We provided three processed data files in CSV format:  'all_samples_counts.csv' contains the raw read count matrix for all biological samples, which was generated by featureCounts and used for differential expression analysis.  'group_mean_tpm_results.csv' contains the normalized mean Transcripts Per Million (TPM) values calculated for each of the five experimental groups (egg, larva, pupa, male adult, and female adult).  'stage- and sex-specific gene.csv' contains the list of identified stage- and sex-specific expressed genes across different developmental stages and sexes of Phyllotreta striolata."

organism: Phyllotreta striolata

source_name: whole body

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer's instructions.
RNA-seq libraries were constructed using the Illumina TruSeq RNA Library Prep Kit.

value: whole body


title: MuSC RNA-seq III control 3h biol rep 2

description:
Library name: Cultured adult mouse MuSC, serum starved, control-treated for 3h, biological replicate 2
TPM_joined.tab: TPM_wt2control3h
FPKM_joined.tab: FPKM_wt2control3h

value: skeletal muscle

value: muscle stem cells

value: control


title: NPS_8778_CD_7

description:
Library name: NPS_8778_CD_7
RNA-Seq of CHIM NPS

value: Nose

value: female


title: RNA-Seq of Phyllotreta striolata:pupal whole-body-Rep2

description: Library name: PSP_2


title: MuSC RNA-seq III BMP6+CHX 3h biol rep 1

description:
Library name: Cultured adult mouse MuSC, serum starved, BMP6-stimulated + cycloheximide-treated for 3h, biological replicate 1
TPM_joined.tab: TPM_wt1BMP6CXD3h
FPKM_joined.tab: FPKM_wt1BMP6CXD3h

value: biol rep 1


title: SN50ug_9days_CTLA

description:
Library name: SN50ug_9days_CTLA
Diversity control, 9 days

value: Untreated, 9 days Replicate A


title: NPS_8879_CD_5

description:
Library name: NPS_8879_CD_5
RNA-Seq of CHIM NPS

value: NPS

value: male


title: RNA-Seq of Phyllotreta striolata:pupal whole-body-Rep3

description: Library name: PSP_3


title: SN50ug_6days_SelB

description:
Library name: SN50ug_6days_SelB
Amplified sgRNA region to identify genes that sensitise or protect againt venom compared to diversity controls, 6 days

value: 50 ug/mL of Chrysaora quinquecirrha venom over 6 days, Replicate B


title: MuSC RNA-seq III BMP6+DAPT 3h biol rep 1

description:
Library name: Cultured adult mouse MuSC, serum starved, BMP6-stimulated + DAPT-treated for 3h, biological replicate 1
TPM_joined.tab: TPM_wt1BMP6DAPT3h
FPKM_joined.tab: FPKM_wt1BMP6DAPT3h


title: RNA-Seq of Phyllotreta striolata:female adult whole-body-Rep1

description: Library name: PSF_1


title: MuSC RNA-seq III BMP6 3h biol rep 1

description:
Library name: Cultured adult mouse MuSC, serum starved, BMP6-stimulated for 3h, biological replicate 1
TPM_joined.tab: TPM_wt1BMP63h
FPKM_joined.tab: FPKM_wt1BMP63h


title: SN50ug_6days_SelA

description:
Library name: SN50ug_6days_SelA
Amplified sgRNA region to identify genes that sensitise or protect againt venom compared to diversity controls, 6 days

value: 50 ug/mL of Chrysaora quinquecirrha venom over 6 days, Replicate A


title: NPS_8877_CD_5

description:
Library name: NPS_8877_CD_5
RNA-Seq of CHIM NPS


title: MuSC RNA-seq III control 3h biol rep 1

description:
Library name: Cultured adult mouse MuSC, serum starved, control-treated for 3h, biological replicate 1
TPM_joined.tab: TPM_wt1control3h
FPKM_joined.tab: FPKM_wt1control3h


title: NPS_8876_CD_6

description:
Library name: NPS_8876_CD_6
RNA-Seq of CHIM NPS


title: SN50ug_6days_CTLA

description:
Library name: SN50ug_6days_CTLA
Diversity control, 6 days

value: Untreated, 6 days Replicate A


title: MuSC RNA-seq III BMP6+CHX 1h biol rep 3

description:
Library name: Cultured adult mouse MuSC, serum starved, BMP6-stimulated + cycloheximide-treated for 1h, biological replicate 3
TPM_joined.tab: TPM_wt3BMP6CXD1h
FPKM_joined.tab: FPKM_wt3BMP6CXD1h

value: biol rep 3


title: NPS_8803_CD_6

description:
Library name: NPS_8803_CD_6
RNA-Seq of CHIM NPS


title: RNA-Seq of Phyllotreta striolata:larval  whole-body-Rep2

description: Library name: PSL_2


title: MuSC RNA-seq III BMP6 1h biol rep 3

description:
Library name: Cultured adult mouse MuSC, serum starved, BMP6-stimulated for 1h, biological replicate 3
TPM_joined.tab: TPM_wt3BMP61h
FPKM_joined.tab: FPKM_wt3BMP61h


title: SN50ug_3days_SelA

description:
Library name: SN50ug_3days_SelA
Amplified sgRNA region to identify genes that sensitise or protect againt venom compared to diversity controls, 3 days

value: 50 ug/mL of Chrysaora quinquecirrha venom over 3 days, Replicate A


title: RNA-Seq of Phyllotreta striolata:larval  whole-body-Rep1

description: Library name: PSL_1


title: NPS_8801_CD_7

description:
Library name: NPS_8801_CD_7
RNA-Seq of CHIM NPS


title: MuSC RNA-seq III control 1h biol rep 3

description:
Library name: Cultured adult mouse MuSC, serum starved, control-treated for 1h, biological replicate 3
TPM_joined.tab: TPM_wt3control1h
FPKM_joined.tab: FPKM_wt3control1h


title: SN50ug_3days_CTLB

description:
Library name: SN50ug_3days_CTLB
Diversity control, 3 days

value: Untreated, 3 days Replicate B


title: NPS_8799_CD_7

description:
Library name: NPS_8799_CD_7
RNA-Seq of CHIM NPS


title: RNA-Seq of Phyllotreta striolata:male adult whole-body-Rep1

description: Library name: PSM_1


title: MuSC RNA-seq III BMP6+CHX 1h biol rep 2

description:
Library name: Cultured adult mouse MuSC, serum starved, BMP6-stimulated + cycloheximide-treated for 1h, biological replicate 2
TPM_joined.tab: TPM_wt2BMP6CXD1h
FPKM_joined.tab: FPKM_wt2BMP6CXD1h

value: biol rep 2


title: SN50ug_3days_CTLA

description:
Library name: SN50ug_3days_CTLA
Diversity control, 3 days

value: Untreated, 3 days Replicate A


title: NPS_8797_CD_6

description:
Library name: NPS_8797_CD_6
RNA-Seq of CHIM NPS


title: RNA-Seq of Phyllotreta striolata:male adult whole-body-Rep2

description: Library name: PSM_2

value: whole body


title: MuSC RNA-seq III BMP6+DAPT 1h biol rep 2

description:
Library name: Cultured adult mouse MuSC, serum starved, BMP6-stimulated + DAPT-treated for 1h, biological replicate 2
TPM_joined.tab: TPM_wt2BMP6DAPT1h
FPKM_joined.tab: FPKM_wt2BMP6DAPT1h

value: skeletal muscle

value: muscle stem cells


title: SCD1

data_processing:
Technical quality of reads was checked with FastQC (version 0.12.0) before and after read trimming. Reads were trimmed and filtered with fastp (version 0.23.4) to remove adapter sequence, low-quality bases near the ends of reads, and to remove reads with fewer than 40 high-quality bases. Library quality was assessed with BBMap (version 38.86) and RSeQC (version 3.0.1).
Filtered reads were mapped to their respective genome with STAR (version 2.7.11). For human the T2T-CHM13v2.0 genome assembly with annotation from Ensembl (release 110.1) was used. Gene-level counts were obtained with featureCounts from Subread (version 2.0.5) and transcript-level expression was quantified with RSEM (version 1.3.3). Up to 20 alignments for a given read were output from STAR, but multi-mapping reads were not counted by featureCounts.
Assembly: T2T-CHM13v2.0 genome assembly with annotation from Ensembl (release 110.1)
Supplementary files format and content: Tab-delimited text file with gene-level counts. Includes original Ensembl Gene IDs from Ensembl annotation, as well as the associated gene symbols and gene types. Genes were filtered to include only those with at least 10 counts in one or more samples. Genes were further filtered to keep only features of annotated type "protein_coding", "processed_pseudogene", "lncRNA", "snoRNA", and "miRNA".

extract_protocol:
Human bone marrow HSPCs (CD45+Lineage-CD34+CD38-) were sorted by FACS from cryopreserved SCD and non-SCD patient bone marrow samples. Cells were sorted by FACS and collected directly into the provided RNA lysis buffer for isolation of total RNA (RNeasy Micro kit; QIAGEN, Germantown, MD).
The SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio, Kusatsu, Japan) was used to prepare sequencing libraries. 150 bp paired-end sequencing was performed on the Illumina NovaSeq 6000, targeting an average of 50 million reads/sample by the Vanderbilt Technologies for Advanced Genomics Genomics core laboratory (Vanderbilt University Medical Center, Nashville, TN).

value: bone marrow

value: HSPCs

tag: age(years)

value: M

value: SCD


title: NPS_8796_CD_8

description:
Library name: NPS_8796_CD_8
RNA-Seq of CHIM NPS

value: Nose

value: NPS

value: female


title: RNA-Seq of Phyllotreta striolata:male adult whole-body-Rep3

description: Library name: PSM_3


title: MuSC RNA-seq III BMP6 1h biol rep 2

description:
Library name: Cultured adult mouse MuSC, serum starved, BMP6-stimulated for 1h, biological replicate 2
TPM_joined.tab: TPM_wt2BMP61h
FPKM_joined.tab: FPKM_wt2BMP61h


title: NPS_8802_CD_7

description:
Library name: NPS_8802_CD_7
RNA-Seq of CHIM NPS

value: male


title: NPS_8793_CD_7

description:
Library name: NPS_8793_CD_7
RNA-Seq of CHIM NPS


title: RNA-Seq of Phyllotreta striolata:egg whole-body-Rep1

description: Library name: PSE_1


title: SCD12


title: NPS_8790_CD_6

description:
Library name: NPS_8790_CD_6
RNA-Seq of CHIM NPS


title: RNA-Seq of Phyllotreta striolata:egg whole-body-Rep2

description: Library name: PSE_2


title: SCD11


title: MuSC RNA-seq III BMP6+CHX 1h biol rep 1

description:
Library name: Cultured adult mouse MuSC, serum starved, BMP6-stimulated + cycloheximide-treated for 1h, biological replicate 1
TPM_joined.tab: TPM_wt1BMP6CXD1h
FPKM_joined.tab: FPKM_wt1BMP6CXD1h

value: biol rep 1


title: NPS_8789_CD_6

description:
Library name: NPS_8789_CD_6
RNA-Seq of CHIM NPS


title: RNA-Seq of Phyllotreta striolata:egg whole-body-Rep3

description: Library name: PSE_3


title: MuSC RNA-seq III BMP6+DAPT 1h biol rep 1

description:
Library name: Cultured adult mouse MuSC, serum starved, BMP6-stimulated + DAPT-treated for 1h, biological replicate 1
TPM_joined.tab: TPM_wt1BMP6DAPT1h
FPKM_joined.tab: FPKM_wt1BMP6DAPT1h


title: SCD2


title: CD8+ T Cells, DiSBey, Acute Stimulation, Day 18, chr4, batch1, biol_rep 4

city: Minneapolis

first: Nuri

middle: Alpay

last: Temiz

state: MN

address: 2231 6th St SE

department: Masonic Cancer Center

institute: University of Minnesota

description: Library name: QI4_001

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

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: Acute Stimulation

tag: day

tag: launch chr

tag: biol rep


title: MuSC RNA-seq III BMP6 1h biol rep 1

description:
Library name: Cultured adult mouse MuSC, serum starved, BMP6-stimulated for 1h, biological replicate 1
TPM_joined.tab: TPM_wt1BMP61h
FPKM_joined.tab: FPKM_wt1BMP61h

tag: tissue


title: NPS_8783_CD_5

description:
Library name: NPS_8783_CD_5
RNA-Seq of CHIM NPS

tag: cell type


title: CD8+ T Cells, DiSBey, Acute Stimulation, Day 18, chr4, batch1, biol_rep 3

description: Library name: QI3_001

tag: genotype


title: MuSC RNA-seq III control 1h biol rep 1

description:
Library name: Cultured adult mouse MuSC, serum starved, control-treated for 1h, biological replicate 1
TPM_joined.tab: TPM_wt1control1h
FPKM_joined.tab: FPKM_wt1control1h

value: control


title: SCD3

value: F


title: SCD7


title: NPS_8782_CD_6

description:
Library name: NPS_8782_CD_6
RNA-Seq of CHIM NPS

tag: age


title: CD8+ T Cells, DiSBey, Acute Stimulation, Day 18, chr4, batch1, biol_rep 2

description: Library name: QI2_001


title: cKO_CT22

city: Fukuoka

first: Keisuke

last: Ikegami

address: Nishi-ku Motooka 744

country: Japan

institute: Kyushu University

description: Library name: Mice_cNr3c1_CT22

data_processing:
FASTQ files were obtained from the sequencing provider for each pooled WT or cKO time-point sample and uploaded to RaNAseq (https://ranaseq.eu/) for RNA-seq data processing.
Quality control, read mapping to the mouse reference genome, and generation of gene-level expression values were performed using RaNAseq.
Differentially expressed genes (DEGs) were identified using RaNAseq by comparing WT (Cre-) and retina-specific Nr3c1 cKO (Cre+) samples at the corresponding circadian time points.
Time-series expression profiles across CT2, CT6, CT10, CT14, CT18 and CT22 were then used to evaluate rhythmic gene expression patterns and genes whose rhythmicity was lost or altered in retina-specific Nr3c1 cKO samples.
Processed expression matrices, DEG analysis results, and rhythmic gene expression analysis results were generated from the RaNAseq-processed time-series RNA-seq data.
Assembly: Mus musculus reference genome; exact genome build/assembly to be confirmed based on the reference used for read mapping.
Supplementary files format and content: Processed data files contain gene-level expression values for each pooled genotype/time-point sample, DEG analysis results generated using RaNAseq, and rhythmic gene expression analysis results comparing WT and retina-specific Nr3c1 KO samples.

source_name: ciliary body

growth_protocol: Male 12-week-old WT (Cre-) and retina-specific Nr3c1 cKO (Cre+) mice were maintained under 12 h light/12 h dark (12L:12D) conditions for 2 weeks , and then tranfered to constant dark conditions before sampling to remove the effects of light slimuli.

extract_protocol:
At each time point, whole eyes were collected from three WT mice and three cKO mice. Each whole-eye sample was homogenized with a pestle, and total RNA was extracted. Equal amounts of RNA from the three individuals in each genotype/time-point group were pooled for RNA-seq analysis.
RNA sequencing libraries were prepared from pooled total RNA samples for each genotype/time-point group and sequenced by an external service provider.

treatment_protocol: No drug treatment was performed. Whole eyes were collected every 4 hours at 2, 6, 10, 14, 18, and 22 hours after circadian time 0 (CT2, CT6, CT10, CT14, CT18 and CT22) under 2nd day of constant dark conditions.

value: ciliary body

value: nonpigmented ciliary epithelial cell line

value: nonpigmented ciliary epithelial cell type


title: NS9

value: bone marrow

value: HSPCs

value: NonSCD


title: NPS_8781_6

first: Lisa

last: Willemsen

institute: Amsterdam UMC - locatie AMC

description:
Library name: NPS_8781_6
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.

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: days post_challenge


title: CD8+ T Cells, DiSBey, Acute Stimulation, Day 18, chr4, batch1, biol_rep 1

description: Library name: QI1_001


title: cKO_CT18

description: Library name: Mice_cNr3c1_CT18


title: NS5

tag: Sex

value: M


title: NPS_8780_CD_5

description:
Library name: NPS_8780_CD_5
RNA-Seq of CHIM NPS

value: NPS

value: female


title: NS3


title: cKO_CT14

description: Library name: Mice_cNr3c1_CT14

tag: cell line


title: NPS_8779_CD_5

description:
Library name: NPS_8779_CD_5
RNA-Seq of CHIM NPS


title: CD8+ T Cells, DiSBey, Chronic Stimulation, Day 18, chr4, batch1, biol_rep 3

description: Library name: QE3_001

value: Chronic Stimulation


title: cKO_CT10

description: Library name: Mice_cNr3c1_CT10


title: NS8

tag: condition


title: NPS_8778_CD_6

description:
Library name: NPS_8778_CD_6
RNA-Seq of CHIM NPS


title: CD8+ T Cells, DiSBey, Chronic Stimulation, Day 18, chr4, batch1, biol_rep 2

description: Library name: QE2_001

value: Spleen

tag: treatment


title: NPS_8784_CD_5

description:
Library name: NPS_8784_CD_5
RNA-Seq of CHIM NPS

value: male


title: cKO_CT6

description: Library name: Mice_cNr3c1_CT6


title: plus dox 24h DMSO+BMP4 rep3

city: South San Francisco

first: Robert

last: Piskol

state: CA

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

data_processing:
Reads were aligned to the human reference genome (NCBI Assembly GRCh38) using GSNAP (Wu and Nacu, 2010) version ‘2013-10-10’, allowing a maximum of two mismatches per 50 base pair sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap’).
Transcript annotation was based on the human RefSeq database NCBI Annotation Releases 106.
To quantify gene expression, the number of reads mapped to the exons of each RefSeq gene was calculated using the HTSeqGenie R package.
Read counts were scaled by library size, quantile normalized and precision weights calculated using the “voom” R package (Law et al., 2014).
Differential expression analysis on the normalized count data was performed using the “limma” R package (Ritchie et al., 2015) by contrasting MIB1 knockout  treated samples with control samples, respectively.  Gene expression was considered significantly different across groups if we observed an |log2-fold change| ≥ 1 (estimated from the model coefficients) associated with an FDR adjusted P-value ≤ 0.05. In addition, gene expression was obtained in the form of normalized Reads Per Kilobase gene model per Million total reads (nRPKM) as described previously (Srinivasan et al., 2016).
Assembly: human genome (NCBI Assembly GRCh38)
Supplementary files format and content: csv (count and rpkm matrix)

source_name: plus dox 24h DMSO+BMP4

extract_protocol:
Total RNA was quantified with Qubit RNA HS Assay Kit (Thermo Fisher Scientific) and quality was assessed using RNA ScreenTape on TapeStation 4200 (Agilent Technologies). For low input RNA, cDNA library was generated from 2 nanograms of total RNA using Smart-Seq V4 Ultra Low Input RNA Kit (Takara) and 150 picograms of cDNA were used to make sequencing libraries by Nextera XT DNA Sample Preparation Kit (Illumina). For regular input RNA, the sequencing library was generated using a Truseq Stranded mRNA kit (Illumina) with an input of 100-1000 nanograms of total RNA.
Libraries were quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and the average library size was determined using D1000 ScreenTape on TapeStation 4200 (Agilent Technologies). Libraries were pooled and sequenced on NovaSeq 6000 (Illumina) to generate 30 millions single-end 50-base pair reads for each sample.

treatment_protocol: MIB1-iKO cells were seeded into 6-well plates (1x105 cells/well) and treated with 50 nM LDN189193 -/+ 0.5 ug/ml doxycycline for 3 days and then placed into dmso +10 ng/ml BMP4 or  LDN189193 +10 ng/ml BMP4 for 24 hours

value: lung

value: plus dox 24h DMSO+BMP4


title: NPS_8879_CD_4

city: Amsterdam

address: Meibergdreef 9

description:
Library name: NPS_8879_CD_4
RNA-Seq of CHIM NPS


title: cKO_CT2

description: Library name: Mice_cNr3c1_CT2


title: CD8+ T Cells, DiSBey, Chronic Stimulation, Day 18, chr4, batch1, biol_rep 1

description: Library name: QE1_001

value: CD8+ T Cells

value: DiSBey


title: plus dox 24h DMSO+BMP4 rep2


title: NPS_8878_CD_5

description:
Library name: NPS_8878_CD_5
RNA-Seq of CHIM NPS


title: CD8+ T Cells, DiSBey, Input, Day 2, chr4, batch1, biol_rep 1

description: Library name: QA_001

value: Input


title: WT_CT22

description: Library name: Mice_WT_CT22

value: ciliary body

value: nonpigmented ciliary epithelial cell line


title: plus dox 24h DMSO+BMP4 rep1


title: NPS_8877_CD_4

description:
Library name: NPS_8877_CD_4
RNA-Seq of CHIM NPS


title: CD8+ T Cells, DiSBey, Acute Stimulation, Day 6, chr1, batch1, biol_rep 3

description: Library name: QI3D6_1

value: Acute Stimulation


title: WT_CT18

description: Library name: Mice_WT_CT18

value: nonpigmented ciliary epithelial cell type


title: plus dox 24h LDN+BMP4 rep3

source_name: plus dox 24h LDN+BMP4

value: plus dox 24h LDN+BMP4


title: CD8+ T Cells, DiSBey, Chronic Stimulation, Day 18, chr4, batch1, biol_rep 4

description: Library name: QE4_001


title: NPS_8876_CD_5

description:
Library name: NPS_8876_CD_5
RNA-Seq of CHIM NPS

value: Nose


title: CD8+ T Cells, DiSBey, Acute Stimulation, Day 14, chr1, batch1, biol_rep 3

description: Library name: QI3D14_1


title: WT_CT14

description: Library name: Mice_WT_CT14


title: NPS_8878_CD_6

description:
Library name: NPS_8878_CD_6
RNA-Seq of CHIM NPS


title: NPS_8803_CD_5

description:
Library name: NPS_8803_CD_5
RNA-Seq of CHIM NPS


title: plus dox 24h LDN+BMP4 rep 2


title: CD8+ T Cells, DiSBey, Acute Stimulation, Day 10, chr1, batch1, biol_rep 3

description: Library name: QI3D10_1


title: WT_CT10

description: Library name: Mice_WT_CT10


title: RNA-Seq of Phyllotreta striolata:female adult whole-body-Rep2

description: Library name: PSF_2

value: whole body


title: SN50ug_6days_CTLB

description:
Library name: SN50ug_6days_CTLB
Diversity control, 6 days

value: Untreated, 6 days Replicate B


title: plus dox 24h LDN+BMP4 rep 1


title: RNA-Seq of Phyllotreta striolata:female adult whole-body-Rep3

description: Library name: PSF_3


title: NPS_8802_CD_6

description:
Library name: NPS_8802_CD_6
RNA-Seq of CHIM NPS

value: NPS


title: CD8+ T Cells, DiSBey, Acute Stimulation, Day 6, chr1, batch1, biol_rep 2

description: Library name: QI2D6_1


title: WT_CT6

description: Library name: Mice_WT_CT6


title: no dox 24h DMSO+BMP4 rep3

source_name: no dox 24h DMSO+BMP4

value: no dox 24h DMSO+BMP4


title: NPS_8801_CD_6

description:
Library name: NPS_8801_CD_6
RNA-Seq of CHIM NPS


title: CD8+ T Cells, DiSBey, Acute Stimulation, Day 14, chr1, batch1, biol_rep 2

description: Library name: QI2D14_1

value: Spleen


title: SN50ug_3days_SelB

description:
Library name: SN50ug_3days_SelB
Amplified sgRNA region to identify genes that sensitise or protect againt venom compared to diversity controls, 3 days

value: 50 ug/mL of Chrysaora quinquecirrha venom over 3 days, Replicate B


title: MuSC RNA-seq III BMP6+DAPT 1h biol rep 3

description:
Library name: Cultured adult mouse MuSC, serum starved, BMP6-stimulated + DAPT-treated for 1h, biological replicate 3
TPM_joined.tab: TPM_wt3BMP6DAPT1h
FPKM_joined.tab: FPKM_wt3BMP6DAPT1h

value: skeletal muscle

value: muscle stem cells

value: biol rep 3


title: no dox 24h DMSO+BMP4 rep2

value: lung


title: WT_CT2

description: Library name: Mice_WT_CT2


title: RNA-Seq of Phyllotreta striolata:larval  whole-body-Rep3

description: Library name: PSL_3


title: NPS_8799_CD_6

description:
Library name: NPS_8799_CD_6
RNA-Seq of CHIM NPS

value: female


title: CD8+ T Cells, DiSBey, Acute Stimulation, Day 10, chr1, batch1, biol_rep 2

description: Library name: QI2D10_1

value: CD8+ T Cells

value: DiSBey


title: FeAAD9

city: Zhengzhou

first: Shuai

address: No.1, East Jian She Road

institute: The First Affiliated Hospital of Zhengzhou University

description:
Library name: Sample 48
Column name in raw_counts.txt:FeAAD9

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.

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.

value: Thoracic aorta

value: Female

value: WT

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


title: no dox 24h DMSO+BMP4 rep1


title: NPS_8797_CD_5

description:
Library name: NPS_8797_CD_5
RNA-Seq of CHIM NPS

value: Nose


title: CD8+ T Cells, DiSBey, Acute Stimulation, Day 6, chr1, batch1, biol_rep 1

description: Library name: QI1D6_1

value: Acute Stimulation


title: FeAAD8

description:
Library name: Sample 47
Column name in raw_counts.txt:FeAAD8


title: no dox 24h LDN+BMP4 rep3

source_name: no dox 24h LDN+BMP4

value: no dox 24h LDN+BMP4


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

description: Library name: QI1D14_1


title: NPS_8796_CD_7

description:
Library name: NPS_8796_CD_7
RNA-Seq of CHIM NPS

value: NPS


title: FeAAD7

description:
Library name: Sample 46
Column name in raw_counts.txt:FeAAD7


title: no dox 24h LDN+BMP4 rep2


title: CD8+ T Cells, DiSBey, Acute Stimulation, Day 10, chr1, batch1, biol_rep 1

description: Library name: QI1D10_1

value: Spleen


title: FeAAD6

description:
Library name: Sample 45
Column name in raw_counts.txt:FeAAD6


title: NPS_8793_CD_6

description:
Library name: NPS_8793_CD_6
RNA-Seq of CHIM NPS


title: no dox 24h LDN+BMP4 rep1


title: NPS_8790_CD_5

description:
Library name: NPS_8790_CD_5
RNA-Seq of CHIM NPS


title: CD8+ T Cells, DiSBey, Chronic Stimulation, Day 6, chr1, batch1, biol_rep 2

description: Library name: QE2D6_1

value: Chronic Stimulation


title: NPS_8789_CD_5

description:
Library name: NPS_8789_CD_5
RNA-Seq of CHIM NPS

value: male


title: FeAAD5

description:
Library name: Sample 44
Column name in raw_counts.txt:FeAAD5


title: CD8+ T Cells, DiSBey, Chronic Stimulation, Day 14, chr1, batch1, biol_rep 2

description: Library name: QE2D14_1


title: FeAAD4

description:
Library name: Sample 43
Column name in raw_counts.txt:FeAAD4


title: Day 3 MIB1 KO dox rep1

source_name: lung

treatment_protocol: MIB1-iKO cells were seeded into 6-well plates (1x10^5 cells/well) and treated with 0.5 ug/ml doxycycline for 3 days.

value: Day 3 MIB1 KO dox


title: SCD13

city: Memphis

first: Shannon

last: McKinney-Freeman

address: 262 Danny Thomas Pl

institute: St. Jude Children's Research Hospital

source_name: bone marrow

value: bone marrow

value: HSPCs

value: M

value: SCD


title: CD8+ T Cells, DiSBey, Chronic Stimulation, Day 10, chr1, batch1, biol_rep 2

description: Library name: QE2D10_1

value: CD8+ T Cells

value: DiSBey


title: Day 3 MIB1 KO no dox rep2

value: lung

value: Day 3 MIB1 KO no dox


title: FeAAD3

description:
Library name: Sample 42
Column name in raw_counts.txt:FeAAD3

value: Thoracic aorta

value: Female

value: WT

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


title: NPS_8783_CD_4

description:
Library name: NPS_8783_CD_4
RNA-Seq of CHIM NPS

source_name: Nose

value: Nose

value: NPS


title: CD8+ T Cells, DiSBey, Chronic Stimulation, Day 6, chr1, batch1, biol_rep 1

description: Library name: QE1D6_1

value: Spleen

value: Chronic Stimulation


title: FeAAD2

description:
Library name: Sample 41
Column name in raw_counts.txt:FeAAD2


title: Day 3 MIB1 KO no dox rep1


title: NPS_8782_CD_5

description:
Library name: NPS_8782_CD_5
RNA-Seq of CHIM NPS

value: female


title: FeAAD1

description:
Library name: Sample 40
Column name in raw_counts.txt:FeAAD1


title: CD34+ d6 erythroid progenitors treated with TGFb1, Replicate 2

city: Bronx

first: Kith

last: Pradhan

state: ny

address: 1300 Morris Park Ave

institute: Einstein College of Medicine

description: Library name: j992_rna_d6T2

data_processing:
Reads were aligned to the reference with tophat2 using the “-g 1” parameter setting.
Gene expression was enumerated with htseq2 using gencode.v24.primary_assembly
Assembly: GRCh38_no_alt_analysis (hg38)
Supplementary files format and content: tab delimited txt file with Ensembl identifier and count columns

source_name: In vitro HSC cultures

growth_protocol: Cells were grown in Condition media containing human serum, FBS and IMDM, supplmented with EPO, IL3 and SCF

extract_protocol:
For RNA-seq, cells were collected 12 hours post-treatment with TGF-β1. The cell pellets were resuspended in lysis buffer from the RNeasy Mini Kit (Qiagen, Valencia, CA) and processed according to the manufacturer’s instructions. RNA was eluted in nuclease-free water and quantified using a Qubit fluorometer. The quality and integrity of the RNA were assessed using an RNA 6000 Bioanalyzer kit (Agilent). Samples with RNA integrity number (RIN) scores ≥8 were selected for further analysis. cDNA was synthesized from 1 µg of RNA using the SuperScript™ VILO™ cDNA Synthesis Kit (Invitrogen, Waltham, MA) following the manufacturer’s protocol.
RNA library preparation The RNA quality was analyzed using a bioanalyzer. RNA samples with RQN scores above an 8 were considered suitable for RNA library preparation. The library preparation process followed the manufacturer's protocol (QIAseq Stranded RNA Lib Kit UDI-B, Cat# 180452). Initially, RNA molecules were fragmented into smaller fragments, and then reverse transcriptase was used to convert the fragmented RNA into double-stranded cDNA. Adaptor ligation was performed, followed by library amplification to ensure sufficient cDNA fragments for sequencing. Prior to sequencing, the library underwent quality control and quantification. Sequencing was conducted using an Illumina sequencer (Nextseq500) with 150 paired-end sequencing, resulting in the generation of approximately 30 million reads per sample.

treatment_protocol:
Cells were treated either with vehicle or TGF-β1
Cells were treated either with vehicle or TGF-β2

value: In vitro HSC cultures

value: HSC


title: NPS_8781_CD_5

description:
Library name: NPS_8781_CD_5
RNA-Seq of CHIM NPS

value: male


title: CD34+ d6 erythroid progenitors treated with vehicle, Replicate 2

description: Library name: j992_rna_d6C2

value: Vehicle


title: FeNonAD8

description:
Library name: Sample 39
Column name in raw_counts.txt:FeNonAD8


title: CD8+ T Cells, DiSBey, Chronic Stimulation, Day 10, chr1, batch1, biol_rep 1

description: Library name: QE1D10_1

value: CD8+ T Cells


title: NPS_8780_CD_4

description:
Library name: NPS_8780_CD_4
RNA-Seq of CHIM NPS


title: Day 3 MIB1 KO dox rep2

value: Day 3 MIB1 KO dox


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

description: Library name: QAD2_1

value: DiSBey

value: Input


title: CD34+ d6 erythroid progenitors treated with TGFb1, Replicate 1

description: Library name: j972_rna_d6T


title: FeNonAD7

description:
Library name: Sample 38
Column name in raw_counts.txt:FeNonAD7

value: Thoracic aorta


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

description: Library name: QI-2-D18_1

value: Acute Stimulation


title: CD34+ d6 erythroid progenitors treated with vehicle, Replicate 1

description: Library name: j972_rna_d6C


title: NPS_8778_CD_5

description:
Library name: NPS_8778_CD_5
RNA-Seq of CHIM NPS


title: FeNonAD5

description:
Library name: Sample 36
Column name in raw_counts.txt:FeNonAD5

value: Female

value: WT


title: NPS_8879_CD_3

description:
Library name: NPS_8879_CD_3
RNA-Seq of CHIM NPS

value: Nose


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

description: Library name: QE-2-D18_1


title: FeNonAD4

description:
Library name: Sample 35
Column name in raw_counts.txt:FeNonAD4

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


title: NPS_8878_CD_4

description:
Library name: NPS_8878_CD_4
RNA-Seq of CHIM NPS

value: NPS


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

description: Library name: QE-1-D18_1

value: Spleen

value: Chronic Stimulation


title: 253949419110_S01_GE1_107_Sep09_1_4

type: RNA

city: Augsburg

first: Victoria

middle: Elisabeth

last: Fincke

address: Stenglinstraße 2

institute: Childens Cancer Center - University hospital Augsburg

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing: NOT PROVIDED; REQUESTED

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.

tag: main diagnosis

value: CoA

value: aortic tissue


title: 253949419207_S01_GE1_107_Sep09_1_2

value: male


title: NPS_8877_CD_3

description:
Library name: NPS_8877_CD_3
RNA-Seq of CHIM NPS


title: 253949419206_S01_GE1_107_Sep09_2_2


title: Non-immunosuppressed wildtype lung transplant recipient, neutrophils

city: Saint Louis

first: Daniel

last: Kreisel

state: MO

address: 660 S Euclid Ave

institute: Washington University School of Medicine

description: Library name: Nonimmunosuppressed_neutrophil_recipient

data_processing:
Alignment with Cell Ranger v6
QC and filtering with Seurat v4
Unsupervised clustering with Seurat v4
Assembly: mm10
Supplementary files format and content: .rds object

extract_protocol: Chromium Single Cell 3ʹ Reagent v3.1 kit from 10X Genomics

value: lung

value: Lung transplant without immunosuppression


title: FeNonAD2

description:
Library name: Sample 33
Column name in raw_counts.txt:FeNonAD2


title: NPS_8876_CD_4

description:
Library name: NPS_8876_CD_4
RNA-Seq of CHIM NPS

value: female


title: 253949419205_S01_GE1_107_Sep09_1_4


title: Il1b-deficient lung transplant recipient, CD45.2 positive recipient cells

description: Library name: Il1bKO_recipient

value: Lung transplant + immunosuppression


title: FeNonAD1

description:
Library name: Sample 32
Column name in raw_counts.txt:FeNonAD1


title: NPS_8803_CD_4

description:
Library name: NPS_8803_CD_4
RNA-Seq of CHIM NPS


title: Wildtype lung transplant recipient, CD45.2 positive recipient cells

description: Library name: Wildtype_recipient


title: 253949419205_S01_GE1_107_Sep09_1_2


title: FeCon10

description:
Library name: Sample 31
Column name in raw_counts.txt:FeCon10

value: Normal drinking water control


title: NPS_8784_CD_4

description:
Library name: NPS_8784_CD_4
RNA-Seq of CHIM NPS


title: NPS_8802_CD_5

description:
Library name: NPS_8802_CD_5
RNA-Seq of CHIM NPS