title: OA_3_1

city: Chengdu

first: Heng

last: Xu

state: Sichuan

address: 17#, section 3, South Renmin Road

institute: Sichuan University

description:
Library name: sample3
treatment-naive osteoarthritis synovial fluid sample 3; Cell Ranger processed feature-barcode matrix archive

data_processing:
FASTQ files generated from the 10x Genomics platform were aligned and quantified against the human GRCh38 reference genome (version 6.1.2) using Cell Ranger v4.3.0 with default settings.
For this GEO submission, the Cell Ranger output for each OA sample was packaged as a sample-specific .tar.gz archive containing the 10x feature-barcode matrix files: matrix.mtx.gz, barcodes.tsv.gz, and features.tsv.gz.
In the published downstream analysis, Cell Ranger outputs were imported with Read10X/Seurat; potential doublets were removed with DoubletFinder, low-quality cells were filtered, data were normalized, highly variable genes were selected, and batch effects were corrected using a FastMNN-based workflow before clustering and annotation.
Assembly: Homo sapiens GRCh38 (10x Genomics/Cell Ranger human reference, version 6.1.2)
Supplementary files format and content: Each processed data file is a .tar.gz archive of Cell Ranger feature-barcode matrix output for one sample, containing matrix.mtx.gz, barcodes.tsv.gz, and features.tsv.gz.

source_name: synovial fluid

extract_protocol:
Fresh knee synovial fluid was collected under aseptic conditions. Hyaluronidase was added to a final concentration of 100 U/ml and samples were incubated at 37 degrees C for 30 min. Samples were centrifuged at 800 x g for 10 min at 4 degrees C; cell pellets were treated with red blood cell lysis buffer on ice for 6 min, washed, and subjected to debris removal by density-gradient centrifugation. Purified cells were washed with PBS, resuspended, and counted before single-cell library preparation.
Single-cell suspensions were loaded onto Chromium microfluidic chips using 10x Genomics Chromium Single Cell 3' v3 chemistry and barcoded with the 10x Chromium Controller. cDNA synthesis and gene expression library construction were performed with the Chromium Single Cell 3' v3 reagent kit according to the manufacturer's instructions. Libraries were sequenced on an Illumina NovaSeq 6000 platform by Novogene Co., Ltd.

treatment_protocol: No ex vivo treatment was applied to the submitted OA synovial fluid control samples.

value: synovial fluid

value: synovial fluid cells

value: none; treatment-naive osteoarthritis control

tag: batch

value: OA control


title: Untreated mouse replicate 5

status: Public on Jul 22 2026

type: SRA

city: Botucatu

first: Guilherme

middle: Ribeiro

last: Romualdo

state: SP

address: Rua Dr José Barbosa de Barros, 1486

country: Brazil

institute: UNESP

description:
Library name: Control5
Column name in Control_FPKM.csv: Control5

library_source: transcriptomic

data_processing:
Raw reads of fastq format were first processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N, and low-quality reads from raw data (Bolger et al., 2014). All the downstream analyses were based on clean data with high quality. Reference genome (GRCm39/mm39) and gene model annotation files were downloaded from the genome website directly. The index of the reference genome was built, and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. The abundance of each transcript was quantified using feature Counts v1.5.0-p3.
Assembly: GRCm39/mm39
Supplementary files format and content: csv. files contain fpkm data for each sample

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
Total RNA was isolated using QIAzol lysis reagent and RNeasy column-based system (Qiagen, UK) according to the manufacturer's instructions.
SMARTer Prep Kit according to the manufacturer's instructions

treatment_protocol: Five-week-old male mice of HCC-susceptible C3H/HeJ mice (n=30 animals) were obtained from the University of São Paulo and kept in the animal facility of the Experimental Research Unit (UNIPEX) at São Paulo State University (Botucatu). After acclimatization, the animals were subjected to a chemically induced model of hepatocarcinogenesis, undergoing 5 cycles of intraperitoneal (i.p.) applications of the diethylnitrosamine (DEN) carcinogen: twice a week, at a dose of 25 mg/kg of body weight (b.w.) for 3 weeks, followed by a one-week rest period. Negative controls received 0.9% saline solution with the same frequency and route of administration. After the five DEN cycles (4 months), the animals had a one-month rest period and were then allocated into 5 experimental groups (Figure 1A) (n=6 animals/group): some were treated with CAF (50 mg/kg b.w., 3×/week) via intragastric (i.g.) administration (Romualdo et al., 2020); SOR (30 mg/kg b.w., i.g., 2×/week, vehicle: corn oil + 2% DMSO) alone (Liu et al., 2006); CAF + SOR (same regimen) or vehicles for 3 weeks (Figure 1A). CAF was administered on Mondays, Wednesdays, and Fridays, while SOR was given on Tuesdays and Thursdays, all in the morning (8-9 h). The remaining animals received the drug vehicles at the respective frequencies and routes of administration: SOR was dissolved in 100% DMSO and diluted in saline corn oil to the desired concentration with a final DMSO concentration of 2% (v/v). CAF was directly diluted in tap water.

tag: tissue

value: Liver


title: ATAC-seq, Bonobo LCL, DMSO, 1 hour, rep 2

city: Boulder

first: Robin

middle: D.

last: Dowell

state: CO

address: 596 UCB

department: Molecular, Cellular and Developmental Biology

country: USA

institute: University of Colorado Boulder

library_source: genomic

data_processing:
Read quality was assessed using FastQC (v0.11.5).
Read quality and adapter trimming was done using BBMap (v38.05) bbduk with options ktrim=r qtrim=10, k=23, mink=11, hdist=1, maq=10, minlen=25, tpe, tbo, literal=AAAAAAAAAAAAAAAAAAAAAAA, ref= The FASTA file containing common adapters found in https://github.com/Dowell-Lab/Nascent-Flow/blob/master/bin/adapters.fa.
Mapping was done using HISAT2 (v2.1.0) with options --new-summary --very-sensitive --no-spliced-alignment to each species' reference genomes.
Converted mapped SAM to BAM files using Samtools (v1.8) view -F 4 to remove unmapped reads.
Read duplicates were removed using Sambamba (v0.6.6) markdup with options --remove-duplicates, --overflow-list-size=300000.
Bedgraph files were obtained using deepTools (v3.0.1) bamCoverage with options --binSize 1, --normalizeUsing CPM.
Assembly: Human (Homo sapiens) datasets were mapped to hg38,  and Bonobo (Pan paniscus) datasets were mapped to panPan3.
Supplementary files format and content: The *.bigwig are bigwig visualization files normalized for coverage using deepTools using --normalizeUsing RPKM.

molecule: genomic DNA

organism: Pan paniscus

growth_protocol: The human, chimp, bonobo, gorilla, orangutan, gibbon, rhesus, baboon, squirrel monkey, owl monkey, and cow LCLs were cultured in RPMI-1640 media (Gibco Ref. 72400-047), 15% FBS (R&D Systems Ref. S11150), and 100 U/mL Penicillin-Streptomycin (Gibco Ref. 15140-122). The chicken LCLs were cultured in RPMI-1640 media (Gibco Ref. 72400-047), 10% FBS (R&D Systems Ref. S11150), 5% Chicken serum (Sigma Ref. C5405-100ML), 10% Tryptose phosphate broth (Sigma Ref. T8154), 0.05 mM β-mercaptoethanol (MP Ref. 194834), and 100 U/mL Penicillin-Streptomycin (Gibco Ref. 15140-122). All LCLs were cultured using vent-cap T-25 flasks (Corning 430639), and kept at a confluency between 400,000 cells/mL and 800,000 cells/mL during cell culture at 37°C with 5% CO2, except for the chicken LCLs which were kept between 1,000,000 cells/mL and 2,500,000 cells/mL.

extract_protocol: The ATAC-seq libraries were made following the [Corces2017] (https://doi.org/10.1038/nmeth.4396) protocol. Briefly, after the 1 hour treatments, the 100,000 cells were transferred from their 12-well plate wells to 1.8 mL eppendorf tubes, and centrifuged at 500 x g for 7 minutes at 4°C. The supernatant was carefully removed and replaced with 50 μL of ice-cold lysis buffer (water with 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL, 0.1% Tween-20, 0.01% Digitonin), the cells resuspended 4 times pipetting up and down, and incubated on ice for 5 minutes. Then, added 1 mL of wash buffer (water with 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20) and the tubes inverted 4 times to mix. The tubes were centrifuged at 500 x g for 10 minutes at 4°C and the supernatant was carefully removed without disturbing the small cell pellet. The pellets were then carefully resuspended by pipetting 6 times with 50 μL of the transposition mix (25 μL Tagment DNA Buffer Illumina Ref. 15027866, 2.5 μL Tagment DNA Enzyme 1 Illumina Ref. 15027865, 0.5 μL Digitonin diluted 1:1 with water, 0.5 μL 10% Tween-20, 5 μL water, 16.5 μL PBS), and were incubated for 30 minutes in a heat block at 37°C, flicking the tube often. Afterwards, the samples were cleaned using the DNA Clean and Concentrator-5 Kit (Zymo Research Ref. D4014) following the manufacturer's instructions, and eluted in 21 μL elution buffer. Then, a PCR pre-amplification was done using NEBNext Ultra II Q5 Master Mix (NEB Ref. M0544S) using 5 cycles. Then, a qPCR was done using NEBNext Ultra II Q5 Master Mix, SYBR Gold (Life Tech Ref. S11494), and 5 μL of the pre-amplified sample, and the results used to determine the additional number of extra PCR cycles using Nextera DNA CD Indices (Illumina Ref. 20015882), which was just 1 additional cycle. The post-amplified ATAC-libraries were cleaned-up with the DNA Clean and Concentrator-5 Kit (Zymo Research Ref. D4014). The libraries were size-selected to remove DNA fragments greater than 1000 bp with a Sage Science BluePippin. The ATAC-seq libraries were quantified with Qubit HS DNA assay and their fragment size-distributions determined with Agilent HS D5000 ScreenTape. All samples were processed in parallel. After the samples were pooled and size-selected, they were cleaned-up using AMPure XP beads (Beckman Coulter Ref. A63881) at 1.5x volume and eluted into 20 μL of EB buffer (Qiagen Ref. 19086).

treatment_protocol: The human and bonobo LCLs were used for obtaining ATAC-seq libraries. They were treated for 1 hour with either 20 μM Nutlin-3a (Sigma Ref. SML0580), treated for 1 hour with either 100 U/mL of human IFN-α2 (Proteintech Ref. HZ-1066), or treated with 0.001% DMSO as a negative control. The treatments were done in 12-well plate wells so that each well had 100,000 cells in 2 mL volume. Each condition was prepared in duplicates, and all samples were processed in parallel.

tag: Sex

value: Female

tag: cell line

tag: cell type

value: Lymphoblastoid cell line

tag: genotype

value: WT

tag: treatment

value: DMSO

tag: time

value: 1 hour


title: FFPE, EarlyStable,nr80

city: Bergen

first: Tony

last: Chen

address: Haukelandsveien 22

country: Norway

institute: Haukeland University Hospital

description:
Library name: ES_80
Novogene

data_processing:
Alignment using Hisat2 v2.0.5
Adapter contamination, uncertain nucleotides constitute more than 10% of reads and low base quality  were filtered for clean reads.
Assembly: Homo_sapiens_Ensemble_94
Supplementary files format and content: raw_gene_count.csv

organism: Homo sapiens

source_name: Formalin Fixed Paraffin embedded kidney tissue

extract_protocol:
For RNA bulk sequencing, the RNA was extracted using miRNeasy extraction kit. 10 ng/ul was used for library construction.
For bulk RNA sequencing, RNA libraries was prepared according to the Truseq Exome library prep kit following manufacturers protocol.


title: Microglia_F6_046, KO male, ZT18

city: Austin

first: Laura

middle: K

last: Fonken

state: TX

address: 107 W Dean Keeton St

department: Pharmacy

institute: The University of Texas at Austin

description:
Library name: Microglia_F6_046
Column name in microglia_counts.csv: F6-046

data_processing:
Samples were sequenced on a NovaSeq S1, SR100.
FASTQ files from multiple sequencing lanes were combined, if needed, and PCR-duplicate sequences were collapsed (deduplicated). The 5' inline barcode Tag, adapter, and polyA tail were removed.
Reads were mapped to the mm39 genome using STAR with default settings and quantMode to produce transcript quantifications.
Library quality and mapping performance was assessed on each sample using the STAR Log.final.out file and by viewing the read alignments using Interactive Genome Viewer. Microglia samples were excluded from analysis if any of the following criteria were met: input reads<1000000, uniquely mapped reads < 900000, uniquely mapped percentage < 85%, mismatch rate per base > 0.85, or if mapping coverage was judged to be poor by a blinded observer in Interactive Genome Viewer.
The counts matrix was created using column 3 (first read strand aligned with RNA) from the ReadsPerGene.out.tab file. Genes with >10 counts in at least 80% (CA1) or 20% (microglia) of samples were considered for analysis.
A PCA was performed on the filtered data to check for outliers. None were detected or excluded here.
Differential gene expression was modelled using limma-voom with TMM normalization. False discovery rate was determined by Benjamini-Hochberg multiplicity correction  (microglia) or permutation analysis (CA1).
Assembly: mm39
Supplementary files format and content: csv file contains raw counts for each sample

source_name: brain

extract_protocol:
Mice were intracardially perfused with PBS on postnatal day 28 at zeitgeber time 6. Brains were removed, flash-frozen whole on dry ice and stored at -80C. The hippocampus was sectioned into 100um-thick coronal slices on a cryostat at 20C, and tissue from area CA1 was collected via micropunch and stored at -80C until RNA extraction. RNA extractions were performed using the RNeasy kit (Qiagen) with on-column DNase digestion according to the manufacturer’s instructions.  300ng total RNA was used for library construction.
Mice were intracardially perfused with PBS on postnatal day 28 at zeitgeber time 6 or 18. Brains were removed and hippocampi were incubated for 15min at 37C in digestion mix containing HBSS, 5% FBS, 10uM HEPES, 2mg/mL collagenase A, and 28U/mL DNase I. Tissue was dissociated using a series of fire-polished glass pipettes, and myelin was removed using Miltenyi Biotec's Debris Removal Kit. Cells were incubated with Miltenyi CD11b microbeads, and microglia were isolated using Mintenyi MACS Separation Columns with MACS MultiStand magnet. Microglia were stored in PBS at -80C until RNA extractions. RNA was extracted using TRizol/chloroform, according to manufacturer's instructions. 150ng total RNA was used for library construction.
Total RNA was fragmented with Mg+ buffer via hydrolysis. cDNA was synthesized with a poly-dT oligo, PCR-amplified, and purified with DNA-binding magnetic beads. Among-sample concentrations were normalized and sample-specific barcodes were added via PCR. Samples were pooled to select a small range of fragment sizes via automated gel extraction (400-500bp). Postextraction products were quantified by Qubit and normalized among pools.

treatment_protocol: Microglia-specific Bmal1 conditional knockout mice (Tmem119wt/CreER2::Bmal1fl/fl, KO ) and wildtype (Tmem119wt/wt::Bmal1fl/fl , WT) littermates were administered 50ug tamoxifen i.p. on postnatal days 3-5.

value: brain

value: microglia

value: ko

value: M

tag: zeitgeber time


title: BulkCA1_B2_010, KO male, ZT6

description:
Library name: BulkCA1_B2_010
Column name in bulkCA1_counts.csv: B2-010

source_name: hippocampus, area CA1

value: hippocampus, area CA1


title: CCI21

city: 贵阳

first: 鹏

last: 陈

state: 贵州

address: 贵州省贵阳市花溪区大学城栋青南路

country: China

institute: 贵州中医药大学

description: Library name: Sample 2

library_source: transcriptomic single cell

data_processing:
Cell Ranger gene quantification quality control.
Post-quantification quality control: Filtering out low-quality cells, filtering out low-abundance genes (depending on the specific circumstances of the project), etc.
Standardization processing of gene expression.
Cell heterogeneity analysis: dimensionality reduction clustering, marker gene identification, cell type identification, cell subpopulation and other downstream personalized analyses.
Gene expression analysis: differential gene analysis, differential gene enrichment analysis, and other downstream personalized analyses.
Assembly: GRCh38，mm10
Supplementary files format and content: Tab-delimited text file including the ratio at which each gene appears cells in each sample cell
Supplementary files format and content: Tab-delimited text file including the cell count of the cluster in each sample

organism: Rattus norvegicus

source_name: spinal cord

extract_protocol:
The 10x Genomics platform utilizes microfluidic technology to encapsulate beads with Cell Barcodes and cells in droplets. The droplets containing cells are collected, and then the cells are lysed within the droplets, allowing the mRNA within the cells to connect with the Cell Barcodes on the beads, forming Single Cell GEMs. Reverse transcription reactions are carried out within the droplets.
Based on 10×genomics technology to establish  library,follow the standard process of 10×genomics,we get the great result

value: spinal cord

value: Stromal cells


title: OA_2_1

description:
Library name: sample2
treatment-naive osteoarthritis synovial fluid sample 2; Cell Ranger processed feature-barcode matrix archive

value: synovial fluid


title: PBMC_8793_CD_4

city: Amsterdam

first: Lisa

last: Willemsen

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC - locatie AMC

description:
Library name: PBMC_8793_CD_4
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

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

value: female


title: PBMC_8778_CD_3

description:
Library name: PBMC_8778_CD_3
RNA-Seq of CHIM PBMC


title: OA_1_1

description:
Library name: sample1
treatment-naive osteoarthritis synovial fluid sample 1; Cell Ranger processed feature-barcode matrix archive

value: synovial fluid cells

value: none; treatment-naive osteoarthritis control

value: OA control


title: CCI7

address: 贵州省贵阳市花溪区大学城栋青南路

description: Library name: Sample 1


title: Microglia_E6_045, WT female, ZT6

description:
Library name: Microglia_E6_045
Column name in microglia_counts.csv: E6-045

value: wt

value: F


title: PBMC_8775_CD_6

description:
Library name: PBMC_8775_CD_6
RNA-Seq of CHIM PBMC

value: male


title: Microglia_D6_044, KO female, ZT18

description:
Library name: Microglia_D6_044
Column name in microglia_counts.csv: D6-044

value: brain


title: porcine alveolar macrophages infected with ASFV WT, rep3

city: Harbin, Heilongjiang Province

first: Linfei

last: Song

address: 678 Haping Road, Xiangfang District

institute: Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences

description:
Library name: WT-3
Column name in raw_counts_All_Samples.txt: WT-3

data_processing:
Illumina Bcltofastq 1.8.4 ver software used for basecalling.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp with default parameters.
Trimmed sequence reads were mapped to Sscrofa11.1 and ASM2981691v1 using HISAT2 (version-2.2.1).
Read count extraction and normalization were performed using featureCounts(version-2.0.6).
Assembly: Sscrofa11.1 and ASM2981691v1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files FPKM values for each Sample

organism: Sus scrofa

source_name: porcine alveolar macrophages

extract_protocol:
RNA was harvested using TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: porcine alveolar macrophages


title: CeA_snRNAseq_Sensitive_M7

first: Elizabeth

last: Osterndorff-Kahanek

address: 2500 Speedway

institute: University of Texas at Austin

description: Library name: M7

data_processing:
Fastq files were processed using the CellRanger (v7.0.0) pipeline. CellRanger outputs were imported to Seurat (v4.3.0) for further processing.
Assembly: mRatBN7
Supplementary files format and content: Tab-separated values files, comma-separated values files, matrix files

source_name: central amygdala (CeA)

extract_protocol:
Rats were immediately sacrificed after last footshock session, and brains were fresh frozen and then stored at −80°C until further processing. We sectioned the brains at a cryostat (Leica CM3050s) and collected 300 µm slices from approximately bregma -1.6mm to -2.8mm based on the rat brain in stereotaxic coordinates. Then CeA tissue was harvested bilaterally from the brain slices using a 1.5 mm diameter biopsy punch and tissue blocks were stored at −80°C. Nuclei were isolated using the Chromium Nuclei Isolation Kit with RNase inhibitor (10X Genomics) following the manufacturer's instructions with a lysis time of 6.5 minutes and a single wash following debris removal. The nuclei were resuspended in a final volume of 50–100 µL at a target concentration of 500–1,200 nuclei/µL.
Single-nucleus RNA-seq libraries were generated using the Chromium Next GEM Single Cell 3′ Kit v3.1 (10x Genomics), targeting 10,000 nuclei per sample. Libraries were sequenced on an  Illumina NovaSeq 6000 system using an S1 flow cell, producing approximately 500 million reads per sample.

value: central amygdala (CeA)

tag: strain

value: Wistar

tag: phenotpe

value: Sensitive


title: PBMC_8662_CD_3

description:
Library name: PBMC_8662_CD_3
RNA-Seq of CHIM PBMC


title: SRRM2-depleted HEK293T replicate 3

city: Hangzhou

first: jinghan

last: rong

state: Zhejiang

address: westlake university

institute: westlake university

description:
Library name: SR_3
Biological replicate 3 of SRRM2-depleted HEK293T cells generated using small interfering RNA.

data_processing:
Raw reads in FASTQ format were processed using fastp to remove adapter-containing reads, reads containing poly-N sequences, and low-quality reads.
High-quality paired-end reads were aligned to the human reference genome using HISAT2 version 2.0.5.
Alternative splicing events were detected and quantified using replicate Multivariate Analysis of Transcript Splicing version 3.2.5.
Skipped-exon events were compared between VRK1-KO and wild-type cells and between SRRM2-depleted and wild-type cells.
Complete rMATS results for all quantified skipped-exon events were retained, and significant differential skipped-exon events were defined using a false discovery rate cutoff of 0.05.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file containing complete rMATS skipped-exon results for VRK1-knockout versus wild-type cells.
Supplementary files format and content: Tab-delimited text file containing complete rMATS skipped-exon results for SRRM2-depleted versus wild-type cells.

growth_protocol: Cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37 °C in a humidified incubator with 5% carbon dioxide.

extract_protocol:
Total RNA was extracted using TRIzol RNA extraction reagent. RNA integrity was assessed using the Agilent Bioanalyzer 2100 system.
Messenger RNA was purified from total RNA using poly-T oligonucleotide-attached magnetic beads. After fragmentation, first-strand complementary DNA was synthesized using random hexamer primers, followed by second-strand complementary DNA synthesis. Libraries were prepared by end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Library quality was assessed using Qubit, real-time polymerase chain reaction, and the Bioanalyzer, followed by paired-end sequencing on an Illumina platform.

treatment_protocol: Vaccinia-related kinase 1-knockout cells were generated using the CRISPR-Cas9 system. HEK293T cells were transfected with 20 nM SRRM2-targeting siRNA using Lipofectamine RNAiMAX and harvested 48 h after transfection.

value: wild-type

value: SRRM2-targeting small interfering RNA


title: porcine alveolar macrophages infected with ASFV WT, rep2

description:
Library name: WT-2
Column name in raw_counts_All_Samples.txt: WT-2


title: PBMC_8591_CD_2

description:
Library name: PBMC_8591_CD_2
RNA-Seq of CHIM PBMC


title: Microglia_B6_042, WT female, ZT18

description:
Library name: Microglia_B6_042
Column name in microglia_counts.csv: B6-042

value: microglia


title: SRRM2-depleted HEK293T replicate 1

description:
Library name: SR_1
Biological replicate 1 of SRRM2-depleted HEK293T cells generated using small interfering RNA.


title: porcine alveolar macrophages infected with ASFV WT, rep1

description:
Library name: WT-1
Column name in raw_counts_All_Samples.txt: WT-1


title: PBMC_8590_CD_3

description:
Library name: PBMC_8590_CD_3
RNA-Seq of CHIM PBMC

value: Blood


title: porcine alveolar macrophages infected with ASFV ΔD250R, rep3

description:
Library name: P73-3
Column name in raw_counts_All_Samples.txt: P73-3


title: Microglia_A6_041, WT male, ZT18

description:
Library name: Microglia_A6_041
Column name in microglia_counts.csv: A6-041

value: M


title: VRK1-knockout HEK293T replicate 3

description:
Library name: V1_3
Biological replicate 3 of VRK1-knockout HEK293T cells generated using CRISPR-Cas9.

value: VRK1 knockout


title: Microglia_H5_040, WT male, ZT18. Data excluded from analysis due to poor library quality and mapping performance.

description:
Library name: Microglia_H5_040
Column name in microglia_counts.csv: H5-040


title: PBMC_8589_CD_10_reprep

description:
Library name: PBMC_8589_CD_10_reprep
RNA-Seq of CHIM PBMC

value: PBMC

tag: reprep

value: Yes

value: female


title: Microglia_G5_039, KO male, ZT18

description:
Library name: Microglia_G5_039
Column name in microglia_counts.csv: G5-039

value: ko


title: VRK1-knockout HEK293T replicate 2

description:
Library name: V1_2
Biological replicate 2 of VRK1-knockout HEK293T cells generated using CRISPR-Cas9.


title: PBMC_8589_CD_10

description:
Library name: PBMC_8589_CD_10
RNA-Seq of CHIM PBMC


title: VRK1-knockout HEK293T replicate 1

description:
Library name: V1_1
Biological replicate 1 of VRK1-knockout HEK293T cells generated using CRISPR-Cas9.


title: porcine alveolar macrophages infected with ASFV ΔD250R, rep1

description:
Library name: P73-1
Column name in raw_counts_All_Samples.txt: P73-1


title: PBMC_8342_CD_2

description:
Library name: PBMC_8342_CD_2
RNA-Seq of CHIM PBMC


title: Microglia_F5_038, KO female, ZT6

description:
Library name: Microglia_F5_038
Column name in microglia_counts.csv: F5-038

value: F


title: PBMC_8781_CD_3

description:
Library name: PBMC_8781_CD_3
RNA-Seq of CHIM PBMC

value: male


title: porcine alveolar macrophages, rep3

description:
Library name: NC-3
Column name in raw_counts_All_Samples.txt: NC-3


title: OEKZ24241-01

address: 贵州省贵阳市花溪区大学城栋青南路

description:
Library name: CCI51_52_53
Fresh frozen Spatial transcriptome sequencing

data_processing:
Evaluation of the quality of raw data
Space Ranger gene quantitative quality control
Quantitative quality control
Genetic expression normalization processing
Assembly: GRCh38，mm10
Supplementary files format and content: Tab-delimited text file including the ratio at which each gene appears cells in each sample cell
Supplementary files format and content: Tab-delimited text file including the cell count of the cluster in each sample
Library strategy: Spatial Transcriptomics

extract_protocol:
Collect fresh tissue, freeze it, slice it, and perform HE staining for imaging. Optimize to determine whether the slices cover the targeted area.
Using the 10xGenomics Visium kit, the sequencing libraries were constructed according to the manufacturer's procedures.

value: spinal cord

value: Murine spinal cord tissue lineage

value: Stromal cells


title: Wild-type HEK293T replicate 3

description:
Library name: T_3
Biological replicate 3 of wild-type HEK293T cells.


title: PBMC_8338_CD_2

description:
Library name: PBMC_8338_CD_2
RNA-Seq of CHIM PBMC


title: porcine alveolar macrophages, rep2

description:
Library name: NC-2
Column name in raw_counts_All_Samples.txt: NC-2

value: porcine alveolar macrophages


title: Microglia_E5_037, KO female, ZT6

description:
Library name: Microglia_E5_037
Column name in microglia_counts.csv: E5-037

value: brain


title: Wild-type HEK293T replicate 2

description:
Library name: T_2
Biological replicate 2 of wild-type HEK293T cells.

value: wild-type


title: PBMC_8336_CD_3

description:
Library name: PBMC_8336_CD_3
RNA-Seq of CHIM PBMC


title: Microglia_D5_036, KO male, ZT6

description:
Library name: Microglia_D5_036
Column name in microglia_counts.csv: D5-036


title: porcine alveolar macrophages, rep1

description:
Library name: NC-1
Column name in raw_counts_All_Samples.txt: NC-1


title: Wild-type HEK293T replicate 1

description:
Library name: T_1
Biological replicate 1 of wild-type HEK293T cells.


title: PBMC_8334_CD_3

description:
Library name: PBMC_8334_CD_3
RNA-Seq of CHIM PBMC


title: LL-37-3

city: Bunkyo-Ku

first: Ge

last: Peng

state: Tokyo

address: 2-1-1 Hongo

country: Japan

institute: Juntendo University Graduate School of Medicine

description:
Library name: SAMPLE-6
Column name in Homo sapiens_tpm_table.csv:LL-37-3

data_processing:
The process includes poly(A) mRNA enrichment and fragmentation followed by cDNA synthesis, end repair, adaptor ligations, and PCR amplification.
Assembly: Homo sapiens: GRCh38；Mus musculus: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: A375 cell line

extract_protocol:
Total RNA was isolated from cultured keratinocytes using an Rneasy Plus Micro Kit according to the manufacturer's instructions
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit

value: A375 cell line

value: LL-37 80 µg/mL


title: PBMC_8325_CD_3

description:
Library name: PBMC_8325_CD_3
RNA-Seq of CHIM PBMC

value: Blood


title: Microglia_B5_034, KO male, ZT18

description:
Library name: Microglia_B5_034
Column name in microglia_counts.csv: B5-034

value: microglia

value: M


title: PBMC_8879_CD_1

description:
Library name: PBMC_8879_CD_1
RNA-Seq of CHIM PBMC

value: PBMC


title: LL-37-2

description:
Library name: SAMPLE-5
Column name in Homo sapiens_tpm_table.csv:LL-37-2


title: knu_meiocyte_biorep2

city: Shanghai

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

institute: Fudan University

description: Library name: Sample 5

data_processing:
pRNASeqTools (https://github.com/ grubbybio/pRNASeqTools) was used for transcriptome data analysis. To find genes with preferential expression in meiocytes, differentially expressed genes of knu-2 compared with ler were identified based on the criteria of fold change ≥2 and p-value < 0.05.
Assembly: Araport11
Supplementary files format and content: tab-delimited text files containing gene ID, raw read counts

organism: Arabidopsis thaliana

source_name: meiocyte

extract_protocol:
Anthers of ler and knu-2 (stage 4~7) were isolated and squeezed by forceps, then the released meiocytes were collected for RNA extraction. Recombinant RNase inhibitor (final concentration with 1 U/μL, Takara, 2313B) was used to prevent RNA degradation by adding to the collection buffer. TRIzol (ThermoFisher, 15596026) and Dr. GenTLE™ Precipitation Carrier (Takara, 9094) were used for extracting RNA.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: meiocyte


title: Microglia_A5_033, KO female, ZT6

description:
Library name: Microglia_A5_033
Column name in microglia_counts.csv: A5-033


title: knu_meiocyte_biorep1

description: Library name: Sample 4


title: LL-37-1

description:
Library name: SAMPLE-4
Column name in Homo sapiens_tpm_table.csv:LL-37-1


title: PBMC_8877_CD_1_reprep

description:
Library name: PBMC_8877_CD_1_reprep
RNA-Seq of CHIM PBMC

value: Yes


title: Ctrl-3

description:
Library name: SAMPLE-3
Column name in Homo sapiens_tpm_table.csv:Ctrl-3

value: Ctrl


title: PBMC_8877_CD_1

description:
Library name: PBMC_8877_CD_1
RNA-Seq of CHIM PBMC


title: Microglia_G4_031, WT male, ZT6

description:
Library name: Microglia_G4_031
Column name in microglia_counts.csv: G4-031

value: wt


title: ler_meiocyte_biorep2

description: Library name: Sample 2

value: Ler


title: PBMC_8876_CD_2

description:
Library name: PBMC_8876_CD_2
RNA-Seq of CHIM PBMC

value: female


title: Microglia_F4_030, WT female, ZT6

description:
Library name: Microglia_F4_030
Column name in microglia_counts.csv: F4-030

value: F


title: Ctrl-2

description:
Library name: SAMPLE-2
Column name in Homo sapiens_tpm_table.csv:Ctrl-2


title: ler_meiocyte_biorep1

description: Library name: Sample 1


title: Ctrl-1

description:
Library name: SAMPLE-1
Column name in Homo sapiens_tpm_table.csv:Ctrl-1


title: Microglia_E4_029, WT female, ZT6

description:
Library name: Microglia_E4_029
Column name in microglia_counts.csv: E4-029


title: siz1,IAA, 3h, rep3

city: Qingdao

first: Qianlan

last: Yin

state: Shandong

address: 72 Coastal Highway

department: College of Life Science

institute: Shandong University

data_processing:
Select the corresponding testing methods for quality inspection according to the requirements of samples and products
A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads.
The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented.
Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA.
After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs.
Assembly: The corresponding library quality control protocol will be selected depending upon product requirements.
Supplementary files format and content: Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested.
Supplementary files format and content: Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

source_name: root

growth_protocol: Arabidopsis seeds were planted in a culture dish containing 1/2 ms medium at 4 ° C for two days and germinated at 22 ° C for seven days

extract_protocol:
RNAsimple Total RNA Kit (TIANGEN) DP419
RNA-Seq (Quantification) uses a new generation of high-throughput sequencing technology to study the gene expression pattern of eukaryotic cells and provide accurate digital expression profile detection by sequencing and comparing transcripts.
Transcriptome research is the basis and starting point of gene function and structure research. Through the new generation of high-throughput sequencing, almost all transcripts of a specific tissue or organ of a species can be obtained comprehensively and quickly.

treatment_protocol: 0.5μM IAA (Sigama)

value: root

value: IAA


title: PC9 TDP1 KO2 untreated replicate 3

city: Toulouse

first: Olivier

last: Sordet

address: 2 Avenue Hubert Curien

department: CRCT

country: France

institute: INSERM

description: Library name: PC9_TDP1_KO2_NT_Rep3

data_processing:
Reads were aligned to human genome (GRChg38, Ensembl release 110).
Gene expression levels were quantified using RSEM (v1.3.1) with Bowtie2 (v2.5.2).
Differential expression analysis was performed using DESeq2 (v1.40.2).
Assembly: GRCh38 (Ensembl release 110).
Supplementary files format and content: Processed data are provided as tab-delimited text (.txt) files containing gene-level expression values estimated by RSEM.
Supplementary files format and content: Each file includes Ensembl gene identifiers and sample-specific expression values corresponding to expected counts.

source_name: Lung

growth_protocol: PC9 cells (human lung adenocarcinoma cell line) were cultured in RPMI-1640 medium  supplemented with 10% fetal bovine serum (FBS) and antibiotics at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions.
Library preparation was performed using the TruSeq Stranded mRNA kit (Illumina), and sequencing was carried out on a NovaSeq 6000 with 101 bp paired-end reads at CeGaT GmbH (Tübingen, Germany).

treatment_protocol: TDP1 WT PC9 cells were treated with 1 µM erlotinib for 7 days (drug-tolerant cells, DTC) or 28 days (drug-tolerant expanded cells, DTEC). TDP1 KO PC9 cells were maintained under untreated conditions.

value: Lung

value: Cancer cell line

value: TDP1 KO

value: Untreated

value: batch 1


title: PBMC_8802_CD_3

description:
Library name: PBMC_8802_CD_3
RNA-Seq of CHIM PBMC

value: Blood

value: male


title: Microglia_D4_028, KO female, ZT6

description:
Library name: Microglia_D4_028
Column name in microglia_counts.csv: D4-028

value: brain

value: microglia

value: ko


title: PC9 TDP1 KO2 untreated replicate 2

description: Library name: PC9_TDP1_KO2_NT_Rep2


title: PBMC_8801_CD_3

description:
Library name: PBMC_8801_CD_3
RNA-Seq of CHIM PBMC

value: PBMC


title: Microglia_C4_027, WT male, ZT6

description:
Library name: Microglia_C4_027
Column name in microglia_counts.csv: C4-027

value: wt

value: M


title: siz1,IAA, 3h, rep1


title: PC9 TDP1 KO2 untreated replicate 1

description: Library name: PC9_TDP1_KO2_NT_Rep1


title: PBMC_8799_CD_3

description:
Library name: PBMC_8799_CD_3
RNA-Seq of CHIM PBMC

value: female


title: Microglia_B4_026, KO male, ZT6

description:
Library name: Microglia_B4_026
Column name in microglia_counts.csv: B4-026


title: siz1, CK, rep3

value: MS


title: PC9 TDP1 WT DTEC replicate 3

description: Library name: PC9_TDP1_WT_DTEC_Rep3

value: TDP1 WT

value: Erlotinib 1µM 28 days


title: PBMC_8797_CD_3_reprep

description:
Library name: PBMC_8797_CD_3_reprep
RNA-Seq of CHIM PBMC

value: Yes


title: Microglia_A4_025, KO male, ZT6

description:
Library name: Microglia_A4_025
Column name in microglia_counts.csv: A4-025


title: Microglia_H3_024, KO male, ZT6

description:
Library name: Microglia_H3_024
Column name in microglia_counts.csv: H3-024


title: PC9 TDP1 WT DTEC replicate 1

description: Library name: PC9_TDP1_WT_DTEC_Rep1

value: Lung

value: Cancer cell line


title: siz1, CK, rep1

value: root


title: PBMC_8796_CD_4_reprep

description:
Library name: PBMC_8796_CD_4_reprep
RNA-Seq of CHIM PBMC


title: Col,IAA, 3h, rep3

value: Col

value: IAA


title: Microglia_G3_023, WT male, ZT18

description:
Library name: Microglia_G3_023
Column name in microglia_counts.csv: G3-023


title: PC9 TDP1 WT DTC replicate 3

description: Library name: PC9_TDP1_WT_DTC_Rep3

value: Erlotinib 1µM 7 days

value: batch 1


title: PBMC_8796_CD_4

description:
Library name: PBMC_8796_CD_4
RNA-Seq of CHIM PBMC

value: Blood


title: Microglia_F3_022, WT male, ZT18

description:
Library name: Microglia_F3_022
Column name in microglia_counts.csv: F3-022

value: brain

value: microglia


title: Col,IAA, 3h, rep2


title: PC9 TDP1 WT DTC replicate 2

description: Library name: PC9_TDP1_WT_DTC_Rep2


title: PBMC_8793_CD_3

description:
Library name: PBMC_8793_CD_3
RNA-Seq of CHIM PBMC

value: PBMC


title: Microglia_C5_035, WT female, ZT18

description:
Library name: Microglia_C5_035
Column name in microglia_counts.csv: C5-035

value: wt

value: F


title: Microglia_E3_021, KO female, ZT6. Data excluded from analysis due to poor coverage in Interactive Genome Viewer.

description:
Library name: Microglia_E3_021
Column name in microglia_counts.csv: E3-021

value: ko


title: knu_meiocyte_biorep3

description: Library name: Sample 6

value: meiocyte


title: PC9 TDP1 WT DTC replicate 1

description: Library name: PC9_TDP1_WT_DTC_Rep1

value: TDP1 WT


title: Col,IAA, 3h, rep1


title: PBMC_8790_CD_2_reprep

description:
Library name: PBMC_8790_CD_2_reprep
RNA-Seq of CHIM PBMC

value: Yes

value: female


title: Microglia_D3_020, KO female, ZT6. Data excluded from analysis due to poor coverage in Interactive Genome Viewer.

description:
Library name: Microglia_D3_020
Column name in microglia_counts.csv: D3-020


title: Col, CK, rep3

value: MS


title: ler_meiocyte_biorep3

description: Library name: Sample 3

value: Ler


title: PC9 TDP1 WT untreated replicate 3

description: Library name: PC9_TDP1_WT_NT_Rep3

value: Lung

value: Cancer cell line

value: Untreated


title: Microglia_H4_032, WT male, ZT6

description:
Library name: Microglia_H4_032
Column name in microglia_counts.csv: H4-032

value: M


title: PBMC_8790_CD_2

description:
Library name: PBMC_8790_CD_2
RNA-Seq of CHIM PBMC

value: Blood


title: Microglia_C3_019, KO male, ZT6

description:
Library name: Microglia_C3_019
Column name in microglia_counts.csv: C3-019

value: brain


title: Col, CK, rep2

value: root

value: Col


title: PC9 TDP1 WT untreated replicate 2

description: Library name: PC9_TDP1_WT_NT_Rep2

value: batch 1


title: PBMC_8789_CD_2

description:
Library name: PBMC_8789_CD_2
RNA-Seq of CHIM PBMC

value: PBMC

value: male


title: Microglia_B3_018, WT male, ZT6

description:
Library name: Microglia_B3_018
Column name in microglia_counts.csv: B3-018

value: microglia

value: wt


title: Col, CK, rep1


title: PC9 TDP1 WT untreated replicate 1

description: Library name: PC9_TDP1_WT_NT_Rep1

value: TDP1 WT


title: PBMC_8803_CD_2

description:
Library name: PBMC_8803_CD_2
RNA-Seq of CHIM PBMC


title: PBMC_8784_CD_2_reprep

description:
Library name: PBMC_8784_CD_2_reprep
RNA-Seq of CHIM PBMC

value: Yes


title: Microglia_A3_017, WT male, ZT6

description:
Library name: Microglia_A3_017
Column name in microglia_counts.csv: A3-017


title: siz1,IAA, 3h, rep2

value: IAA


title: TSDP_2

city: Taipei City

first: Sheng

last: Yang

address: No. 128, Sec. 2, Academia Rd., Nangang Dist.

department: Bioengineering

country: Taiwan

institute: National Tsing Hua University

description: Library name: TSDP_2

data_processing:
Illumina Casava software used for basecalling.
FastQC and MultiQC were used to check fastq files for quality.The obtained raw paired-end reads were filtered by Trimmomatic (v0.38) to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36.
Read pairs from each sample were aligned to the reference genome by the HISAT2 software (v2.1.0).
FeatureCounts (v2.0.0) was used to count the reads numbers mapped to individual genes. For gene expression, the “Relative Log Expression” normalization (RLE) was performed DEGseq2 (v1.26.0).
Assembly: mm_GRChm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include TMM values for each Sample

source_name: tumor

growth_protocol: Murine HCC HCA-1 cells were orthotopically implanted in the liver of 6-8-week-old male C3H mice. 1*10^6 HCA-1 cells were injected in the subcapsular region through 28-gauge needle

extract_protocol:
The integrity of RNA extracted from the treatment and control groups using the RNeasy Kit (Qiagen) was evaluated with the RNA Nano6000 assay kit (Agilent Technologies, CA, USA)
RNA libraries were prepared for sequencing using KAPA mRNA HyperPrep Kit Illumina® Platforms protocol

treatment_protocol: The experimental design involved orthotopically implanting murine HCC (HCA-1) cells in C3H mice, followed by IV administration of nanoparticle loaded with DNIC and sorafenib on days 10,12,14,17,20 and 23. Subsequent transcriptome analysis of the tumors was performed on day 24.

value: tumor

value: HCC


title: Microglia_H2_016, WT female, ZT18

description:
Library name: Microglia_H2_016
Column name in microglia_counts.csv: H2-016

value: F


title: PBMC_8784_CD_2

description:
Library name: PBMC_8784_CD_2
RNA-Seq of CHIM PBMC


title: TSDP_5

description: Library name: TSDP_5

value: nanoparticle loaded with DNIC and sorafenib


title: Subject 32 PBMC

city: Denver

last: Wynn

address: 1400 Jackson St.

institute: National Jewish Health

description: Library name: Subject 32 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: Subject 31 PBMC

description: Library name: Subject 31 PBMC


title: Microglia_G2_015, KO female, ZT18

description:
Library name: Microglia_G2_015
Column name in microglia_counts.csv: G2-015

value: ko


title: PBMC_8783_CD_2

description:
Library name: PBMC_8783_CD_2
RNA-Seq of CHIM PBMC

value: Blood


title: TSDP_1

description: Library name: TSDP_1


title: PBMC_8782_CD_2

description:
Library name: PBMC_8782_CD_2
RNA-Seq of CHIM PBMC

value: female


title: Subject 29 PBMC

description: Library name: Subject 29 PBMC

value: Female


title: Microglia_F2_014, WT female, ZT18. Data excluded from analysis due to poor library quality and mapping performance.

description:
Library name: Microglia_F2_014
Column name in microglia_counts.csv: F2-014

value: brain


title: Control_5

description: Library name: Control_5

value: Untreated


title: Subject 28 PBMC

description: Library name: Subject 28 PBMC

value: PBMC


title: PBMC_8781_CD_2

description:
Library name: PBMC_8781_CD_2
RNA-Seq of CHIM PBMC

value: male


title: siz1, CK, rep2

value: root

value: MS


title: Subject 27 PBMC

description: Library name: Subject 27 PBMC


title: Control_4

description: Library name: Control_4


title: Microglia_E2_013, WT female, ZT18. Data excluded from analysis due to poor library quality and mapping performance.

description:
Library name: Microglia_E2_013
Column name in microglia_counts.csv: E2-013

value: microglia

value: wt


title: Microglia_D2_012, KO female, ZT18. Data excluded from analysis due to poor library quality and mapping performance.

description:
Library name: Microglia_D2_012
Column name in microglia_counts.csv: D2-012


title: Control_3

description: Library name: Control_3

value: tumor


title: PBMC_8780_CD_2_reprep

description:
Library name: PBMC_8780_CD_2_reprep
RNA-Seq of CHIM PBMC

value: Yes


title: PBMC_8797_CD_3

description:
Library name: PBMC_8797_CD_3
RNA-Seq of CHIM PBMC


title: PC9 TDP1 WT DTEC replicate 2

description: Library name: PC9_TDP1_WT_DTEC_Rep2

value: Lung

value: Cancer cell line

value: TDP1 WT

value: Erlotinib 1µM 28 days

value: batch 1


title: PBMC_8780_CD_2

description:
Library name: PBMC_8780_CD_2
RNA-Seq of CHIM PBMC

value: Blood

value: female


title: Subject 26 PBMC

description: Library name: Subject 26 PBMC

value: Male


title: Microglia_C2_011, KO male, ZT18. Data excluded from analysis due to poor library quality and mapping performance.

description:
Library name: Microglia_C2_011
Column name in microglia_counts.csv: C2-011

value: brain

value: ko

value: M


title: PBMC_8779_CD_2_reprep

description:
Library name: PBMC_8779_CD_2_reprep
RNA-Seq of CHIM PBMC

value: PBMC


title: CD8+ T cells, Arid3b/Runx3-dKO, untreated, replicate3

city: Beijing

first: Zhidong

last: Gao

address: No.11 Xizhimen South Street

institute: Peking University People’s Hospital

description:
Library name: sg-Arid3b+sg-Runx3 untreat 3
AR3

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: Arid3b/Runx3 knockout


title: Subject 25 PBMC

description: Library name: Subject 25 PBMC

value: Female


title: Microglia_B2_010, WT male, ZT18. Data excluded from analysis due to poor library quality and mapping performance.

description:
Library name: Microglia_B2_010
Column name in microglia_counts.csv: B2-010

value: microglia

value: wt


title: CD8+ T cells, Arid3b/Runx3-dKO, untreated, replicate2

description:
Library name: sg-Arid3b+sg-Runx3 untreat 2
AR2


title: Subject 24 PBMC

description: Library name: Subject 24 PBMC


title: PBMC_8779_CD_2

description:
Library name: PBMC_8779_CD_2
RNA-Seq of CHIM PBMC


title: CD8+ T cells, Arid3b/Runx3-dKO, untreated, replicate1

description:
Library name: sg-Arid3b+sg-Runx3 untreat 1
AR1


title: Microglia_A2_009, WT female, ZT6. Data excluded from analysis due to poor library quality and mapping performance.

description:
Library name: Microglia_A2_009
Column name in microglia_counts.csv: A2-009

value: F


title: Subject 23 PBMC

description: Library name: Subject 23 PBMC


title: PBMC_8778_CD_2_reprep

description:
Library name: PBMC_8778_CD_2_reprep
RNA-Seq of CHIM PBMC

value: Yes


title: Microglia_H1_008, WT female, ZT6

description:
Library name: Microglia_H1_008
Column name in microglia_counts.csv: H1-008


title: Subject 22 PBMC

description: Library name: Subject 22 PBMC


title: Microglia_G1_007, KO male, ZT6. Data excluded from analysis due to poor library quality and mapping performance.

description:
Library name: Microglia_G1_007
Column name in microglia_counts.csv: G1-007


title: CD8+ T cells, Arid3b-KO, untreated, replicate3

description:
Library name: sg-Arid3b+sg-Int untreat 3
AI3

value: Arid3b knockout


title: PBMC_8778_CD_2

description:
Library name: PBMC_8778_CD_2
RNA-Seq of CHIM PBMC


title: CD8+ T cells, Arid3b-KO, untreated, replicate2

description:
Library name: sg-Arid3b+sg-Int untreat 2
AI2


title: Subject 20 PBMC

description: Library name: Subject 20 PBMC


title: PBMC_8775_CD_2

description:
Library name: PBMC_8775_CD_2
RNA-Seq of CHIM PBMC

value: male


title: Microglia_F1_006, WT male, ZT6. Data excluded from analysis due to poor library quality and mapping performance.

description:
Library name: Microglia_F1_006
Column name in microglia_counts.csv: F1-006


title: PBMC_8662_CD_2

description:
Library name: PBMC_8662_CD_2
RNA-Seq of CHIM PBMC


title: CD8+ T cells, Arid3b-KO, untreated, replicate1

description:
Library name: sg-Arid3b+sg-Int untreat 1
AI1


title: Subject 19 PBMC

description: Library name: Subject 19 PBMC


title: Microglia_E1_005, KO male, ZT6. Data excluded from analysis due to poor coverage in Interactive Genome Viewer.

description:
Library name: Microglia_E1_005
Column name in microglia_counts.csv: E1-005


title: CD8+ T cells,Runx3-KO, untreated, replicate3

description:
Library name: sg-Int+sg-Runx3 untreat 3
IR3

value: Runx3 knockout


title: PBMC_8591_CD_9

description:
Library name: PBMC_8591_CD_9
RNA-Seq of CHIM PBMC

value: Blood


title: Microglia_D1_004, WT female, ZT18. Data excluded from analysis due to poor library quality and mapping performance.

description:
Library name: Microglia_D1_004
Column name in microglia_counts.csv: D1-004


title: CD8+ T cells,Runx3-KO, untreated, replicate2

description:
Library name: sg-Int+sg-Runx3 untreat 2
IR2


title: Subject 18 PBMC

description: Library name: Subject 18 PBMC


title: Subject 17 PBMC

description: Library name: Subject 17 PBMC


title: Microglia_C1_003, KO female, ZT18. Data excluded from analysis due to poor library quality and mapping performance.

description:
Library name: Microglia_C1_003
Column name in microglia_counts.csv: C1-003


title: Subject 16 PBMC

description: Library name: Subject 16 PBMC


title: CD8+ T cells,Runx3-KO, untreated, replicate1

description:
Library name: sg-Int+sg-Runx3 untreat 1
IR1


title: PBMC_8589_CD_2

description:
Library name: PBMC_8589_CD_2
RNA-Seq of CHIM PBMC

value: female


title: Microglia_B1_002, KO male, ZT18. Data excluded from analysis due to poor library quality and mapping performance.

description:
Library name: Microglia B1_002
Column name in microglia_counts.csv: B1-002


title: PBMC_8590_CD_2

description:
Library name: PBMC_8590_CD_2
RNA-Seq of CHIM PBMC


title: CeA_snRNAseq_Resistant_M17

description: Library name: M17

value: central amygdala (CeA)

value: Wistar

value: Resistant


title: FFPE, EarlyProgressive,nr90

description:
Library name: EP_90
Novogene

value: Formalin Fixed Paraffin embedded kidney tissue


title: CD8+ T cells, Control, untreated, replicate3

description:
Library name: sg-Int+sg-Int untreat 3
II3

value: intergenic sequence knockout


title: Subject 15 PBMC

description: Library name: Subject 15 PBMC

value: PBMC

value: Male


title: PBMC_8342_CD_1

description:
Library name: PBMC_8342_CD_1
RNA-Seq of CHIM PBMC


title: Microglia A1_001, WT male, ZT18. Data excluded from analysis due to poor library quality and mapping performance.

description:
Library name: Microglia A1_001
Column name in microglia_counts.csv: A1_001

value: brain

value: M


title: CD8+ T cells, Control, untreated, replicate2

description:
Library name: sg-Int+sg-Int untreat 2
II2

value: CD8+ T cells


title: CeA_snRNAseq_Resistant_M14

description: Library name: M14


title: PBMC_8338_CD_1

description:
Library name: PBMC_8338_CD_1
RNA-Seq of CHIM PBMC


title: Subject 14 PBMC

description: Library name: Subject 14 PBMC


title: Old

first: liu

last: cihang

address: Xueyuan Road

institute: Peking University Health Science Center

description:
Library name: Sample4
Old vs Young_processed data.txt

data_processing:
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 in- house perl scripts. In this step, clean data ( clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
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).
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.
Differential expression analysis of two conditions/ groups ( two biological replicates per condition) was performed using the DESeq2 R package ( 1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P- values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: platelets

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: platelets

value: WT

value: 24 month-old; Old


title: Young

description:
Library name: Sample3
Old vs Young_processed data.txt

value: 3 month-old; Young

value: male


title: Subject 13 PBMC

description: Library name: Subject 13 PBMC

value: Female


title: CeA_snRNAseq_Resistant_M13

description: Library name: M13


title: PBMC_8336_CD_2

description:
Library name: PBMC_8336_CD_2
RNA-Seq of CHIM PBMC

value: Blood

value: female


title: PBMC_8801_CD_4

description:
Library name: PBMC_8801_CD_4
RNA-Seq of CHIM PBMC


title: CD8+ T cells, Control, untreated, replicate1

description:
Library name: sg-Int+sg-Int untreat 1
II1


title: Subject 12 PBMC

description: Library name: Subject 12 PBMC


title: PBMC_8334_CD_2

description:
Library name: PBMC_8334_CD_2
RNA-Seq of CHIM PBMC


title: CD8+ T cells, Arid3b/Runx3-dKO, co-cultured with CMT93-OVA cells, replicate3

description:
Library name: sg-Arid3b+sg-Runx3 treat 3
cAR3

value: Arid3b/Runx3 knockout

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

value: 4 hours


title: PBMC_8325_CD_2

description:
Library name: PBMC_8325_CD_2
RNA-Seq of CHIM PBMC


title: Subject 11 PBMC

description: Library name: Subject 11 PBMC


title: Subject 10 PBMC

description: Library name: Subject 10 PBMC


title: cKO

description:
Library name: Sample2
cKO vs WT_processed data.txt

value: HuR cKO

value: 3 month-old


title: CD8+ T cells, Arid3b/Runx3-dKO, co-cultured with CMT93-OVA cells, replicate1

description:
Library name: sg-Arid3b+sg-Runx3 treat 1
cAR1


title: WT

description:
Library name: Sample1
cKO vs WT_processed data.txt


title: PBMC_8796_CD_3

description:
Library name: PBMC_8796_CD_3
RNA-Seq of CHIM PBMC

value: PBMC


title: Subject 9 PBMC

description: Library name: Subject 9 PBMC


title: PBMC_8878_CD_1

description:
Library name: PBMC_8878_CD_1
RNA-Seq of CHIM PBMC


title: single-nucleus RNA-seq, postnatal day 21, replicate 1

city: Chapel Hill

first: LI

last: QIAN

address: 111 Mason Farm Road, MBRB

department: Department of pathology

institute: UNC

description: Library name: P21_1

data_processing:
Single-nucleus RNA sequencing data were processed and analyzed using the Seurat package (v5) in R. Raw count matrices were first filtered to remove low-quality cells based on mitochondrial gene expression (> 5%) and gene detection thresholds (nFeature > 7500 or nFeature <750). Then the doublet was identified and removed using the default setting of scDblFinder. Data normalization was performed using a regularized negative binomial regression method (SCTransform) to account for technical variability. Highly variable genes were then identified and used for dimensionality reduction via principal component analysis (PCA).
Assembly: mm10
Supplementary files format and content: Cellranger output file:barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: nuclear RNA

source_name: Heart

extract_protocol:
Hearts were harvested from mice at postnatal day 0 (p0, 2 replicates), day 7 (p7, 2 replicates), day 14 (p14, 2 replicates), and day 21 (p21, 2 replicates), respectively. Hearts were perfused with KCl and PBS before harvesting. After removing the heart from the chest, hearts were minced into pieces on a glass petri dish on ice using a razor blade. Minced heart tissue was then transferred to a 15 ml falcon tube for tissue homogenization with 1 ml of homogenization buffer (0.32M sucrose, 1mM Tris-HCl PH8.0, 3mM Magnesium Acetate, 0.1mM EDTA, 5mM Calcium Chloride, 0.1% Triton, 1x cOmplete Protease Inhibitor Cocktail, 200 U/ml RNase OUT, 1mM DTT). The tissue homogenization was performed on ice with two cycles of 30 second on and 60 sec off. After the tissue was completely homogenized, the tissue lysate was then transferred to a 7 ml tissue grinder. 1 ml of tissue homogenization buffer was used to wash the falcon tube before adding it to the tissue grinder. Eight strokes were performed with a loose pestle (A) on ice. 30 strokes were performed with a tight pestle (B) on ice. Then the tissue lysate was passed through a 70 μm and followed with a 40 μm cell strainer. Wash off any left-over tissue lysate from the 40 μm cell strainer with 1 ml of the homogenization buffer. Then the nuclei were pelleted by centrifuging at 500 g for 5 min at 4°C. Wash the pellet twice with resuspension buffer (PBS/1%BSA, 200 U/ml RNase OUT, 1 mM DTT). The nuclei pellets were then resuspended in 0.5 ml resuspension buffer. Before running the nuclei pellet with a 10x 3’ scRNA-seq kit, isolated nuclei were labeled with DRAQ5 and sorted with flow cytometry to ensure the purity of the nuclei.
The single-nucleus library preparations were performed strictly following the manufacturer’s manual (Chromium Single Cell 3' Reagent Kits User Guide, CG000315).

value: Heart

value: Wildtype


title: single-nucleus RNA-seq, postnatal day 21, replicate 2

description: Library name: P21_2


title: Subject 8 PBMC

description: Library name: Subject 8 PBMC


title: CD8+ T cells, Arid3b-KO, co-cultured with CMT93-OVA cells, replicate3

description:
Library name: sg-Arid3b+sg-Int treat 3
cAI3

value: CD8+ T cells

value: Arid3b knockout


title: single-nucleus RNA-seq, postnatal day 14, replicate 2

description: Library name: P14_2


title: PBMC_8876_CD_1

description:
Library name: PBMC_8876_CD_1
RNA-Seq of CHIM PBMC


title: Subject 7 PBMC

description: Library name: Subject 7 PBMC

value: Male


title: PBMC_8802_CD_2

description:
Library name: PBMC_8802_CD_2
RNA-Seq of CHIM PBMC


title: CD8+ T cells,Runx3-KO, co-cultured with CMT93-OVA cells, replicate3

description:
Library name: sg-Int+sg-Runx3 treat 3
cIR3

value: Runx3 knockout


title: PBMC_8799_CD_2

description:
Library name: PBMC_8799_CD_2
RNA-Seq of CHIM PBMC


title: single-nucleus RNA-seq, postnatal day 7, replicate 2

description: Library name: P7_2


title: Subject 6 PBMC

description: Library name: Subject 6 PBMC


title: PBMC_8797_CD_2

description:
Library name: PBMC_8797_CD_2
RNA-Seq of CHIM PBMC


title: CD8+ T cells,Runx3-KO, co-cultured with CMT93-OVA cells, replicate2

description:
Library name: sg-Int+sg-Runx3 treat 2
cIR2


title: Subject 5 PBMC

description: Library name: Subject 5 PBMC


title: CD8+ T cells,Runx3-KO, co-cultured with CMT93-OVA cells, replicate1

description:
Library name: sg-Int+sg-Runx3 treat 1
cIR1


title: PBMC_8796_CD_2

description:
Library name: PBMC_8796_CD_2
RNA-Seq of CHIM PBMC


title: single-nucleus RNA-seq, postnatal day 0, replicate 2

description: Library name: P0_2


title: CD8+ T cells, Control, co-cultured with CMT93-OVA cells, replicate3

description:
Library name: sg-Int+sg-Int treat 3
cII3

value: intergenic sequence knockout


title: PBMC_8793_CD_2

description:
Library name: PBMC_8793_CD_2
RNA-Seq of CHIM PBMC


title: PBMC_8784_CD_1_reprep

description:
Library name: PBMC_8784_CD_1_reprep
RNA-Seq of CHIM PBMC

value: Yes

value: male


title: single-nucleus RNA-seq, postnatal day 0, replicate 1

description: Library name: P0_1


title: CD8+ T cells, Control, co-cultured with CMT93-OVA cells, replicate1

description:
Library name: sg-Int+sg-Int treat 1
cII1


title: PBMC_8784_CD_1

description:
Library name: PBMC_8784_CD_1
RNA-Seq of CHIM PBMC

value: Blood


title: Subject 1 PBMC

description: Library name: Subject 1 PBMC

value: Female


title: spleen, CD8+ Non-Tfc, rep3

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: S-Non3

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.

source_name: Spleen

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.

value: Spleen

value: CD8 T lymphocytes


title: PBMC_8783_CD_1

description:
Library name: PBMC_8783_CD_1
RNA-Seq of CHIM PBMC


title: PIP-seq, postnatal day 14, replicate 1

description: Library name: PIP-seq library 1

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

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.


title: siBRG1_H3k27

first: Zishanbai

last: Zhang

address: No.1 Dongjiaominxiang, Dongcheng District

institute: Beijing Tongren Hospital

description:
Library name: siBRG1_H3k27
The raw data are being made available by Bowtie2 and MACS2 callpeak

data_processing:
Upload fq.gz data to Galaxy version 23.2 rc1, Using FastQC to evaluate the quality of data, using cutadapt to de concatenate raw data
Reads were aligned to the UCSC hg38 genome using Bowtie version 2.5.0.
To create coverage plots, the locations of the mapped reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called using MACS2 callpeak v3.5.4 with the significance cut-off p-value <=0.00001
Assembly: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Supplementary files format and content: hg38
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag

source_name: FaDu

growth_protocol: FaDu were cultured in MEM medium supplemented with 10 % fetal bovine serum, 100 U mL-1 penicillin, and 100 U mL-1 streptomycin (Gibco)

extract_protocol:
1 × 105 FaDu cells were collected,for the CUT&Tag analysis, we utilized the Hyperactive Universal CUT&Tag Assay Kit for Illumina (TD903, Vazyme)
For the CUT&Tag analysis, we utilized the Hyperactive Universal CUT&Tag Assay Kit for Illumina (TD903, Vazyme). Briefly, 1 × 105 FaDu cells were collected, resuspended in 100 μL wash buffer, transferred to an 8-tube strip containing activated ConA beads, and incubated for 10 min. Subsequently, 50 μL prechilled antibody buffer containing BACH1 or BRG1 antibodies was added to cells and incubated at 4 °C overnight, followed by the addition of diluted secondary antibodies and incubation for 60 min. After washing thrice with DIG wash buffer, samples were incubated with diluted pA/G-Tnp transposase for 1 h. Next, 50 μL diluted TTBL was added, and samples were incubated at 37 °C in a PCR instrument for 60 min for fragmentation. Subsequently, DNA extraction was performed by adding 5 μL proteinase K, 100 μL buffer L/B, and 20 μL DNA extract beads on the fragmented samples and incubating at 55 °C for 10 min. Following washes with WA and WB buffers, samples were eluted using sterile ultrapure water. The extracted DNA underwent library amplification using the TruePrep Index Kit V2 for Illumina (TD202, Vazyme). PCR products were treated with VAHTS DNA clean beads (N411, Vazyme) for 5 min, the supernatant then was discarded, samples were washed with 80% ethanol, eluted using sterile ultrapure water, and the library was sequenced on the Illumina NovaSeq platform.

value: FaDu

value: Human medulloblastoma cell

value: H3K27 (ABclonal, A22006)


title: spleen, CD8+ Non-Tfc, rep2

description: Library name: S-Non2


title: siBRG1_BACH1

description:
Library name: siBRG1_BACH1
The raw data are being made available by Bowtie2 and MACS2 callpeak

value: BACH1(Proteintech, 14018-1-AP)


title: PBMC_8781_CD_1

description:
Library name: PBMC_8781_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.

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: PBMC


title: spleen, CD8+ Non-Tfc, rep1

description: Library name: S-Non1


title: SCD,6mo,rep4

city: Memphis

first: Shannon

last: McKinney-Freeman

state: TN

address: 262 Danny Thomas Pl

department: Experimental Hematology

institute: St. Jude Children's Research Hospital

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 mouse the GRCm39 genome assembly with annotation from Gencode (version M35) 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: GRCm39, Gencode M35
Supplementary files format and content: Tab-delimited text file with gene-level counts. Includes original Ensembl Gene IDs from Gencode M35 annotation, as well as the associated gene symbols and gene types. Gene types were not filtered for this file, so all features in the GTF are included.

source_name: bone marrow

extract_protocol:
Cells sorted via FACS were collected directly into the provided RNA lysis buffer for isolation of total RNA (RNeasy Micro kit; QIAGEN, Germantown, MD).
The Ovation RNA Seq System V2 kit (Tecan, Männedorf, Switzerland) was used for library preparation. 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).

treatment_protocol: Mouse bone marrow LT-HSCs were collected by FACS from either SCD or non-SCD littermates (i.e. Townes mice), at 2 or 6 months of age.

value: bone marrow

value: LT-HSCs

tag: condition

value: SCD

value: SS

value: 6 months

value: M


title: PBMC_8780_CD_1_reprep

description:
Library name: PBMC_8780_CD_1_reprep
RNA-Seq of CHIM PBMC

value: Yes

value: female


title: SCD,6mo,rep3


title: spleen, CD8+ Tfc, rep3

description: Library name: S-Tfc3


title: siBACH1_BRG1

description:
Library name: siBACH1_BRG1
The raw data are being made available by Bowtie2 and MACS2 callpeak

value: BRG1(Proteintech, ab110641)


title: SCD,6mo,rep2


title: spleen, CD8+ Tfc, rep2

description: Library name: S-Tfc2


title: NC_H3k27

description:
Library name: NC_H3k27
The raw data are being made available by Bowtie2 and MACS2 callpeak

value: WT


title: SCD,6mo,rep1

value: F


title: spleen, CD8+ Tfc, rep1

description: Library name: S-Tfc1

value: Spleen

value: CD8 T lymphocytes


title: NC_BRG1

description:
Library name: NC_BRG1
The raw data are being made available by Bowtie2 and MACS2 callpeak

value: FaDu

value: Human medulloblastoma cell


title: NonSCD,6mo,rep5

value: non-SCD

value: AA


title: lymph node, CD8+ Non-Tfc, rep3

description: Library name: LN-Non3

source_name: inguinal lymph nodes

value: inguinal lymph nodes


title: NC_BACH1

description:
Library name: NC_BACH1
The raw data are being made available by Bowtie2 and MACS2 callpeak

value: BACH1(Proteintech, 14018-1-AP)


title: PBMC_8778_CD_1

description:
Library name: PBMC_8778_CD_1
RNA-Seq of CHIM PBMC

value: Blood

value: PBMC


title: NonSCD,6mo,rep4

value: bone marrow

value: LT-HSCs

value: 6 months


title: lymph node, CD8+ Non-Tfc, rep2

description: Library name: LN-Non2


title: IL1B_3

description:
Library name: FIS3
FPKM.FIS3

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

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.

value: IL1B knockdown


title: NonSCD,6mo,rep3

value: M


title: PBMC_8779_CD_1

description:
Library name: PBMC_8779_CD_1
RNA-Seq of CHIM PBMC

value: female


title: lymph node, CD8+ Non-Tfc, rep1

description: Library name: LN-Non1


title: IL1B_2

description:
Library name: FIS2
FPKM.FIS2


title: Brain single cell 287

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description: Library name: Sample 287

data_processing:
The sequencing reads were first aligned to the Ensembl mouse reference genome GRCm39 with STRA (version 2.7.3a). The duplicated reads were removed using samtools software (version 1.16.1). The raw read counts for each gene were then calculated using featureCounts function from the Subread package (version 1.4.6-p5)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include raw counts values for each sample

source_name: brain

extract_protocol:
Brain tissue from adult mice was mechanically and enzymatically dissociated, and vascular fragments were isolated, followed by further digestion to obtain a single-cell suspension.
Libraries for RNA-seq were prepared by using SMART-seq2 methodology

value: brain

value: endothelial


title: CD8+ T cells, Arid3b/Runx3-dKO, co-cultured with CMT93-OVA cells, replicate2

description:
Library name: sg-Arid3b+sg-Runx3 treat 2
cAR2

value: CD8+ T cells

value: Arid3b/Runx3 knockout

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

value: 4 hours


title: PBMC_8662_CD_1

last: Willemsen

address: Meibergdreef 9

institute: Amsterdam UMC - locatie AMC

description:
Library name: PBMC_8662_CD_1
RNA-Seq of CHIM PBMC

source_name: Blood

value: male


title: NonSCD,6mo,rep2

value: non-SCD

value: AA


title: lymph node, CD8+ Tfc, rep3

description: Library name: LN-Tfc3

value: inguinal lymph nodes

value: CD8 T lymphocytes


title: Brain single cell 286

description: Library name: Sample 286


title: CD8+ T cells, Arid3b-KO, co-cultured with CMT93-OVA cells, replicate2

description:
Library name: sg-Arid3b+sg-Int treat 2
cAI2

value: Arid3b knockout


title: IL1B_1

description:
Library name: FIS1
FPKM.FIS1

value: FaDu

value: Human medulloblastoma cell


title: PBMC_8591_CD_1_reprep

description:
Library name: PBMC_8591_CD_1_reprep
RNA-Seq of CHIM PBMC

value: Blood

value: PBMC

value: Yes


title: CD8+ T cells, Arid3b-KO, co-cultured with CMT93-OVA cells, replicate1

description:
Library name: sg-Arid3b+sg-Int treat 1
cAI1


title: MCbs1 PBS biorep 3

city: Richardson

first: Nikki

last: Delk

address: 800 West Campbell Road

department: Biological Sciences

institute: University of Texas at Dallas

description: Library name: 300-15

data_processing:
Fastq files were checked for quality using fastqc and fastq_screen and were quality trimmed using fastq-mcf
Trimmed fastq files were mapped to hg19 (UCSC version from igenomes) using TopHat
duplicates were marked using picard-tools, read counts were generated using featureCounts and differential expression analysis was performed using edgeR
Assembly: hg19
Supplementary files format and content: The Excel files contain RNA-seq differential expression analysis results, gene overlap analyses identifying shared and unique differentially expressed genes, genes of interest (GOI), and Gene Ontology (GO) over-representation analysis (ORA) results with associated enrichment statistics.

growth_protocol: To establish stable chronic IL-1-exposed sublines, MCF7 cells were cultured in DMEM/10% FB Essence (FBE) containing 0.5ng/mL IL-1α or 0.5ng/mL IL-1β for 6 months and T47D cells were cultured in RPMI 1640/10% FBE containing 0.5 ng/mL IL-1α or IL-1β for 6 months (7 months for the T47Dbs1 subline due to slowed prolifer-ation and expansion). Following chronic IL-1 exposure, cells were moved out of IL-1-containing medium and maintained in normal growth medium without IL-1 for phenotype characterization. Parental cell lines (MCF71, T47D1) were cultured in vehicle control (1× phosphate buffer saline, PBS) alongside the sublines. Sublines: MCF7 chronic IL-1α subline termed MCas1, MCF7 chronic IL-1β sublines termed MCbs1, T47D chronic IL-1α subline termed T47Das1, and termed T47D chronic IL-1β subline T47Dbs1.

extract_protocol:
RNA was extracted from cells treated with cytokines using GeneJET RNA Purification kit (Thermo Fisher Scientific, Waltham, MA; K0732) as per manufacturer’s instructions. Genomic DNA contamination was removed by treating 1 ug of RNA with 1 U of DNase-I (Thermo scientific, Waltham, MA; EN0521) following manufacturer’s instructions.
RNA-seq was performed by the Genome Center at tThe University of Texas at Dallas (Richardson, TX). Total RNA library was prepared using Illumina Truseq Stranded Total RNA prep Gold kit (Illumina). The prepared libraries were sequenced on an Illumina NextSeq 500 platform (San Diego, CA) with 100bp single-end reads.

treatment_protocol: We performed RNA sequencing (RNA-seq) and differential gene expression analysis for the parental (MCF71, T47D1) cells treated acutely with vehicle control, 25ng/mL IL-1α or 25ng/mL IL-1β for 4 days and for the chronic IL-1 sublines (MCas1, MCbs1, T47Das1, T47Dbs1) grown in vehicle control only.

value: breast cancer


title: NonSCD,6mo,rep1

value: bone marrow

value: LT-HSCs

value: 6 months

value: M


title: single-nucleus RNA-seq, postnatal day 14, replicate 1

description: Library name: P14_1

value: Heart

value: Wildtype


title: PBMC_8775_CD_1

first: Lisa

description:
Library name: PBMC_8775_CD_1
RNA-Seq of CHIM PBMC

value: male


title: single-nucleus RNA-seq, postnatal day 7, replicate 1

description: Library name: P7_1


title: PBMC_8591_CD_1

description:
Library name: PBMC_8591_CD_1
RNA-Seq of CHIM PBMC

value: female


title: NC_6

description:
Library name: FIN3
FPKM.FIN3

value: NC


title: Subject 4 PBMC

description: Library name: Subject 4 PBMC

value: Male