title: C. elegans, JUb19, R2

city: Washington

first: Jordan

middle: D

last: West

state: District of Columbia

institute: The George Washington

description: Library name: Sample 2

data_processing:
Sequencing reads were aligned to the C. elegans reference genome (WormBase release WS235) using Rsubread (run in RStudio). Gene-level counts were normalized and analyzed for differential expression with the limma-voom pipeline on the Galaxy platform (usegalaxy.org). Genes with <1 count per million (CPM) across all samples were excluded, and differentially expressed genes were defined at an adjusted p-value < 0.05.  Differential expression results were visualized as a volcano plot showing log₂ fold change versus −log₁₀ (adjusted p-value). Functional enrichment was assessed using Gene Set Enrichment Analysis (GSEA v4.3.2)59 against curated immune gene sets, with normalized enrichment scores (NES), nominal p-values, and false discovery rate (FDR) q-values reported. Category-level enrichment of differentially expressed genes (DEGs) was performed with WormCat 2.0 (wormcat.com)60 and visualized as category-level enrichment plots. Overlap with published immune-response datasets was summarized with Venn diagrams generated using Intervene (https://intervene.readthedocs.io/en/latest/index.html), highlighting shared and unique DEGs.
Assembly: WBcel235
Supplementary files format and content: tab-delimited text file contains raw counts for each sample

organism: Caenorhabditis elegans

source_name: Whole organism

extract_protocol:
Animals were rinsed from OP50- and JUb19-seeded plates with M9 buffer and transferred into TRI Reagent. Suspensions were incubated at room temperature for 30 min, thoroughly homogenized, and stored at −80 °C. Total RNA was isolated by BCP phase separation, then purified by isopropanol precipitation followed by a 75% ethanol wash. For RNA-seq, JUb19 fed conditions were collected 2h later than OP50 conditions to better match developmental differences across conditions. Samples received an additional cleanup with the RNeasy Universal Mini Kit per manufacturer’s instructions (Qiagen).
cDNA libraries were prepared and sequenced (paired end) by Genewiz Azenta.

value: Whole organism


title: C. elegans, OP50, R3

status: Public on Jun 17 2026

type: SRA

department: Biological Sciences

country: USA

description: Library name: Sample 6

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: genotype

value: WT

tag: treatment

tag: time


title: C. elegans, OP50, R1

description: Library name: Sample 4


title: C. elegans, JUb19, R3

description: Library name: Sample 3


title: 3N2WTShamSaline

city: Charlottesville

first: Vikram

last: Sabapathy

state: Virginia

address: 1340 Jefferson Park Ave., Pinn Hall, Room No: 4043

department: Center for Immunity, Inflammation and Regenerative Medicine

institute: University of Virginia

description: Library name: Sample 3

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using fastp v.0.23.1.
Trimmed and de-duplicated reads were then mapped to the Mus musculus GRCm38 ERCC reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed.
Assembly: Mus musculus GRCm38
Supplementary files format and content: CSV file include featurecounts for all the sample

organism: Mus musculus

source_name: Kidney

extract_protocol:
RNA was isolated from FACS-sorted cells using RNeasy Plus mini kit (Qiagen) and the quality was assessed with an HS-RNA Agilent Tape Station
mRNA sequencing with Twist UMI system

value: Kidney

value: Saline


title: C. elegans, OP50, R2

description: Library name: Sample 5


title: 2N2WTShamSaline

description: Library name: Sample 2


title: SSV1-infected Saccharolobus solfataricus S441 carrier state; control

city: Brussels

first: Wouter

last: Magnus

address: Pleinlaan 2

country: Belgium

institute: Vrije Universiteit Brussel

description:
Library name: PROM9_BC02
TSS_enr_ratios_WM_SSV1.plus.csv
TSS_enr_ratios_WM_SSV1.minus.csv
TTS_eff_ratios_WM_SSV1.plus.drop.coverage
TTS_eff_ratios_WM_SSV1.minus.drop.coverage

library_source: other

data_processing:
Real time basecalling and demultiplexing by the Guppy software (v3.2.10) in high accuracy mode.
read processing, mapping and identification of the viral transcription start sites (TSS) and termination sites (TTS) was performed according to the ONT-cappable-seq v2.0.0 automated data-analysis workflow (https://github.com/LoGT-KULeuven/ONT-cappable-seq/releases/tag/v2.0.0)
Assembly: SSV1 (NC_001338.1)
Supplementary files format and content: .csv files contain information on the location of transcription start sites of SSV1
Supplementary files format and content: .drop.coverage files contain information on the efficiency of transcription termination sites of SSV1

molecule: other

organism:
Saccharolobus solfataricus
Sulfolobus spindle-shaped virus 1

source_name: archaeal cells infected with virus

growth_protocol: SSV1-infected Saccharolobus solfataricus S441 was cultivated in liquid DT medium to OD600 of 0.5 (mid-exponential phase). For studying carrier state infection, culture samples were taken, while for studying infection post-UV-induction, which 20 mL aliquots were transferred to 95 mm diameter Petri dishes for UV-irradiation, after which samples were collected at 1, 2, 3, 4, 5, 6, 7, 8.5 and 12 hours post-UV-induction.

extract_protocol:
For every post-UV-induction RNA sample, RNA was extracted using hot phenol treatment and ethanol precipitation to extract and purify the RNA.
Total RNA was enriched for primary transcripts using the ONT-cappable-seq enrichment protocol. In parallel, control samples were subjected to similar environmental conditions. The RNA was reverse transcribed, PCR amplified and barcoded accoriding to Oxford Nanopore Technology cDNA-PCR protocol (SQK-PCB109)

treatment_protocol: Total RNA was extracted using hot-phenol extraction, followed by DNAse treatment. The enriched samples were subjected to an enrichment procedure based on streptavidin beads to enrich for primary transcripts. For the control samples the enrichment steps were omitted.

tag: strain

tag: cell type

value: archaeal cells infected with virus

value: no enrichment

tag: infection stage

value: carrier state


title: C. elegans, JUb19, R1

description: Library name: Sample 1


title: PA01, control, ChIP seq

city: Honolulu

first: Hung

last: Vo

state: Hawaii

address: 1800 East-West Road Life Sciences Building, Rm 318

department: Microbiology

institute: University of Hawaii at Manoa

description: Library name: PA01ChIPseq

data_processing:
ChIP-seq data were aligned to the Pa wt PA01 genome with Bowtie2 (Langmead, 2012), peaks called with MACS2 (Feng, 2012), and consensus binding regions determined with MEME (Bailey, 2009) (https://meme-suite.org/meme/).
Assembly: NC_002516.2
Supplementary files format and content: tab delimited text file include raw data of each sample
Supplementary files format and content: txt sample include -log10 of q value and Fold Enrichment compared between PA3321::Tn complement with 3xTY1 taq  and wild type control

organism: Pseudomonas aeruginosa

source_name: Bacteria

growth_protocol: The mutant PA3321::Tn and the wt PA01 strain were grown overnight in LB broth, diluted 100-fold into fresh LB broth, and grown in the same biofilm growth condition (30oC, no shake, 48 hours)

extract_protocol:
The ChIP-seq assays were performed as previously described (Heacock-Kang, 2018). Briefly, the regulator mutant strain PA3321∷Tn containing IPlac-3xTY1-PA3321 was grown and induced by isopropyl β-D-1-thiogalactopyranoside (IPTG) (0.25 mM) in LB at 30 °C for 48h without shaking. After induction, bacterial cells were cross-linked with paraformaldehyde, harvested, and lysed by freezing and thawing. Supernatants containing the DNA-regulator complexes were sheared to an average size of 100–500 bp in a Roche® nebulizer. The TY1-tagged PA3321 regulator bound to its regulated DNA region/fragment was enriched and captured using TY1 mouse monoclonal antibody and DiaMag® anti-mouse IgG-coated magnetic beads (Diagenode®), respectively. Captured DNA-regulator complexes were reversed cross-linked and purified using the QIAquick PCR Purification Kit (QIAGEN).
Purified DNA fragments were used as a template for library construction according to the Illumina ChIP-seq sample preparation protocol and sequenced at TUCF Genomics, where DNA libraries were prepped and 50 bp single-end reads were sequenced with the Illumina HiSeq 2500.

treatment_protocol: ChIP-seq profile of PA3321::Tn complement with PA3321-TY1x3 in static biofilm growth with control is Pa wt PA01

value: Bacteria

tag: cell line

value: Pseudomonas

value: aeruginosa

value: PA01 wild type

value: static biofiilm growth


title: 1N2WTShamSaline

description: Library name: Sample 1


status: Public on Jun 16 2026

city: Singapore

first: Swarnaseetha

last: Adusumalli

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

description: Library name: wk12-Replicate-2 pig heart with human CVPs

data_processing:
The spatial transcriptomes reads were aligned to a combined genome reference from human and pig ensembl genomes using 10X spaceranger counts.
The paired histology H&E images were also processed using spaceRanger to select locations covered by tissue by aligning to spot locations with fiducial border spots in the histology image.
Assembly: Human: GRCh38 (v102) and Pig: Ssus11 (v102)
Supplementary files format and content: h5 format
Supplementary files format and content: hires tissue image in png format
Library strategy: Spatial Transcriptomics

molecule: polyA RNA

organism: Sus scrofa

source_name: Heart

growth_protocol: Cells were differentiaed on LN521+221 for 11 days and transplanted into MI pig hearts (refer to the growth protocol from mouse paper)

extract_protocol:
Tissue were permeabilised by enzymes and released poly-A mRNA was captured by primers on the spots. RT master mix containing reverse transcription reagents was added to the permeabilized tissue reagents. Incubation with the regaents produces spatially barcoded, full-length cDNA from poly-A mRNA on the slides. Second strand synthesis and denaturation were perforemd and finally cDNA amplication and checked with quality control Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size. P5, P7, i7 and i5 sample indexes, and TruSeq Read 2 (read 2 primer sequence) are added via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina amplification.
10X Visium Spatial Transcriptome

treatment_protocol: Tissue were cryopreserved in OCT and liquid nitrogen and cryosectioned into 5 microns tissue slices. The tissue slice is placed into the 10x visium slides within the square boundary.

value: Heart

value: Cardiomyocytes

value: developmental stage:3 months old 15-20 kg

value: Tissue were cryopreserved in OCT and liquid nitrogen and cryosectioned into 5 microns tissue slices. The tissue slice is placed into the 10x vivium slides within the square boundary.


title: PA3321, mutant complement, ChIP seq

description: Library name: PA3321ChIPSeq

value: PA3321::Tn complement with TY 1x3 tag


title: SSV1-infected Saccharolobus solfataricus S441 carrier state; enriched

description:
Library name: PROM9_BC01
TSS_enr_ratios_WM_SSV1.plus.csv
TSS_enr_ratios_WM_SSV1.minus.csv
TTS_eff_ratios_WM_SSV1.plus.drop.coverage
TTS_eff_ratios_WM_SSV1.minus.drop.coverage

value: enriched for primary transcripts


title: wk12-Media pig heart tissue

description: Library name: wk12-Media pig heart tissue


description: Library name: wk12-Replicate-1 pig heart with human CVPs


title: wk4-Sham pig heart tissue

description: Library name: wk4-Sham pig heart tissue


description: Library name: wk4-Replicate-1 pig heart with human CVPs


description: Library name: wk4-Replicate-2 pig heart with human CVPs


description: Library name: wk1-Replicate-2 pig heart with human CVPs


title: wk12-Sham pig heart tissue

description: Library name: wk12-Sham pig heart tissue


description: Library name: wk1-Replicate-1 pig heart with human CVPs


title: wk4-Media pig heart tissue

description: Library name: wk4-Media pig heart tissue


title: wk1-Sham pig heart tissue

description: Library name: wk1-Sham pig heart tissue


title: wk1-Media pig heart tissue

description: Library name: wk1-Media pig heart tissue


title: scRNA-seq_4NQO_OSCC_Tongue_Rep3

city: Hung Hom

first: Xiaofan

last: Xu

address: 11 Yuk Choi Rd

country: Hong Kong

institute: The Hong Kong Polytechnic University

description: Library name: scRNA-seq_4NQO_OSCC_Tongue_Rep3

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using the Cell Ranger pipeline (10x Genomics) for demultiplexing, alignment to the mouse reference genome (mm10), and gene expression quantification. Downstream analysis, including quality control (filtering cells with <200 detected genes or >20% mitochondrial reads), data normalization, scaling, principal component analysis (PCA), graph-based clustering, and UMAP dimensionality reduction, was performed using the Seurat package (version 5.0) in R.
Assembly: mm10
Supplementary files format and content: count matrix, feature annotations, cell barcodes

source_name: Bulk tongue tissue

extract_protocol:
Tongue tissues were placed in ice-cold PBS with 1% penicillin-streptomycin, dissected, and cut into ~1 mm³ pieces. Enzymatic digestion was performed using 0.25% trypsin and 0.1% collagenase type I at 37°C for 30 minutes with agitation. The reaction was stopped with fetal bovine serum (FBS), and the suspension was filtered through a 70 µm strainer. Only samples with >90% viability (Trypan Blue) proceeded to sequencing.
Single-cell RNA sequencing libraries were constructed using the 10x Genomics Chromium platform. Approximately 10,000 cells per sample were loaded. Following cDNA synthesis and library preparation, sequencing was performed on an Illumina NovaSeq 6000 platform.

treatment_protocol: Experimental group (OSCC): 100 µg/mL 4-nitroquinoline 1-oxide (4-NQO, Sigma-Aldrich #N8141) dissolved in propylene glycol:water (1:10 v/v) administered in drinking water for 16 weeks. Control group (Vehicle): propylene glycol:water (1:10 v/v) only for 16 weeks.

value: Bulk tongue tissue


title: scRNA-seq_4NQO_OSCC_Tongue_Rep2

description: Library name: scRNA-seq_4NQO_OSCC_Tongue_Rep2


title: scRNA-seq_4NQO_OSCC_Tongue_Rep1

description: Library name: scRNA-seq_4NQO_OSCC_Tongue_Rep1


title: scRNA-seq_Control_Tongue_Rep1

description: Library name: scRNA-seq_Control_Tongue_Rep1

value: Control


title: scRNA-seq_Control_Tongue_Rep2

description: Library name: scRNA-seq_Control_Tongue_Rep2


title: scRNA-seq_Control_Tongue_Rep3

description: Library name: scRNA-seq_Control_Tongue_Rep3


title: C26shCS_2_iWAT

city: Munich

first: Mauricio

last: Berriel Diaz

state: Bavaria

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Cancer

country: Germany

institute: Helmholtz Center Munich

description: Library name: Sample 32

data_processing:
Downstream analysis was performed using a combination of programs including STAR, HTseq, Cufflink and our wrapped scripts. Alignments were parsed using Tophat program and differential expressions were determined through DESeq2/edgeR. GO and KEGG enrichment were implemented by the ClusterProfiler. Gene fusion and difference of alternative splicing event were detected by Star-fusion and rMATS software
Assembly: mm10
Supplementary files format and content: a single tab-delimited text file include read counts  for each Sample

source_name: iWAT

extract_protocol:
Total RNA was extracted from frozen organs by performing a tissue lysis in TRIzol™ (Life Technologies, #15596018) with Qiagen's TissueLyser II (Qiagen, # 85300).
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: iWAT

value: C26 tumor carrying control shRNA

tag: repeat


title: Testis, reproductive season, sRNA-seq, rep3

city: Kunming

first: xu

last: dai

state: Yunnan

address: No. 452 Fenyuan Road, Panlong District

country: China

institute: Yunnan Agricultural University

description: Library name: R_TESTIS_sRNA_3

data_processing:
All sequencing services were performed by E-GENE Technology Co., Ltd. (Shenzhen, China).
Assembly: Tree Shrew Database V3.0 (https://www.treeshrewdb.org)
Supplementary files format and content: gene_expression.csv CSV file containing raw read counts for all genes across all samples, generated by featureCounts. Rows represent gene IDs, columns represent sample names. mirna_expression.csv CSV file containing raw read counts for known and novel miRNAs across all samples, generated by miRDeep2 quantifier.pl. Rows represent miRNA IDs, columns represent sample names. piRNA_expression.csv CSV file containing raw read counts for individual piRNAs across all samples, generated by pirAT. Rows represent piRNA IDs, columns represent sample names. piRNA_cluster_expression.csv CSV file containing raw read counts for piRNA clusters across all samples, quantified by intersecting proTRAC cluster coordinates with BAM files using bedtools. Rows represent cluster IDs, columns represent sample names.

organism: Tupaia belangeri chinensis

source_name: Testis

extract_protocol:
Total RNA was extracted from testis, caput epididymis, and cauda epididymis tissues of Tupaia belangeri using TRIzol reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions. Tissue samples were homogenized in liquid nitrogen prior to extraction. RNA integrity was assessed using an Agilent Bioanalyzer 2100 (RNA Integrity Number, RIN ≥ 7.0). RNA concentration and purity were measured using a NanoDrop spectrophotometer (A260/A280 ratio between 1.8 and 2.0).
mRNA sequencing (RNA-seq): For each sample, 1–2 μg of total RNA was treated with DNase I to remove residual genomic DNA and subsequently purified using RNA Clean XP magnetic beads. Poly(A)+ mRNA was enriched using Oligo(dT) magnetic beads. The enriched mRNA was fragmented according to the kit protocol to generate RNA fragments of approximately 150–300 nt. First-strand cDNA was synthesized using random hexamer primers and SuperScript II reverse transcriptase, followed by second-strand cDNA synthesis using RNase H and DNA polymerase I. Double-stranded cDNA was purified with AMPure XP beads and subjected to end repair, 3′ A-tailing, and ligation of Illumina sequencing adapters. The final libraries were generated by PCR amplification. Library quality control included initial quantification using Qubit 2.0 and dilution to 1 ng/μL, assessment of insert size distribution using the Agilent 2100 Bioanalyzer, and accurate quantification by qPCR (effective concentration > 2 nM). Qualified libraries were pooled at equimolar ratios and sequenced on an Illumina NovaSeq 6000 platform to generate paired-end 150 bp reads (PE150). Small RNA sequencing (sRNA-seq): Total RNA was used as the input material for small RNA library construction. Sequencing adapters were sequentially ligated to the 3′ and 5′ ends of small RNAs according to the manufacturer’s protocol, followed by reverse transcription and PCR amplification. The amplified products were separated by 6% polyacrylamide gel electrophoresis, and fragments of approximately 140–160 bp were excised and recovered for library construction. Library quality control procedures were identical to those used for RNA-seq libraries. Qualified libraries were pooled and sequenced on an Illumina NovaSeq 6000 platform to generate single-end 50 bp reads (SE50). All sequencing services were performed by E-GENE Technology Co., Ltd. (Shenzhen, China).

value: Testis


title: C26shCS_1_iWAT

description: Library name: Sample 31


title: Testis, reproductive season, sRNA-seq, rep1

description: Library name: R_TESTIS_sRNA_1


title: C26shAS_2_iWAT

description: Library name: Sample 30

value: ADAMTSL4 knockdown in C26 tumor


title: Caput epididymis, reproductive season, sRNA-seq, rep3

description: Library name: R_CAPUT_sRNA_3

source_name: Caput epididymis

value: Caput epididymis


title: Testis, reproductive season, sRNA-seq, rep2

description: Library name: R_TESTIS_sRNA_2


title: C26shAS_1_iWAT

description: Library name: Sample 29


title: adipose tissue, CD, rep1

city: Xi'an

first: Chen

last: Wang

address: Yanta West Road No.277

institute: The First Affiliated Hospital of Xi’an Jiaotong University

description:
Library name: Ctrl
10XGenomics

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software （ version5.01 ）.
Assembly: mm39
Supplementary files format and content: Mouse mm10

molecule: nuclear RNA

source_name: adipose tissue

extract_protocol:
Samples were cut into ~1 mm pieces and homogenized using a Dounce homogenizer (885302-0002; Kimble Chase) in 2 ml of ice-cold Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) supplemented with protease inhibitor(5892791001; Roche) and RNase inhibitor(N2615;Promega and AM2696; Life Technologies). They were incubated on ice for 5 minutes with an additional 2 ml of lysis buffer. Grounded with a dounce(Sigma), resuspended by pipette，gentlely; Incubated on ice for 6 min, then add 2 ml of ice-cold 4% BSA, resuspended by Pasteur pipette, then stop the reaction; Centrifuged at 300g for 5 minutes at 4°C; Add 2 ml of lysis buffer and 4% BSA, resuspended, Incubated on ice for 3 min; De-fragment with Miltenyi (Debris Removal Solution); The pellet was resuspended and washed with 4 ml of the buffer, and then, it was incubated on ice for 5 minutes. After another centrifugation; The pellet was resuspended in Nuclei Suspension Buffer (1x PBS,0.07% BSA, and 0.1% RNase inhibitor); Filtered through a 20-mm cell strainer(43-50020-50; pluriSelect), and counted using a haemocytometer/ Countess II Automated Cell Counter and concentration adjusted to 700-1200 cells/μl.
Single-nuclei suspensions were loaded to 10x Chromium to capture 8000 single cell according to the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’ kit (V3) . The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150bp) by LC-Bio Technology co.ltd., (HangZhou,China) at a minimum depth of 20,000 reads per cell.

value: adipose tissue

value: chow diet


title: Caput epididymis, reproductive season, sRNA-seq, rep2

description: Library name: R_CAPUT_sRNA_2


title: adipose tissue, HFD, rep1

description:
Library name: AS
10XGenomics

value: high fed diet


title: Cauda epididymis, eproductive season, sRNA-seq, rep3

description: Library name: R_CAUDA_sRNA_3

source_name: Cauda epididymis

value: Cauda epididymis


title: Caput epididymis, reproductive season, sRNA-seq, rep1

description: Library name: R_CAPUT_sRNA_1


title: WT3-SVF-D4

city: Hangzhou

first: Shun

last: Chen

address: No. 866 Yuhangtang Road, Hangzhou, Zhejiang Province, China

institute: Zhejiang University

description:
Library name: WT3-SVF-D4-LEF1306_L0
Column name in Ythdf1_SVF_D4_gene_count_matrix.txt: WT3-SVF-D4-LEF1306_L0

data_processing:
Raw reads were filtered to remove adapter sequences and low-quality reads.
Clean reads were aligned to the Mus musculus reference genome using STAR.
Gene-level raw read counts were generated from aligned reads using featureCounts.
Differential gene expression analysis was performed between Ythdf1 knockout and wild-type SVF-derived adipocytes.
Assembly: Mus musculus genome assembly mm10/GRCm38
Supplementary files format and content: Tab-delimited text file containing raw gene-level read counts. Rows are Ensembl gene IDs and columns are RNA-seq samples.

source_name: inguinal white adipose tissue

growth_protocol: SVF cells were isolated from inguinal white adipose tissue of wild-type and Ythdf1 knockout mice and cultured under standard conditions before adipogenic induction.

extract_protocol:
Total RNA was extracted from differentiated SVF-derived adipocytes. Ribosomal RNA was removed, and RNA quality was assessed before library preparation.
RNA-seq libraries were generated from rRNA-depleted total RNA and sequenced on an Illumina NovaSeq 6000 platform to generate paired-end 150 bp reads.

treatment_protocol: SVF cells were induced to undergo adipogenic differentiation in vitro for 4 days before RNA isolation.

value: inguinal white adipose tissue

value: SVF-derived adipocytes

value: wild type

value: in vitro adipogenic differentiation for 4 days


title: Cauda epididymis, eproductive season, sRNA-seq, rep2

description: Library name: R_CAUDA_sRNA_2


title: WT2-SVF-D4

description:
Library name: WT2-SVF-D4-LEF1305_L1
Column name in Ythdf1_SVF_D4_gene_count_matrix.txt: WT2-SVF-D4-LEF1305_L1


title: WT1-SVF-D4

description:
Library name: WT1-SVF-D4-LEF1304_L1
Column name in Ythdf1_SVF_D4_gene_count_matrix.txt: WT1-SVF-D4-LEF1304_L1


title: Cauda epididymis, eproductive season, sRNA-seq, rep1

description: Library name: R_CAUDA_sRNA_1


title: KO3-SVF-D4

description:
Library name: KO3-SVF-D4-LEF1309_L1
Column name in Ythdf1_SVF_D4_gene_count_matrix.txt: KO3-SVF-D4-LEF1309_L1

value: Ythdf1 knockout


title: Testis, non-reproductive season, sRNA-seq, rep3

description: Library name: NR_TESTIS_sRNA_3


title: KO2-SVF-D4

description:
Library name: KO2-SVF-D4-LEF1308_L0
Column name in Ythdf1_SVF_D4_gene_count_matrix.txt: KO2-SVF-D4-LEF1308_L0


title: Testis, non-reproductive season, sRNA-seq, rep2

description: Library name: NR_TESTIS_sRNA_2


title: KO1-SVF-D4

description:
Library name: KO1-SVF-D4-LEF1307_L1
Column name in Ythdf1_SVF_D4_gene_count_matrix.txt: KO1-SVF-D4-LEF1307_L1


title: Testis, non-reproductive season, sRNA-seq, rep1

description: Library name: NR_TESTIS_sRNA_1


title: Caput epididymis, non-reproductive season, sRNA-seq, rep3

description: Library name: NR_CAPUT_sRNA_3


title: Caput epididymis, non-reproductive season, sRNA-seq, rep2

description: Library name: NR_CAPUT_sRNA_2


title: Subchondral bone from DMM-operated Pvalb cKO mouse (8 weeks post-surgery), biological replicate 4

city: Shanghai

first: Jiansen

last: Su

address: No. 600, Yishan Road, Shanghai

institute: Shanghai Sixth People's Hospital

description: Library name: OA_PV4

data_processing:
Raw sequencing reads (FASTQ format) were first subjected to quality control using FastQC v0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Adapter sequences and low-quality reads (Phred quality score < 20, read length < 50 bp) were trimmed using Trimmomatic v0.39 with parameters: ILLUMINACLIP:adapters.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:50.
Clean reads were aligned to the mouse reference genome using STAR v2.7.10a with default parameters.
Gene-level read counts were quantified using featureCounts v2.0.3 from the Subread package, with parameters: -p -t exon -g gene_id -s 0.
Differential gene expression analysis was performed using DESeq2 v1.42.0 in R v4.3.1. Genes with adjusted p-value < 0.05 and
Assembly: mm39 (GRCm39)
Supplementary files format and content: gene_raw_counts.csv: Comma-separated values (CSV) file containing FPKM for all genes across all samples. Rows represent Ensembl gene IDs, columns represent sample library names.

source_name: Tibial subchondral bone

growth_protocol: 8-week-old male C57BL/6J wild-type mice and Dmp1-Cre;Pvalbfl/fl conditional knockout mice were housed in a specific pathogen-free (SPF) facility under a 12-hour light/dark cycle at 22±2°C with 50±10% humidity, and had free access to standard chow and water.

extract_protocol:
Total RNA was extracted from frozen tibial subchondral bone tissues using TRIzol reagent (Invitrogen, #15596026) combined with the RNeasy Mini Kit (Qiagen, #74104) following the manufacturer's instructions. Briefly, bone tissues were ground into fine powder in liquid nitrogen, lysed in TRIzol, and centrifuged to remove debris. The aqueous phase was collected, mixed with 70% ethanol, and loaded onto RNeasy spin columns. On-column DNase I digestion (Qiagen, #79254) was performed to eliminate genomic DNA contamination. RNA concentration and purity were measured using a NanoDrop 2000 spectrophotometer (Thermo Fisher), and RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). Only samples with RNA Integrity Number (RIN) ≥ 8.0 were used for library construction.
mRNA-seq libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, #E7770) according to the manufacturer's protocol. Briefly, 1 μg of total RNA per sample was used for poly(A) mRNA enrichment using oligo(dT) magnetic beads. The enriched mRNA was fragmented into 200-300 bp fragments at 94°C for 15 minutes. First-strand cDNA was synthesized using random hexamer primers and reverse transcriptase, followed by second-strand cDNA synthesis with dUTP instead of dTTP. The double-stranded cDNA was subjected to end repair, dA-tailing, and ligation of NEBNext adaptors with unique barcodes. After size selection (250-350 bp) using AMPure XP beads (Beckman Coulter), the libraries were amplified by PCR for 12-15 cycles. The final libraries were quantified using a Qubit 3.0 fluorometer (Thermo Fisher) and validated for size distribution using an Agilent 2100 Bioanalyzer.

treatment_protocol: Mice were randomly divided into sham surgery group and DMM (Destabilization of the medial meniscus) surgery group. For DMM surgery, the medial meniscotibial ligament was transected to induce osteoarthritis. For sham surgery, the joint capsule was opened but the ligament was left intact. Mice were sacrificed 8 weeks after surgery, and tibial subchondral bone tissues were harvested for RNA extraction.

value: Tibial subchondral bone

value: Pvalb cKO

value: DMM-operated


title: Subchondral bone from DMM-operated Pvalb cKO mouse (8 weeks post-surgery), biological replicate 5

description: Library name: OA_PV5


title: Subchondral bone from DMM-operated Pvalb cKO mouse (8 weeks post-surgery), biological replicate 3

description: Library name: OA_PV3


title: Caput epididymis, non-reproductive season, sRNA-seq, rep1

description: Library name: NR_CAPUT_sRNA_1


title: Subchondral bone from DMM-operated Pvalb cKO mouse (8 weeks post-surgery), biological replicate 2

description: Library name: OA_PV2


title: Cauda epididymis, non-reproductive season, sRNA-seq, rep3

description: Library name: NR_CAUDA_sRNA_3


title: Subchondral bone from DMM-operated Pvalb cKO mouse (8 weeks post-surgery), biological replicate 1

description: Library name: OA_PV1


title: Cauda epididymis, non-reproductive season, sRNA-seq, rep2

description: Library name: NR_CAUDA_sRNA_2


title: Subchondral bone from DMM-operated wild-type mouse (8 weeks post-surgery), biological replicate 5

description: Library name: OA_wt5

value: wild-type


title: Cauda epididymis, non-reproductive season, sRNA-seq, rep1

description: Library name: NR_CAUDA_sRNA_1


title: Testis, reproductive season, RNA-seq, rep3

description: Library name: R_TESTIS_RNA_3


title: Subchondral bone from DMM-operated wild-type mouse (8 weeks post-surgery), biological replicate 4

description: Library name: OA_wt4


title: Subchondral bone from DMM-operated wild-type mouse (8 weeks post-surgery), biological replicate 3

description: Library name: OA_wt3


title: Testis, reproductive season, RNA-seq, rep2

description: Library name: R_TESTIS_RNA_2


title: Subchondral bone from DMM-operated wild-type mouse (8 weeks post-surgery), biological replicate 2

description: Library name: OA_wt2


title: Subchondral bone from DMM-operated wild-type mouse (8 weeks post-surgery), biological replicate 1

description: Library name: OA_wt1


title: Testis, reproductive season, RNA-seq, rep1

description: Library name: R_TESTIS_RNA_1


title: Caput epididymis, reproductive season, RNA-seq, rep3

description: Library name: R_CAPUT_RNA_3


title: Subchondral bone from sham-operated wild-type C57BL/6 mouse, biological replicate 5

description: Library name: sham5

value: sham-operated


title: Caput epididymis, reproductive season, RNA-seq, rep2

description: Library name: R_CAPUT_RNA_2


title: Subchondral bone from sham-operated wild-type C57BL/6 mouse, biological replicate 4

description: Library name: sham4


title: Caput epididymis, reproductive season, RNA-seq, rep1

description: Library name: R_CAPUT_RNA_1


title: Subchondral bone from sham-operated wild-type C57BL/6 mouse, biological replicate 2

description: Library name: sham2


title: Cauda epididymis, eproductive season, RNA-seq, rep2

description: Library name: R_CAUDA_RNA_2


title: Subchondral bone from sham-operated wild-type C57BL/6 mouse, biological replicate 1

description: Library name: sham1


title: Cauda epididymis, eproductive season, RNA-seq, rep1

description: Library name: R_CAUDA_RNA_1


title: Testis, non-reproductive season, RNA-seq, rep3

description: Library name: NR_TESTIS_RNA_3

value: Testis


title: Tibialis anterior WT Rep4

city: Edmonton

first: Toshifumi

last: Yokota

state: Alberta

department: Medical Genetics

country: Canada

institute: University of Alberta

description: Library name: WT4

data_processing:
CutAdapt 1.10 and FastQC 0.10.1 were used to clean raw data and remove adapters.
Reads were mapped to GRCm39 using HISAT 2.0.
Transcript assembly and expression profiling was completed with StringTie 1.3.4.
Assembly: GRCm39
Supplementary files format and content: FPKM values for each sample are provided in a single CSV file

source_name: Tibialis anterior

extract_protocol:
RNA was isolated using the Agilent Total RNA Isolation Mini Kit. Samples quality was assessed with Agilent 2100 Bioanalyzer to ensure that all RNA RIN >7.0.
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol.

value: Tibialis anterior

value: WT


title: Testis, non-reproductive season, RNA-seq, rep2

description: Library name: NR_TESTIS_RNA_2


title: Tibialis anterior WT Rep3

description: Library name: WT3


title: Tibialis anterior WT Rep2

description: Library name: WT2


title: Testis, non-reproductive season, RNA-seq, rep1

description: Library name: NR_TESTIS_RNA_1


title: Tibialis anterior WT Rep1

description: Library name: WT1


title: Caput epididymis, non-reproductive season, RNA-seq, rep3

description: Library name: NR_CAPUT_RNA_3

value: Caput epididymis


title: Tibialis anterior mdx Rep4

description: Library name: MDX4

value: mdx


title: Caput epididymis, non-reproductive season, RNA-seq, rep2

description: Library name: NR_CAPUT_RNA_2


title: Tibialis anterior mdx Rep3

description: Library name: MDX3


title: Caput epididymis, non-reproductive season, RNA-seq, rep1

description: Library name: NR_CAPUT_RNA_1


title: Tibialis anterior mdx Rep2

description: Library name: MDX2


title: Cauda epididymis, non-reproductive season, RNA-seq, rep3

description: Library name: NR_CAUDA_RNA_3


title: Cauda epididymis, non-reproductive season, RNA-seq, rep2

description: Library name: NR_CAUDA_RNA_2


title: Tibialis anterior DMD-Null Rep4

description: Library name: Null4

value: DMD-Null


title: Cauda epididymis, non-reproductive season, RNA-seq, rep1

description: Library name: NR_CAUDA_RNA_1

value: Cauda epididymis


title: GFHD101, untreated control

city: Kraków

first: Mariia

last: Melnykova

address: ul. Gołębia 24

department: Microbiology Department

country: Poland

institute: Uniwersytet Jagielloński

description: Library name: IF9

data_processing:
Raw sequencing reads in FASTQ format were generated by Illumina base calling.
Raw reads were filtered to remove reads containing adapters, reads with more than 10% undetermined bases (N), and reads with low-quality bases (Q < 5) accounting for more than 50% of the read.
Clean reads were aligned to the human reference genome using HISAT2.
Gene-level read counts were generated from uniquely mapped reads using reference genome annotation.
Assembly: Homo sapiens genome assembly GRCh38/hg38
Supplementary files format and content: Comma-delimited text file containing gene-level raw read counts. Rows correspond to genes, identified by Ensembl gene IDs; columns correspond to individual RNA-seq samples.

organism: Homo sapiens

source_name: gingiva

growth_protocol: Primary human gingival fibroblasts (GFs) were isolated from gingival tissue specimens obtained from study participants and cultured in DMEM supplemented with fetal bovine serum. The day before stimulation and throughout the experiment, cells were cultured in antibiotic-free DMEM supplemented with 2% FBS.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
mRNA libraries were prepared by Novogene using poly(A) enrichment. Briefly, mRNA was enriched from total RNA, fragmented, reverse-transcribed into cDNA, end-repaired, adapter-ligated, PCR-amplified, and sequenced on an Illumina platform.

treatment_protocol: GFs were seeded in 6-well plates at 5 × 10^5 cells/well and were either left untreated, stimulated with IFNg (100 ng/ml), infected with Fusobacterium nucleatum (Fn) at MOI 50, or treated simultaneously with IFN-γ and Fn for 24 h.

value: gingiva

value: primary human gingival fibroblast

value: ctrl


title: Tibialis anterior DMD-Null Rep3

description: Library name: Null3


title: Tibialis anterior DMD-Null Rep2

description: Library name: Null2


title: GFHD06, Fn and IFNg treated

description: Library name: IF8

value: FnIFNg


title: GFHD06, IFNg treated

description: Library name: IF7

value: IFNg


title: Tibialis anterior DMD-Null Rep1

description: Library name: Null1


title: GFHD06, Fn treated

description: Library name: IF6

value: Fn


title: ATAC counts of multiplex sSL0212 containing tissue & timepoint(s) CTX (L); P14

city: Klosterneuburg

first: Gaia

last: Novarino

address: Am Campus 1

country: Austria

institute: Institute of Science and Technology Austria (ISTA)

description:
Library name: sSL0212_ATAC
sSL0212_ATAC_filtered_feature_bc_matrix.h5
sSL0212_ATAC_fragments.tsv.gz
sSL0212_ATAC_fragments.tsv.gz.tbi
sSL0212_ATAC_peak_annotation.tsv
sSL0212_ATAC_peaks.bed
cx_p14_diet_seurat_RNA_assay.rds

library_source: genomic single cell

data_processing:
Pre-processing was done per 10X lane (i.e., per multiplexing group of 4-6 samples). Peaks for the snATAC-seq modality were called for each run separately using MACS2 (v2.2.7.1) within Signac. A set of consensus peaks for the snATAC-seq analysis was created according to Signac. CMO demultiplexing information was taken from Cellranger output and added as metadata. Doublets were identified using scDblFinder6 (v1.14.0), separately for snRNA-seq and snATAC-seq modality. snRNA-seq parameters for the scDblFinder function were dims = 50, cluster = TRUE, knownUse = “discard”. snATAC-seq features were first aggregated (aggregateFeatures function, k = 500) and parameters for scDblFinder were dims = 50, aggegateFeatures = TRUE. Cells identified as doublets based on CMO data were included as known doublets (knownDoublets parameter). Quality control metrics such as the percentage of mitochondrial reads, nucleosome signal, and transcription start site (TSS) enrichment were calculated per run. After removing known and estimated doublets outlier thresholds for snRNA-seq read counts (nCount_RNA) or snATAC-seq read counts (nCount_ATAC) were derived using the isOutlier function from the scuttle package7 (v1.10.2) with parameters nmads = 3, type = “both”, log = TRUE. Nuclei falling outside these thresholds or with more than 5% of mitochondrial reads were removed. Complete datasets for each time point/tissue were created by integrating individual Seurat objects representing separate 10X lanes (i.e., multiplexing groups). snRNA-seq data were normalized using SCTransform8,9 from Seurat with parameter vst.flavor = “v2”. Integration of normalized snRNA-seq data was performed according to Seurat using the reciprocal PCA method with the following non-default parameters: SelectIntegrationFeatures(nfeatures = 2500), FindIntegrationAnchors(reduction = “rpca”), IntegrateData(dims = 1:50). Integration of snATAC-seq data was performed at the level of the LSI embedding using IntegrateEmbeddings(dims.to.integrate = 1:50) function with the integration anchors derived from snRNA-seq data. Identification of cell types was performed using the combination of both modalities, snRNA-seq and snATAC-seq. A PCA embedding was derived for the integrated snRNA-seq data, weighted nearest neighbor (WNN) graph was calculated using the FindMultimodalNeighbors function with the integrated LSI and integrated PCA reductions as input and dims_atac = 2:50, dims_rna = 1:50. The resulting WNN graph was used for UMAP visualization of the dataset and identification of clusters
Samples used for multi-omics analyses were de-multiplexed, and the raw sequencing data was converted to FASTQ format using bcl2fastq (v2.20.0.422). Joint processing of the gene expression and ATAC modalities was performed using the cellranger-arc software (v2.0.0). The mm10 reference genome was used for the alignment (refdata-cellranger-arc-mm10-2020-A-2.0.0, obtained from https://cf.10xgenomics.com/supp/cell-arc/refdata-cellranger-arc-mm10-2020-A-2.0.0.tar.gz). To capture CMO reads, the gene expression modality was separately processed using the cellranger count pipeline (v7.0.0 and v7.1.0), aligning it against the mm10 reference genome (refdata-gex-mm10-2020-A, obtained from https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz). Each nucleus was assigned to the sample of origin as part of further demultiplexing, for which a Gaussian mixture model was fitted to the CMO count distributions. The probability that a given CMO read count was derived from background or positive signal was then inferred (as described in2).
Assembly: mm10
Supplementary files format and content: Cellranger output files (GEX): filtered feature matrix (h5 format); QC categories (csv)
Supplementary files format and content: Cellranger output files (ATAC): filtered feature matrix (h5 format); atac fragments (tsv & index); atac peak annotation (tsv & bed)
Supplementary files format and content: Downstream pipeline: integrated seurat object (RDS); pipeline input sample table (xlsx)

molecule: genomic DNA

source_name: Cortex

extract_protocol:
Single nuclei were extracted using the 10X Genomics nuclei isolation kit (Chromium Nuclei Isolation Kit CG000505, Rev A). Samples were pooled after barcoding with cholesterol-modified oligos (CMOs) and a CMO Co-Anchor. Afterwards, single nuclei of pooled samples were encapsulated in Gel-Beads-in  emulsions (GEMs) on a 10X Chromium Controller using Chromium Next GEM Chip J Single Cell kit (PN-1000230), Chromium Next GEM Single Cell Multiome GEM Kit A (PN-1000232), Chromium Next GEM Single Cell Multiome Gel Bead Kit A (PN-1000231) as instructed by the manufacturer.
The library was prepared according to the 10X protocol using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression, CG000338 Rev F. The hasthag oligo (HTO) libraries were prepared alongside cDNA amplification. Here, an ADT additive primer was added to the reaction. During cDNA cleanup, supernatant was saved to purify Hash-DNA. HTO libraries were generated using unique combinations of i5 and i7 indices.

value: Cortex

value: mixed

value: mixed samples (multiplex)

tag: batch


title: GEX counts of multiplex sSL0212 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0212_GEX
sSL0212_GEX_filtered_feature_bc_matrix.h5
sSL0212_GEX_QC_categories.csv
cx_p14_diet_seurat_RNA_assay.rds


title: HTO counts of multiplex sSL0212 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0212_HTO
Samples GN3F/22/2387, GN3F/22/2384, GN22/3866, GN22/3873, GN22/3F/2101, GN22/3F/2104, GN3F/22/2387, GN3F/22/2384, GN22/3866, GN22/3873, GN22/3F/2101, GN22/3F/2104 with genotypes Ash1l+/-, Ash1l+/-, Cul3+/-, Cul3+/-, Usp7+/-, Usp7+/-, Ash1l+/-, Ash1l+/-, Cul3+/-, Cul3+/-, Usp7+/-, Usp7+/- and sex f, m, m, f, m, f, f, m, m, f, m, f from tissue CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L) at timepoints P14, P14, P14, P14, P14, P14, P14, P14, P14, P14, P14, P14
cx_p14_diet_seurat_RNA_assay.rds

molecule: protein


title: GFHD06, untreated control

description: Library name: IF5


title: GFHD105, Fn and IFNg treated

description: Library name: IF20


title: GFHD105, IFNg treated

description: Library name: IF19


title: ATAC counts of multiplex sSL0249 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0249_ATAC
sSL0249_ATAC_filtered_feature_bc_matrix.h5
sSL0249_ATAC_fragments.tsv.gz
sSL0249_ATAC_fragments.tsv.gz.tbi
sSL0249_ATAC_peak_annotation.tsv
sSL0249_ATAC_peaks.bed
cx_p14_diet_seurat_RNA_assay.rds


title: GFHD105, Fn treated

description: Library name: IF18


title: GEX counts of multiplex sSL0249 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0249_GEX
sSL0249_GEX_filtered_feature_bc_matrix.h5
sSL0249_GEX_QC_categories.csv
cx_p14_diet_seurat_RNA_assay.rds


title: HTO counts of multiplex sSL0249 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0249_HTO
Samples GN23/22, GN23/45, GN22/2824, GN22/4129, GN23/22, GN23/45, GN22/2824, GN22/4129 with genotypes Hnrnpu+/-, Hnrnpu+/-, Trip12+/-, Ptchd1 -/y, Hnrnpu+/-, Hnrnpu+/-, Trip12+/-, Ptchd1 -/y and sex f, m, m, m, f, m, m, m from tissue CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L) at timepoints P14, P14, P14, P14, P14, P14, P14, P14
cx_p14_diet_seurat_RNA_assay.rds


title: GFHD105, untreated control

description: Library name: IF17


title: GFHD102, Fn and IFNg treated

description: Library name: IF16


title: ATAC counts of multiplex sSL0246 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0246_ATAC
sSL0246_ATAC_filtered_feature_bc_matrix.h5
sSL0246_ATAC_fragments.tsv.gz
sSL0246_ATAC_fragments.tsv.gz.tbi
sSL0246_ATAC_peak_annotation.tsv
sSL0246_ATAC_peaks.bed
cx_p14_diet_seurat_RNA_assay.rds


title: HTO counts of multiplex sSL0246 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0246_HTO
Samples GN3F/22/1913, GN3F/22/2112, GN3F/22/2381, GN3F/22/2356, GN21/7361, GN3F/22/1913, GN3F/22/2112, GN3F/22/2381, GN3F/22/2356, GN21/7361 with genotypes Kdm6b+/-, Kdm6b+/-, Usp7+/-, Usp7+/-, Ptchd1 -/y, Kdm6b+/-, Kdm6b+/-, Usp7+/-, Usp7+/-, Ptchd1 -/y and sex f, m, f, m, m, f, m, f, m, m from tissue CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L) at timepoints P14, P14, P14, P14, P14, P14, P14, P14, P14, P14
cx_p14_diet_seurat_RNA_assay.rds


title: GFHD102, IFNg treated

description: Library name: IF15


title: GEX counts of multiplex sSL0246 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0246_GEX
sSL0246_GEX_filtered_feature_bc_matrix.h5
sSL0246_GEX_QC_categories.csv
cx_p14_diet_seurat_RNA_assay.rds


title: GFHD102, Fn treated

description: Library name: IF14


title: HTO counts of multiplex sSL0245 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0245_HTO
Samples GN22/4746, GN22/4741, GN3F/22/2583, GN3F/22/2580, GN22/3924, GN22/4095, GN22/4746, GN22/4741, GN3F/22/2583, GN3F/22/2580, GN22/3924, GN22/4095 with genotypes Cul3+/-, Cul3+/-, Kmt5b+/-, Kmt5b+/-, Setd5+/-, Setd5+/-, Cul3+/-, Cul3+/-, Kmt5b+/-, Kmt5b+/-, Setd5+/-, Setd5+/- and sex m, f, f, m, m, m, m, f, f, m, m, m from tissue CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L) at timepoints P14, P14, P14, P14, P14, P14, P14, P14, P14, P14, P14, P14
cx_p14_diet_seurat_RNA_assay.rds


title: GFHD102, untreated control

description: Library name: IF13


title: GFHD101, Fn and IFNg treated

description: Library name: IF12


title: ATAC counts of multiplex sSL0245 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0245_ATAC
sSL0245_ATAC_filtered_feature_bc_matrix.h5
sSL0245_ATAC_fragments.tsv.gz
sSL0245_ATAC_fragments.tsv.gz.tbi
sSL0245_ATAC_peak_annotation.tsv
sSL0245_ATAC_peaks.bed
cx_p14_diet_seurat_RNA_assay.rds


title: GEX counts of multiplex sSL0245 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0245_GEX
sSL0245_GEX_filtered_feature_bc_matrix.h5
sSL0245_GEX_QC_categories.csv
cx_p14_diet_seurat_RNA_assay.rds


title: GEX counts of multiplex sSL0247 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0247_GEX
sSL0247_GEX_filtered_feature_bc_matrix.h5
sSL0247_GEX_QC_categories.csv
cx_p14_diet_seurat_RNA_assay.rds


title: GFHD101, Fn treated

description: Library name: IF10


title: GFHD101, IFNg treated

description: Library name: IF11


title: ATAC counts of multiplex sSL0247 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0247_ATAC
sSL0247_ATAC_filtered_feature_bc_matrix.h5
sSL0247_ATAC_fragments.tsv.gz
sSL0247_ATAC_fragments.tsv.gz.tbi
sSL0247_ATAC_peak_annotation.tsv
sSL0247_ATAC_peaks.bed
cx_p14_diet_seurat_RNA_assay.rds


title: HTO counts of multiplex sSL0247 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0247_HTO
Samples GN23/46, GN23/235, GN22/3F/2541, GN22/3F/2394, #LSMO428, GN23/46, GN23/235, GN22/3F/2541, GN22/3F/2394, #LSMO428 with genotypes Hnrnpu+/-, Hnrnpu+/-, Usp7+/-, Usp7+/-, C57BL6/J, Hnrnpu+/-, Hnrnpu+/-, Usp7+/-, Usp7+/-, C57BL6/J and sex f, m, f, m, m, f, m, f, m, m from tissue CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L) at timepoints P14, P14, P14, P14, P14, P14, P14, P14, P14, P14
cx_p14_diet_seurat_RNA_assay.rds


title: HTO counts of multiplex sSL0250 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0250_HTO
Samples GN23/262, GN23/264, GN3F/23/546, GN3F/23/103, GN23/262, GN23/264, GN3F/23/546, GN3F/23/103 with genotypes Hnrnpu+/-, Hnrnpu+/-, Trip12+/-, Trip12+/-, Hnrnpu+/-, Hnrnpu+/-, Trip12+/-, Trip12+/- and sex f, m, f, m, f, m, f, m from tissue CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L) at timepoints P14, P14, P14, P14, P14, P14, P14, P14
cx_p14_diet_seurat_RNA_assay.rds


title: ICRH135-Cyto (Cytokine) RNA

city: St Louis

first: Ricardo

last: D'Oliveira Albanus

state: MO

address: 4370 Duncan Avenue, Suite 6306D, Jeffrey T. Fort Neuroscience Bdg.

department: Neurology

institute: Washington University School of Medicine

description:
Library name: ICRH135-Cyto_RNA
10X Genomics Single Cell 3' v3 (scRNA-seq): R1 contains the 16 bp cell barcode and 12 bp UMI; R2 contains the cDNA transcript sequence; I1 contains the sample index.

data_processing:
snATAC-seq: reads were adapter-trimmed with cta (v0.12) and aligned to the hg19 reference genome with bwa mem (v0.7.15-r1140) using -I 200,200,5000.
snATAC-seq: cell barcodes were corrected against the 10X Genomics barcode whitelist allowing Hamming distance <= 2. Duplicate reads were marked with Picard MarkDuplicates (v2.8.1).
scRNA-seq: reads were processed with the Parker Lab snRNA-seq pipeline (https://github.com/porchard/snRNAseq-NextFlow) and aligned to hg19 + GENCODE v19 with STARsolo (STAR v2.5.4). Cell barcodes were corrected against the 10X allowlist.
scRNA-seq: QC was applied per barcode (>=1000 UMIs; non-empty by EmptyDrops at 1% FDR; mitochondrial-read fraction below per-library knee). Doublets were flagged with DoubletFinder (v2.0.2) and ambient RNA was controlled with DecontX (Celda v1.2.4) using two-pass clustering (delta1=10, delta2=20).
CVB4 quantification: scRNA-seq and snATAC-seq reads were re-aligned to a hybrid hg19+CVB4 (GenBank AF311939.1) reference to quantify CVB4 infection efficiency.
Assembly: hg19 (GRCh37); CVB4 reads aligned against a hybrid hg19+AF311939.1 reference
Supplementary files format and content: scRNA-seq: per-library Seurat objects (.rds) containing ambient-subtracted count matrices for autosomal, protein-coding genes, with QC metadata and cluster assignments. Available via Zenodo (DOI: 10.5281/zenodo.13362658).
Supplementary files format and content: snATAC-seq: per-library fragment files (.tsv.gz) and peak-by-barcode count matrices. Available via Zenodo (DOI: 10.5281/zenodo.13362658).  Intentionally left empty file to indicate insufficient data for peak calls for these cell types.

source_name: pancreatic islet

extract_protocol:
Human pancreatic islets were isolated in the Human Islet Core at the University of Pennsylvania following the requirements of the Clinical Islet Transplantation consortium procedure. Islets were grown in CIT culture medium in a humidified incubator with 5% CO2 at 37 C. For perturbation samples (HPAP059, ICRH134, ICRH135), islets were treated with cytokine cocktail or infected with CVB4, alongside a mock control. Single-cell suspensions and single-nucleus preparations were generated for scRNA-seq and snATAC-seq, respectively, following the 10X Genomics sample-preparation protocols.
scRNA-seq libraries were prepared using the 10X Chromium Single Cell 3' Library Kit (v3 chemistry). snATAC-seq libraries were prepared using the 10X Chromium Single Cell ATAC Library Kit (v1 chemistry). Libraries were sequenced on an Illumina NovaSeq 6000 at the Weill Cornell Medicine genomics resources core facility. The three HPAP059 snATAC-seq libraries were sequenced on an Illumina NovaSeq SP at Novogene.

value: pancreatic islet

value: Cytokine


title: ICRH135-CVB4 (CVB4) ATAC

description:
Library name: ICRH135-CVB4_ATAC
10X Genomics Single Cell ATAC v1 (snATAC-seq): R1 and R3 contain genomic DNA paired-end mates; R2 contains the 16 bp cell barcode; I1 contains the sample index.


title: GEX counts of multiplex sSL0250 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0250_GEX
sSL0250_GEX_filtered_feature_bc_matrix.h5
sSL0250_GEX_QC_categories.csv
cx_p14_diet_seurat_RNA_assay.rds


title: ICRH135-Cyto (Cytokine) ATAC

description:
Library name: ICRH135-Cyto_ATAC
10X Genomics Single Cell ATAC v1 (snATAC-seq): R1 and R3 contain genomic DNA paired-end mates; R2 contains the 16 bp cell barcode; I1 contains the sample index.


title: ICRH135-Mock (Baseline) RNA

description:
Library name: ICRH135-Mock_RNA
10X Genomics Single Cell 3' v3 (scRNA-seq): R1 contains the 16 bp cell barcode and 12 bp UMI; R2 contains the cDNA transcript sequence; I1 contains the sample index.

value: Baseline


title: ATAC counts of multiplex sSL0250 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0250_ATAC
sSL0250_ATAC_filtered_feature_bc_matrix.h5
sSL0250_ATAC_fragments.tsv.gz
sSL0250_ATAC_fragments.tsv.gz.tbi
sSL0250_ATAC_peak_annotation.tsv
sSL0250_ATAC_peaks.bed
cx_p14_diet_seurat_RNA_assay.rds


title: Subchondral bone from sham-operated wild-type C57BL/6 mouse, biological replicate 3

description: Library name: sham3

value: Tibial subchondral bone

value: wild-type

value: sham-operated


title: ICRH135-Mock (Baseline) ATAC

description:
Library name: ICRH135-Mock_ATAC
10X Genomics Single Cell ATAC v1 (snATAC-seq): R1 and R3 contain genomic DNA paired-end mates; R2 contains the 16 bp cell barcode; I1 contains the sample index.


title: Cauda epididymis, eproductive season, RNA-seq, rep3

description: Library name: R_CAUDA_RNA_3


title: GEX counts of multiplex sSL0215 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0215_GEX
sSL0215_GEX_filtered_feature_bc_matrix.h5
sSL0215_GEX_QC_categories.csv
cx_p14_diet_seurat_RNA_assay.rds


title: HTO counts of multiplex sSL0215 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0215_HTO
Samples GN/22/87, GN/21/6715, GN3F/22/2666, GN3F/22/2668, GN3F/22/2549, GN3F/22/2550, GN/22/87, GN/21/6715, GN3F/22/2666, GN3F/22/2668, GN3F/22/2549, GN3F/22/2550 with genotypes Bckdk-/-, Bckdk-/-, Ash1l+/-, Ash1l+/-, Wac+/-, Wac+/-, Bckdk-/-, Bckdk-/-, Ash1l+/-, Ash1l+/-, Wac+/-, Wac+/- and sex f, m, m, f, m, f, f, m, m, f, m, f from tissue CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L) at timepoints P14, P14, P14, P14, P14, P14, P14, P14, P14, P14, P14, P14
cx_p14_diet_seurat_RNA_assay.rds


title: ICRH134-CVB4 (CVB4) RNA

description:
Library name: ICRH134-CVB4_RNA
10X Genomics Single Cell 3' v3 (scRNA-seq): R1 contains the 16 bp cell barcode and 12 bp UMI; R2 contains the cDNA transcript sequence; I1 contains the sample index.


title: 10x lib 8, donor E6, healthy

city: Rehovot

first: Liran

last: Shlush

address: 234 Herzl Street

country: Israel

institute: Weizmann Institute of Science

description: Library name: 10x_lib_8_donor_E6_blood_sample_1

data_processing:
Count matrices were generated using 10x Genomics' Cell Ranger v6.1.2 (https://www.10xgenomics.com/support/software/cell-ranger/latest).
As each 10x scRNA library contained pooled cells of multiple individuals, both Vireo (https://github.com/single-cell-genetics/vireo) and Souporcell (https://github.com/wheaton5/souporcell) were used (on each 10x library separately) to cluster cells based on SNPs found in the sequenced RNA. Cells that were identified as doublets by Vireo or Souporcell were discarded.
As part of additional doublet detection, A metacell model was constructed using Metacell with a target metacell size of 50 cells, including cells previously identified as doublets. Metacells containing at least threefold more doublet-marked cells than expected from the overall doublet rate were classified as doublet-enriched. All cells that belonged to a doublet metacell were then marked as doublets. We also identified doublet metacells based on the expression of marker genes of two cell states
We filtered out cells with at least 15% mitochondrial and MALAT1 expression, then removed mitochondrial and ribosomal genes and further filtered cells with ≤500 UMIs.
Assembly: GRCh38-3.0.0
Supplementary files format and content: h5ad file (https://anndata.readthedocs.io/en/stable/) containing count matrix and cell metadata.

source_name: peripheral blood

growth_protocol: CD34⁺ hematopoietic stem and progenitor cells (HSPCs) were isolated from peripheral blood of healthy adult donors by magnetic enrichment. Cells were pre-stimulated overnight in StemSpan SFEM II medium supplemented with SCF, FLT3L, TPO, IL-3, SR1, and UM729 before being transduced with a CellTaggin lentiviral library. Following lentiviral barcoding, GFP⁺ transduced cells were single-cell sorted into 384-well plates and cultured in StemSpan SFEM II supplemented with defined cytokine combinations. Cells were maintained at 37°C and 5% CO₂ and sampled longitudinally at 2–3 time points during differentiation.

extract_protocol:
At each sampling time point, half of the cells from each culture well cells were harvested and pooled for single-cell RNA sequencing. Cell suspensions were washed and processed immediately for Chromium Single Cell 3′ library preparation according to the manufacturer's instructions. For final time points, a fraction of cells was additionally collected for genomic DNA extraction and CellTag barcode recovery.
Single-cell RNA-seq libraries were generated using the Chromium Single Cell 3′ Reagent Kit v3.1 (10x Genomics). 10,000 - 20,000 cells were loaded for GEM generation. Following reverse transcription, cDNA amplification, and library construction according to the manufacturer's protocol, libraries were sequenced on an Illumina NovaSeq 6000 platform. Transcriptomic libraries captured both cellular mRNA and expressed CellTag barcode sequences.

treatment_protocol: CD34⁺ cells were transduced with the CellTag-V1 lentiviral barcode library on retronectin-coated plates in the presence of LentiBoost and protamine sulfate. After transduction, single GFP⁺ cells were sorted and cultured under distinct cytokine stimulation conditions designed to promote different myeloid differentiation trajectories. Cytokine compositions varied between experimental conditions as described in Supplementary Table S3.

value: peripheral blood

tag: Sex

value: male

value: immune cells

tag: age

tag: disease state

value: healthy


title: Puck_240108_16

city: New Haven

first: Hattie

last: Chung

state: CT

address: 300 George St

institute: Yale University

description: Library name: 2024-02-12_Puck_240108_16

data_processing:
Raw sequencing data were processed using the Slide-seq pipeline following Stickels et al. Nat Biotech 2021.
Assembly: mm10
Supplementary files format and content: [puck_name].h5ad: processed raw counts of beads (rows) and genes (columns)
Library strategy: Spatial Transcriptomics

source_name: Ovary

growth_protocol: Female C57BL/6 mice were maintained under SPF conditions on a 12-hour light-dark cycle with standard chow and water provided ad libitum.

extract_protocol:
10µm frozen sections were cut on the cryostat
Spatial transcriptome libraries were prepared using the Slide-seq V2 protocol

treatment_protocol: Mice were staged near-daily for their estrous cycle and harvested at the estrus or metestrus stage via intracardial perfusion with PBS. Ovaries were fresh frozen embedded in OCT.

value: Ovary

tag: Stage

value: Estrus

tag: group

value: Old


title: Healthy human donor (1), CAR T cells, JUN-FOS-BATF, RNA

city: Stanford

first: Oliver

last: Takacsi-Nagy

state: CA

address: 234 Pasteur Dr. (BMI 4600)

department: Pathology

institute: Stanford University School of Medicine

description:
Library name: Acute_1A-JUN-FOS-BATF_RNA
Column name in both processed data files: 'Acute_1A'

data_processing:
Basecalls were performed using bcl-convert Version 4.4.6 from Illumina
Reads were pre-processed and pseudoaligned for transcript quantification using Salmon (v1.5.2) and the nf-core/rnaseq pipeline (v3.5) with default parameters.
DESeq2 (v1.50.2) was used to variance-stabilize (normalized) Salmon quantifications (raw).
Assembly: hg38
Supplementary files format and content: Two csv files, one for raw counts and one for normalized (DESeq VST) counts; column names correspond to Samples in both.

source_name: Primary Human T Cell

growth_protocol: Primary human T cells were negatively selected from PBMCs isolated from leukoreduction chambers from three healthy blood donors and activated by CD3/28 agonism in X-VIVO 15 supplemented with 5% FBS and 50 IU/mL recombinant human IL-2. 48 hours post-activation, T cells were electroporated with Cas9 ribonucleoprotein and a plasmid homology-directed repair template to enable integration of a multicistronic cassette encoding tNGFR, CD19-28z and variable natural and engineered FLAG-tagged AP-1 transcription factors within the continuous reading frame of the TRAC locus. Pre- and post-editing cells were maintained at 0.5-1e6/ml. Six days post-editing, CAR T cells were challenged with CD19-expressing Nalm6 targets (leukemia cell line, 1:8 Effector:Target ratio, 72-hour co-culture).

extract_protocol:
2e5-5e5 live CAR T cells (tNGFR+) were enriched magnetically and RNA was isolated using Qiagen RNeasy Micro or Mini Kits, including DNase treatment.
25-100ng of RNA based on Qubit quantification (Thermo Fisher) was inputted into the Illumina Stranded mRNA Prep workflow and resultant libraries were quantified by Qubit and size-verified on an Agilent TapeStation. Sequencing was performed on a NovaSeq X (Illumina) with the following read structure: 151 bp Read 1, 12 bp i7 Index, 24 bp i5 Index, 151 bp Read 2.

treatment_protocol: All T cells in this sample were treated the same, the only difference between the T cells is which healthy human donor they were isolated from and which transcription factor they were edited to express.

value: Primary Human T Cell

tag: individual

value: Healthy Donor 1

tag: tf expressed

value: JUN-FOS-BATF


title: ATAC counts of multiplex sSL0215 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0215_ATAC
sSL0215_ATAC_filtered_feature_bc_matrix.h5
sSL0215_ATAC_fragments.tsv.gz
sSL0215_ATAC_fragments.tsv.gz.tbi
sSL0215_ATAC_peak_annotation.tsv
sSL0215_ATAC_peaks.bed
cx_p14_diet_seurat_RNA_assay.rds

tag: tissue

value: Cortex

value: mixed

value: mixed samples (multiplex)


title: Puck_230807_04

description: Library name: 2024-02-13_Puck_230807_04

tag: genotype

value: Young


title: Healthy human donor (3), CAR T cells, JUN+FOS, RNA

description:
Library name: Chronic_HA_3G-JUN+FOS_RNA
Column name in both processed data files: Donor3_JUN+FOS

data_processing:
Basecalls were performed using bcl-convert Version 4.3.6 from Illumina and samples demultiplexed using Fulcrum Genomics fqtk v0.3.1.
Reads were pre-processed and pseudoaligned for transcript quantification using Salmon (v1.5.2) and the nf-core/rnaseq pipeline (v3.5) with default parameters.
DESeq2 (v1.50.2) was used to variance-stabilize (normalized) Salmon quantifications (raw).
Assembly: hg38
Supplementary files format and content: Two csv files, one for raw counts and one for normalized (DESeq VST) counts; column names correspond to Samples in both.

growth_protocol: Primary human T cells were negatively selected from PBMCs isolated from leukoreduction chambers from three healthy blood donors and activated by CD3/28 agonism in X-VIVO 15 supplemented with 5% FBS and 50 IU/mL recombinant human IL-2. 48 hours post-activation, T cells were electroporated with Cas9 ribonucleoprotein and a plasmid homology-directed repair template to enable integration of a multicistronic cassette encoding tNGFR, CD19-28z and variable natural and engineered FLAG-tagged AP-1 transcription factors within the continuous reading frame of the TRAC locus. Pre- and post-editing cells were maintained at 0.5-1e6/ml. Six days post-editing, CAR T cells were challenged with GD2-expressing Nalm6 targets for two days and then challenged a second time for three days (engineered leukemia cell line, 1:4 Effector:Target ratio).

extract_protocol:
2e5-5e5 live CAR T cells (tNGFR+) were enriched magnetically and preserved in Zymo DNA/RNA shield. RNA extraction was performed by Plasmidsaurus.
Performed by Plasmidsaurus. The general workflow consisted of: reverse transcription, second strand synthesis, tagmentation, indexing and amplification.

value: Healthy Donor 3

value: JUN+FOS


title: ICRH134-CVB4 (CVB4) ATAC

description:
Library name: ICRH134-CVB4_ATAC
10X Genomics Single Cell ATAC v1 (snATAC-seq): R1 and R3 contain genomic DNA paired-end mates; R2 contains the 16 bp cell barcode; I1 contains the sample index.

value: pancreatic islet

tag: treatment


title: GEX counts of multiplex sSL0196 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0196_GEX
sSL0196_GEX_filtered_feature_bc_matrix.h5
sSL0196_GEX_QC_categories.csv
cx_p14_diet_seurat_RNA_assay.rds


title: ATAC counts of multiplex sSL0196 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0196_ATAC
sSL0196_ATAC_filtered_feature_bc_matrix.h5
sSL0196_ATAC_fragments.tsv.gz
sSL0196_ATAC_fragments.tsv.gz.tbi
sSL0196_ATAC_peak_annotation.tsv
sSL0196_ATAC_peaks.bed
cx_p14_diet_seurat_RNA_assay.rds


title: ICRH134-Cyto (Cytokine) RNA

description:
Library name: ICRH134-Cyto_RNA
10X Genomics Single Cell 3' v3 (scRNA-seq): R1 contains the 16 bp cell barcode and 12 bp UMI; R2 contains the cDNA transcript sequence; I1 contains the sample index.

value: Cytokine


title: ICRH134-Cyto (Cytokine) ATAC

description:
Library name: ICRH134-Cyto_ATAC
10X Genomics Single Cell ATAC v1 (snATAC-seq): R1 and R3 contain genomic DNA paired-end mates; R2 contains the 16 bp cell barcode; I1 contains the sample index.


title: ICRH135-CVB4 (CVB4) RNA

description:
Library name: ICRH135-CVB4_RNA
10X Genomics Single Cell 3' v3 (scRNA-seq): R1 contains the 16 bp cell barcode and 12 bp UMI; R2 contains the cDNA transcript sequence; I1 contains the sample index.


title: HTO counts of multiplex sSL0196 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0196_HTO
Samples 323380, 21/6706, 22/3417, 22/3923, 323380, 21/6706, 22/3417, 22/3923 with genotypes C57BL6/J, Bckdk-/-, Ptchd1 -/y, Setd5+/-, C57BL6/J, Bckdk-/-, Ptchd1 -/y, Setd5+/- and sex f, f, m, m, f, f, m, m from tissue CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L) at timepoints P14, P14, P14, P14, P14, P14, P14, P14
cx_p14_diet_seurat_RNA_assay.rds


title: ICRH134-Mock (Baseline) RNA

description:
Library name: ICRH134-Mock_RNA
10X Genomics Single Cell 3' v3 (scRNA-seq): R1 contains the 16 bp cell barcode and 12 bp UMI; R2 contains the cDNA transcript sequence; I1 contains the sample index.

value: Baseline


title: HTO counts of multiplex sSL0211 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0211_HTO
Samples GN3F/22/1690, GN3F/22/1691, GN3F/22/2454, GN3F/22/2133, GN22/4463, GN22/4477, GN3F/22/1690, GN3F/22/1691, GN3F/22/2454, GN3F/22/2133, GN22/4463, GN22/4477 with genotypes Wac+/-, Wac+/-, Kdm6b+/-, Kdm6b+/-, Setd5+/-, Setd5+/-, Wac+/-, Wac+/-, Kdm6b+/-, Kdm6b+/-, Setd5+/-, Setd5+/- and sex m, f, m, f, m, f, m, f, m, f, m, f from tissue CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L) at timepoints P14, P14, P14, P14, P14, P14, P14, P14, P14, P14, P14, P14
cx_p14_diet_seurat_RNA_assay.rds


title: HPAP059-Cyto (Cytokine) RNA

description:
Library name: HPAP059-Cyto_RNA
10X Genomics Single Cell 3' v3 (scRNA-seq): R1 contains the 16 bp cell barcode and 12 bp UMI; R2 contains the cDNA transcript sequence; I1 contains the sample index.


title: ATAC counts of multiplex sSL0211 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0211_ATAC
sSL0211_ATAC_filtered_feature_bc_matrix.h5
sSL0211_ATAC_fragments.tsv.gz
sSL0211_ATAC_fragments.tsv.gz.tbi
sSL0211_ATAC_peak_annotation.tsv
sSL0211_ATAC_peaks.bed
cx_p14_diet_seurat_RNA_assay.rds


title: GEX counts of multiplex sSL0211 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0211_GEX
sSL0211_GEX_filtered_feature_bc_matrix.h5
sSL0211_GEX_QC_categories.csv
cx_p14_diet_seurat_RNA_assay.rds


title: HPAP059-Cyto (Cytokine) ATAC

description:
Library name: HPAP059-Cyto_ATAC
10X Genomics Single Cell ATAC v1 (snATAC-seq): R1 and R3 contain genomic DNA paired-end mates; R2 contains the 16 bp cell barcode; I1 contains the sample index.


title: ICRH134-Mock (Baseline) ATAC

description:
Library name: ICRH134-Mock_ATAC
10X Genomics Single Cell ATAC v1 (snATAC-seq): R1 and R3 contain genomic DNA paired-end mates; R2 contains the 16 bp cell barcode; I1 contains the sample index.


title: HPAP059-CVB4 (CVB4) ATAC

description:
Library name: HPAP059-CVB4_ATAC
10X Genomics Single Cell ATAC v1 (snATAC-seq): R1 and R3 contain genomic DNA paired-end mates; R2 contains the 16 bp cell barcode; I1 contains the sample index.


title: HTO counts of multiplex sSL0214 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0214_HTO
Samples LSMO429, 323378, GN3F/22/2015, GN3F/22/2017, GN3F/22/2391, GN3F/22/2392, LSMO429, 323378, GN3F/22/2015, GN3F/22/2017, GN3F/22/2391, GN3F/22/2392 with genotypes C57BL6/J, C57BL6/J, Wac+/-, Wac+/-, Kmt5b+/-, Kmt5b+/-, C57BL6/J, C57BL6/J, Wac+/-, Wac+/-, Kmt5b+/-, Kmt5b+/- and sex f, m, m, f, m, f, f, m, m, f, m, f from tissue CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L) at timepoints P14, P14, P14, P14, P14, P14, P14, P14, P14, P14, P14, P14
cx_p14_diet_seurat_RNA_assay.rds


title: HPAP059-Mock (Baseline) RNA

description:
Library name: HPAP059-Mock_RNA
10X Genomics Single Cell 3' v3 (scRNA-seq): R1 contains the 16 bp cell barcode and 12 bp UMI; R2 contains the cDNA transcript sequence; I1 contains the sample index.


title: HPAP059-CVB4 (CVB4) RNA

description:
Library name: HPAP059-CVB4_RNA
10X Genomics Single Cell 3' v3 (scRNA-seq): R1 contains the 16 bp cell barcode and 12 bp UMI; R2 contains the cDNA transcript sequence; I1 contains the sample index.


title: GEX counts of multiplex sSL0214 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0214_GEX
sSL0214_GEX_filtered_feature_bc_matrix.h5
sSL0214_GEX_QC_categories.csv
cx_p14_diet_seurat_RNA_assay.rds


title: ATAC counts of multiplex sSL0214 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0214_ATAC
sSL0214_ATAC_filtered_feature_bc_matrix.h5
sSL0214_ATAC_fragments.tsv.gz
sSL0214_ATAC_fragments.tsv.gz.tbi
sSL0214_ATAC_peak_annotation.tsv
sSL0214_ATAC_peaks.bed
cx_p14_diet_seurat_RNA_assay.rds


title: HPAP059-Mock (Baseline) ATAC

description:
Library name: HPAP059-Mock_ATAC
10X Genomics Single Cell ATAC v1 (snATAC-seq): R1 and R3 contain genomic DNA paired-end mates; R2 contains the 16 bp cell barcode; I1 contains the sample index.


title: Tibialis anterior mdx Rep1

description: Library name: MDX1

value: Tibialis anterior

value: mdx


title: HTO counts of multiplex sSL0195 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0195_HTO
Samples 326647, 323298, 21/6714, 22/4092, 326647, 323298, 21/6714, 22/4092 with genotypes C57BL6/J, C57BL6/J, Bckdk-/-, Setd5+/-, C57BL6/J, C57BL6/J, Bckdk-/-, Setd5+/- and sex f, m, m, f, f, m, m, f from tissue CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L) at timepoints P14, P14, P14, P14, P14, P14, P14, P14
cx_p14_diet_seurat_RNA_assay.rds


title: ATAC counts of multiplex sSL0195 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0195_ATAC
sSL0195_ATAC_filtered_feature_bc_matrix.h5
sSL0195_ATAC_fragments.tsv.gz
sSL0195_ATAC_fragments.tsv.gz.tbi
sSL0195_ATAC_peak_annotation.tsv
sSL0195_ATAC_peaks.bed
cx_p14_diet_seurat_RNA_assay.rds


title: ICRH122 (Baseline) ATAC

description:
Library name: ICRH122_ATAC
10X Genomics Single Cell ATAC v1 (snATAC-seq): R1 and R3 contain genomic DNA paired-end mates; R2 contains the 16 bp cell barcode; I1 contains the sample index.


title: GEX counts of multiplex sSL0195 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0195_GEX
sSL0195_GEX_filtered_feature_bc_matrix.h5
sSL0195_GEX_QC_categories.csv
cx_p14_diet_seurat_RNA_assay.rds


title: ICRH122 (Baseline) RNA

description:
Library name: ICRH122_RNA
10X Genomics Single Cell 3' v3 (scRNA-seq): R1 contains the 16 bp cell barcode and 12 bp UMI; R2 contains the cDNA transcript sequence; I1 contains the sample index.


title: HTO counts of multiplex sSL0248 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0248_HTO
Samples GN3F/22/2792, GN3F/22/2926, GN22/5768, GN22/5131, GN23/545, GN3F/22/2591, GN3F/22/2792, GN3F/22/2926, GN22/5768, GN22/5131, GN23/545, GN3F/22/2591 with genotypes Ash1l+/-, Ash1l+/-, Bckdk-/-, Bckdk-/-, Trip12+/-, Trip12+/-, Ash1l+/-, Ash1l+/-, Bckdk-/-, Bckdk-/-, Trip12+/-, Trip12+/- and sex f, m, f, m, f, m, f, m, f, m, f, m from tissue CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L) at timepoints P14, P14, P14, P14, P14, P14, P14, P14, P14, P14, P14, P14
cx_p14_diet_seurat_RNA_assay.rds


title: HPAP044 (Baseline) RNA

description:
Library name: HPAP044_RNA
10X Genomics Single Cell 3' v3 (scRNA-seq): R1 contains the 16 bp cell barcode and 12 bp UMI; R2 contains the cDNA transcript sequence; I1 contains the sample index.


title: GEX counts of multiplex sSL0248 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0248_GEX
sSL0248_GEX_filtered_feature_bc_matrix.h5
sSL0248_GEX_QC_categories.csv
cx_p14_diet_seurat_RNA_assay.rds


title: HPAP044 (Baseline) ATAC

description:
Library name: HPAP044_ATAC
10X Genomics Single Cell ATAC v1 (snATAC-seq): R1 and R3 contain genomic DNA paired-end mates; R2 contains the 16 bp cell barcode; I1 contains the sample index.


title: HPAP040 (Baseline) RNA

description:
Library name: HPAP040_RNA
10X Genomics Single Cell 3' v3 (scRNA-seq): R1 contains the 16 bp cell barcode and 12 bp UMI; R2 contains the cDNA transcript sequence; I1 contains the sample index.


title: ATAC counts of multiplex sSL0248 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0248_ATAC
sSL0248_ATAC_filtered_feature_bc_matrix.h5
sSL0248_ATAC_fragments.tsv.gz
sSL0248_ATAC_fragments.tsv.gz.tbi
sSL0248_ATAC_peak_annotation.tsv
sSL0248_ATAC_peaks.bed
cx_p14_diet_seurat_RNA_assay.rds


title: HTO counts of multiplex sSL0213 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0213_HTO
Samples GN22/3960, GN22/3966, GN3F/22/2484, GN3F/22/2449, GN22/3F/2370, GN22/3F/2371, GN22/3960, GN22/3966, GN3F/22/2484, GN3F/22/2449, GN22/3F/2370, GN22/3F/2371 with genotypes Cul3+/-, Cul3+/-, Kdm6b+/-, Kdm6b+/-, Kmt5b+/-, Kmt5b+/-, Cul3+/-, Cul3+/-, Kdm6b+/-, Kdm6b+/-, Kmt5b+/-, Kmt5b+/- and sex m, f, m, f, m, f, m, f, m, f, m, f from tissue CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L) at timepoints P14, P14, P14, P14, P14, P14, P14, P14, P14, P14, P14, P14
cx_p14_diet_seurat_RNA_assay.rds


title: ATAC counts of multiplex sSL0213 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0213_ATAC
sSL0213_ATAC_filtered_feature_bc_matrix.h5
sSL0213_ATAC_fragments.tsv.gz
sSL0213_ATAC_fragments.tsv.gz.tbi
sSL0213_ATAC_peak_annotation.tsv
sSL0213_ATAC_peaks.bed
cx_p14_diet_seurat_RNA_assay.rds


title: HPAP040 (Baseline) ATAC

description:
Library name: HPAP040_ATAC
10X Genomics Single Cell ATAC v1 (snATAC-seq): R1 and R3 contain genomic DNA paired-end mates; R2 contains the 16 bp cell barcode; I1 contains the sample index.


title: GEX counts of multiplex sSL0213 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0213_GEX
sSL0213_GEX_filtered_feature_bc_matrix.h5
sSL0213_GEX_QC_categories.csv
cx_p14_diet_seurat_RNA_assay.rds


title: HPAP036 (Baseline) RNA

description:
Library name: HPAP036_RNA
10X Genomics Single Cell 3' v3 (scRNA-seq): R1 contains the 16 bp cell barcode and 12 bp UMI; R2 contains the cDNA transcript sequence; I1 contains the sample index.


title: HPAP039 (Baseline) ATAC

description:
Library name: HPAP039_ATAC
10X Genomics Single Cell ATAC v1 (snATAC-seq): R1 and R3 contain genomic DNA paired-end mates; R2 contains the 16 bp cell barcode; I1 contains the sample index.


title: HPAP039 (Baseline) RNA

description:
Library name: HPAP039_RNA
10X Genomics Single Cell 3' v3 (scRNA-seq): R1 contains the 16 bp cell barcode and 12 bp UMI; R2 contains the cDNA transcript sequence; I1 contains the sample index.


title: HPAP036 (Baseline) ATAC

description:
Library name: HPAP036_ATAC
10X Genomics Single Cell ATAC v1 (snATAC-seq): R1 and R3 contain genomic DNA paired-end mates; R2 contains the 16 bp cell barcode; I1 contains the sample index.


title: GEX counts of multiplex sSL0255 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0255_GEX
sSL0255_GEX_filtered_feature_bc_matrix.h5
sSL0255_GEX_QC_categories.csv
cx_p14_diet_seurat_RNA_assay.rds


title: ATAC counts of multiplex sSL0255 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0255_ATAC
sSL0255_ATAC_filtered_feature_bc_matrix.h5
sSL0255_ATAC_fragments.tsv.gz
sSL0255_ATAC_fragments.tsv.gz.tbi
sSL0255_ATAC_peak_annotation.tsv
sSL0255_ATAC_peaks.bed
cx_p14_diet_seurat_RNA_assay.rds


title: GEX counts of multiplex sSL0239 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0239_GEX
sSL0239_GEX_filtered_feature_bc_matrix.h5
sSL0239_GEX_QC_categories.csv
cx_p4_diet_seurat_RNA_assay.rds


title: HTO counts of multiplex sSL0255 containing tissue & timepoint(s) CTX (L); P14

description:
Library name: sSL0255_HTO
Samples #22/2927, #22/2787, #23/1378, #LSMO430, #23/779, #22/4529, #22/2927, #22/2787, #23/1378, #LSMO430, #23/779, #22/4529 with genotypes Ash1l+/-, Ash1l+/-, Cul3+/-, C57BL6/J, Trip12+/-, Cul3+/-, Ash1l+/-, Ash1l+/-, Cul3+/-, C57BL6/J, Trip12+/-, Cul3+/- and sex f, m, m, f, f, f, f, m, m, f, f, f from tissue CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L) at timepoints P14, P14, P14, P14, P14, P14, P14, P14, P14, P14, P14, P14
cx_p14_diet_seurat_RNA_assay.rds


title: zxq005_v

city: Huzhou

first: Yan

last: qiang

address: No. 1558, North Third Ring Road, Wuxing District, Huzhou City.

institute: huzhou central hospital

description:
Library name: zxq005_v
Fresh frozen Spatial transcriptome sequencing

data_processing:
Raw sequencing data were demultiplexed and converted to FASTQ format using Illumina bcl2fastq (version 2.20). We used the 10× Genomics official analysis software Cell Ranger (version 3.1.0) to perform quality control on the raw sequencing data of each sample and to align reads to the reference genome (GRCh38). The Cell Ranger output was loaded into Seurat (version 3.1.1) for dimensionality reduction, clustering, and analysis of scRNA-seq data. Quality control thresholds were set based on standard practices in scRNA‑seq analysis. Cells with fewer than 500 detected genes were excluded as they likely represent empty droplets or damaged cells. Cells with more than 5,000 detected genes were considered potential doublets or multiplets and were also removed. The mitochondrial gene expression threshold was set at <25%, as a high percentage of mitochondrial reads is a common indicator of cell stress or compromised membrane integrity.
ST was performed on five FFPE PDAC sections using the 10× Genomics Visium Spatial platform. Raw sequencing data were processed with Space Ranger (version 1.1). Gene point matrices generated after processing data from ST and Visium samples were analyzed using the Seurat software package (version 3.1.1). Genes with a minimum number of detected genes of 200 were screened, and genes with fewer than 10 readings or expression below 3 points were removed. The different spots were normalized using the LogVMR function. After dimensionality reduction and clustering, the SpatialFeaturePlot function in Seurat (version 1.1.1) was used to generate spatial feature expression maps.
Assembly: GRCh38
Supplementary files format and content: processed data.tar.gz
Library strategy: Spatial Transcriptomics

source_name: Human pancreatic tumor tissue

extract_protocol:
Fresh PDAC tissues were placed in sterile RNase‑free dishes containing ice‑cold calcium‑ and magnesium‑free 1× PBS. Tissues were minced into approximately 0.5 mm² pieces, washed with PBS, and carefully dissected to remove blood clots and adipose tissue. Dissociation was performed in enzyme solution at 37°C with shaking at 100 rpm for 20 min. Digestion was stopped by adding 1× PBS supplemented with 10% fetal bovine serum, followed by gentle pipetting 5–10 times. The suspension was passed through a 70 μm cell strainer and centrifuged at 300×g for 5 min at 4°C. The cell pellet was resuspended in 100 μL of 1× PBS containing 0.04% BSA, mixed with 1 mL of 1× red blood cell lysis buffer, and incubated at room temperature or on ice for 2–10 min to eliminate erythrocytes. After centrifugation (300×g, 5 min, room temperature), dead cells were removed using the Miltenyi Dead Cell Removal Kit according to the manufacturer’s instructions. The resulting single‑cell suspension was washed twice with 1× PBS/0.04% BSA, resuspended in 50 μL of the same buffer, and assessed for viability by trypan blue exclusion. Only suspensions with >85% viability were used; cell counts were determined using a Countess II Automated Cell Counter, and concentrations were adjusted to 700–1200 cells/μL.
Single‑cell suspensions were loaded onto the 10× Genomics Chromium platform to generate gel beads in emulsion using the Chromium Single‑Cell 3′Reagent Kit (v3) following the manufacturer’s protocol. Subsequent cDNA amplification and library construction were performed according to standard procedures. Libraries were sequenced on an Illumina NovaSeq 6000 system with paired‑end 150 bp reads, targeting a minimum depth of 20,000 reads per cell. Sequencing was carried out by LC‑Bio Technology Co., Ltd. (Hangzhou, China).

value: Human pancreatic tumor tissue


title: ATAC counts of multiplex sSL0239 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0239_ATAC
sSL0239_ATAC_filtered_feature_bc_matrix.h5
sSL0239_ATAC_fragments.tsv.gz
sSL0239_ATAC_fragments.tsv.gz.tbi
sSL0239_ATAC_peak_annotation.tsv
sSL0239_ATAC_peaks.bed
cx_p4_diet_seurat_RNA_assay.rds


title: lsy004_v

description:
Library name: lsy004_v
Fresh frozen Spatial transcriptome sequencing


title: Healthy human donor (3), CAR T cells, FOS+BATF, RNA

description:
Library name: Chronic_HA_3B-FOS+BATF_RNA
Column name in both processed data files: Donor3_FOS+BATF

value: FOS+BATF


title: cgq003_v

description:
Library name: cgq003_v
Fresh frozen Spatial transcriptome sequencing


title: xlc002_v

description:
Library name: xlc002_v
Fresh frozen Spatial transcriptome sequencing


title: ATAC counts of multiplex sSL0227 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0227_ATAC
sSL0227_ATAC_filtered_feature_bc_matrix.h5
sSL0227_ATAC_fragments.tsv.gz
sSL0227_ATAC_fragments.tsv.gz.tbi
sSL0227_ATAC_peak_annotation.tsv
sSL0227_ATAC_peaks.bed
cx_p4_diet_seurat_RNA_assay.rds


title: HTO counts of multiplex sSL0239 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0239_HTO
Samples GN22/4291, GN22/3951, GN3F/22/2158, GN3F/22/2160, GN22/4909, GN22/4188, GN22/4291, GN22/3951, GN3F/22/2158, GN3F/22/2160, GN22/4909, GN22/4188 with genotypes Cul3+/-, Cul3+/-, Wac+/-, Wac+/-, Setd5+/-, Setd5+/-, Cul3+/-, Cul3+/-, Wac+/-, Wac+/-, Setd5+/-, Setd5+/- and sex f, m, m, f, f, m, f, m, m, f, f, m from tissue CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L) at timepoints P4, P4, P4, P4, P4, P4, P4, P4, P4, P4, P4, P4
cx_p4_diet_seurat_RNA_assay.rds


title: wbq001_v

description:
Library name: wbq001_v
Fresh frozen Spatial transcriptome sequencing


title: HTO counts of multiplex sSL0227 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0227_HTO
Samples GN3F/22/2605, GN3F/22/2758, GN22/4794, GN22/4298, GN22/4701, GN3F/22/2605, GN3F/22/2758, GN22/4794, GN22/4298, GN22/4701 with genotypes Ash1l+/-, Ash1l+/-, Cul3+/-, Cul3+/-, Ptchd1 -/y, Ash1l+/-, Ash1l+/-, Cul3+/-, Cul3+/-, Ptchd1 -/y and sex m, f, f, m, m, m, f, f, m, m from tissue CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L) at timepoints P4, P4, P4, P4, P4, P4, P4, P4, P4, P4
cx_p4_diet_seurat_RNA_assay.rds


title: zxq005_p

description:
Library name: zxq005_p
10x Genomics

data_processing:
Raw sequencing data were demultiplexed and converted to FASTQ format using Illumina bcl2fastq (version 2.20). We used the 10× Genomics official analysis software Cell Ranger (version 3.1.0) to perform quality control on the raw sequencing data of each sample and to align reads to the reference genome (GRCh38). The Cell Ranger output was loaded into Seurat (version 3.1.1) for dimensionality reduction, clustering, and analysis of scRNA-seq data. Quality control thresholds were set based on standard practices in scRNA‑seq analysis. Cells with fewer than 500 detected genes were excluded as they likely represent empty droplets or damaged cells. Cells with more than 5,000 detected genes were considered potential doublets or multiplets and were also removed. The mitochondrial gene expression threshold was set at <25%, as a high percentage of mitochondrial reads is a common indicator of cell stress or compromised membrane integrity.
ST was performed on five FFPE PDAC sections using the 10× Genomics Visium Spatial platform. Raw sequencing data were processed with Space Ranger (version 1.1). Gene point matrices generated after processing data from ST and Visium samples were analyzed using the Seurat software package (version 3.1.1). Genes with a minimum number of detected genes of 200 were screened, and genes with fewer than 10 readings or expression below 3 points were removed. The different spots were normalized using the LogVMR function. After dimensionality reduction and clustering, the SpatialFeaturePlot function in Seurat (version 1.1.1) was used to generate spatial feature expression maps.
Assembly: GRCh38
Supplementary files format and content: processed data.tar.gz

source_name: PBMC

value: PBMC


title: GEX counts of multiplex sSL0227 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0227_GEX
sSL0227_GEX_filtered_feature_bc_matrix.h5
sSL0227_GEX_QC_categories.csv
cx_p4_diet_seurat_RNA_assay.rds


title: lsy004_p

description:
Library name: lsy004_p
10x Genomics


title: HTO counts of multiplex sSL0229 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0229_HTO
Samples GN3F/22/2852, GN3F/22/2390, GN3F/22/2840, GN3F/22/2965, GN22/5558, GN3F/22/2852, GN3F/22/2390, GN3F/22/2840, GN3F/22/2965, GN22/5558 with genotypes Wac+/-, Wac+/-, Kdm6b+/-, Kdm6b+/-, Ptchd1 -/y, Wac+/-, Wac+/-, Kdm6b+/-, Kdm6b+/-, Ptchd1 -/y and sex m, f, f, m, m, m, f, f, m, m from tissue CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L) at timepoints P4, P4, P4, P4, P4, P4, P4, P4, P4, P4
cx_p4_diet_seurat_RNA_assay.rds


title: GEX counts of multiplex sSL0229 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0229_GEX
sSL0229_GEX_filtered_feature_bc_matrix.h5
sSL0229_GEX_QC_categories.csv
cx_p4_diet_seurat_RNA_assay.rds


title: xlc002_p

description:
Library name: xlc002_p
10x Genomics


title: ATAC counts of multiplex sSL0229 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0229_ATAC
sSL0229_ATAC_filtered_feature_bc_matrix.h5
sSL0229_ATAC_fragments.tsv.gz
sSL0229_ATAC_fragments.tsv.gz.tbi
sSL0229_ATAC_peak_annotation.tsv
sSL0229_ATAC_peaks.bed
cx_p4_diet_seurat_RNA_assay.rds


title: wbq001_p

description:
Library name: wbq001_p
10x Genomics


title: HTO counts of multiplex sSL0238 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0238_HTO
Samples GN22/4096, GN22/4097, GN3F/22/3099, GN3F/22/3104, GN22/3F/2474, GN22/3F/2476, GN22/4096, GN22/4097, GN3F/22/3099, GN3F/22/3104, GN22/3F/2474, GN22/3F/2476 with genotypes Setd5+/-, Setd5+/-, Usp7+/-, Usp7+/-, Kmt5b+/-, Kmt5b+/-, Setd5+/-, Setd5+/-, Usp7+/-, Usp7+/-, Kmt5b+/-, Kmt5b+/- and sex f, m, m, f, m, f, f, m, m, f, m, f from tissue CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L) at timepoints P4, P4, P4, P4, P4, P4, P4, P4, P4, P4, P4, P4
cx_p4_diet_seurat_RNA_assay.rds


title: GEX counts of multiplex sSL0238 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0238_GEX
sSL0238_GEX_filtered_feature_bc_matrix.h5
sSL0238_GEX_QC_categories.csv
cx_p4_diet_seurat_RNA_assay.rds


title: zxq005-t

description:
Library name: zxq005-t
10x Genomics

source_name: pancreatic tumor tissue

value: pancreatic tumor tissue


title: cgq003_p

description:
Library name: cgq003_p
10x Genomics


title: lsy004-t

description:
Library name: lsy004-t
10x Genomics


title: ATAC counts of multiplex sSL0228 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0228_ATAC
sSL0228_ATAC_filtered_feature_bc_matrix.h5
sSL0228_ATAC_fragments.tsv.gz
sSL0228_ATAC_fragments.tsv.gz.tbi
sSL0228_ATAC_peak_annotation.tsv
sSL0228_ATAC_peaks.bed
cx_p4_diet_seurat_RNA_assay.rds


title: xlc002-t

description:
Library name: xlc002-t
10x Genomics


title: cgq003-t

description:
Library name: cgq003-t
10x Genomics


title: GEX counts of multiplex sSL0228 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0228_GEX
sSL0228_GEX_filtered_feature_bc_matrix.h5
sSL0228_GEX_QC_categories.csv
cx_p4_diet_seurat_RNA_assay.rds


title: HTO counts of multiplex sSL0228 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0228_HTO
Samples GN22/5364, GN22/5361, #GN22/3F/2777, #GN22/3F/2780, GN22/5232, GN22/5364, GN22/5361, #GN22/3F/2777, #GN22/3F/2780, GN22/5232 with genotypes Cul3+/-, Cul3+/-, Kmt5b+/-, Kmt5b+/-, Ptchd1 -/y, Cul3+/-, Cul3+/-, Kmt5b+/-, Kmt5b+/-, Ptchd1 -/y and sex f, m, m, f, m, f, m, m, f, m from tissue CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L) at timepoints P4, P4, P4, P4, P4, P4, P4, P4, P4, P4
cx_p4_diet_seurat_RNA_assay.rds


title: HCT116 mAID2-RAD21 + auxin 6h replicate 1 RNA-seq

city: Chapel Hill

first: John Patrick

last: Flores

state: NC

address: 104 Manning Dr

institute: UNC Chapel Hill

description:
Library name: HCT116-mAID2-RAD21-auxin-6h-1
RNA-seq of HCT116 mAID2-RAD21 cells treated with auxin for 6h (RAD21 depleted), replicate 1

data_processing:
Adapters were trimmed using Trim Galore and read quality was assessed with FastQC and MultiQC. Transcript abundance was quantified using Salmon v1.10.0 with --validateMappings --seqBias --gcBias --posBias against the GENCODE hg38 transcriptome index. Quantifications were imported into R using tximeta, and counts were summarized to gene-level abundance using tximport. Genes with fewer than 10 counts in at least four samples were excluded. This GEO submission includes raw FASTQ files and gene-level expression matrices in both raw count and TPM formats.
Assembly: hg38 (GRCh38) human reference genome.
Supplementary files format and content: Strand-specific bigWig files containing normalized RNA-seq signal tracks for each replicate and timepoint. This includes merged untreated and sorbitol replicate bigWig files. Files are provided separately for forward and reverse strands.

growth_protocol: HCT116-RAD21-mAID2 cells were cultured in standard conditions (37 °C, 5% CO₂) in McCoy's 5A medium supplemented with 10% fetal bovine serum and penicillin/streptomycin. Cells were regularly monitored for mycoplasma contamination and maintained at 30–80% confluence prior to experimental treatments.

extract_protocol:
Cells were detached, counted, and pelleted at 4 °C. For RNA-seq, total RNA was extracted using a column-based RNA purification kit following the manufacturer’s instructions. For CUT&Tag and Hi-C, nuclei were isolated by gentle lysis in detergent-containing buffer prior to downstream processing.
mRNA or total RNA input was subjected to library preparation compatible with strand-specific sequencing. Libraries were constructed using manufacturer protocols, indexed, pooled, and sequenced.

treatment_protocol: HCT116-RAD21-mAID2 cells were serum-starved for 1 h and treated with 1 µM 5-phenyl-indole-3-acetic acid (5-Ph-IAA; BioAcademia #30-003) for 6 h to deplete RAD21, adapted from Yesbolatova et al. For RNA-seq, cells received one of three conditions in serum-free media: control (no treatment) for 6 h, 0.2 M sorbitol for 6 h, or 0.2 M sorbitol with 1 µM 5-Ph-IAA for 6 h. Cells were harvested immediately and processed for downstream library preparation.

value: 1uM 5-Ph-IAA for 6h (RAD21 depletion)


title: wbq001-t

description:
Library name: wbq001-t
10x Genomics


title: HTO counts of multiplex sSL0241 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0241_HTO
Samples 324727, 327556, GN3F/22/2830, GN3F/22/2176, GN22/4890, GN22/4907, 324727, 327556, GN3F/22/2830, GN3F/22/2176, GN22/4890, GN22/4907 with genotypes C57BL6/J, C57BL6/J, Wac+/-, Wac+/-, Setd5+/-, Setd5+/-, C57BL6/J, C57BL6/J, Wac+/-, Wac+/-, Setd5+/-, Setd5+/- and sex f, m, m, f, f, m, f, m, m, f, f, m from tissue CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L) at timepoints P4, P4, P4, P4, P4, P4, P4, P4, P4, P4, P4, P4
cx_p4_diet_seurat_RNA_assay.rds


title: ATAC counts of multiplex sSL0241 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0241_ATAC
sSL0241_ATAC_filtered_feature_bc_matrix.h5
sSL0241_ATAC_fragments.tsv.gz
sSL0241_ATAC_fragments.tsv.gz.tbi
sSL0241_ATAC_peak_annotation.tsv
sSL0241_ATAC_peaks.bed
cx_p4_diet_seurat_RNA_assay.rds


title: HCT116 mAID2-RAD21 sorbitol 6h replicate 1 RNA-seq

description:
Library name: HCT116-mAID2-RAD21-sorbitol-6h-1
RNA-seq of HCT116 mAID2-RAD21 cells treated with sorbitol for 6h, replicate 1

value: 0.2M sorbitol for 6h


title: HCT116 mAID2-RAD21 serum starvation replicate 1 RNA-seq

description:
Library name: HCT116-mAID2-RAD21-serum-starve-1
RNA-seq of HCT116 mAID2-RAD21 cells after serum starvation (untreated control), replicate 1

value: serum starvation (untreated control)


title: HTO counts of multiplex sSL0242 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0242_HTO
Samples GN22/313, GN23/444, GN22/5252, GN22/5251, GN3F/2828, GN3F/2752, GN22/313, GN23/444, GN22/5252, GN22/5251, GN3F/2828, GN3F/2752 with genotypes Bckdk-/-, Bckdk-/-, Hnrnpu+/-, Hnrnpu+/-, Trip12+/-, Trip12+/-, Bckdk-/-, Bckdk-/-, Hnrnpu+/-, Hnrnpu+/-, Trip12+/-, Trip12+/- and sex f, m, f, m, f, m, f, m, f, m, f, m from tissue CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L) at timepoints P4, P4, P4, P4, P4, P4, P4, P4, P4, P4, P4, P4
cx_p4_diet_seurat_RNA_assay.rds

value: Cortex

value: mixed


title: GEX counts of multiplex sSL0243 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0243_GEX
sSL0243_GEX_filtered_feature_bc_matrix.h5
sSL0243_GEX_QC_categories.csv
cx_p4_diet_seurat_RNA_assay.rds

value: mixed samples (multiplex)


title: ATAC counts of multiplex sSL0242 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0242_ATAC
sSL0242_ATAC_filtered_feature_bc_matrix.h5
sSL0242_ATAC_fragments.tsv.gz
sSL0242_ATAC_fragments.tsv.gz.tbi
sSL0242_ATAC_peak_annotation.tsv
sSL0242_ATAC_peaks.bed
cx_p4_diet_seurat_RNA_assay.rds