title: MCF7 cells,VI-10H,rep3

city: wuhan

first: song

last: zemin

address: no.185 the road of eastlake

institute: wuhan university

description: Library name: Sample 9

data_processing:
For RNAseq, raw fastq reads underwent alignment to the mouse genome (hg38) utilizing HISAT2 version 2.1.0. The raw read counts were normalized to Reads per Million (RPM) per sample. To quantify read counts within specific genomic regions, featurecounts was employed, and these counts were subsequently utilized by DESeq2 (version 1.32.0) for differential gene expression analysis.
Assembly: hg38
Supplementary files format and content: txt

extract_protocol:
For RNAseq, poly(A)-containing mRNA was selectively enriched from 1 μg of total RNA utilizing VAHTS mRNA capture beads (Vazyme, N401-02).
To generate fragments of 200-500 nucleotides in length, the enriched mRNA was fragmented through treatment with 2× ProtoScript II buffer (NEB, M0368). Following fragmentation, the first- and second-strand cDNA were generated, and adaptor ligation was carried out, followed by 12-15 cycles of PCR amplification.

value: human breast cancer


title: C57BL/6J 8-10 weeks female, Colon epithelium, 10dpi, Biological replicate 3

status: Public on Jul 29 2026

type: SRA

city: Boston

first: Yuko

last: Hasegawa

state: MA

address: 181 Longwood Ave.

country: USA

institute: Brigham and Women's Hospital

description:
Library name: ColonEpi-day10-3
ColonEpi_featureCounts.txt

library_source: transcriptomic

data_processing:
Low-quality bases and the adaptors were trimmed using Trim Galore. The reads were mapped to the mouse reference genome (mm10) using STAR with default parameters, and the gene-level raw read count matrix was obtained using the featureCounts function in the subread using mouse GENCODE annotation M25 (GRCm38.p6)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: Colon

extract_protocol:
RNA was harvested by bead-beating the tissue in TRIzol
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols

treatment_protocol: Mice were orally gavaged with 5 × 10⁹ Citrobacter rodentium

tag: tissue

value: Colon

tag: genotype

value: WT

tag: treatment

value: Cr infection

tag: time


title: 203991400162_R02C01_PD705_PFC

type: genomic

city: Exeter

first: Joshua

last: Harvey

state: Devon

address: RILD Building, RD&E, Barrack Road

department: Clinical and Biomedical Sciences

country: United Kingdom

institute: University of Exeter

hyb_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the Zymo EZ 96 DNA methylation kit (Zymo Research) according to the manufacturer’s standard protocol.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) using a Illumina iScan System (Illumina)

data_processing:
Data was imported using the R package methylumi methylumIDAT function. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions.
[ukbbn_betas_normalised.Rdata] wateRmelon processed beta values, dasen quantile normalised

label: Cy3 & Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Prefrontal cortex

label_protocol: Standard Illumina Protocol

extract_protocol: ~30mg of brain tissue was milled over liquid nitrogen and extracted following the Qiagen AllPrep DNA/RNA/miRNA Universal kit following standard protocol. Samples were pre-checked using nanodrop fluorometer prior to further processing.

value: Prefrontal cortex

tag: regiondescription

tag: plate

tag: centre

value: Imperial Brain Bank

tag: Sex

value: male

tag: thal

value: FALSE


title: 203991390118_R02C01_PD913_PFC

value: female


title: C57BL/6J 8-10 weeks female, Colon epithelium, 10dpi, Biological replicate 2

description:
Library name: ColonEpi-day10-2
ColonEpi_featureCounts.txt


title: control, shNT TGFb treated, biol rep 2

city: Chapel Hill

first: Shea

middle: N

last: Ricketts

state: NC

address: 111 Mason Farm Road

department: Pathology and Laboratory Medicine

institute: UNC Chapel Hill

description: Library name: shNTtgfb2

data_processing:
Data was assessed for quality with FastQC and aligned to mouse genome using STAR
Transcript expression was inferred using featureCounts
Assembly: mm10
Supplementary files format and content: tab-delimited text file includs TPM values for each sample

molecule: total RNA

source_name: Heart

growth_protocol: Cardiac fibroblasts isolated from wildtype C57BL/6  mice were maintained in DMEM supplemented with 20% fetal bovine serum, 1% nonessential amino acids and 1% penicillin-streptomycin in humidified atmosphere at 37 ºC under 5% CO2

extract_protocol:
RNA was harvested with QIA shredder homogenization (Qiagen #795654) and RNeasy Plus Mini Kit (Qiagen #74134pi). 1.3 ug of total RNA was used for sequencing libraries.
Library preparation was performed by Novogene

treatment_protocol: For FGFR1 knockdown assays, cardiac fibroblasts were treated with lentiviral shFgfr1 to deplete FGFR1 for and treated with lentiviral shNT for control. For FGFR1 overexpression assays, cardiac firboblasts were treated with lentiviral overexpression constructs (Fgfr1a1, Fgfr1a2, or Fgfr1b) and treated with lentiviral LacZ for Control. All lentiviral treatments were supplemented with 8ug/mL of polybrene.

value: Heart

tag: cell type

value: Fibroblast

value: WildType, shNT

value: Profibrotic stimulation by TGFb (10 ng/ul)


title: C57BL/6J 8-10 weeks female, Colon epithelium, 21dpi, Biological replicate 3

description:
Library name: ColonEpi-day21-3
ColonEpi_featureCounts.txt


title: 203991400139_R05C01_PD385_PFC


title: C57BL/6J 8-10 weeks female, Colon epithelium, 10dpi, Biological replicate 1

description:
Library name: ColonEpi-day10-1
ColonEpi_featureCounts.txt


title: 203991400139_R04C01_PD330_PFC


title: 203991410064_R05C01_P60/10_PFC

value: QSBB

value: TRUE


title: control, shNT TGFb treated, biol rep 1

description: Library name: shNTtgfb1


title: C57BL/6J 8-10 weeks female, Colon epithelium, 6dpi, Biological replicate 4

description:
Library name: ColonEpi-day6-4
ColonEpi_featureCounts.txt


title: 203991400139_R02C01_20040063_PFC

value: Newcastle Brain Tissue Resource


title: C57BL/6J 8-10 weeks female, Colon epithelium, 6dpi, Biological replicate 3

description:
Library name: ColonEpi-day6-3
ColonEpi_featureCounts.txt


title: 203991400119_R06C01_P83/16_PFC


title: 203991410066_R07C01_PD896_PFC


title: anti-human CTLA-4

city: Lund

first: Björn

last: Frendeus

state: Skane

address: Ideongatan 1

country: Sweden

institute: BioInvent International

description:
Library name: Sample2
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting anf aggregation were made using the Cell Ranger software v7.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest/release-notes/cr-release-notes#v7-0-0)
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

extract_protocol:
Tumors from 11 mice/group was harvested and pooled together into 1 sample, in total 4 samples. Harvested tumors were cut into small (2-3 mm) pieces using scalpels. Tissue pieces were enzymatically digested using 0,5 mg/ml Liberase TM (Merck) and 200 kunitz/ml DNAse (Merck) for 2x5 min at 37 degrees with slight vortex in between. Digestion reaction was quenched with 5 mL of RPMI (containing 10% FCS) and cells were filtered through a 70 mm cell-strainer. Viable lymphocytes were isolated using Lympholyte-M Separation Media (Cedarlane) gradients. Lymphocytes were stained with viability dye and CD45 antibody and live CD45+ cells were sorted using a FACS AriaFusion (Becton Dickinson). Cells were counted (NucleoCounter NC-202, ChemoMetec) and fixed according to “10x sample fixation Protocol” from 10x Genomics and kept at -80 °C until analyzed using scRNA- seq.
Viable CD45+ cells were sorted using FACS and samples were fixed using 4% formaldehyde for 20 hours at 4 °C, followed by long-term storage at –80 °C according to ‘10x Genomics’ flex fixation kit recommendations. In short, prior to library preparation, samples were thawed, washed, and hybridized with barcoded probe sets according to the Chromium Next-GEM Flex protocol (10x Genomics). Approximately 10k cells per sample were targeted for capture, and the pooled samples were loaded onto a Chromium X instrument using a Chip Q. The sequencing Libraries were sequenced on an Illumina NovaSeq 600

value: Tumor

value: CD45 positive cells

tag: host strain

value: anti-mouse FcgRII

tag: batch

value: batch 1


title: 203991410110_R03C01_PD537_PFC


title: C57BL/6J 8-10 weeks female, Colon epithelium, 6dpi, Biological replicate 1

description:
Library name: ColonEpi-day6-1
ColonEpi_featureCounts.txt

value: Colon

value: WT

value: Cr infection


title: C57BL/6J 8-10 weeks female, Colon epithelium, 6dpi, Biological replicate 2

description:
Library name: ColonEpi-day6-2
ColonEpi_featureCounts.txt


title: C57BL/6J 8-10 weeks female, Colon epithelium, 3dpi, Biological replicate 3

description:
Library name: ColonEpi-day3-3
ColonEpi_featureCounts.txt


title: C57BL/6J 8-10 weeks female, Colon epithelium, 3dpi, Biological replicate 4

description:
Library name: ColonEpi-day3-4
ColonEpi_featureCounts.txt


title: 203991390105_R08C01_C026_PFC

value: Prefrontal cortex

value: Imperial Brain Bank


title: C57BL/6J 8-10 weeks female, Colon epithelium, 3dpi, Biological replicate 1

description:
Library name: ColonEpi-day3-1
ColonEpi_featureCounts.txt


title: C57BL/6J 8-10 weeks female, Colon epithelium, 1dpi, Biological replicate 4

description:
Library name: ColonEpi-day1-4
ColonEpi_featureCounts.txt


title: 203991390105_R06C01_20185903_PFC

value: male

value: FALSE


title: 203991390105_R04C01_20152919_PFC


title: 203991390105_R01C01_PDC131_PFC

value: female


title: C57BL/6J 8-10 weeks female, Colon epithelium, 1dpi, Biological replicate 2

description:
Library name: ColonEpi-day1-2
ColonEpi_featureCounts.txt


title: C57BL/6J 8-10 weeks female, Colon epithelium, 1dpi, Biological replicate 1

description:
Library name: ColonEpi-day1-1
ColonEpi_featureCounts.txt


title: 203991390076_R01C01_19980060_PFC


title: C57BL/6J 8-10 weeks female, Colon epithelium, 0dpi, Biological replicate 4

description:
Library name: ColonEpi-day0-4
ColonEpi_featureCounts.txt

value: Control (PBS)


title: C57BL/6J 8-10 weeks female, Colon epithelium, 0dpi, Biological replicate 3

description:
Library name: ColonEpi-day0-3
ColonEpi_featureCounts.txt


title: 203968030087_R07C01_PDC114_PFC


title: 203991390076_R02C01_PD905_PFC


title: C57BL/6J 8-10 weeks female, Colon epithelium, 0dpi, Biological replicate 2

description:
Library name: ColonEpi-day0-2
ColonEpi_featureCounts.txt


title: C57BL/6J 8-10 weeks female, Colon epithelium, 0dpi, Biological replicate 1

description:
Library name: ColonEpi-day0-1
ColonEpi_featureCounts.txt


title: 203968030087_R03C01_PD911_PFC


title: Patient 6_2

city: Lexington

first: Robert

last: Helsley

state: KY

address: 741 S. Limestone St.

department: Intern

institute: University of Kentucky

description:
Library name: Sample 12
S12

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Novogenes methods
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
Assembly: Homo Sapiens (GRCh38/hg38)
Supplementary files format and content: xls files include RPKM and total counts for each Sample

source_name: Liver

extract_protocol:
Total RNA was isolated from livers using the Qiagen Rneasy Mini kit. Novogene isolated mRNA from the total RNA provided by the investigators using poly-T oligo-attached magnetic beads.
mRNA libraries were constructed by Novogene using random hexamers and dUTP. The library was complete after end repair, A-tailing, adapter ligation, size selection, amplification, and purification, following Novogenes methods.

value: Liver

tag: cell line

value: Adjacent


title: 203968030003_R05C01_PD916_PFC


title: Cardiac nuclei, I/R surgery, Enpatoran treatment, replicate 3

city: Baltimore

first: Yijia

last: Li

state: MD

address: HSF2 G-S003, 20 Penn street

department: Anesthesiology

institute: University of Maryland, Baltimore

description:
Library name: Enp3
10X Genomics

data_processing:
FastQ files produced by the 10x Genomics sequencing pipeline were aligned to the human reference genome (GRCh38) using CellRanger (v6.1.1, 10x Genomics). Samples were combined into a single dataset using the ‘Seurat’ R package, followed by checks for batch effects due to technical variations or cell cycle influences on proliferative states.
Assembly: mouse reference genome (GRCm39)
Supplementary files format and content: Tab-separated values files

molecule: nuclear RNA

extract_protocol:
Nuclei were isolated from flash-frozen and powdered heart tissue. A detergent-mechanical cell lysis method was used, involving three major steps: lysis, homogenization, and density barrier centrifugation. In a laminar hood, a ~50-mg powered heart tissue was placed into a pre-frozen BioPulverizer (BioSpec), then immediately added lysis buffer (10mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1 Nonidet P40, 1 X RNase inhibitor, 1ul/mL DEPC). Tissue was disaggregated, flushing up and down, first using a 1 ml pipette tip. Homogenized tissue was diluted to 2 ml with lysis buffer and filtered through a 70 µm filter. Homogenate was spun at 350 g for 5 min at 4°C. The pellet was washed twice by washing buffer (1 X PBS, 1% BSA, 1 X RNase inhibitor). Pellet was then resuspended and 500 µl of pellet suspension was diluted with 500 µl 5% iodixanol solution (5% iodixanol, 250 mM sucrose, 150 mM KCl, 130 mM MgCl2, 1 X RNase inhibitor, and 60mM Tris-HCl, pH 8.0), filtered for the second time with a 20 µm mesh and placed on bottom of 500 µl layer of 8.5% iodixanol solution (8.5% iodixanol, 250 mM sucrose, 150 mM KCl, 130 mM MgCl2, 1 X RNase inhibitor, 60mM Tris-HCl, pH 8.0). The density barrier was centrifuged at 10,000 g for 10 minutes at 4°C. The pellet was collected and washed with washing buffer, centrifuged at 350 g for 5 min at 4°C, and finally suspended in 50 µl washing buffer. Single nuclei suspensions were counted and evaluated for integrity using Propidium Iodide in a MoxiGo cytometer using 650 nm filter. The nuclei count was adjusted to 1000 nuclei/ml.
Single-cell RNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) (10x Genomics, Pleasanton, CA, USA), following the manufacturer's user guide (CG000315 Rev C). Briefly, single cells were encapsulated into Gel Beads-in-Emulsion (GEMs) using the Chromium Controller and a microfluidic Chip G. Each GEM contains a single cell, a uniquely barcoded gel bead, reverse transcription reagents, and partitioning oil. Within each GEM, polyadenylated mRNAs were reverse transcribed to generate barcoded full-length cDNA, incorporating a 10x Barcode and Unique Molecular Identifier (UMI) through oligo(dT) primers. After reverse transcription, GEMs were broken, and barcoded cDNA was purified using Silane DynaBeads. The purified cDNA was PCR amplified and size-selected using SPRIselect magnetic beads. For library construction, cDNA was enzymatically fragmented, end-repaired, A-tailed, and ligated with Illumina-compatible adaptors. Dual indices (i7 and i5) were incorporated during sample index PCR. Final libraries included P5 and P7 adapter sequences and were compatible with Illumina sequencing. Libraries were quantified and assessed for quality using an Agilent Bioanalyzer, TapeStation, or equivalent platform, and sequenced on an Illumina instrument using paired-end mode (e.g., 28 bp for Read 1, 8 bp i7 index, 10 bp i5 index, and 90 bp for Read 2).

treatment_protocol: WT mice were given 2 doses of either Enpatoran, each at 5mg/kg BW (InvivoGen, San Diego, CA) or normal saline (NS) by intraperitoneal (i.p) injection. Two doses of NS or Enpatoran were given 1 hour before LAD occlusion (i.e., before ischemia) and again right after ischemia.

value: Heart

tag: age

value: 9-10 weeks old

tag: exposure

value: I/R surgery

value: Enpa


title: Cardiac nuclei, I/R surgery, Enpatoran treatment, replicate 2

description:
Library name: Enp2
10X Genomics


title: 203968030003_R02C01_PD120_PFC


title: 203968030003_R01C01_P28/11_PFC

value: QSBB


title: Cardiac nuclei, I/R surgery, Enpatoran treatment, replicate 1

description:
Library name: Enp1
10X Genomics


title: Cardiac nuclei, I/R surgery, NS treatment, replicate 3

description:
Library name: NS3
10X Genomics

value: NS


title: 203973690040_R07C01_P32/10_PFC

value: TRUE


title: Cardiac nuclei, I/R surgery, NS treatment, replicate 2

description:
Library name: NS2
10X Genomics

value: WT


title: 203973690040_R05C01_NP12/161_PFC

value: Oxford Brain Bank


title: Cardiac nuclei, I/R surgery, NS treatment, replicate 1

description:
Library name: NS1
10X Genomics


title: 203973690040_R02C01_P90/17_PFC

value: Prefrontal cortex


title: Cardiac nuclei, Sham surgery, NS treatment, replicate 3

description:
Library name: Sham3
10X Genomics

value: Sham surgery


title: Cardiac nuclei, Sham surgery, NS treatment, replicate 2

description:
Library name: Sham2
10X Genomics

value: male


title: 203973690063_R08C01_PDC078_PFC

value: Imperial Brain Bank

value: FALSE


title: 203973690063_R06C01_PD803_PFC


title: 203977090045_R06C01_PD900_PFC

value: female


title: Mono-mac-6-sgMETTL1.6-Rep2

city: Duarte

first: Rui

last: Su

state: CA

address: 1500 E Duarte Rd

institute: City of Hope

description:
Library name: Mono-mac-6-sgMETTL1.6-Rep2
mm6.sgM1.6.EV.2

data_processing:
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
the TPM were calculated using RSEM 1.2.31 with default parameters
Assembly: GRCh38
Supplementary files format and content: RSEM output file containing the expression of genes

growth_protocol: Human Mono-mac-6 cell line was grown in RPMI 1640 media supplemented with 10% FBS, 1% Penicillin-Streptomycin, 2 mM L-glutamine, 1x non-essential amino acids, 1 mM sodium pyruvate, 10 μg/ml human insulin, 10 mM HEPES and 0.1% Plasmocin™ Prophylactic

extract_protocol:
Total RNA was extracted using TRIZOL reagent
RNA library preparation was conducted using KAPA Stranded mRNA-Seq Kit

treatment_protocol: Mono-mac-6 cells were havested at approximately 8-10 days post lentivitus transduction.

value: AML

value: carry MLL-AF9 fusion gene


title: Liver tissue, KO-4, 12 hours after PHx

city: Hefei

first: Taofei

last: Zeng

state: Anhui

address: 17 Lujiang Road

country: China

institute: The First Affiliated Hospital of USTC

description: Library name: KO-4

data_processing:
The sequencing reads were aligned to the mm10 genome with the STAR algorithm, and unique gene counts were calculated using the Htseq-count algorithm. Differentially expressed genes (DEGs) between groups were identified with the DESeq2 R package. Pathway enrichment analysis for Reactome pathways was performed using the ClusterProfiler (v4.0) R package. Gene Set Enrichment Analysis (GSEA) was applied to identify gene sets showing significant differences between the specified groups.
Assembly: mm10
Supplementary files format and content: csv files include  raw counts for each sample

growth_protocol: Mice were maintained under pathogen-free conditions with controlled humidity, a 12-hour light/dark cycle, and ad libitum access to food and water.

extract_protocol:
RNA was extracted from tissue using a standard protocol with TRIzol reagent. Samples were homogenized in lysis buffer, and RNA was isolated by separating the aqueous phase and precipitating with isopropanol. After ethanol washing and drying, RNA was resuspended in RNase-free water. RNA quality was assessed using an Agilent 2100 Bioanalyzer and verified by RNase-free agarose gel electrophoresis.
After total RNA was extracted from mouse liver tissues, eukaryotic mRNA was enriched using Oligo(dT) beads. The enriched mRNA was then fragmented into short fragments and reverse transcribed into cDNA using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530, New England Biolabs, Ipswich, MA, USA). The purified double-stranded cDNA was end-repaired, an A-base was added, and Illumina sequencing adapters were ligated. The ligation products were purified using AMPure XP Beads (1.0X), size-selected by agarose gel electrophoresis, and PCR amplified. The final cDNA library was sequenced using the Illumina NovaSeq 6000 at Gene Denovo Biotechnology Co. (Guangzhou, China).

treatment_protocol: Mice were anesthetized with isoflurane after hair removal and disinfection of the abdominal skin. A midline incision was made to expose the liver, and the left lateral and median lobes were resected. The peritoneum was sutured with absorbable sutures, and the skin was closed with standard sutures. Postoperative care included rewarming with a heating blanket.

value: Liver

value: Partial Hepatectomy


title: 203977090045_R05C01_PD443_PFC


title: Mono-mac-6-sgNS (control)-Rep2

description:
Library name: Mono-mac-6-sgNS-Rep2
mm6.sgNS.EV.2


title: Liver tissue, KO-3, 12 hours after PHx

description: Library name: KO-3


title: Mono-mac-6-sgMETTL1.3-Rep1

description:
Library name: Mono-mac-6-sgMETTL1.3-Rep1
mm6.sgM1.3.EV.1


title: 203977090021_R08C01_PD153_PFC


title: Liver tissue, KO-2, 12 hours after PHx

description: Library name: KO-2


title: Mono-mac-6-sgNS (control)-Rep1

description:
Library name: Mono-mac-6-sgNS-Rep1
mm6.sgNS.EV.1


title: 203977090021_R07C01_20090027_PFC

value: Newcastle Brain Tissue Resource


title: IP2_76NTERT

city: Omaha

first: Jordan

last: Rowley

state: NE

address: 3828 Jones St, Apt 202

institute: University of Nebraska Medical Center

description: Library name: Sample 10_eCLIP_IP

data_processing:
RNAseq Reads were aligned and mapped to reference genome using STAR
Peaks from bigwig files were visualized using IGV
TPM values were calculated using DESeq2
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample and Deseqresults file for RNAseq
Supplementary files format and content: peaks and bigwig for eCLIP data

extract_protocol:
Total RNA was isolated using the Trizol reagent from control or ECD depleted 76NTERT cells. The quality of purified RNA samples was determined using a Bioanalyzer
RNA-seq libraries were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) following the manufacturer's protocols and subjected to 100 bp paired-end sequencing on an Illumina NovaSeq 6000 system at the UNMC next generation sequencing facility.

treatment_protocol: The ECD (GeneID: 11319) CDS in the mammalian expression vector pLenti-C-Myc-DDK-P2A-Puro and empty Vector control plasmids were obtained from (Origene Biotech cat # PS100092). RNA binding region was deleted from WT ECD containing plasmid using PCR-based site-directed mutagenesis as mentioned above. Lentiviral supernatants were generated by transient co-transfection of Lenti-X 293T cells with lentiviral packaging plasmid, psPAX2 (Addgene, #12260) envelope pMD2.G plasmid (Addgene#12259) and either empty mammalian expression vector or ECD (WT and mutant) CDS carrying vectors using X-treme GENE HP DNA transfection reagent (Roche#06366236001). 76NTERT cells were transduced with collected lentiviral supernatant in the presence of polybrene (8 µg/ml, Sigma#H9268). 72 hours post-transduction, cells were selected in 1 μg/ml puromycin for 5 days, and ECD levels assessed by Western blotting (WB) using an anti-ECD monoclonal antibody (Kim et al., 2009).

value: mammary epithelial cells from normal breast tissue


title: Liver tissue, KO-1, 12 hours after PHx

description: Library name: KO-1


title: IP1_76NTERT

description: Library name: Sample 9_eCLIP_IP


title: 203977090021_R06C01_19900165_PFC


title: Input2_76NTERT

description: Library name: Sample 8_eCLIP_control


title: Liver tissue, WT-6, 12 hours after PHx

description: Library name: WT-6


title: Input1_76NTERT

description: Library name: Sample 7_eCLIP_control


title: 203977090021_R04C01_RI04/099_PFC


title: MiceHippocampalTissue_RNA_SchizophreniaPool2_5

city: Barcelona

first: Marcos

last: Galán-Ganga

address: C/ Casanova, 143.

department: Biomedicine

country: Spain

institute: University of Barcelona

description:
Library name: SCZP2-5
Two rounds of sequencing for each sample (R1 and R2)

data_processing:
The quality of the sequencing data was checked using the FastQC software (v0.11.5). FastQC: a quality control tool for high throughput sequence data (available online at http://www.bioinformatics.babraham.ac.uk/projects/fastqchttp://www.bioinformatics.babraham.ac.uk/projects/fastqc). An estimation of ribosomal RNA in the raw data was obtained using riboPicker (v0.4.3). Reads were aligned to the GENCODE version of the Mus musculus genome, release M20 (GRMm38/mm10 assembly) using the STAR mapper (v2.5.3a). The raw read counts per gene was also obtained using STAR (–quantMode TranscriptomeSAM GeneCounts option) and the GENCODE release M20 annotation (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M20/gencode.vM20.annotation.gtf.gz)
Assembly: GRMm38/mm10 assembly
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

source_name: Hippocampal brain tissue

extract_protocol:
For the hippocampal RNA extraction and quality control, mouse samples were homogenized in QIAzol solution (QIAGEN, 79306) and lysed using a polytron, followed by RNA extraction using the miRNeasy mini kit (QIAGEN, 217004) according to the manufacturer’s instructions. All samples were eluted in 40 µL of RNAse-free water and total RNA quantity and purity were measured using a ND-1000 spectrophotometer (Thermo Fisher Scientific). RNA integrity was assessed using a 2100 Bioanalyser (Agilent Technologies Inc.), according to manufacturers' protocols. The average RIN value for our mouse samples was 8.5.
Libraries were prepared using the TruSeq Stranded mRNA Sample Prep kit v2 (RS-122-2101/2) according to the manufacturer's protocol. Briefly, 500 ng of total RNA were used for poly(A)-mRNA selection using streptavidin-coated magnetic beads and were subsequently fragmented to ∼300 bp. cDNA was synthesized using reverse transcriptase (SuperScript II, Invitrogen, 18064-014) and random primers. The second strand of the cDNA incorporated dUTP in place of dTTP. Double-stranded DNA was further used for library preparation. dsDNA was subjected to A-tailing and ligation of the barcoded Truseq adapters. Library amplification was performed by PCR using the primer cocktail supplied in the kit. All purification steps were performed using AMPure XP beads. Final libraries were analysed using Fragment Analyser to estimate the quantity and check size distribution and were then quantified by qPCR using the KAPA Library Quantification kit (KK4835, KapaBiosystems) before amplification with Illumina's cBot. Sequencing was performed using the HiSeq2500 equipment (Illumina), and 50 nt single-end reads were generated, using the v4 chemistry.

value: Hippocampal brain tissue

tag: sex and_age

value: 4-moths-old male

tag: strain

value: wild-type

value: Schizophrenia 2 RNA


title: Liver tissue, WT-5, 12 hours after PHx

description: Library name: WT-5

tag: tissue

value: WT


title: Cardiac nuclei, Sham surgery, NS treatment, replicate 1

description:
Library name: Sham1
10X Genomics

value: Heart

value: 9-10 weeks old

tag: genotype

value: NS


title: MiceHippocampalTissue_RNA_SchizophreniaPool2_4

description:
Library name: SCZP2-4
Two rounds of sequencing for each sample (R1 and R2)

tag: treatment


title: 203991400161_R06C01_PD171_PFC

value: Prefrontal cortex

value: Imperial Brain Bank

value: male


title: Mono-mac-6-sgMETTL1.3-Rep2

description:
Library name: Mono-mac-6-sgMETTL1.3-Rep2
mm6.sgM1.3.EV.2

value: AML


title: 203977090021_R02C01_PD113_PFC

value: FALSE


title: MiceHippocampalTissue_RNA_SchizophreniaPool2_3

description:
Library name: SCZP2-3
Two rounds of sequencing for each sample (R1 and R2)


title: Liver tissue, WT-4, 12 hours after PHx

description: Library name: WT-4

value: Liver


title: 203968030057_R06C01_PD501_PFC

value: female


title: MiceHippocampalTissue_RNA_SchizophreniaPool2_1

description:
Library name: SCZP2-1
Two rounds of sequencing for each sample (R1 and R2)


title: MCF7 cells,VI-10J,rep2

description: Library name: Sample 5

value: human breast cancer


title: Liver tissue, WT-3, 12 hours after PHx

description: Library name: WT-3

value: Partial Hepatectomy


title: Mono-mac-6-sgMETTL1.6-Rep1

description:
Library name: Mono-mac-6-sgMETTL1.6-Rep1
mm6.sgM1.6.EV.1

value: carry MLL-AF9 fusion gene


title: 203991400161_R02C01_PDC040_PFC


title: MiceHippocampalTissue_RNA_SchizophreniaPool1_5

description:
Library name: SCZP1-5
Two rounds of sequencing for each sample (R1 and R2)

value: Hippocampal brain tissue

value: 4-moths-old male

value: Schizophrenia 1 RNA


title: 203968030057_R04C01_P46/10_PFC

value: QSBB

value: TRUE


title: MiceHippocampalTissue_RNA_SchizophreniaPool1_4

description:
Library name: SCZP1-4
Two rounds of sequencing for each sample (R1 and R2)

value: wild-type


title: Liver tissue, WT-2, 12 hours after PHx

description: Library name: WT-2

value: WT


title: MiceHippocampalTissue_RNA_SchizophreniaPool1_3

description:
Library name: SCZP1-3
Two rounds of sequencing for each sample (R1 and R2)


title: 203968030057_R02C01_20150159_PFC

value: Prefrontal cortex

value: Newcastle Brain Tissue Resource


title: Liver tissue, WT-1, 12 hours after PHx

description: Library name: WT-1


title: MiceHippocampalTissue_RNA_SchizophreniaPool1_2

description:
Library name: SCZP1-2
Two rounds of sequencing for each sample (R1 and R2)


title: 203968030065_R07C01_PD902_PFC

value: Imperial Brain Bank


title: MiceHippocampalTissue_RNA_SchizophreniaPool1_1

description:
Library name: SCZP1-1
Two rounds of sequencing for each sample (R1 and R2)


title: MiceHippocampalTissue_RNA_HealthyControlPool_5

description:
Library name: CTL-5
Two rounds of sequencing for each sample (R1 and R2)

value: Control RNA


title: MiceHippocampalTissue_RNA_HealthyControlPool_4

description:
Library name: CTL-4
Two rounds of sequencing for each sample (R1 and R2)


title: Liver, HSWDF

city: Singapore

first: Jin

last: Zhou

address: 8 College Road Singapore

country: Singapore

institute: Duke-NUS Medical School

description: Library name: HSWDF

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using CeleScope version 2.0.7 (https://singleron.bio/products/celescope/)
Assembly: Mus_musculus_ensembl_99
Supplementary files format and content: matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz

extract_protocol:
Liver tissue was dissociated using the PythoN Junior Tissue Dissociation Buffer (product number 11300603, Singleron) and the PythoN Junior automated dissociator (Singleron). The resulting cell suspension was filtered through 70 µm and 40 µm filters, and the cells were centrifuged at 300g for 5 minutes. The cell pellets were then resuspended in 1 mL of pre-chilled resuspension buffer followed by a short centrifugation at 100g for 1 minute. Following this, the cells in the supernatant were stained with acridine orange/propidium iodide (product number F23001, Logos Biosystems) and counted using the LUNA-FX7 automated cell counter (Logos Biosystems).
Single cell RNA-seq libraries were constructed using sCircle® Single Cell Full Length Immuno-TCR Library Kit (4153011, Singleron Biotechnologies) according to the manufacturer´s instructions. Briefly, for each library, a cell suspension of a specified cell concentration was loaded onto a microfluidic chip to capture the target number of cells. The single-cell capture, lysis and mRNA capture steps were automated using the Singleron Matrix NEO system. The final single-cell RNA libraries were sequenced on the Illumina NovaSeq platform with paired-end 150 bp.

tag: mouse strain

value: male

value: 24-26 weeks old

value: HSWDF


title: 203968030065_R05C01_PD792_PFC

tag: regiondescription

value: female

value: FALSE


title: MiceHippocampalTissue_RNA_HealthyControlPool_3

description:
Library name: CTL-3
Two rounds of sequencing for each sample (R1 and R2)


title: Liver, WDF

description: Library name: WDF

value: Liver

value: WDF


title: MiceHippocampalTissue_RNA_HealthyControlPool_2

description:
Library name: CTL-2
Two rounds of sequencing for each sample (R1 and R2)

value: Hippocampal brain tissue

value: 4-moths-old male


title: 203968030034_R08C01_20160475_PFC

tag: plate


title: MiceHippocampalTissue_RNA_HealthyControlPool_1

description:
Library name: CTL-1
Two rounds of sequencing for each sample (R1 and R2)


title: MiceHippocampalTissue_RNA_Vehicle_5

description:
Library name: VEH-5
Two rounds of sequencing for each sample (R1 and R2)

value: Vehicle


title: 203968030034_R06C01_C036_PFC

tag: centre


title: MiceHippocampalTissue_RNA_Vehicle_4

description:
Library name: VEH-4
Two rounds of sequencing for each sample (R1 and R2)


title: Liver, HSD

description: Library name: HSD

tag: Sex

value: HSD


title: Liver, NCD

description: Library name: NCD

value: NCD


title: MiceHippocampalTissue_RNA_Vehicle_3

description:
Library name: VEH-3
Two rounds of sequencing for each sample (R1 and R2)

value: wild-type


title: 203991400119_R05C01_PD704_PFC

value: Prefrontal cortex

tag: thal


title: 203991400119_R02C01_PD816_PFC


title: MiceHippocampalTissue_RNA_Vehicle_2

description:
Library name: VEH-2
Two rounds of sequencing for each sample (R1 and R2)


title: 203968030034_R03C01_PD976_PFC


title: 203991400119_R01C01_20040105_PFC

value: Newcastle Brain Tissue Resource


title: MCAO,72h

city: BEIJING

first: Qianqian

last: Yin

address: 49 North Garden Road, Haidian District

department: Center of Basic Medical Research

institute: Peking University Third Hospital

description:
Library name: MCAO
BD Rhapsody platform

data_processing:
The FASTQ files were processed using the BD Rhapsody™ Sequence Analysis Pipeline 2.3 with the GRCm39 mouse genome as reference.
Assembly: GRCm39
Supplementary files format and content: rds files for each sample

source_name: brain

extract_protocol:
We performed single cell separation and library preparation on CD45+ cells using the microwell-based BD Rhapsody scRNA-Seq platform with the BD Rhapsody Whole Transcriptome Analysis (WTA) reagent kit (BD Biosciences), following the manufacturer’s instructions. Briefly, forty-thousand CD45+ cells from mice of sham or MCAO group were loaded on the BD Rhapsody cartridge for single cell separation, respectively. Within 30 minutes of retrieving cell capture beads, we initiated reverse transcription to prepare cDNA.
We then prepared libraries for RNA transcripts, sample tags according to the manufacturer’s instructions. Libraries were sequenced on the NovaSeq 6000 (Illumina) to generate 150 bp paired-end reads.

value: brain

value: MCAO


title: 203968030034_R02C01_PD876_PFC

value: Imperial Brain Bank

value: male


title: MiceHippocampalTissue_RNA_Vehicle_1

description:
Library name: VEH-1
Two rounds of sequencing for each sample (R1 and R2)


title: WT-6

city: Shenyang,China

first: Dan

address: No. 146, Huanghe North Street, Yuhong District, Shenyang City, Liaoning Province，China

institute: Shenyang Medical College

description: Library name: sample4

data_processing:
Illumina Hiseq platform
Assembly: mm10
Supplementary files format and content: .gz includes raw counts for each Sample
Supplementary files format and content: xls. include FPKM values for each Sample

source_name: ovary tissue

extract_protocol:
Total RNA was purified from mouse white adipose tissue using Trizol reagent (Takara).1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.

value: ovary tissue

value: wt


title: sham, 72h

description:
Library name: sham
BD Rhapsody platform

value: sham


title: C57BL/6J 8-10 weeks female, Colon epithelium, 3dpi, Biological replicate 2

description:
Library name: ColonEpi-day3-2
ColonEpi_featureCounts.txt

value: Colon

value: WT

value: Cr infection

tag: time


title: 203968030034_R01C01_NP10/083_PFC

value: Oxford Brain Bank

value: FALSE


title: WT-5

description: Library name: sample3


title: ++Oxtr-4

description: Library name: sample2

value: tg


title: siLCP1, replicat3

description: Library name: SI3

data_processing:
After quality control, the reads were aligned to the GRCm39 genome assembly via HISAT2 (version 2.0.4). We used HTSeq (v0.9.1) statistics to compare the read count values for each gene with the original expression of the gene and then used FPKM to standardize the expression.
Assembly: GRCm39
Supplementary files format and content: txt file includes raw counts and FPKM for each sample

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany) following the manufacturer’s instructions.
To confirm the insert size and calculate the molar concentration, mRNA was quantified with a Qubit® 2.0 fluorometer (Life Technologies, USA) and validated with an Agilent 2100 bioanalyzer (Agilent Technologies, USA). cDNA libraries were sequenced on the Illumina NovaSeq 6000 platform (Illumina, USA).

tag: cell type

value: Monocyte/macrophage

value: LCP1 knockdown


title: ++Oxtr-3

description: Library name: sample1


title: MiceHippocampalTissue_RNA_SchizophreniaPool2_2

description:
Library name: SCZP2-2
Two rounds of sequencing for each sample (R1 and R2)

value: Hippocampal brain tissue

value: 4-moths-old male

value: wild-type

value: Schizophrenia 2 RNA


title: Sta3_519

description: Library name: sample3

library_source: genomic

data_processing:
illumina novaseq Xplus
Assembly: mm10
Supplementary files format and content: .gz includes raw counts for each sample
Supplementary files format and content: bigwig for each sample
Library strategy: CUT&Tag

extract_protocol:
Ovaries were immediately dissected and homogenized for nuclear extracts using a Nuclear Extraction Kit (SN0020, Solarbio).  The CUT&Tag procedure (Vazyme, TD904-C2) began with nuclei incubation using ConA Beads Pro (10 min, RT), followed by centrifugation and supernatant removal. Nuclear-bead complexes were resuspended in 50μL chilled Antibody Buffer containing either anti-H3K4me3 (CST #9145T; 1:50) or anti-p-Stat3 (CST #9751S; 1:100) primary antibodies with gentle inversion mixing, then incubated overnight at 4°C. After secondary antibody incubation (goat anti-rabbit/mouse IgG, 1:100; 1 h, RT) and washing, tagmentation was performed using pA/G-Tnp Pro (1 h, 37°C) followed by DNA extraction, library amplification, and purification (Vazyme N411).
CUT&Tag libraries were prepared using  Hyperactive Universal CUT&Tag Assay Kit (Vazyme). Libraries were amplified using 11 cycles on the thermocycler. Post amplification libraries were size selected at 280-450bp in length. Libraries were validated using the Agilent High Sensitivity DNA Kit.


title: 203968030064_R05C01_PDC053_PFC

value: Prefrontal cortex

value: Imperial Brain Bank

value: female


title: siLCP1, replicat2

description: Library name: SI2


title: 203968030064_R06C01_PD612_PFC

value: male


title: H3K4_543

description: Library name: sample1

value: ovary tissue

value: wt


title: Sta3_517

description: Library name: sample2


title: siLCP1, replicat1

description: Library name: SI1


title: Sample10_IB6239

city: Groningen

first: Bart

last: Eggen

state: Groningen

address: Antonius Deusinglaan 1

department: Department of Biomedical Sciences

country: Netherlands

institute: UMCG Groningen

description:
Library name: Sample10
Libraries were sequenced multiple times, and were mapped together using CellRanger7. Processed data files are CellRanger7 raw and filtered feature matrices.

data_processing:
Data processing was performed with Cellranger v7.0.0
Assembly: GrCh38-2020-A
Supplementary files format and content: Processed data files contain the filtered feature matrix returned by CellRanger v7.0.0
Supplementary files format and content: Each sample has one file, where columns are barcodes and rows are genes

source_name: Fresh frozen brain, occipitotemporal cortex

growth_protocol: N/A, samples were obtained from a postmortem brain bank from donors diagnosed with AD and non-neurological controls.

extract_protocol:
Nuclei were isolated from fresh frozen human occipitotemporal cortex brain tissue using a sucrose gradient ultracentrifugation protocol. Samples were a subset of those originally reported in (Gerrits et al., Acta Neuropathologica, 2021). Nuclei were separated into 3 populations using FANS: NeuN+ nuclei, Olig2+ nuclei, and the double negative nuclei. We collected 30,000 NEUN+ nuclei, 15,000 OLIG2+ nuclei, and 5,000 double negative nuclei. All collected nuclei were then loaded onto the Chromium v3 single cell chips (10x Genomics). This strategy has previously been used to enrich for less abundant CNS cell types (Gerrits et al., Acta Neuropathologica, 2021).
Single-nucleus cDNA libraries were constructed and dual-indexed using the Chromium Single Cell 3′ Reagents Kit v3 and corresponding user guide (10× Genomics).

tag: diagnosis

value: AD


title: 203968030064_R02C01_19980026_PFC

value: Newcastle Brain Tissue Resource


title: Sample9_IB6237

description:
Library name: Sample9
Libraries were sequenced multiple times, and were mapped together using CellRanger7. Processed data files are CellRanger7 raw and filtered feature matrices.

treatment_protocol: N/A, samples were obtained from a postmortem brain bank from donors diagnosed with AD and non-neurological controls.

value: Fresh frozen brain, occipitotemporal cortex


title: Sample8_IB6125

description:
Library name: Sample8
Libraries were sequenced multiple times, and were mapped together using CellRanger7. Processed data files are CellRanger7 raw and filtered feature matrices.

value: CTR


title: 203968030064_R01C01_20020080_PFC

value: FALSE


title: Control, replicate 3

description: Library name: Contro3

tag: cell line

value: Monocyte/macrophage

value: Wide type


title: Sample7_IB6001

description:
Library name: Sample7
Libraries were sequenced multiple times, and were mapped together using CellRanger7. Processed data files are CellRanger7 raw and filtered feature matrices.

tag: age


title: Sample6_IB5875

description:
Library name: Sample6
Libraries were sequenced multiple times, and were mapped together using CellRanger7. Processed data files are CellRanger7 raw and filtered feature matrices.


title: Control, replicate 1

description: Library name: Contro1


title: 203977090043_R08C01_PD268_PFC


title: Sample4_IB5816

description:
Library name: Sample4
Libraries were sequenced multiple times, and were mapped together using CellRanger7. Processed data files are CellRanger7 raw and filtered feature matrices.


title: 203977090043_R07C01_PD143_PFC


title: Quadriceps, injured limb, SPiDER pos

first: Alexander

middle: Romano

last: Keeble

address: 900 S Limestone st

institute: Northwestern University

description: Library name: Quad_Rpos

data_processing:
Raw sequencing reads were demultiplexed and converted into fastqs before analysis with CellRanger (v6.0). CellRanger was used to pre-process and align single-cell reads from both datasets to the mm10-2020A reference genome using v3 chemistry. CellRanger h5 output files were produced that contained filtered count matrices labeled with gene symbols and nuclei barcodes.
Assembly: mm39
Supplementary files format and content: filtered hdf5 files containing raw alinged counts

source_name: Quadriceps

extract_protocol:
Quadriceps. Mouse quadriceps were dissected and pooled from n = 8 mice 14 days following ACL transection surgery. Muscles were mechanically minced in a petri dish before transferring to a 50mL conical containing muscle dissociation buffer comprised of Ham’s-F10 (Thermo Scientific, 11550043) media supplemented with 10% normal horse serum (Sigma, 22H319) and 800U/mL of Collagenase II (Thermo Scientific, 17101-015). The muscle slurry was agitated at 37⁰ C for 1 hour, centrifuged (500 X g for 5 minutes at 4 °C), and the resultant pellet was resuspended in Collagenase II and 11U/mL Dispase (Roche, 04942078001) and the slurry was incubated (30 minutes) with agitation. After incubation, the suspension was centrifuged again under the same parameters, the supernatant aspirated and the pellet resuspended and filtered through a 40µm cell strainer. Finally, the suspension was centrifuged again and the remaining cell pellet was resuspended and ready for staining. Joint capsule. Tissue from ACLT and uninjured knee joints was collected and pooled from n = 8 (same mice for quadriceps scRNA-seq) and digested with a protocol adapted from (5). Approximately 1 mm wide articular cartilage tissue and myotendinous tissue from the proximal articular surface of the tibia and the distal articular surface of the femur were scraped with a scalpel and placed into a suspension buffer containing 0.2% collagenase II (Thermo Fisher Scientific). The joint tissue homogenate was agitated for a cumulative period of 2 hours with cell straining (70 μm filter) performed at 30 minute-intervals. After the final digestion interval, cells were pelleted by centrifugation, resuspended, passed through a 40 µm filter to obtain a single cell suspension, which was pelleted and resuspended for staining. For FACS sorting, cells were incubated with SPiDER-βgal and DAPI as a viability stain, debris and dead cells were gated out using forward/side scatter profiles, and SPiDER-GFP+ / DAPI- cells were collected as SA βgal positive, and SPiDER-GFP- / DAPI- cells were collected as SA βgal negative fractions
Through collaboration with the UKY Arts and Sciences Imaging Center, cell suspensions were counted with a hemocytometer and loaded onto a 10x chromium controller. Single-cell RNAseq libraries were prepared using the Chromium Single Cell 3′ reagent kit version 3.1 (10x Genomics, PN-1000075; Pleasanton, CA) following manufacturer’s guidelines. 4,000-10,000 single cell transcriptomes were recovered for sequencing. Single cell libraries were sequenced by Novogene on an Illumina NovaSeq 6000 at with 150 bp pair-end reads.

value: Quadriceps

value: ACLT


title: Sample2_IB5431

description:
Library name: Sample2
Libraries were sequenced multiple times, and were mapped together using CellRanger7. Processed data files are CellRanger7 raw and filtered feature matrices.


title: 203977090043_R04C01_20060025_PFC


title: Sample1_IB5328

description:
Library name: Sample1
Libraries were sequenced multiple times, and were mapped together using CellRanger7. Processed data files are CellRanger7 raw and filtered feature matrices.


title: Quadriceps, injured limb, SPiDER neg

description: Library name: Quad_Rneg


title: OT118A, OBMI

first: Anna

last: Ramos-Triguero

address: C/ del Rosselló, 149

institute: FRCB-IDIBAPS

description:
Library name: OT118A
150x2 bp

data_processing:
Quality control and preprocessing were performed using FastQC (v0.11.8), MultiQC (v1.9) and Trimmomatic (v0.39), alignment to Homo_sapiens.GRCh38.102 reference genome using STAR (v2.7.10.a) and quality control of alignment with Qualimap (v.2.2.2).
Gene counts were estimated using featureCounts (v1.6.4) and differentially expressed genes using DESeq2 (v1.36.0).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: cord blood

extract_protocol:
Cord blood was collected at birth for transcriptomic analysis. 10 mL of whole blood were collected in BD Vacutainer® K3E 15% Aprotinin 250KIU (SGSH;BD361017). Peripheral blood mononuclear cells (PBMCs) were isolated by Blood Collection tube BD Vacutainer®, BD CPT™ (Avantor, BDAM362781). Total RNA was extracted with RNeasy Mini Kit (Qiagen,74106).
RNA samples were analyzed in Microomics Systems S.L. (Barcelona, Spain). Sequencing was performed using Illumina-NextSeq (150x2bp).

value: cord blood

value: PBMCs


title: 203977090043_R03C01_P33/12_PFC

data_processing:
Data was imported using the R package methylumi methylumIDAT function. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions.
[ukbbn_betas_normalised.Rdata] wateRmelon processed beta values, dasen quantile normalised

extract_protocol: ~30mg of brain tissue was milled over liquid nitrogen and extracted following the Qiagen AllPrep DNA/RNA/miRNA Universal kit following standard protocol. Samples were pre-checked using nanodrop fluorometer prior to further processing.

value: Prefrontal cortex

value: QSBB


title: OT116A, OBMI

description:
Library name: OT116A
150x2 bp

value: Peripheral blood mononuclear cells (PBMCs)


title: Quadriceps, uninjured limb

description: Library name: Quad_Lneg

value: Uninjured


title: OT113A, OBMI

description:
Library name: OT113A
150x2 bp


title: 203977090043_R01C01_PD1029_PFC

value: Imperial Brain Bank

value: male


title: OT98_B, OBMI

description:
Library name: OT98_B
150x2 bp


title: Joint capsule, injured limb, SPiDER pos

description: Library name: Cart_Rpos

source_name: Joint capsule

value: Joint capsule


title: OT85_A, OBMI

description:
Library name: OT85_A
150x2 bp


title: 203977090066_R06C01_RI94/1335_PFC

value: Oxford Brain Bank


title: OT69_A, OBMI

description:
Library name: OT69_A
150x2 bp


title: OT38_A, OBMI

description:
Library name: OT38_A
150x2 bp


title: Joint capsule, injured limb, SPiDER neg

description: Library name: Cart_Rneg


title: OT34_A, OBMI

description:
Library name: OT34_A
150x2 bp


title: Joint capsule, uninjured limb

description: Library name: Cart_Lneg


title: OT27_A, OBMI

description:
Library name: OT27_A
150x2 bp


title: 203977090066_R01C01_PD659_PFC


title: OT26_B, OBMI

description:
Library name: OT26_B
150x2 bp


title: MSCs in senescent media 3

description: Library name: SEN_C

data_processing:
Raw fastqs were trimmed and quality controlled prior to aligning with STAR aligner (reference genome: mm39). DESEQ2 was used for comparison analyses between MSCs treated with conditioned media from senescent macrophages or from control macrophages. Raw p-values were adjusted for multiple testing using the Benjamini-Hochberg false discovery rate (FDR) step-up method.
Assembly: mm39
Supplementary files format and content: tab delimited text file containing DESEQ2 normalized counts for each sample

source_name: Skeletal muscle

extract_protocol:
Following 72h incubation in conditioned media, cells were washed and RNA was isolated using Tri Reagent (Zymo Research, #R2050-1-200).
Approximately 600 nanograms of RNA per sample (n=3 per group) were shipped to Novogene on dry ice for library construction and sequencing. RNA was sequenced using an Illumina NovaSeq 6000 platform using a paired-end 150 bp dual-indexing protocol.

value: Skeletal muscle

value: Mesenchymal stem cells


title: OT24_A, OBMI

description:
Library name: OT24_A
150x2 bp


title: 203991400140_R06C01_20174934_PFC

value: Newcastle Brain Tissue Resource

value: FALSE


title: OT19_A, OBMI

description:
Library name: OT19_A
150x2 bp


title: OT14_A, OBMI

description:
Library name: OT14_A
150x2 bp


title: 203991400140_R02C01_PD550_PFC

value: female


title: MSCs in senescent media 1

description: Library name: SEN_A


title: OT13_A, OBMI

description:
Library name: OT13_A
150x2 bp


title: 203991400117_R08C01_P69/13_PFC


title: C57BL/6 mice, kidney, adenine diet & AA, 2

city: Suzhou

first: liwei

last: zhu

state: Jiangsu

address: 77th, Changan South Street

institute: Zhangjiagang TCM Hospital Affiliated to Nanjing University ofChinese Medicine

description: Library name: AA_2

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: kidney

growth_protocol: Eight-week-old male C57BL/6 mice (20 ± 2 g)

extract_protocol:
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H.
Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: The CKD model was established by administering adenine-enriched chow for 4 week, AA groups received daily oral gavage of AA, while the control animals were maintained on adenine-free chow. Weeks 5–8, all groups were transitioned to standard diet while AA treatment continued.

value: kidney

value: adenine diet & AA


title: MSCs in control media 3

description: Library name: CON_C


title: OT12_A, OBMI

description:
Library name: OT12_A
150x2 bp

value: cord blood


title: OT10_A, OBMI

description:
Library name: OT10_A
150x2 bp

value: PBMCs


title: 203991400117_R07C01_PD897_PFC

value: Prefrontal cortex


title: OT7_A, OBMI

description:
Library name: OT7_A
150x2 bp


title: MSCs in control media 2

description: Library name: CON_B


title: OT5_A, OBMI

description:
Library name: OT5_A
150x2 bp


title: 203991400117_R06C01_PD690_PFC


title: OT1_A, OBMI

description:
Library name: OT1_A
150x2 bp


title: MSCs in control media 1

description: Library name: CON_A


title: NT93_A, NBMI

description:
Library name: NT93_A
150x2 bp


title: C57BL/6 mice, kidney, adenine diet, 1

description: Library name: M_1

value: adenine diet


title: Sample5_IB5869

description:
Library name: Sample5
Libraries were sequenced multiple times, and were mapped together using CellRanger7. Processed data files are CellRanger7 raw and filtered feature matrices.

value: Fresh frozen brain, occipitotemporal cortex

value: AD


title: 203991400117_R01C01_20185902_PFC


title: NT84_A, NBMI

description:
Library name: NT84_A
150x2 bp

value: Peripheral blood mononuclear cells (PBMCs)


title: Sample3_IB5508

description:
Library name: Sample3
Libraries were sequenced multiple times, and were mapped together using CellRanger7. Processed data files are CellRanger7 raw and filtered feature matrices.

value: CTR


title: NT83_A, NBMI

description:
Library name: NT83_A
150x2 bp


title: 203991400152_R03C01_P72/12_PFC

value: QSBB


title: Induction day 7 Pex19 KO-3

city: Durham

first: Jian-Liang

address: 111 TW Alexander Dr

institute: NIEHS

description:
Library name: F-27
Pex19 KO 46C mESCs induced for neural differentiation in NDiff227 medium for 7 days

data_processing:
Illumina’s bcl2fastq was used to convert bcl files to FASTQ files and de-multiplex the samples.
The raw reads were mapped to mm10 using STAR aligner (STAR_2.6.0c)
Subread featureCounts (version 2.0.3) was applied for gene quantification based on GENCODE annotation (gencode.vM23)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read count and DESeq2 vst normalized counts for each sample

source_name: 46C mESCs

growth_protocol: WT, Pex5 KO and Pex19 KO 46C mESCs cultured in ESGRO maintenance medium were induced for neural differentiation in the NDiff 227 neural differentiation medium (Takaba Y40002) for 4 or 7 days.

extract_protocol:
Total RNAs were extracted from mESCs using Qiagen RNeasy mini-kit (Qiagen, 74104).
The integrity of the total RNA was determined using a Tapestation (Agilent) and concentration were assessed by Qubit (ThermoFisher Scientific).  RNA-seq libraries were prepared with the TruSeq Stranded/Ribo kit (Illumina, San Diego, CA) and sequenced using the single-end 75bp protocol using the Next-Seq 500 platform (Illumina) per the manufacturer’s protocol.

treatment_protocol: Neural differentiation was induced in the NDiff 227 neural differentiation medium (Takaba Y40002) for 4 or 7 days.

value: 46C mESCs

value: embryonic stem cells (mESCs)

value: Pex19 KO

value: NDiff227 neural differentiation medium (Takaba Y40002) for 7 days


title: NT77_A, NBMI

description:
Library name: NT77_A
150x2 bp


title: Induction day 7 Pex19 KO-2

description:
Library name: F-26
Pex19 KO 46C mESCs induced for neural differentiation in NDiff227 medium for 7 days


title: NT76_A, NBMI

description:
Library name: NT76_A
150x2 bp


title: 203991400152_R01C01_20174906_PFC

first: Joshua

address: RILD Building, RD&E, Barrack Road

institute: University of Exeter

value: Newcastle Brain Tissue Resource

value: FALSE


title: NT75_A, NBMI

description:
Library name: NT75_A
150x2 bp


title: NT74_A, NBMI

description:
Library name: NT74_A
150x2 bp


title: Induction day 7 Pex19 KO-1

description:
Library name: F-25
Pex19 KO 46C mESCs induced for neural differentiation in NDiff227 medium for 7 days


title: 203991400160_R05C01_RI02/203_PFC

value: Oxford Brain Bank

value: female


title: NT72_A, NBMI

description:
Library name: NT72_A
150x2 bp

value: cord blood


title: 203991400160_R03C01_NP17/003_PFC


title: Induction day 7 Pex5 KO-3

description:
Library name: F-24
Pex5 KO 46C mESCs induced for neural differentiation in NDiff227 medium for 7 days

value: Pex5 KO


title: NT71_B, NBMI

description:
Library name: NT71_B
150x2 bp

value: PBMCs


title: NT70_B, NBMI

description:
Library name: NT70_B
150x2 bp


title: NT53_A, NBMI

description:
Library name: NT53_A
150x2 bp


title: Induction day 7 Pex5 KO-2

description:
Library name: F-23
Pex5 KO 46C mESCs induced for neural differentiation in NDiff227 medium for 7 days


title: 203991400160_R02C01_20100575_PFC

value: Prefrontal cortex

value: male


title: Induction day 7 Pex5 KO-1

description:
Library name: F-22
Pex5 KO 46C mESCs induced for neural differentiation in NDiff227 medium for 7 days


title: 203991400160_R01C01_PD730_PFC

value: Imperial Brain Bank


title: NT39_A, NBMI

description:
Library name: NT39_A
150x2 bp

value: Peripheral blood mononuclear cells (PBMCs)


title: NT36_A, NBMI

description:
Library name: NT36_A
150x2 bp


title: 203977090066_R02C01_20010072_PFC


title: NT23_A, NBMI

description:
Library name: NT23_A
150x2 bp


title: 203973690018_R06C01_PD765_PFC


title: Induction day 7 WT-3

description:
Library name: F-21
WT 46C mESCs induced for neural differentiation in NDiff227 medium for 7 days

value: WT


title: NT17_A, NBMI

description:
Library name: NT17_A
150x2 bp


title: Induction day 7 WT-2

description:
Library name: F-20
WT 46C mESCs induced for neural differentiation in NDiff227 medium for 7 days


title: MSCs in senescent media 2

description: Library name: SEN_B

value: Skeletal muscle

value: Mesenchymal stem cells


title: 203973690018_R05C01_20130020_PFC


title: NT11_A, NBMI

description:
Library name: NT11_A
150x2 bp


title: NT3_A, NBMI

description:
Library name: NT3_A
150x2 bp


title: C57BL/6J 8-10 weeks female, Colon epithelium, 36dpi, Biological replicate 4

first: Yuko

address: 181 Longwood Ave.

institute: Brigham and Women's Hospital

description:
Library name: ColonEpi-day36-4
ColonEpi_featureCounts.txt

data_processing:
Low-quality bases and the adaptors were trimmed using Trim Galore. The reads were mapped to the mouse reference genome (mm10) using STAR with default parameters, and the gene-level raw read count matrix was obtained using the featureCounts function in the subread using mouse GENCODE annotation M25 (GRCm38.p6)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
RNA was harvested by bead-beating the tissue in TRIzol
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols

value: Colon

value: Cr infection


title: Induction day 7 WT-1

description:
Library name: F-19
WT 46C mESCs induced for neural differentiation in NDiff227 medium for 7 days

value: 46C mESCs

value: embryonic stem cells (mESCs)

value: NDiff227 neural differentiation medium (Takaba Y40002) for 7 days


title: MM.1R_BRD4

city: Pamplona

first: Nahia

last: Gomez-Echarte

address: Avenida Pio XII, 55

institute: CIMA

description: Library name: sample 16

data_processing:
The reads were aligned to the human genome hg38 (GRCh38.p13) for all the samples.
CUT&RUN peaks were determined using MACS2. Peaks were compared and consensus matrixes were generated with the peaks common to two of the samples.
Assembly: GRCh38.p13
Supplementary files format and content: CUT&RUN BigWig file containing the genomic annotation for each TF.
Library strategy: CUT&Run

source_name: cell line culture

growth_protocol: MM cell lines were maintained in RPMI-1640 medium containing L-Glutamine supplemented with 1% of penicillin-treptomycin, 2% HEPES Buffer and 20% of Fetal Bovine Serum.

extract_protocol:
CUT&RUN was performed following CUTANA™ ChIC/CUT&RUN Kit and DNA was isolated using Pheno:Chloroform:Isoamyl protocol.
Libraries for CUT&RUN were carried out using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England Biolabs) following the modified protocol for TF by Liu, et al.

treatment_protocol: transduction of lentiviral particles containing the empty vector (scramble) or the vector containing the sgRNAs against IRF2 (IRF2-ssg1 and IRF2-ssg2).

value: Multiple Myeloma

tag: chip antibody

value: EpiCypher, 13-2003


title: OT16_A, OBMI

description:
Library name: OT16_A
150x2 bp

value: cord blood


title: 203973690018_R04C01_C048_PFC

value: FALSE


title: MM.1R_IRF2_2

description: Library name: sample 15

value: Invitrogen, 700226


title: Induction day 4 Pex19 KO-3

description:
Library name: F-18
Pex19 KO 46C mESCs induced for neural differentiation in NDiff227 medium for 4 days

value: Pex19 KO

value: NDiff227 neural differentiation medium (Takaba Y40002) for 4 days


title: MM.1R_IRF1_2

description: Library name: sample 14

value: Cell Signaling, #8478


title: 203976760050_R06C01_PD636_PFC

value: Prefrontal cortex

value: Imperial Brain Bank

value: male


title: MM.1R_IgG

description: Library name: sample 13

value: WT

value: Millipore, 12-370


title: 203976760050_R05C01_20185946_PFC

value: Newcastle Brain Tissue Resource

value: female


title: Induction day 4 Pex19 KO-2

description:
Library name: F-17
Pex19 KO 46C mESCs induced for neural differentiation in NDiff227 medium for 4 days

value: 46C mESCs

value: embryonic stem cells (mESCs)


title: MM.1R_IRF2

description: Library name: sample 12

value: Multiple Myeloma

value: abcam, ab124744


title: MM.1R_IRF4_2

description: Library name: sample 11

value: abcam, ab124691


title: Induction day 4 Pex19 KO-1

description:
Library name: F-16
Pex19 KO 46C mESCs induced for neural differentiation in NDiff227 medium for 4 days


title: MM.1R_IRF4

description: Library name: sample 10

value: Cell Signaling, #4964


title: 203976760050_R04C01_PD366_PFC

value: FALSE


title: Induction day 4 Pex5 KO-3

description:
Library name: F-15
Pex5 KO 46C mESCs induced for neural differentiation in NDiff227 medium for 4 days

value: Pex5 KO


title: KMS11_IRF1_2

description: Library name: sample 8

value: abcam, ab243895


title: 203976760050_R03C01_PD870_PFC


title: KMS11_BRD4

description: Library name: sample 7

value: EpiCypher, 13-2003


title: Induction day 4 Pex5 KO-2

description:
Library name: F-14
Pex5 KO 46C mESCs induced for neural differentiation in NDiff227 medium for 4 days

value: NDiff227 neural differentiation medium (Takaba Y40002) for 4 days


title: MM.1R_IRF1

description: Library name: sample 9


title: KMS11_IRF4_2

description: Library name: sample 6


title: 203991400062_R03C01_PD755_PFC

value: Prefrontal cortex

value: Imperial Brain Bank


title: KMS11_IRF2_2

description: Library name: sample 5

value: WT

value: Invitrogen, 700226


title: Induction day 4 Pex5 KO-1

description:
Library name: F-13
Pex5 KO 46C mESCs induced for neural differentiation in NDiff227 medium for 4 days


title: KMS11_IRF1

description: Library name: sample 4

value: Cell Signaling, #8478


title: 203991400062_R02C01_PD915_PFC

value: female


title: KMS11_IgG

description: Library name: sample 3

value: Millipore, 12-370


title: Induction day 4 WT-3

description:
Library name: F-12
WT 46C mESCs induced for neural differentiation in NDiff227 medium for 4 days

value: 46C mESCs

value: embryonic stem cells (mESCs)


title: KMS11_IRF4

description: Library name: sample 2

value: Multiple Myeloma


title: 203991390104_R06C01_19970033_PFC

value: Newcastle Brain Tissue Resource


title: KMS11_IRF2

description: Library name: sample 1

value: abcam, ab124744


title: Induction day 4 WT-2

description:
Library name: F-11
WT 46C mESCs induced for neural differentiation in NDiff227 medium for 4 days


title: 203991390104_R05C01_PDC093_PFC

value: FALSE


title: LNCaP:C42 siKDM1A siKDM7A R1881 #3

city: Nottingham

first: Nigel

middle: P

last: Mongan

address: University Park

department: Biodiscovery Institute

institute: University of Nottingham

data_processing:
Contaminating adapters and low quality reads with phred scores <30 were removed using the Trimgalore wrapper for Cutadapt and Fastqc
The resultant quality controlled fastq files were aligned to the Ensembl annoted Human genome (GRCh38.83) using STAR
Gene expression was quantified using FeatureCounts
Genome_build: GRCh38.83
Supplementary_files_format_and_content: Tab delimited text file contain gene expression in counts

growth_protocol: Cells were maintained at 37C and 5% CO2 in phenol red containing RPMI-1640 medium supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin-glutamine, 2 mM L-Glutamine and 1 mM sodium pyruvate.

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini kit
Illumina

treatment_protocol: The determine the effect of KDM1A and KDM7A depletion on androgen regulated transcription, LNCaP and LNCaP:C42 cells were grown in phenol red-free RPMI-1640 medium supplemented with 1% penicillin-streptomycin, 2mM L-Glutamine and 1 mM sodium pyruvate and 10% charcoal-stripped FBS. Functional depletion of KDM1A and KDM7A was performed via siRNA technique using ON-TARGETplus siRNA–SMART pools for Human KDM1A (#L-009223-00-0005) and KDM7A (#L-025357-01-0005) (GE DharmaconTM). ON-TARGETplus non-targeting control siRNAs (#D-001810-10-05, GE DharmaconTM) were employed as negative controls. Cells were transfected using DharmaFECT 2 Transfection Reagent (GE DharmaconTM) and transfection was performed accoding to the manufacturer's instructions.

value: Prostate cancer cells

tag: transfection

value: siKDM1A siKDM7A


title: LNCaP:C42 siKDM1A siKDM7A R1881 #2


title: Induction day 4 WT-1

description:
Library name: F-10
WT 46C mESCs induced for neural differentiation in NDiff227 medium for 4 days


title: LNCaP:C42 siKDM1A siKDM7A R1881 #1


title: 203991390104_R02C01_PD036_PFC

city: Exeter

last: Harvey

value: male


title: LNCaP:C42 siRNA Scramble non-gene targetting R1881 #3

value: siRNA Scramble


title: Induction day 0 Pex19 KO-3

description:
Library name: F-9
Pex19 KO mESCs cultured in regular maintenance medium

value: Pex19 KO

value: ESGRO medium (Millipore SF001-500P)


title: LNCaP:C42 siRNA Scramble non-gene targetting R1881 #2


title: 203991400061_R07C01_20141915_PFC

value: Prefrontal cortex


title: LNCaP:C42 siRNA Scramble non-gene targetting R1881 #1


title: LNCaP:C42 siRNA Scramble non-gene targetting Vehicle Control #3

source_name: LNCaP

value: LNCaP

value: Vehicle


title: Induction day 0 Pex19 KO-2

description:
Library name: F-8
Pex19 KO mESCs cultured in regular maintenance medium


title: 203991400061_R03C01_20163928_PFC


title: LNCaP:C42 siRNA Scramble non-gene targetting Vehicle Control #2


title: Induction day 0 Pex19 KO-1

description:
Library name: F-7
Pex19 KO mESCs cultured in regular maintenance medium


title: LNCaP:C42 siRNA Scramble non-gene targetting Vehicle Control #1


title: 203991400061_R02C01_P58/10_PFC

value: QSBB

value: female


title: LNCaP siKDM1A siKDM7A R1881 #3


title: Induction day 0 Pex5 KO-3

description:
Library name: F-6
Pex5 KO mESCs cultured in regular maintenance medium

value: 46C mESCs

value: Pex5 KO


title: LNCaP siKDM1A siKDM7A R1881 #2


title: 203990170009_R05C01_PD763_PFC

value: Imperial Brain Bank


title: Induction day 0 Pex5 KO-2

description:
Library name: F-5
Pex5 KO mESCs cultured in regular maintenance medium

value: embryonic stem cells (mESCs)


title: LNCaP siKDM1A siKDM7A R1881 #1


title: 203990170009_R02C01_20140411_PFC

value: Newcastle Brain Tissue Resource


title: Induction day 0 Pex5 KO-1

description:
Library name: F-4
Pex5 KO 46C mESCs cultured in regular maintenance medium


title: LNCaP siRNA Scramble non-gene targetting R1881 #2


title: 203973690073_R07C01_PD739_PFC

value: FALSE


title: LNCaP siRNA Scramble non-gene targetting R1881 #1

value: Prostate cancer cells


title: LNCaP siRNA Scramble non-gene targetting Vehicle Control #3


title: LNCaP siRNA Scramble non-gene targetting Vehicle Control #2


title: Induction day 0 WT-3

description:
Library name: F-3
WT 46C mESCs cultured in regular maintenance medium

value: WT


title: LNCaP siRNA Scramble non-gene targetting R1881 #3


title: 203973690073_R06C01_P21/13_PFC

value: male


title: LNCaP siRNA Scramble non-gene targetting Vehicle Control #1

value: siRNA Scramble


title: 203973690073_R03C01_PDC084_PFC


title: Induction day 0 WT-2

description:
Library name: F-2
WT 46C mESCs cultured in regular maintenance medium


title: LNCaP:C42 R1881 + Namoline + TCE-5002 rep 2

data_processing:
Contaminating adapters and low quality reads with phred scores <30 were removed using the Trimgalore wrapper for Cutadapt and FastQC
The resultant quality controlled fastq files were aligned to the Ensembl annoted Human genome (GRCh38.83) using STAR
Gene expression was quantified using FeatureCounts
Genome_build: GRCh38.83
Supplementary_files_format_and_content: Tab delimited text file contain gene expression in counts

tag: tag

value: R1881 + Namoline + TCE-5002


title: LNCaP:C42 R1881 + Namoline + TCE-5002 rep 1


title: Induction day 0 WT-1

description:
Library name: F-1
WT 46C mESCs cultured in regular maintenance medium

value: ESGRO medium (Millipore SF001-500P)


title: 203973690036_R06C01_PD701_PFC

tag: tissue

value: Prefrontal cortex


title: LNCaP:C42 R1881 + Namoline rep 1

value: R1881 + Namoline


title: BMDMs, TMV-OEG8-Man regulated M2, rep 3

city: Beijing

first: Jiaodan

last: Jin

address: 29  Zhongguancun East  Road,  Haidian District, Beijing, 100190,  China

institute: Technical Institute of Physics and Chemistry

description:
Library name: Sample 9
Colume name in raw_counts_all_samples.txt: TMV-OEG8-Man_3

data_processing:
fastp v 0.20.1
Raw reads of fastq format were firstly processed using fastp (parameter: --length_required 50) and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2 (parameter: --rna-strandness rf --fr).
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count (v 0.11.2, parameter: -s reverse).
Differential expression analysis was performed using the DESeq2 (v 1.22.2, parameter: qvalue(pvalue)<0.05, |log2FoldChange|>1).
Assembly: GRCm39
Supplementary files format and content: csv files include FPKM values for each Sample
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Bone marrow derived macrophages (BMDMs)

growth_protocol: Balb/c (female, 6-8 weeks) mice were sacrificed and dissected to extract the femur and tibia. The bones were then cut, and the marrow was flushed out using PBS. After filtering out bone debris and lysing erythrocytes, the bone cells were resuspended in high-glucose DMEM containing 25 ng/mL M-CSF, 10% FBS, and 1% P/S, and incubated at 37℃ with 5% CO2. The date of cell extraction was recorded as Day 0. The culture medium was refreshed on the 3rd and 5th days, leading to the harvest of mature resting BMDMs (M0 macrophages) on the 6th day.

extract_protocol:
Each cell sample was washed with PBS, and then total RNA was extracted using the TRIzol reagent under the manufacturer’s guidance. Total RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer, and RNA integrity was assessed using the Agilent 2100 bioanalyzer.
The VAHTS Universal V6 RNA-seq Library Prep Kit was used to construct libraries according to the manufacturer’s instructions.

treatment_protocol: Mature BMDMs were stimulated with 25ng/mL IL-4 for 48 hours to achieve M2 polarization (M2 group), and then the culture medium containing 50μg/mL TMV-OEG8-Man was replaced to obtain TMV-OEG8-Man regulated M2 macrophages (TMV-OEG8-Man regulated M2 group). Resting macrophages (M0 group) are untreated mature BMDMs, which were replaced with fresh culture medium when stimulated in the other two groups.

value: Bone marrow derived macrophages (BMDMs)

tag: genotype

value: TMV-OEG8-Man treatment for 24 hours after IL-4 treatment


title: LNCaP:C42 R1881 + Namoline rep 2


title: LNCaP:C42 R1881 TCE-5002 rep 2


title: 203973690036_R03C01_PD980_PFC

source_name: Prefrontal cortex


title: LNCaP:C42 R1881 TCE-5002 rep 1


title: BMDMs, TMV-OEG8-Man regulated M2, rep 2

description:
Library name: Sample 8
Colume name in raw_counts_all_samples.txt: TMV-OEG8-Man_2

tag: treatment


title: LNCaP:C42 R1881 rep 2


title: 203973690036_R02C01_PD973_PFC


title: LNCaP R1881 + Namoline + TCE-5002 rep 2

value: LNCaP


title: BMDMs, TMV-OEG8-Man regulated M2, rep 1

description:
Library name: Sample 7
Colume name in raw_counts_all_samples.txt: TMV-OEG8-Man_1


title: LNCaP:C42 R1881 rep 1


title: 203991410125_R06C01_PD758_PFC


title: LNCaP R1881 + Namoline + TCE-5002 rep 1


title: BMDMs, M0,rep 3

description:
Library name: Sample 6
Colume name in raw_counts_all_samples.txt: Control_3

value: untreated


title: 203991410125_R03C01_NP14/075_PFC

value: Oxford Brain Bank


title: LNCaP R1881 rep 2


title: BMDMs, M0,rep 2

description:
Library name: Sample 5
Colume name in raw_counts_all_samples.txt: Control_2


title: LNCaP R1881 rep 1


title: MT3_LSK

city: South Bend

first: Richard

last: Dahl

state: IN

address: Harper Hall 227, 1234 Notre Dame Ave.

department: Microbiology and Immunology

institute: Indiana University School of Medicine, South Bend

description: Library name: Sample 1

data_processing:
Reads aligned to genome with STAR/ C++ code.
Gene level expression was calculated (Fragments per Kilobase per Million-FPKM) using Cufflinks
Assembly: MM10
Supplementary files format and content: tab-delimited text file of FPKMs for each sample

source_name: Bone Marrow

growth_protocol: Bone Marrow isolated from 6-8 week old Wildtype or Mir11-/- mice.

extract_protocol:
Total RNA prepared using Qiagen MiREasy Kit
cDNA libraries were generated using NEBNext Ultra II RNA Library Prep Kit

treatment_protocol: Lin-Sca1+cKit+ cells population isolated by FACsAriaIII cell sorter.

value: Bone Marrow

tag: strain background

value: Normal hematopoiesis

tag: batch


title: 203991410002_R08C01_P64/11_PFC

tag: regiondescription

tag: plate

value: QSBB

value: female


title: MT2_LSK

description: Library name: Sample 2


title: BMDMs, M0,rep 1

description:
Library name: Sample 4
Colume name in raw_counts_all_samples.txt: Control_1


title: MT1_LSK

description: Library name: Sample 3


title: 203991410002_R06C01_20111135_PFC

tag: centre

value: Newcastle Brain Tissue Resource

tag: Sex

value: FALSE


title: WT3_LSK

description: Library name: Sample 4

value: Wildtype


title: WT2_LSK

description: Library name: Sample 5


title: 203991410002_R05C01_PDC023_PFC

value: Imperial Brain Bank

tag: thal


title: WT1_LSK

description: Library name: Sample 6

tag: cell type


title: BMDMs, M2, rep 2

description:
Library name: Sample 2
Colume name in raw_counts_all_samples.txt: IL-4_2

value: WT

value: IL-4 treatment for 48 hours


title: Ezh2_KO_CD8_d5_rep3

city: Toon

last: Matsuoka

state: Ehime

address: Shitsukawa

department: Immunology

country: Japan

institute: Ehime university

description: Library name: Ezh2_KO_d5_3

data_processing:
CLC Genomics Workbench v24.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC Genomics Workbench (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GRCm39/mm10 using CLC Genomics Workbench (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC Genomics Workbench
Assembly: mm10
Supplementary files format and content: XLSX files include TPM values for each Sample

source_name: Splenic CD8 T cells

growth_protocol: WT and Ezh2-deficient (Ezh2 KO) naïve CD8 T (CD44lowCD62Lhigh) cells were prepared using a CD8+ T cell Isolation kit (BioLegend) with biotin anti-CD44 antibody (BioLegend).  Naïve CD8 T cells (0.75 × 10^6) were stimulated with immobilized anti-TCR-β mAb (3 μg/ml, BioLegend) and anti-CD28 mAb (1 μg/ml,BioLegend) for 2 days in the presence of IL-2 (10 ng/ml, BioLegend). Next, the cells were transferred to a new plate and further cultured in the presence of IL-2 (10 ng/ml) for one or five days.

extract_protocol:
RNA was extracted using RNeasy plus Micro plus kit (Qiagen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using QuabtSeq 3'mRNA-Seq Library Prep Kit for illumina following manufacturer's protocols.

value: Splenic CD8 T cells

value: Ezh2 knockout

tag: strain


title: 203991410002_R03C01_P30/14_PFC

value: Prefrontal cortex

value: male


title: Ezh2_KO_CD8_d5_rep2

description: Library name: Ezh2_KO_d5_2


title: BMDMs, M2, rep 1

description:
Library name: Sample 1
Colume name in raw_counts_all_samples.txt: IL-4_1

value: Bone marrow derived macrophages (BMDMs)


title: 203991410001_R08C01_PD572_PFC


title: Ezh2_KO_CD8_d5_rep1

description: Library name: Ezh2_KO_d5_1


title: 203991410001_R07C01_20100082_PFC


title: WT_CD8_d5_rep1

description: Library name: WT_d5_1


title: WT_CD8_d5_rep2

description: Library name: WT_d5_2


title: Ctrl 4

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

country: Belgium

institute: University of Liège

description:
Library name: WT_4_88
88_R1

data_processing:
Data have been processed through the nf-core-rnaseq 3.0 pipeline using STAR/Salmon method for mapping and quantification.
Assembly: GRCm38 Ensembl release 102
Supplementary files format and content: Count matrice with tab-separated columns

source_name: Sciatic nerve

extract_protocol:
Samples were lysed and RNA was extracted using the Rneasy Mini kit (Qiagen), including a step to remove contaminating DNA using the Rnase-free DNase set (Qiagen). 250ng of total RNA was used to prepare sequencing libraries.
Libraries were prepared using the Illumina Stranded mRNA Prep Ligation kit following manufacturer's protocol.

value: Sciatic nerve

value: CNP+/+ Cdk7lox/lox

value: Postnatal day 6 (P6)


title: WT_CD8_d5_rep3

description: Library name: WT_d5_3


title: CNP-Cdk7cKO 4

description:
Library name: CKO_4_87
87_R1

value: CNPcre/+ Cdk7lox/lox


title: Ezh2_KO_CD8_d3_rep3

description: Library name: Ezh2_KO_d3_3


title: Ezh2_KO_CD8_d3_rep2

description: Library name: Ezh2_KO_d3_2


title: 203991410001_R04C01_PD959_PFC


title: CNP-Cdk7cKO 3

description:
Library name: CKO_3_85
85_R1


title: BMDMs, M2, rep 3

description:
Library name: Sample 3
Colume name in raw_counts_all_samples.txt: IL-4_3


title: 203991410001_R03C01_PD744_PFC


title: Ezh2_KO_CD8_d3_rep1

description: Library name: Ezh2_KO_d3_1


title: WT_CD8_d3_rep3

description: Library name: WT_d3_3


title: CNP-Cdk7cKO 2

description:
Library name: CKO_2_83
83_R1


title: WT_CD8_d3_rep2

description: Library name: WT_d3_2


title: 203991410001_R02C01_PD726_PFC


title: Ctrl 3

description:
Library name: WT_3_82
82_R1


title: WT_CD8_d3_rep1

description: Library name: WT_d3_1


title: exp22_W3_multiome_ATAC_Data

city: Prague

first: Juraj

last: Michalik

address: Vídeňská 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the Czech Academy of Sciences

description:
Library name: exp22-W3-ATAC
GEX+FB and GEX+ATAC were processed separately due to non-standard 10X protocol.

data_processing:
Sequencing was performed on NextSeq500 platform.
Base calling and FASTQ generation were performed using bcl2fastq v2.2.0 tool (Illumina). All files were demultiplexed manually (see publication and associated GitHub for details).
Due to non-standard 10X protocol, FB+GEX and GEX+ATAC were mapped manually (the former being used to generate FB counts only). The murine reference genome used for read alignment was obtained from Ensembl release 102 and prepared using the mkref tool from 10x Cell Ranger v7.1.0 (to generate Feature Barcode counts, used along with GEX) and Cell Ranger ARC v2.0.2 (to generate counts for GEX and peak counts). For ATAC, mouse genome annotations were added from EnsDb.Mmusculus.v79/mm10 (v2.99.0).
Subsequent analyses were performed in R v4.5.2 using the Seurat v5.1.0 and Signac v1.13.0.
Assembly: GRCm38 v102 (Ensembl) - GEX/EnsDb.Mmusculus.v79/mm10 (v2.99.0) - ATAC.
Supplementary files format and content: File containing specification of each hashtag and sample for Well 2 (W2) samples, in CSV format, used by 10X Cell Ranger to quantify each hashtag for each cell. Feature Barcode reference file.
Supplementary files format and content: File containing specification of each hashtag and sample for Well 3 (W3) samples, in CSV format, used by 10X Cell Ranger to quantify each hashtag for each cell. Feature Barcode reference file.
Supplementary files format and content: 10X Cell Ranger ARC output: list of barcodes in TSV format (W2) - contains GEX and peak counts
Supplementary files format and content: 10X Cell Ranger ARC output: list of genes/features and their type in TSV format (W2)  - contains GEX and peak counts
Supplementary files format and content: 10X Cell Ranger ARC output: sparse matrix quantifying results (W2)  - contains GEX and peak counts
Supplementary files format and content: 10X Cell Ranger output: list of barcodes in TSV format (W2) - contains GEX and FB counts. FB counts are then combined with ARC output, GEX is not used in final data and is counted only for comparison.
Supplementary files format and content: 10X Cell Ranger output: list of genes/features and their type in TSV format (W2)  - contains GEX and FB counts. FB counts are then combined with ARC output, GEX is not used in final data and is counted only for comparison.
Supplementary files format and content: 10X Cell Ranger output: sparse matrix quantifying results (W2)  - contains GEX and FB counts. FB counts are then combined with ARC output, GEX is not used in final data and is counted only for comparison.
Supplementary files format and content: 10X Cell Ranger output: fragments file (W2)
Supplementary files format and content: 10X Cell Ranger output: fragments file index (W2)
Supplementary files format and content: 10X Cell Ranger ARC output: list of barcodes in TSV format (W3) - contains GEX and peak counts
Supplementary files format and content: 10X Cell Ranger ARC output: list of genes/features and their type in TSV format (W3)  - contains GEX and peak counts
Supplementary files format and content: 10X Cell Ranger ARC output: sparse matrix quantifying results (W3)  - contains GEX and peak counts
Supplementary files format and content: 10X Cell Ranger output: list of barcodes in TSV format (W3) - contains GEX and FB counts. FB counts are then combined with ARC output, GEX is not used in final data and is counted only for comparison.
Supplementary files format and content: 10X Cell Ranger output: list of genes/features and their type in TSV format (W3)  - contains GEX and FB counts. FB counts are then combined with ARC output, GEX is not used in final data and is counted only for comparison.
Supplementary files format and content: 10X Cell Ranger output: sparse matrix quantifying results (W3)  - contains GEX and FB counts. FB counts are then combined with ARC output, GEX is not used in final data and is counted only for comparison.
Supplementary files format and content: 10X Cell Ranger output: fragments file (W3)
Supplementary files format and content: 10X Cell Ranger output: fragments file index (W3)
Supplementary files format and content: RDS file of Seurat object with GEX, FB and ATAC results, merged from both wells.

source_name: spleen

growth_protocol: FACS-sorted Tcm (CD8a+ CD45.1- CD45.2+ CD62L+ CX3CR1-), Tem (CD8a+ CD45.1- CD45.2+ CD62L- CX3CR1+), and naïve cells (CD8a+ CD44-) were adoptively transferred into congenic (CD45.1).

extract_protocol:
In indicated data points, spleens were harvested and processed into cell suspension. Donor cells were resorted (CD8a+ CD45.1- CD45.2+ CD44+) together with resting memory (CD8+ CD45.2+ CD44+) and naïve (CD8+ CD44-) cells. Samples were pooled together based on the condition.
Nuclei were isolated according to the 10x Genomics Demonstrated Protocol CG000365 (Rev C) with small adaptations. For sample multiplexing, isolated nuclei from each sample were labelled with MULTI-seq Lipid-Modified Oligos kit (Sigma-Aldrich, #LMO001A, #LMO001B) according to the original protocol (McGinnis et al., 2019). Single-nucleus ATAC and gene expression libraries were generated using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression reagents (10x Genomics, #PN-1000285) according to the manufacturer’s protocol (CG000338, Rev B), except for modifications introduced to recover the lipid-hashtag barcode library.

treatment_protocol: Mice were infected with Lm-OVA, with 2 mice per condition.

value: spleen

tag: cell line

value: CD8+ T cells

value: Progeny of Tn/Tem/Tcm

value: Lm-OVA

tag: time

value: Day 0/Day 7


title: 203991410124_R08C01_20152920_PFC

value: Newcastle Brain Tissue Resource

value: FALSE


title: exp22_W3_multiome_Hashtags_Data

description:
Library name: exp22-W3-CSP
Features specified in FeatureReference_W3.csv. GEX+FB and GEX+ATAC were processed separately due to non-standard 10X protocol.

library_source: other

data_processing:
Sequencing was performed on NextSeq500 platform.
Base calling and FASTQ generation were performed using bcl2fastq v2.2.0 tool (Illumina). All files were demultiplexed manually (see publication and associated GitHub for details).
Due to non-standard 10X protocol, FB+GEX and GEX+ATAC were mapped manually (the former being used to generate FB counts only). The murine reference genome used for read alignment was obtained from Ensembl release 102 and prepared using the mkref tool from 10x Cell Ranger v7.1.0 (to generate Feature Barcode counts, used along with GEX) and Cell Ranger ARC v2.0.2 (to generate counts for GEX and peak counts). For ATAC, mouse genome annotations were added from EnsDb.Mmusculus.v79/mm10 (v2.99.0).
Subsequent analyses were performed in R v4.5.2 using the Seurat v5.1.0 and Signac v1.13.0.
Assembly: GRCm38 v102 (Ensembl) - GEX/EnsDb.Mmusculus.v79/mm10 (v2.99.0) - ATAC.
Supplementary files format and content: File containing specification of each hashtag and sample for Well 2 (W2) samples, in CSV format, used by 10X Cell Ranger to quantify each hashtag for each cell. Feature Barcode reference file.
Supplementary files format and content: File containing specification of each hashtag and sample for Well 3 (W3) samples, in CSV format, used by 10X Cell Ranger to quantify each hashtag for each cell. Feature Barcode reference file.
Supplementary files format and content: 10X Cell Ranger ARC output: list of barcodes in TSV format (W2) - contains GEX and peak counts
Supplementary files format and content: 10X Cell Ranger ARC output: list of genes/features and their type in TSV format (W2)  - contains GEX and peak counts
Supplementary files format and content: 10X Cell Ranger ARC output: sparse matrix quantifying results (W2)  - contains GEX and peak counts
Supplementary files format and content: 10X Cell Ranger output: list of barcodes in TSV format (W2) - contains GEX and FB counts. FB counts are then combined with ARC output, GEX is not used in final data and is counted only for comparison.
Supplementary files format and content: 10X Cell Ranger output: list of genes/features and their type in TSV format (W2)  - contains GEX and FB counts. FB counts are then combined with ARC output, GEX is not used in final data and is counted only for comparison.
Supplementary files format and content: 10X Cell Ranger output: sparse matrix quantifying results (W2)  - contains GEX and FB counts. FB counts are then combined with ARC output, GEX is not used in final data and is counted only for comparison.
Supplementary files format and content: 10X Cell Ranger output: fragments file (W2)
Supplementary files format and content: 10X Cell Ranger output: fragments file index (W2)
Supplementary files format and content: 10X Cell Ranger ARC output: list of barcodes in TSV format (W3) - contains GEX and peak counts
Supplementary files format and content: 10X Cell Ranger ARC output: list of genes/features and their type in TSV format (W3)  - contains GEX and peak counts
Supplementary files format and content: 10X Cell Ranger ARC output: sparse matrix quantifying results (W3)  - contains GEX and peak counts
Supplementary files format and content: 10X Cell Ranger output: list of barcodes in TSV format (W3) - contains GEX and FB counts. FB counts are then combined with ARC output, GEX is not used in final data and is counted only for comparison.
Supplementary files format and content: 10X Cell Ranger output: list of genes/features and their type in TSV format (W3)  - contains GEX and FB counts. FB counts are then combined with ARC output, GEX is not used in final data and is counted only for comparison.
Supplementary files format and content: 10X Cell Ranger output: sparse matrix quantifying results (W3)  - contains GEX and FB counts. FB counts are then combined with ARC output, GEX is not used in final data and is counted only for comparison.
Supplementary files format and content: 10X Cell Ranger output: fragments file (W3)
Supplementary files format and content: 10X Cell Ranger output: fragments file index (W3)
Supplementary files format and content: RDS file of Seurat object with GEX, FB and ATAC results, merged from both wells.
Library strategy: CITE-seq

molecule: protein


title: Ctrl 2

description:
Library name: WT_2_81
81_R1

tag: age


title: exp22_W3_multiome_GEX_Data

description:
Library name: exp22-W3-GEX
GEX+FB and GEX+ATAC were processed separately due to non-standard 10X protocol.


title: 203991410124_R07C01_PDC016_PFC

value: Imperial Brain Bank

value: female


title: exp22_W2_multiome_ATAC_Data

description:
Library name: exp22-W2-ATAC
GEX+FB and GEX+ATAC were processed separately due to non-standard 10X protocol.

value: Progeny of Tn/Tem/Tcm (TM control)

value: Day 0/Day 12


title: CNP-Cdk7cKO 1

description:
Library name: CKO_1_79
79_R1


title: exp22_W2_multiome_Hashtags_Data

description:
Library name: exp22-W2-CSP
Features specified in FeatureReference_W2.csv. GEX+FB and GEX+ATAC were processed separately due to non-standard 10X protocol.


title: exp22_W2_multiome_GEX_Data

description:
Library name: exp22-W2-GEX
GEX+FB and GEX+ATAC were processed separately due to non-standard 10X protocol.


title: Ctrl 1

description:
Library name: WT_1_78
78_R1


title: 203991400131_R07C01_20185910_PFC

value: Prefrontal cortex


title: C57BL/6J 8-10 weeks female, Liver, 3dpi, eae infected, Biological replicate 4

city: Boston

last: Hasegawa

description:
Library name: Liver_eae_4
eae_featureCounts.txt

source_name: Liver

value: Liver

value: WT

value: eae infected


title: 203991410124_R06C01_P66/11_PFC

value: QSBB

value: TRUE


title: C57BL/6J 8-10 weeks female, Liver, 3dpi, eae infected, Biological replicate 3

description:
Library name: Liver_eae_3
eae_featureCounts.txt


title: C57BL/6J 8-10 weeks female, Liver, 3dpi, eae infected, Biological replicate 2

description:
Library name: Liver_eae_2
eae_featureCounts.txt


title: 203991400131_R06C01_PD820_PFC


title: Acetate3

city: Guangzhou

first: Zhiwen

last: Zhang

address: Lujing Road 2

institute: Southern Medical University

description:
Library name: Sample6
Count6

data_processing:
Sequencing output was normalized and expressed as RPKM (reads per kilobase of exon per million mapped reads). Raw reads were adapter-trimmed with cutadapt v1.18 and aligned to the GENCODE v30 mouse reference genome using HISAT2 v2.1.0 (default settings).
Assembly: mm10
Supplementary files format and content: gene_fpkm

growth_protocol: CD8⁺ T cells were isolated from mouse spleens using a positive selection kit (Miltenyi Biotec, 130‑104‑075). Purified CD8⁺ T cells were seeded onto culture plates pre‑coated with anti‑CD3 (5 µg/mL) and anti‑CD28 (2 µg/mL) antibodies at 4 °C for 24 h. Cells were cultured in RPMI‑1640 medium supplemented with 30 U/mL recombinant murine IL‑2, 1% non‑essential amino acids, 1% sodium pyruvate, and 50 µM 2‑mercaptoethanol. According to experimental grouping, PYG, ECCS, BSSC, acetate, or CUCPT 4a was added, and cells were incubated at 37 °C in 5% CO₂ for 72 h. Activated T cells were then used for subsequent functional assays.

extract_protocol:
Total RNA was extracted from mouse CD8⁺ T cells (acetate-treated and control) using TRIzol reagent (Thermo Fisher Scientific).
Qualified RNA samples were submitted to Novogene (Beijing) for paired-end sequencing on an Illumina NovaSeq 6000 platform. Libraries were prepared with the TruSeq RNA Sample Prep Kit (Illumina).

treatment_protocol: Final concentration of 5mm mol/L acetate treatment for 48 hours

value: spleen

value: mice primary cells

value: CD8+T cell

value: Acetate treatment


title: C57BL/6J 8-10 weeks female, Liver, 3dpi, eae infected, Biological replicate 1

description:
Library name: Liver_eae_1
eae_featureCounts.txt


title: Acetate2

description:
Library name: Sample5
Count5


title: 203991400131_R05C01_RI94/1280_PFC

value: Oxford Brain Bank


title: C57BL/6J 8-10 weeks female, Colon epithelium, 1dpi, Biological replicate 3

description:
Library name: ColonEpi-day1-3
ColonEpi_featureCounts.txt

source_name: Colon

value: Colon

value: Cr infection


title: C57BL/6J 8-10 weeks female, Liver, 3dpi, wt infected, Biological replicate 3

description:
Library name: Liver_wt_3
eae_featureCounts.txt

value: wt infected


title: Acetate1

description:
Library name: Sample4
Count4


title: C57BL/6J 8-10 weeks female, Liver, 3dpi, wt infected, Biological replicate 2

description:
Library name: Liver_wt_2
eae_featureCounts.txt


title: C57BL/6J 8-10 weeks female, Liver, 3dpi, wt infected, Biological replicate 4

description:
Library name: Liver_wt_4
eae_featureCounts.txt


title: C57BL/6J 8-10 weeks female, Liver, 3dpi, wt infected, Biological replicate 1

description:
Library name: Liver_wt_1
eae_featureCounts.txt


title: 203991400131_R02C01_C087_PFC

value: Imperial Brain Bank

value: female

value: FALSE


title: Control, replicate 2

address: 49 North Garden Road, Haidian District

institute: Peking University Third Hospital

description: Library name: Contro2

data_processing:
After quality control, the reads were aligned to the GRCm39 genome assembly via HISAT2 (version 2.0.4). We used HTSeq (v0.9.1) statistics to compare the read count values for each gene with the original expression of the gene and then used FPKM to standardize the expression.
Assembly: GRCm39
Supplementary files format and content: txt file includes raw counts and FPKM for each sample

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany) following the manufacturer’s instructions.
To confirm the insert size and calculate the molar concentration, mRNA was quantified with a Qubit® 2.0 fluorometer (Life Technologies, USA) and validated with an Agilent 2100 bioanalyzer (Agilent Technologies, USA). cDNA libraries were sequenced on the Illumina NovaSeq 6000 platform (Illumina, USA).

value: Monocyte/macrophage

value: Wide type


title: Control3

description:
Library name: Sample3
Count3

value: WT

value: No treatment


title: 203991400131_R01C01_PD874_PFC

value: Prefrontal cortex

value: male