title: CD8 T cells, 1 stimultation,  rep 4

description:
D2071
In the processed data file, there are these columns: Geneid (ENSEMBLE ID), Chr (Chromosome where gene is anotated), Start (position of the chromosome where the gene starts), End position of the chromosome where the gene ends), Strand (DNA strand that codifies for the gene, + or -), Length (length of the gene in base pairs), the following columns are the names for each studied sample


title: pan pol II DMSO 24h rep2

status: Public on Feb 12 2026

type: SRA

city: Nam-gu, Pohang-si

first: Hyerim

last: Jung

state: Gyeongsangbuk-do

address: 47, Jigok-ro

department: Dept. of Life Sciences

country: South Korea

institute: Pohang University of Science & Technology (POSTECH)

description: Library name: pan-pol-II-DMSO-24h-rep2

library_source: genomic

data_processing:
ChIP-seq data were trimmed with Trim Galore (0.6.7)[37] and aligned to hg38 (v36) using Bowtie 2 (2.4.5)[38]. The bigWig files were generated by HOMER (v4.11)[39] makeUCSCfile and visualized with UCSC genome browser. For pan pol II, Ser5P, and Ser2P ChIP-seq, read counting was generated by HOMER analyzeRepeats.pl and DESeq2 (1.40.0)[40]. For CDK7, MYC, E2F1, and TOP1 ChIP-seq, peakcalling was performed with MACS3 (3.0.0b1)[41] and IDR (2.0.3)[42].
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: MCF-7 was maintained in DMEM (Thermo Fisher Scientific, Waltham, MA, USA, Gibco™, 31053028) with 10% FBS (Invitrogen, Carlsbad, CA, USA, 10091148), GlutaMAX (Thermo Fisher Scientific, Gibco™, 35050061) and Penicillin-Streptomycin (Welgene, Gyeongsansi, South Korea, LS202-02) ), and for short-term treatment, DMEM (Gibco™, 31053028) with 10% charcoal stripped FBS (Gibco™, A3382101), and GlutaMAX (Gibco™, 35050061) was used.

extract_protocol:
For ChIP-seq, MCF-7 cells were crosslinked for 10 (MYC, E2F1 and TOP1) or 15 (other protein) min at RT by crosslinking buffer (50mM HEPES pH 8.0, 100mM NaCl, 1mM EDTA pH 8.0, 0.5mM EGTA pH 8.0) with 1% formaldehyde (Sigma-Aldrich, F8775-4X25ML) followed by quenching with 125mM glycine (Daejung, Siheung-si, South Korea, 4068-4105) for 5 min. Cells were washed with ice cold 1X PBS and pellets were stored at -80℃.
ChIP-seq libraries were generated with NEBNext End Repair Module (NEB, E6050L), NEBNext dA-Tailing Module (NEB, E6053L), Quick Ligation Kit (NEB, M2200L), and NEBNext Multiplex Oligos for Illumina (NEB, E7335S, E7500S, E7710S) according to the manufacturer's protocol.

treatment_protocol: For the short-term condition, MCF-7 cells were treated with DMSO or 100 nM Q901 for 1 h followed by 1 h of EtOH/E2 treatment (the E2 condition was not used in this study). For long-term treatment, MCF-7 cells were treated with DMSO or 100 nM Q901 for 4, 24 h. For TPT treatment, cells were treated with 100 nM Q901 for 2 h followed by 1 μM TPT for 6 h.

tag: cell line

tag: treatment

value: DMSO 24h

tag: chip antibody

value: pan Rpb1 CTD (Cell Signaling Technology, 2629)


title: CD8 T cells, 4 stimulations normoxia,  rep 1

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

description:
D1784N
In the processed data file, there are these columns: Geneid (ENSEMBLE ID), Chr (Chromosome where gene is anotated), Start (position of the chromosome where the gene starts), End position of the chromosome where the gene ends), Strand (DNA strand that codifies for the gene, + or -), Length (length of the gene in base pairs), the following columns are the names for each studied sample

library_source: transcriptomic

data_processing:
Using STAR software [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/], FASTQ files were aligned to Genome data base (GRCh38) and read counts obtained for each gene
Assembly: GRCh38
Supplementary files format and content: A matrix is generated as a plain text file (*.txt) with Program featureCounts v2.0.3 (Command:"featureCounts" "-p" "--primary" "-C" "-t" "exon" "-g" "gene_id" "-a"), in which each column is a sample, each row is a gene (ensembl_ID), and in each cell indicates the number of raw counts obtained by STAR per sample and gene.

molecule: total RNA

source_name: PBMC

growth_protocol: Human peripheral blood mononuclear cells (PBMCs) were isolated from buffy coats of blood donors by Ficoll-Paque Plus (Cytiva Cat. #: 17144003) density centrifugation (1200 xg for 10 min at RT) using SepMate-50 tubes (StemCell Cat. #: 85450). CD8+ T cells were isolated from PBMCs using the EasySep Human CD8+ T Cell Isolation Kit (StemCell Cat. #: 17953RF) and a RoboSep cell separator (StemCell) according to the manufacturer’s indications. Human CD8+ T cells were stimulated four times (every two days) on culture plates coated with 5 μg/mL anti-CD3 (BD Biosciences Cat. #: 567118) and soluble 1 μg/mL anti-CD28 antibodies (Invitrogen Cat. #: 16-0289-81) in RPMI 1640 GlutaMAX medium (Gibco Cat. #: 61870044) supplemented with 10% FBS (Thermo Fisher Cat. #: 10270106) and 100 IU/mL human IL-2 IS premium grade (Miltenyi Biotec Cat. #: 130-097-748). The last two stimulations were performed in a glucose-reduced medium composed of glucose-free RPMI (Gibco Cat. #: 11879020) and RPMI 1640 GlutaMAX media (1:3), under normoxia (21% O2) or hypoxia (1% O2). T cell concentration in the initial and following stimulations was 1 million cells/mL and 0.5 million/mL, respectively.

extract_protocol:
NucleoSpin RNA kit (Macherey-Nagel Cat. No.740955.250), with Dnase treatment. Total RNA was eluted in RNase-free water
Sequencing libraries were prepared following the protocol "TruSeq Stranded mRNA Sample Preparation Guide (Part#15031047 Rev.E)" with the “TruSeq® Stranded mRNA Library Prep” kit  (Illumina Inc. Cat. # 20020594) and TruSeq RNA CD Index Plate (96 Indexes, 96 Samples) (Illumina Inc. Cat. # 20019792)

treatment_protocol: CD8+ T cells were stimulated once or four times. From the third stimulacion a reduction to 66% glucose was performed and T cell were subjected to either normoxia or hypoxia

tag: tissue

value: PBMC

tag: cell type

value: CD8+ T cells


title: pan pol II Q901 4h rep2

description: Library name: pan-pol-II-QS1409-4h-rep2


title: Y665F_male_rep1

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

country: USA

institute: National Institutes of Health (NIH)

description: Library name: Sample 5

data_processing:
The fastq files were subjected to QC analyses using the FastQC tool (version 0.11.9). Quality filtering and alignment of the raw reads was done using Trimmomatic (version 0.36) and subsequently aligned to the reference genome mm10 applying STAR RNA-seq aligner (version 2.7.11b), Samtools (version 1.9) and Picard (version 2.9.2). Htseq (version 0.9.1) was applied to calculate raw read counts.
Assembly: mm10
Supplementary files format and content: raw read counts from RNA-seq samples

organism: Mus musculus

source_name: Adipose

growth_protocol: Total RNA-seq was done for the  adipose tissue of wild-type and mutant mice carrying a point mutation in Stat5-Y665.

extract_protocol:
Total RNA was extracted from the tissue from mice and purified with RNeasy Plus Mini Kit (Invitrogen, 12183018A). Ribosomal RNA was removed from 1ug of total RNAs and cDNA was synthesized using SuperScript III (Invitrogen). Libraries for sequencing were prepared according to the manufacturer’s instructions with TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina, RS-122-2301) and paired-end sequencing was done with a Novaseq 6000 instrument (Illumina).
Libraries for sequencing were prepared using standard New England Biolabs's protocols.

value: Adipose

tag: strain

tag: Stage

value: 2-month-old age

tag: genotype

tag: Sex

value: male


title: CD8 T cells, 1 stimultation,  rep 3

description:
D1991
In the processed data file, there are these columns: Geneid (ENSEMBLE ID), Chr (Chromosome where gene is anotated), Start (position of the chromosome where the gene starts), End position of the chromosome where the gene ends), Strand (DNA strand that codifies for the gene, + or -), Length (length of the gene in base pairs), the following columns are the names for each studied sample


title: WT_male_rep4

description: Library name: Sample 4

value: WT


title: CDK7 DMSO 24h rep1

description: Library name: CDK7-DMSO-24h-rep1

value: CDK7 (Bethyl, A300-405A)


title: pan pol II, Ser5P, Ser2P, CDK7 4h, 24h input rep2

description: Library name: pan-pol-II-Ser5P-Ser2P-CDK7-input-4h-24h-rep2


title: CDK7 Q901 4h rep1

description: Library name: CDK7-QS1409-4h-rep1


title: WT_male_rep3

description: Library name: Sample 3


title: pan pol II DMSO 4h rep2

description: Library name: pan-pol-II-DMSO-4h-rep2

value: DMSO 4h


title: CD8 T cells, 1 stimultation,  rep 2

description:
D1951
In the processed data file, there are these columns: Geneid (ENSEMBLE ID), Chr (Chromosome where gene is anotated), Start (position of the chromosome where the gene starts), End position of the chromosome where the gene ends), Strand (DNA strand that codifies for the gene, + or -), Length (length of the gene in base pairs), the following columns are the names for each studied sample


title: CDK7 DMSO 4h rep1

description: Library name: CDK7-DMSO-4h-rep1


title: CDK7 Q901 24h rep1

description: Library name: CDK7-QS1409-24h-rep1


title: CD8 T cells, 1 stimultation,  rep 1

description:
D1781
In the processed data file, there are these columns: Geneid (ENSEMBLE ID), Chr (Chromosome where gene is anotated), Start (position of the chromosome where the gene starts), End position of the chromosome where the gene ends), Strand (DNA strand that codifies for the gene, + or -), Length (length of the gene in base pairs), the following columns are the names for each studied sample


title: Ser2P Q901 24h rep1

description: Library name: Ser2P-QS1409-24h-rep1

value: phospho-Rpb1 CTD Ser2 (Abcam, ab5095)


title: WT_male_rep2

description: Library name: Sample 2


title: rp_larp6kd_rep2

city: La Jolla

first: Brian

last: Yee

state: CA

address: 9500 Gilman Dr

department: Health

institute: UCSD

data_processing:
for ribosome profiling, reads were processed with CTGTAGGCACCATCAAT adapter trimming using cutadapt.
Bowtie1 alignment was used for hg38 rrna and trna.
Unaligned reads from previous step were aligned to genomic hg38 , followed to trasncriptomic hg38.
Assembly: GRCh38
Supplementary files format and content: wiggle files of 5' aligned rna-seq and ribosome profiling p-site. Each file is separated for plus and minus strand.

source_name: HSCs

growth_protocol: HSCs were cultured in DMEM with 10% FBS at 37C.

extract_protocol: For RNA-seq cells were harvested with Trizol followed by chloroform-based RNA exraction. For Ribosome profiling- Cells were treated with CHX 100ug/mL for 1min, followed by PBS wash supllemented with 100ug/mLCHX and lysed with lysis buffer (12.5 mM Tris, pH 7.0; 7.5mM Tris, pH 8.0; 150 mM NaCl; 5 mM MgCl2; 100 μg/mL cycloheximide; 1 mM DTT; 1% (v/v) Triton X-100; 20 U/mL DNase). cell lysate were collected by centrifugation 10min 15,000xg 4c. Lysate were treated 45min with 250U RNAse I, and quenched with SUPERase Inhibitor, and ribosome pellet was collected by 1h 100k rpm centrifugation  at 4c with TRIZOL, and chloroform-based separation.

treatment_protocol: dsi-control or dsiLARP6 HSCs

value: HSCs

value: Hepatic Stellate Cells

value: LARP6 kd


title: Ser2P DMSO 4h rep1

description: Library name: Ser2P-DMSO-4h-rep1


title: Ser2P Q901 4h rep1

description: Library name: Ser2P-QS1409-4h-rep1


title: Y665F_female_PolII_rep2

description: Library name: Sample 24

data_processing:
The fastq files were subjected to QC analyses using the FastQC tool (version 0.11.9). Quality filtering and alignment of the raw reads was done using Trimmomatic (version 0.36) and Bowtie (version 1.2.2) and Samtools (version 1.8), with the parameter ‘-m 1’ to keep only uniquely mapped reads, using the reference genome mm10. Homer30 (version 4.9.1) software was applied to generate bedGraph files, seperately. Integrative Genomics Viewer (version 2.3.98) was used for visualization with the parameter of -m 1 to retrieve only uniquely mapped reads, and Picard Tools to remove duplicates. Homer software was applied  for the generation of bedGraph files.
Assembly: mm10
Supplementary files format and content: bedgraph

source_name: Liver

growth_protocol: Mouse liver tissues were harvested at 2-month-old age for wild-type and mutant mice carrying a point mutation in Stat5b-Y665.

extract_protocol:
Chromatin was fixed with formaldehyde (1% final concentration) for 10min at room temperature, and then quenched with glycine (0.125 M final concentration). Samples were processed as previously described. The following antibodies were used for ChIP-seq: STAT5A (Santa Cruz Biotechnology, sc-271542), STAT5B (ThermoFisher scientific, 13-5300), NFIB (Sigma-Aldrich, HPA003956), H3K27ac (Abcam, ab4729) and RNA polymerase II (Abcam, ab5408). Libraries for next-generation sequencing were prepared and sequenced with a HiSeq 3000 or Novaseq 6000 instrument (Illumina). Libraries for sequencing were prepared using standard Illumina protocols.
Libraries for sequencing were prepared using standard Illumina protocols.

value: Liver

tag: chip-seq antibody

value: RNA polymerase II (Abcam, ab5408)


title: rp_control_rep2

value: dsi-control


title: Ser5P DMSO 24h rep1

description: Library name: Ser5P-DMSO-24h-rep1

value: DMSO 24h

value: phospho-Rpb1 CTD Ser5 (Abcam, ab5408)


title: Ser5P Q901 24h rep1

description: Library name: Ser5P-QS1409-24h-rep1


title: Ser5P Q901 4h rep1

description: Library name: Ser5P-QS1409-4h-rep1


title: CD8 T cells, 4 stimulations normoxia,  rep 4

description:
D2074N
In the processed data file, there are these columns: Geneid (ENSEMBLE ID), Chr (Chromosome where gene is anotated), Start (position of the chromosome where the gene starts), End position of the chromosome where the gene ends), Strand (DNA strand that codifies for the gene, + or -), Length (length of the gene in base pairs), the following columns are the names for each studied sample

value: PBMC


title: Ser2P DMSO 24h rep1

description: Library name: Ser2P-DMSO-24h-rep1


title: Ser5P DMSO 4h rep1

description: Library name: Ser5P-DMSO-4h-rep1


title: Y665F_female_PolII_rep1

description: Library name: Sample 23


title: Y665F_female_H3K27ac_rep2

description: Library name: Sample 22

value: H3K27ac (Abcam, ab4729)


title: rp_control_rep1


title: WT_male_rep1

description: Library name: Sample 1

value: Adipose


title: pan pol II Q901 24h rep1

description: Library name: pan-pol-II-QS1409-24h-rep1

value: pan Rpb1 CTD (Cell Signaling Technology, 2629)


title: rnaseq_larp6kd_rep2


title: pan pol II DMSO 24h rep1

description: Library name: pan-pol-II-DMSO-24h-rep1


title: pan pol II Q901 4h rep1

description: Library name: pan-pol-II-QS1409-4h-rep1


title: Y665F_female_H3K27ac_rep1

description: Library name: Sample 21

value: 2-month-old age


title: pan pol II, Ser5P, Ser2P, CDK7 4h, 24h input rep1

description: Library name: pan-pol-II-Ser5P-Ser2P-CDK7-input-4h-24h-rep1


title: rnaseq_larp6kd_rep1


title: pan pol II DMSO 4h rep1

description: Library name: pan-pol-II-DMSO-4h-rep1


title: rnaseq_control_rep2

value: WT


title: Y665F_female_STAT5B_rep1

description: Library name: Sample 19

value: STAT5B (ThermoFisher scientific, 13-5300)


title: E2F1 1h input rep2

description: Library name: E2F1-input-rep2


title: rnaseq_control_rep1


title: E2F1 Q901 1h, EtOH 1h rep1

description: Library name: E2F1-QS1409-1h-EtOH-1h-rep1

value: Q901 1h, EtOH 1h

value: E2F1 (Cell Signaling Technology, 3742)


title: E2F1 DMSO 1h, EtOH 1h rep2

description: Library name: E2F1-DMSO-1h-EtOH-1h-rep2

value: DMSO 1h, EtOH 1h


title: Y665H_PolII_rep2

description: Library name: Sample 18


title: Y665F_female_STAT5B_rep2

description: Library name: Sample 20


title: TGFb_IN_rep2

data_processing:
Data was processed using the eCLIP pipeline and available at: http://github.com/yeolab/eclip
Unique Molecular Identifiers (UMIs) were extracted from raw sequencing reads with umi_tools extract
Post-umi-extracted reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using cutadapt.
Trimmed reads were mapped against RepBase with STAR to remove reads mapping to repetitive sequences (--outFilterMultimapNmax 30 --alignEndsType EndToEnd --outFilterMultimapScoreRange 1 --outSAMmode Full --outFilterType BySJout --outSAMtype BAM Unsorted --outFilterScoreMin 10 --outReadsUnmapped Fastx --outSAMattributes All)
Remaining reads were mapped to the appropriate genome build (GRCh38) using STAR aligner (--outFilterMultimapNmax 1 --alignEndsType EndToEnd --outFilterMultimapScoreRange 1 --outSAMmode Full --outFilterType BySJout --outSAMtype BAM Unsorted --outFilterScoreMin 10 --outReadsUnmapped Fastx --outSAMattributes All)
Uniquely mapped reads were removed of PCR duplicates with umi_tools
Peak clusters were identified with CLIPper, available at: https://github.com/YeoLab/clipper
Clusters enriched over corresponding size-matched input (SMInput) were identified using a custom Perl script, available in the main eCLIP repository as: overlap_peakfi_with_bam.pl
Overlapping enriched clusters (peaks) were merged with a custom perl script, available in the main eCLIP repository as: compress_l2foldenrpeakfi_for_replicate_overlapping_bedformat.pl
Assembly: GRCh38
Supplementary files format and content: bigwigs contain RPM-normalized read densities of uniquely-mapped reads
Supplementary files format and content: BED files contain CLIPper peak clusters. Columns 4 and 5 describe the -log10(p-value) and log2(fold) enrichment IP over corresponding SMInput.
Supplementary files format and content: Tab-delimited text file contains the translation efficiency table comparing "rp" to "rnaseq" samples

extract_protocol:
cells were lysed with eCLIP buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate), and RNA was fragmented using RNAse I. Then, samples were subjected for overnight incubation at 4C with corresponding beads-conjugated antibodies.
RNA fragments 3' end were dephosphorylated with FastAP (Thermo) and PNK (NEB), followed by 3' barcoded linker ligation (T4 RNA ligase I, NEB). Then, samples were ran on protein gel for an hour on 150V, followed by overnight transfer on nitrocellulose membrane. protein kDa size and 75kDa above it were extracted for IP and size-matched input and extracted from membrane with proteinase K. the samples subjected to reverse transcription (SSIII Thermo Fisher), and subsequent ExoSAP-IP and EDTA, NaOH and HCl treatment for degradation of excess RT primers and rna template. Additional 3' end ligation and PCR amplification (Q5 2X mix NEB) generated the final library products.

treatment_protocol: cells in 10cm plates were washed once with PBS followed by crosslinking with UV (254 nm, 400 mJ/cm2). TGFb concentration in treated cells was TGFβ1 (5 ng/ml)

value: HSCs

value: Hepatic Stellate Cells

value: TGFb

tag: rip antibody

value: none (input)


title: E2F1 Q901 1h, EtOH 1h rep2

description: Library name: E2F1-QS1409-1h-EtOH-1h-rep2


title: E2F1 1h input rep1

description: Library name: E2F1-input-rep1


title: MYC Q901 1h, EtOH 1h rep2

description: Library name: MYC-QS1409-1h-EtOH-1h-rep2

value: c-Myc/N-Myc (D3N8F) (Cell Signaling Technology, 13987)


title: E2F1 DMSO 1h, EtOH 1h rep1

description: Library name: E2F1-DMSO-1h-EtOH-1h-rep1


title: TGFb_IP_rep2


title: MYC 1h input rep2

description: Library name: MYC-input-rep2


title: Y665H_PolII_rep1

description: Library name: Sample 17

value: Liver

value: RNA polymerase II (Abcam, ab5408)


title: MYC Q901 1h, EtOH 1h rep1

description: Library name: MYC-QS1409-1h-EtOH-1h-rep1


title: TGFb_IN_rep1


title: TGFb_IP_rep1


title: Y665H_H3K27ac_rep2

description: Library name: Sample 16


title: Y665H_H3K27ac_rep1

description: Library name: Sample 15


title: MYC 1h input rep1

description: Library name: MYC-input-rep1


title: MYC DMSO 1h, EtOH 1h rep1

description: Library name: MYC-DMSO-1h-EtOH-1h-rep1


title: CDK7 DMSO 1h, EtOH 1h rep3

description: Library name: CDK7-DMSO-1h-EtOH-1h-rep3

value: CDK7 (Bethyl, A300-405A)


title: ctrl_IP_rep2

source_name: DMSO

value: Untreated


title: CDK7 1h input rep3

description: Library name: CDK7-input-rep3


title: Y665H_STAT5B_rep2

description: Library name: Sample 14


title: ctrl_IN_rep2


title: CDK7 Q901 1h, EtOH 1h rep3

description: Library name: CDK7-QS1409-1h-EtOH-1h-rep3


title: Y665H_STAT5B_rep1

description: Library name: Sample 13


title: Y665F_PolII_rep2

description: Library name: Sample 12


title: CDK7 Q901 1h, EtOH 1h rep2

description: Library name: CDK7-QS1409-1h-EtOH-1h-rep2


title: CDK7 Q901 1h, EtOH 1h rep1

description: Library name: CDK7-QS1409-1h-EtOH-1h-rep1


title: CDK7 DMSO 1h, EtOH 1h rep2

description: Library name: CDK7-DMSO-1h-EtOH-1h-rep2


title: Y665F_PolII_rep1

description: Library name: Sample 11


title: CDK7 DMSO 1h, EtOH 1h rep1

description: Library name: CDK7-DMSO-1h-EtOH-1h-rep1


title: ctrl_IP_rep1


title: ctrl_IN_rep1


title: CDK7 1h input rep2

description: Library name: CDK7-input-rep2


title: Y665F_H3K27ac_rep2

description: Library name: Sample 10

value: H3K27ac (Abcam, ab4729)


title: YSH1_GFP

city: Fayetteville

first: Pieter

middle: Jan

last: Koopmans

state: AR

address: 155 N Stadium Drive

department: Cell and Molecular Biology

institute: University of Arkansas - Fayetteville

description:
Library name: zr17671_1
Young adult mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload sham surgery

data_processing:
For total RNA-Seq, raw FASTQ files were imported into Partek Cloud Platfor aligned to mm39 with STAR 2.7.8a with default parameters. Aligned reads were quantified to annovation model and filtered to exclude genes with maximum count of less than 5. Normalized with DESeq2 median ratio. Tested for significance using DESeq2, with lowest average coverage filter of 1 prior to false discovery correction.
For myonuclear DNA RRBS (methylation), Base calling with Illumina Software. Raw FASTQ files were adapter, filled-in nucleotides, and quality trimmed using TrimGalore. The effect of trimming and overall quality distribution was determined using FastQC. Alignment was performed using Bismark. Read totals were called using Bismark Methylation Extractor. Bismark coverage data (.cov files) are generated from Bismark Methylation Extractor and contains the methylated count and total count at each position within the genome
Following library construction, libraries were sequenced on the Illumina Nova NextSeq X Plus System by Novogene to 200 million reads per sample. Raw FASTQ files were imported into Cell Ranger 9.0 for alignment to reference transcriptome, and report of UMIs/reads/nuclei barcodes. h5 files were exported and imported into Python environment, where ambient RNA correction tool CellBender was used. Processed files were imported into Seurat v5, and data quality control was performed by removing nuclei with <200 UMIs, nuclei with >5% of mitochondrial reads, and genes expressed in <3 nuclei.
Assembly: mm39
Supplementary files format and content: For total RNA-seq, DESeq2 Normalized Counts. For RRBS, bismark files.
Supplementary files format and content: For single myonucleus RNA-seq, .h5 Cell Ranger files

source_name: Plantaris, myonuclei

extract_protocol:
Total RNA was extracted via Trizol-Chloroform precpitiation of RNA using Zymo Direct-Zol RNA extraction kit. Genomic DNA was extracted from myonuclei isolated from the plantaris muscle via fluorescent activated nuclear sorting. The Quick-DNA™ Miniprep Plus kit (Zymo Research, D4068) was used as specified in the protocol. For single myonucleus RNA-seq, myonuclei were isolated from plantaris muscle chunks were minced with scissors in homogenization buffer (500 µl HEPES (1 M) 3 ml KCl (1 M) 250 µl spermidine (100 mM) 750 µl spermine tetrahydrochloride (10 mM) 10 ml EDTA (10 mM) 250 µl EGTA (100 mM) 2.5 ml MgCl (100 mM) 5.13 g sucrose, Dounce homogenized on ice with a plastic pestle in homogenization buffer, then passed through a 40 µm and 20 µm filter into directly into the MACSQuant High Speed Tyto Cardtridge. PI was added to label nuclei. Fluorescently labeled nuclei (GFP+/PI+) were purified via Fluorescence-activated nuclear sorting (FANS) and sorted into re-suspension buffer (1X PBS, 1% BSA, 0.2U/uL RNase inhibitors).
Total RNA-seq libraries were prepared for seqeuencing using standard Illumina protocols and underwent 150 bp PE sequencing. The DNA RRBS was rered to Zymo Research Corporation (RRBS Basic Srvise Package, 15-20 million read pairs per sample). Myouclei were mixed with reverse transcriptase buffer and loaded into the 10X Chromium system using the Single Cell 3’ Reagent Kit v4 according to the manufacturer’s protocol. Following library construction, libraries were sequenced on the Illumina NovaSeq X Plus System at the Novogene.

treatment_protocol: Mice were treated with doxycycline for 7 days to label myonuclei with green fluorescent protein, followed by a 7-13 day washout period. Then mice underwent 72 hours of ambulation after synergist ablation mechanical overload (MOV) surgery.

value: Plantaris, myonuclei

value: HSA-GFP

value: 72 hour Sham

tag: batch


title: Ser2P DMSO 1h, EtOH 1h rep2

description: Library name: Ser2P-DMSO-1h-EtOH-1h-rep2

value: phospho-Rpb1 CTD Ser2 (Abcam, ab5095)


title: Y665F_H3K27ac_rep1

description: Library name: Sample 9

value: 2-month-old age


title: rp_larp6kd_rep1

value: LARP6 kd


title: CDK7 1h input rep1

description: Library name: CDK7-input-rep1


title: pan pol II Q901 1h, EtOH 1h rep2

description: Library name: pan-pol-II-QS1409-1h-EtOH-1h-rep2

value: Q901 1h, EtOH 1h

value: pan Rpb1 CTD (Cell Signaling Technology, 2629)


title: APEX2-DFCP1 construct, no H₂O₂ replicate 2

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

description: Library name: DFCP1_omit_3

data_processing:
The raw data from the DNBSEQ platform was processed using nf-core/rnaseq v3.14.0 (doi: https://doi.org/10.5281/zenodo.1400710) of the nf-core collection of workflows86.  Sequences were aligned to the human GRCh38 genome and v45 GENCODE annotations using STAR 2.7.9a87 and quantified using Salmon 1.10.188, generating gene based read counts and TPM files. Limma-Voom was used to quantify the adjusted P-value and fold change of genes between H2O2 groups and omit conditions from APEX2-DFCP1, -Cyto-V5, and -Perilipin groups. 
Assembly: GRCh38
Supplementary files format and content: Excel file RNAseqYunpingXueLimma.xlsx containing Lmma-Voom fold cahnge analysis

source_name: Hela

growth_protocol: Cell  HeLa  cells were cultured in complete medium (Dulbecco’s Modified Eagle’s Medium containing 10% fetal bovine serum and 1% penicillin-streptomycin) in the incubator at 37°C with 5% CO2. APEX2 expressing cells were seeded on 15 cm plates until they were 90% confluent. 24 h before collection, APEX2 expression was induced with doxycycline (40 µg/mL).

extract_protocol:
Molecules in proximity to APEX2 constructrs were biotinylated following hydrogen peroxide activation. Proximity-labeled RNAs were enriched using streptavidin-coated beads. RNA was extracted from streptavidin pulldown material for downstream analyses.
RNA sequencing was performed on mRNAs proximity-labeled byAPEX2 constructs. RNA-seq libraries were generated from enriched RNA samples and used for transcriptome-wide analysis of proximity-associated mRNAs.

treatment_protocol: On the day of collection, cells were treated with Torin1 to induce autophagy. APEX2 labeling was then initiated by changing the medium to fresh DMEM medium containing 500 mM (Biotin-Phenol/ biotin-tyramide) BP and Torin1. The cells were incubated at 37°C under 5% CO2 for 30 min, followed by gentle agitation for one min after the addition of 1 mM H2O2. The unlabeled controls were processed identically, except that the H2O2 addition step was omitted. The APEX2 reaction was quenched by replacing the medium with an equal volume of quenching buffer (5 mM Trolox, 10 mM sodium ascorbate and 10 mM sodium azide in DPBS) and gently agitated plate for 10 min. Cells were further washed with cold PBS for two times, scraped with cell lifters, and transferred to 1.5-mL Eppendorf tubes. The cells were pelleted by centrifugation at 300 g for three minutes at 4°C and stored at -80°C for further experiments.

tag: replicate

value: Hela

tag: genetic modification

value: APEX2-DFCP1 plasmid

value: H₂O₂ -


title: Ser5P Q901 1h, EtOH 1h rep2

description: Library name: Ser5P-QS1409-1h-EtOH-1h-rep2

value: phospho-Rpb1 CTD Ser5 (Abcam, ab5408)


title: Y665F_STAT5B_rep1

description: Library name: Sample 7

value: Liver

value: STAT5B (ThermoFisher scientific, 13-5300)


title: Ser5P DMSO 1h, EtOH 1h rep2

description: Library name: Ser5P-DMSO-1h-EtOH-1h-rep2

value: DMSO 1h, EtOH 1h


title: YSH2_GFP

description:
Library name: zr17671_3
Young adult mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload sham surgery,


title: APEX2-DFCP1 construct, no H₂O₂ replicate 1

description: Library name: DFCP1_omit_1


title: Ser2P Q901 1h, EtOH 1h rep2

description: Library name: Ser2P-QS1409-1h-EtOH-1h-rep2


title: WT_PolII_rep2

description: Library name: Sample 6

value: WT

value: RNA polymerase II (Abcam, ab5408)


title: pan pol II DMSO 1h, EtOH 1h rep2

description: Library name: pan-pol-II-DMSO-1h-EtOH-1h-rep2


title: Ser2P Q901 1h, EtOH 1h rep1

description: Library name: Ser2P-QS1409-1h-EtOH-1h-rep1


title: WT_PolII_rep1

description: Library name: Sample 5


title: APEX2-DFCP1 construct, H₂O₂ replicate 1

description: Library name: DFCP1_h202_1

value: H₂O₂ +


title: Ser5P DMSO 1h, EtOH 1h rep1

description: Library name: Ser5P-DMSO-1h-EtOH-1h-rep1


title: MYC DMSO 1h, EtOH 1h rep2

description: Library name: MYC-DMSO-1h-EtOH-1h-rep2

value: c-Myc/N-Myc (D3N8F) (Cell Signaling Technology, 13987)


title: Ser2P DMSO 1h, EtOH 1h rep1

description: Library name: Ser2P-DMSO-1h-EtOH-1h-rep1


title: Y665F_STAT5B_rep2

description: Library name: Sample 8


title: pan pol II, Ser5P, Ser2P 1h input rep2

description: Library name: pan-pol-II-Ser5P-Ser2P-input-rep2


title: APEX2-DFCP1 construct, H₂O₂ replicate 2

description: Library name: DFCP1_h202_3


title: Ser5P Q901 1h, EtOH 1h rep1

description: Library name: Ser5P-QS1409-1h-EtOH-1h-rep1


title: APEX2-V5 construct, H₂O₂ replicate 3

description: Library name: 14_cyto_h202

value: APEX2-V5 plasmid


title: pan pol II DMSO 1h, EtOH 1h rep1

description: Library name: pan-pol-II-DMSO-1h-EtOH-1h-rep1


title: pan pol II, Ser5P, Ser2P 1h input rep1

description: Library name: pan-pol-II-Ser5P-Ser2P-input-rep1


title: APEX2-V5 construct, H₂O₂ replicate 2

description: Library name: 13_cyto_h202


title: WT_H3K27ac_rep1

description: Library name: Sample 3

value: H3K27ac (Abcam, ab4729)


title: WT_STAT5B_rep2

description: Library name: Sample 2

value: 2-month-old age


title: APEX2-V5 construct, H₂O₂ replicate 1

description: Library name: 12_cyto_h202


title: sci_L3_Strand_seq_yi314

city: Los Angeles

first: Yi

last: Yin

address: 695 Charles E. Young Dr. S.

department: Human Genetics

institute: University of California, Los Angeles

description: Library name: nextseq190927_yi314

data_processing:
Reads were aligned to hs37d5 or a hybrid reference of hs37d5 and mm10. Using the 1st and 2nd barcodes in the read names, the 3rd round barcode BAM files were additionally split into individual single cell BAMs. Barcode combinations with less than 10000 reads were discarded. Single cell hybrid genome BAMs were additionally split by mouse or human contigs, retaining only standard chromosomes. Each BAM was filtered for proper read pairs, a maximum insert size of 2000, and excessively soft-clipped reads based on a maximum soft-clipping ratio of 0.5 (defined as the number of soft-clipped bases over the number of matched bases). To avoid collisions, any split and filtered BAM that had less than 30% of total reads of the correct species or less than 10000 reads was discarded.
Assembly: mm10, hs37d5
Supplementary files format and content: Final breakpoint files, breakpoint files without the region filter, and sciStrand_objects provided as processed data.

source_name: cell line

growth_protocol: BJ-5ta (CRL-4001, ATCC) and Patski (gift from Disteche lab) cells were cultured in DMEM medium supplemented with 10% FBS and 1x Pen-Strep. HAP1 cells were cultured in IMDM medium supplemented 10% FBS and 1x Pen-Strep. All cells were cultured at 37°C, 5% CO2. For sci-L3-Strand-seq, cells were cultured with BrdU at 40 µM final concentration for 24 hours prior to fixation. HAP1 knockout cells for LIG4- (referred to as HAP1lig4-) are as described in (Findlay et al. 2018) (gift from Shendure lab).

extract_protocol: Fixation and nucleosome depletion was performed as previously described in ‘Methods and molecular design of sci-L3-WGS and sci-L3-target-seq’, subsections ‘Single Cell Preparation and Nucleosome Depletion’ and ‘Tagmentation (first-round barcodes) and ligation (second-round barcodes)’ (Yin et al. 2019). Notably, cells were trypsinized and fixed with 37% formaldehyde (final 1.5% concentration) in 1x PBS at a cell density of 1 million/mL for 10 minutes at room temperature with gentle tube inversion. For first round barcoding,nuclei were distributed into individual wells. Any remaining nuclei were stained with DAPI at a final concentration of 5 ng/µL and used for FACS as previously described (Chovanec and Yin 2025). After the ligation reaction was stopped by the addition of the stop solution (lysis buffer (LB: 60 mM Tris-Ac pH 8.3, 2 mM EDTA pH 8.0, 15 mM DTT) with 0.1% Triton-X100 (LBT)), nuclei were pooled and stained with Hoechst-33258 to a final concentration of 5 ng/µL and the quenched population was sorted (100-300 nuclei per well) into a 96-well plate containing 3 µL of LB. Right after gap extension with the Bst WarmStart 2.0 polymerase at 68°C for 5 minutes and its inactivation with 80°C for 10 minutes, Hoechst-33258 was added at a final concentration of 10ng/µL and incubated at room temperature for 10 minutes in the dark. A 1 or 5 minute exposure in a Bio-Rad Gel Doc with a 365nm UV bulb, or a dose of 27-4000 mJ/cm2 was administered with a UVP crosslinker (CL-3000L) as previously described (Chovanec and Yin 2025). At this stage, each well had a volume of around 7.7 µL, to which 0.3uL of USER enzyme (a mix of uracil DNA glycosylase and endonuclease VIII, referred to as UDG+EndoVIII in the text, NEB) was added and incubated at 37°C for 15 minutes. Next, 0.9 µL of its inhibitor UGI (NEB) was added with a further incubation at 37°C for 10 minutes. Finally, the T7 in vitro transcription system was assembled by adding 2 µL H2O, 2 µL T7 Pol mix and 10 µL rNMP mix (NEB, HiScribe T7 Quick High Yield RNA Synthesis Kit) and incubated at 37°C for 10-16 hours. The remaining section, ‘RNA purification, RT and SSS’, was performed exactly as previously described (Yin et al. 2019).

value: cell line

value: BJ-5ta, BLM-/-

value: Combination of 2 cell lines


title: sci_L3_Strand_seq_yi311

description: Library name: nextseq190906_yi311

value: Patski, HAP1, HAP1lig4-, BJ-5ta, BLM-/-

value: Combination of 5 cell lines


title: sci_L3_Strand_seq_yi310

description: Library name: nextseq190830_yi310


title: APEX2-V5 construct, no H₂O₂ replicate 3

description: Library name: 11_cyto_omit

value: Hela

value: H₂O₂ -


title: WT_STAT5B_rep1

description: Library name: Sample 1

value: Liver


title: sci_L3_Strand_seq_yi312

description: Library name: nextseq190907_yi312

value: Patski, HAP1


title: APEX2-V5 construct, no H₂O₂ replicate 1

description: Library name: 9_cyto_omit


title: sci_L3_Strand_seq_yi309

description: Library name: nextseq190830_yi309


title: female, WT-iβARK, 5

city: Guangzhou

first: Yamei

last: Tang

state: Guangdong

address: 107 Yan Jiang West Road

department: Department of Neurology

country: China

institute: Sun Yat-Sen Memorial Hospital

description:
Library name: female-WT-iβARK-5
200

data_processing:
Low-quality reads were filtered from the raw FASTQ data using fastp (v0.23.2; https://github.com/OpenGene/fastp) with default parameters. The remaining reads were then aligned to the NCBI ribosomal database using Bowtie2 (v2.4.5; https://github.com/BenLangmead/bowtie2) to remove rRNA sequences.
The rRNA-depleted reads were aligned to the GRCm38 reference genome using HISAT2 (v2.2.1; https://github.com/DaehwanKimLab/hisat2). Transcript abundances were then quantified using RSEM (v1.3.3; https://github.com/deweylab/RSEM).
Differentially expressed genes (DEGs) were designated as those with FDR adjusted p-value < 0.05.
Assembly: GRCm38
Supplementary files format and content: Excel file include feature counts for each Sample

molecule: polyA RNA

source_name: mPFC

growth_protocol: Both female and male wild-type mice were housed in a controlled environment, including a 12-hour light/dark cycle, consistent humidity and temperature, and ad libitum access to food and water.

extract_protocol:
Total RNA was extracted from mPFC tissues using the RNeasy Mini Kit (74106, QIAGEN, Germany). RNA concentration was quantified using the Qubit 3.0 and Nanodrop One (Thermo Fisher Scientific, MA, USA), while RNA integrity (RIN) was assessed using the Agilent 4200 TapeStation (Agilent Technologies, Waldbronn, Germany).
mRNA was isolated from total RNA samples meeting integrity criteria (RIN > 7) using poly(T) oligo-attached magnetic beads, followed by processing with the ALFA-SEQ Directional RNA Library Prep Kit (Findrop, China) according to the manufacturer's protocol. Library preparation and subsequent RNA sequencing were performed on an Illumina NovaSeq 6000 platform (MAGIGENE, Guangzhou, China).

treatment_protocol: Mice were injected with AAV2/5 carrying either iβARK-mCherry or mCherry alone at 3-4 months of age, and transcriptional profiles were evaluated 45 days post-intervention.

value: mPFC

value: female

value: iβARK-mCherry


title: sci_L3_Strand_seq_yi317

description: Library name: nextseq190927_yi317


title: sci_L3_Strand_seq_yi307

description: Library name: nextseq190830_yi307


title: APEX2-V5 construct, no H₂O₂ replicate 2

description: Library name: 10_cyto_omit


title: WT_H3K27ac_rep2

description: Library name: Sample 4

value: WT


title: sci_L3_Strand_seq_yi305

description: Library name: nextseq190830_yi305


title: female, WT-iβARK, 3

description:
Library name: female-WT-iβARK-3
198


title: sci_L3_Strand_seq_yi308

description: Library name: nextseq190907_yi308


title: female, WT-iβARK, 4

description:
Library name: female-WT-iβARK-4
199


title: sci_L3_Strand_seq_yi287

description: Library name: nextseq190419_yi287


title: APEX2-Perilipin construct,  H₂O₂ replicate 3

description: Library name: 6_peri_h2o2

value: APEX2-Perilipin plasmid

value: H₂O₂ +


title: sci_L3_Strand_seq_yi284

description: Library name: nextseq190419_yi284


title: sci_L3_Strand_seq_yi285

description: Library name: nextseq190419_yi285


title: female, WT-iβARK, 2

description:
Library name: female-WT-iβARK-2
197


title: APEX2-Perilipin construct,  H₂O₂ replicate 2

description: Library name: 5_peri_h2o2


title: female, WT-iβARK, 1

description:
Library name: female-WT-iβARK-1
196


title: sci_L3_Strand_seq_yi282

description: Library name: nextseq190729_yi282


title: Donor 3, Thoracic, simultaneous ATAC and H3K4me1, sample 3

city: Madison

first: Abbas

middle: Haider

last: Rizvi

state: WI

address: 1500 Highland Ave, Room 715 Room 715

department: Neuroscience

institute: University of Wisconsin-Madison

description: Library name: STAB_Thoracic_H3K4me1_Sample3

data_processing:
Non-mapping sequences were removed from fastq files and histone-associated barcodes were tagged to paired-end reads.
Bio-Rad ATAC-seq analysis toolkit was used for read mapping and nuclei demultiplexing
Sinto was used for barcode de-crosstalk
MACS2 v2.2.7.1 was used for peak calling
ArchR v1.0.3 was used for nuclei quality control filtration
Assembly: GRCh38
Supplementary files format and content: STABseq_DualCC_cells.txt Histone modification associated single nuclei demultiplexing file for all samples
Supplementary files format and content: STABseq_DualCC_matrix.mtx Histone modification associated fragments-by-nuclei file for all samples
Supplementary files format and content: STABseq_DualCC_peaks.bed Histone modification associated peaks annotations file for all samples
Supplementary files format and content: STABseq_noCC_cells.txt ATAC associated single nuclei demultiplexing file for all samples
Supplementary files format and content: STABseq_noCC_matrix.mtx ATAC associated fragments-by-nuclei file for all samples
Supplementary files format and content: STABseq_noCC_peaks.bed ATAC associated peaks annotations file for all samples

source_name: spinal cord

extract_protocol:
Spinal cord tissue was surgically resected from organ donors during organ donation. Individual nuclei were isolated through homogenization and gradient centrifugation.
Nuclei were processed through a modified Cut&Tag protocol followed by BioRad ddSeq ATAC tagmentation, with library generation using custom amplification primers following the Cut&Tag PCR extension

value: spinal cord


title: APEX2-Perilipin construct,  H₂O₂ replicate 1

description: Library name: 4_peri_h2o2


title: Donor 3, Thoracic, simultaneous ATAC and H3K4me1, sample 2

description: Library name: STAB_Thoracic_H3K4me1_Sample2


title: female, WT-mCherry, 5

description:
Library name: female-WT-mCherry-5
195

value: mCherry


title: female, WT-mCherry, 4

description:
Library name: female-WT-mCherry-4
194


title: female, WT-mCherry, 3

description:
Library name: female-WT-mCherry-3
193


title: Donor 3, Thoracic, simultaneous ATAC and H3K27me3, sample 1

description: Library name: STAB_Thoracic_H3K27me3_Sample1


title: APEX2-Perilipin construct, no H₂O₂ replicate 3

description: Library name: 3_peri_omit


title: APEX2-Perilipin construct, no H₂O₂ replicate 2

description: Library name: 2_peri_omit


title: Donor 3, Thoracic, simultaneous ATAC and H3K4me1, sample 1

description: Library name: STAB_Thoracic_H3K4me1_Sample1


title: Donor 3, Thoracic, simultaneous ATAC and H3K27ac, sample 2

description: Library name: STAB_Thoracic_H3K27ac_Sample2


title: APEX2-Perilipin construct, no H₂O₂ replicate 1

description: Library name: 1_peri_omit


title: Donor 3, Thoracic, simultaneous ATAC and H3K27ac, sample 3

description: Library name: STAB_Thoracic_H3K27ac_Sample3


title: female, WT-mCherry, 2

description:
Library name: female-WT-mCherry-2
192


title: Donor 2, Lumbar, simultaneous ATAC and H3K4me1, sample 3

description: Library name: STAB_Lumbar_H3K4me1_Sample3


title: female, WT-mCherry, 1

description:
Library name: female-WT-mCherry-1
191


title: Donor 2, Lumbar, simultaneous ATAC and H3K4me1, sample 2

description: Library name: STAB_Lumbar_H3K4me1_Sample2


title: Donor 2, Lumbar, simultaneous ATAC and H3K4me1, sample 1

description: Library name: STAB_Lumbar_H3K4me1_Sample1


title: Donor 2, Lumbar, simultaneous ATAC and H3K27me3, sample 2

description: Library name: STAB_Lumbar_H3K27me3_Sample2


title: Donor 3, Thoracic, simultaneous ATAC and H3K27ac, sample 1

description: Library name: STAB_Thoracic_H3K27ac_Sample1


title: male, WT-iβARK, 4

description:
Library name: male-WT-iβARK-4
188

value: male


title: Donor 2, Lumbar, simultaneous ATAC and H3K27me3, sample 1

description: Library name: STAB_Lumbar_H3K27me3_Sample1


title: Donor 2, Lumbar, simultaneous ATAC and H3K27ac, sample 3

description: Library name: STAB_Lumbar_H3K27ac_Sample3


title: HS-07 Heat Stroke T1

type: RNA

city: Thuwal

first: Maria

middle: de los Angeles

last: Gomez

address: 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia

department: Bioengineering

country: Saudi Arabia

institute: KAUST

description: Gene expression from heatstroke

hyb_protocol: 5.5 μg of biotinylated cDNA combined with human Clariom D arrays in Affymetrix GeneChip 645 hybridization oven at 45°C with rotation at 60 rpm for 16 hours. We then washed and stained the arrays using the Affymetrix GeneChip Fluidics Station 450

scan_protocol: GeneChip Scanner 3000 7G was used to scan the chip arrays

data_processing: Raw CEL files generated from Affymetrix Human Clariom D arrays (version 22; library: clariomdhumanhsrefseq) were processed using R (Bioconductor 3.19). Quality control and preprocessing were performed with the oligo (v1.68.2) package. Array quality was assessed using Relative Log Expression (RLE) and Normalized Unscaled Standard Error (NUSE) metrics to identify potential outlier arrays.    Background correction, quantile normalization, and summarization were carried out using the Robust Multi-array Average (RMA) algorithm, as implemented in affy (v1.82.0) and affycoretools (v1.76.0). Expression values were exported as log2-transformed probe-set intensities.    Low-abundance transcripts were filtered prior to downstream analysis. A probe set was retained only if its expression exceeded log2 intensity = 4 in at least 17 samples, corresponding to the smallest experimental group size. Probe sets not meeting this criterion were excluded.    For probe sets mapping to multiple gene identifiers, only those corresponding to protein-coding genes were retained in the final expression matrix.

label: biotin

source_name: Heat Stroke T1

label_protocol: 250 ng of total RNA were used to synthesis cDNA and fragmented cDNA labelled with biotin using the GeneChip® WT Plus Reagent Kit.          11 µg of labeled and fragmented cRNA were hybridized for 16 hours at 54 C on Clariom D Human array. After that, washing and staining of the GeneChips were performed using the Affymetrix Fluidics Station 450.          GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

extract_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated using Leucosep seperation tube. RNA was extracted using TRIzol Reagent (Invitrogen) and the SV Total RNA Isolation System (Promega, USA) following the company protocol

tag: age

tag: gender

value: Male


title: Donor 2, Lumbar, simultaneous ATAC and H3K27ac, sample 2

description: Library name: STAB_Lumbar_H3K27ac_Sample2


title: Donor 1, Thoracic spinal cord, snRNA sample 20

description: Library name: Donor1_Thoracic_Plate20

library_source: transcriptomic single cell

data_processing:
read alignment with STAR v2.7.8
nulceus-by-counts generation with Velocyto v0.17.17
Assembly: GRCh38
Supplementary files format and content: RNA_barcodes.tsv nuclei demultiplexing file for each sample
Supplementary files format and content: RNA_matrix.mtx counts-by-nucleus matrix for each sample
Supplementary files format and content: RNA_features.tsv features annotation file for each sample

molecule: nuclear RNA

extract_protocol:
Spinal cord tissue was surgically resected from a tissue donor. Individual nuclei were isolated through homogenization and gradient centrifugation.
384well plate-based snRNA-seq protocol modified from SCRB-seq.


title: Donor 2, Lumbar, simultaneous ATAC and H3K27ac, sample 1

description: Library name: STAB_Lumbar_H3K27ac_Sample1


title: male, WT-iβARK, 3

description:
Library name: male-WT-iβARK-3
187


title: male, WT-iβARK, 1

description:
Library name: male-WT-iβARK-1
185


title: Donor 2, Lumbar, simultaneous ATAC and H3K27ac, sample 4

description: Library name: STAB_Lumbar_H3K27ac_Sample4


title: Donor 1, Thoracic spinal cord, snRNA sample 19

description: Library name: Donor1_Thoracic_Plate19


title: Donor 1, Thoracic spinal cord, snRNA sample 18

description: Library name: Donor1_Thoracic_Plate18


title: male, WT-mCherry, 3

description:
Library name: male-WT-mCherry-3
184


title: Donor 1, Thoracic spinal cord, snRNA sample 14

description: Library name: Donor1_Thoracic_Plate14


title: HS-05 Heat Stroke T1

description: Gene expression from heatstroke

value: Female


title: pan pol II Q901 1h, EtOH 1h rep1

description: Library name: pan-pol-II-QS1409-1h-EtOH-1h-rep1

value: Q901 1h, EtOH 1h

value: pan Rpb1 CTD (Cell Signaling Technology, 2629)


title: male, WT-mCherry, 2

description:
Library name: male-WT-mCherry-2
183


title: Donor 1, Thoracic spinal cord, snRNA sample 17

description: Library name: Donor1_Thoracic_Plate17


title: Donor 1, Thoracic spinal cord, snRNA sample 16

description: Library name: Donor1_Thoracic_Plate16


title: HS-02 Heat Stroke T1

description: Gene expression from heatstroke


title: Donor 1, Thoracic spinal cord, snRNA sample 13

description: Library name: Donor1_Thoracic_Plate13


title: HS-03 Heat Stroke T1

description: Gene expression from heatstroke


title: male, WT-mCherry, 1

description:
Library name: male-WT-mCherry-1
181


title: male, WT-iβARK, 2

description:
Library name: male-WT-iβARK-2
186


title: Donor 1, Thoracic spinal cord, snRNA sample 12

description: Library name: Donor1_Thoracic_Plate12


title: Donor 1, Thoracic spinal cord, snRNA sample 15

description: Library name: Donor1_Thoracic_Plate15


title: HS-18 Heat Stroke T0

description: Gene expression from heatstroke

source_name: Heat Stroke T0


title: Donor 1, Thoracic spinal cord, snRNA sample 10

description: Library name: Donor1_Thoracic_Plate10


title: Donor 1, Thoracic spinal cord, snRNA sample 11

description: Library name: Donor1_Thoracic_Plate11


title: HS-01 Heat Stroke T1

description: Gene expression from heatstroke


title: HS-19 Heat Stroke T0

description: Gene expression from heatstroke


title: M6alone_1_M6alone_2, CITE-seq

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

description: Library name: M6alone_1_M6alone_2, CITE-seq

data_processing:
Demultiplexing and Counting - CellRanger v3.1.0
Assembly: 10X hosted mm10 reference with custom eGFP and tdTomato sequences
Supplementary files format and content: MEX formatted output folders corresponding to the samples
Library strategy: CITE-seq

source_name: heart

extract_protocol:
Single cell libraries were generated from non-myocytes acquired by differential adherence to plastic following langendorff digestion of mice of the following genotype: wildtype Cre controls (Myh6MerCreMer ;Wt1CreERT2;Pkp2+/+), Pkp2myoKO (Myh6MerCreMer ; Pkp2fl/fl), and Pkp2myo/epi-KO (Wt1CreERT2;Pkp2fl/fl).
TotalSeq-A antibodies (BioLegend, San Diego, CA) were added to the flow-sort antibody panel during cell labeling and following sorting, cell suspensions were loaded on a Chromium controller (10x Genomics, Pleasanton, CA, USA) to generate single-cell Gel Bead-in-Emulsions (GEMs). Single-cell RNA-Seq libraries were prepared using Chromium Next GEM Single Cell 3′ GEM, Library and Gel Bead Kit v3.1 (10x Genomics), per manufacturer’s recommendations. Briefly, the beads were dissolved, cells were lysed, and GEM reverse transcription (GEM-RT) was performed to produce barcoded, full-length cDNA. After incubation, GEMs were broken and the pooled post-GEM-RT reaction mixtures were recovered and cDNA was purified with silane magnetic beads (DynaBeads MyOne Silane Beads, ThermoFisher Scientific, Waltham, MA). cDNA was amplified by PCR and fractionated by SPRI bead size-selection to separate mRNA-derived cDNA and CITEseq amplicons. cDNA amplicon size was optimized by enzymatic fragmentation and size selection. Indexed sequencing libraries were constructed by End Repair, A-tailing, Adaptor Ligation, and PCR. In parallel, CITE-seq library construction was performed following SPRI bead purification using Q5 Hot Start HiFi Master Mix (New England Biolabs, Ipswich, MA), SI PCR primer (IDT, Coralville, IA), and indexed TruSeq Small RNA PCR primers (Illumina, San Diego, CA) as specified in Stoeckius et al. Amplified CITE-seq libraries were purified using AMPure XP (Beckman Coulter, Indianapolis, IN) beads and quantified by Qubit dsDNA assay (ThermoFisher) and Bioanalyzer HSDNA (Agilent, Santa Clara, CA) analysis.  CITE-seq libraries were pooled with 10x Genomics gene expression libraries for sequencing on Illumina’s NovaSeq 6000.

value: heart

value: 12 week old

value: Pkp2-CM KO (Myh6-MerCreMer; Pkp2-Fl/Fl)

value: TMX

tag: timepoint

value: 21 days post-TMX


title: Donor 1, Thoracic spinal cord, snRNA sample 8

description: Library name: Donor1_Thoracic_Plate08


title: M6WB_1_M6WB_2_M6WB_3, CITE-seq

description: Library name: M6WB_1_M6WB_2_M6WB_3, CITE-seq

value: Pkp2-Epi / CM KO (WT1-CreERT2; Myh6-MerCreMer; Pkp2-Fl/Fl)


title: Donor 1, Thoracic spinal cord, snRNA sample 9

description: Library name: Donor1_Thoracic_Plate09


title: Donor 1, Thoracic spinal cord, snRNA sample 7

description: Library name: Donor1_Thoracic_Plate07


title: Donor 1, Thoracic spinal cord, snRNA sample 5

description: Library name: Donor1_Thoracic_Plate05


title: dCRE_ctrl_1_dCRE_ctrl_2, CITE-seq

description: Library name: dCRE_ctrl_1_dCRE_ctrl_2, CITE-seq

value: Cre Control (WT1-CreERT2; Myh6-MerCreMer)


title: M6WB_1_M6WB_2_M6WB_3

description: Library name: M6WB_1_M6WB_2_M6WB_3

data_processing:
Demultiplexing and Counting - CellRanger v3.1.0
Assembly: 10X hosted mm10 reference with custom eGFP and tdTomato sequences
Supplementary files format and content: MEX formatted output folders corresponding to the samples


title: Donor 1, Thoracic spinal cord, snRNA sample 6

description: Library name: Donor1_Thoracic_Plate06


title: HS-04 Heat Stroke T0

description: Gene expression from heatstroke


title: HS-03 Heat Stroke T0

description: Gene expression from heatstroke


title: Donor 1, Thoracic spinal cord, snRNA sample 3

description: Library name: Donor1_Thoracic_Plate03


title: Donor 1, Thoracic spinal cord, snRNA sample 4

description: Library name: Donor1_Thoracic_Plate04


title: M6alone_1_M6alone_2

description: Library name: M6alone_1_M6alone_2


title: Donor 1, Thoracic spinal cord, snRNA sample 2

description: Library name: Donor1_Thoracic_Plate02


title: Donor 1, Thoracic spinal cord, snRNA sample 1

description: Library name: Donor1_Thoracic_Plate01


title: dCRE_ctrl_1_dCRE_ctrl_2

description: Library name: dCRE_ctrl_1_dCRE_ctrl_2


title: Donor 1, Lumbar spinal cord, snRNA sample 22

description: Library name: Donor1_Lumbar_Plate22


title: HS-04 Heat Stroke T1

description: Gene expression from heatstroke


title: Donor 1, Lumbar spinal cord, snRNA sample 23

description: Library name: Donor1_Lumbar_Plate23


title: P8 Cardiomyocytes, RBM22

city: Shanghai

first: Zhenzhen

last: Zhan

address: Jimo Road 150

department: Research Center for Translational Medicine

institute: Shanghai East Hospital, Tongji University School of Medicine,

description: Library name: P8-CMs-RBM22

data_processing:
Genome mapping was performed using Bowtie (version:0.12.8) and clean reads were compared to reference genome mm10. MACS (version 2.2.7.1) was applied to call peaks.
The bam file and R package DiffBind were used to analyze the differences between the peaks of the specified two samples. The default parameters were set as fold change ≥ 2 or ≤ 1/2, and P value < 0.05. The differences between the obtained peaks were annotated.
The annotation program was the same as the above peak annotation program, including different peak location and annotation information, etc.  The motif analysis was conducted using “HOMER” tool. And the result of HOMER motif is the motif information predicted based on the existing database within the peak.
Assembly: mm10
Supplementary files format and content: bigWig files
Library strategy: CUT&Tag

growth_protocol: Hearts from neonatal C57BL/6J mice at P1 (regenerative) and P8 (non-regenerative) were harvested. The Neonatal Heart Dissociation Kit, along with the gentleMACS™ Octo Dissociator (Miltenyi Biotec, Teterow, Germany), was used to isolate cardiomyocytes from neonatal hearts. The cardiomyocytes were then incubated in DMEM supplemented with 10% fetal bovine serum overnight at 37°C with 5% CO₂. The cells were stained to confirm the expression of c-TnT. Cells with a purity >97.5% were used for subsequent experiments.

extract_protocol:
CUT&Tag was performed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) following the manufacturer’s protocol. Briefly, Cardiomyocytes were isolated from mouse hearts at postnatal days 1 (P1) and 8 (P8),  and harvested after PBS wash. Cardiomyocytes  (1 × 10⁵) were bound with concanavalin A-coated  magnetic beads and incubated with a primary antibody against RBM22 (Bethyl) at 4 °C overnight. On the next day, samples were incubated with a second antibody and then with Hyperactive pA/G-Transposon for 1 h. DNA was treated with TTBL at 37 °C for 1 h and extracted.
The librarys were constructed by purified DNA, and amplified using Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the product instructions.

tag: developmental stage

value: Postnatal day 8

value: neonatal mouse cardiomyocytes

tag: antibody


title: HS-17 Heat Stroke T0

description: Gene expression from heatstroke


title: Donor 1, Lumbar spinal cord, snRNA sample 20

description: Library name: Donor1_Lumbar_Plate20


title: Donor 1, Lumbar spinal cord, snRNA sample 19

description: Library name: Donor1_Lumbar_Plate19


title: HS-01 Heat Stroke T0

description: Gene expression from heatstroke


title: P1 Cardiomyocytes, RBM22

description: Library name: P1-CMs-RBM22

value: Postnatal day 1


title: Donor 1, Lumbar spinal cord, snRNA sample 18

description: Library name: Donor1_Lumbar_Plate18

value: spinal cord


title: Donor 1, Lumbar spinal cord, snRNA sample 21

description: Library name: Donor1_Lumbar_Plate21


title: HT-19 Control

description: Gene expression from heatstroke

source_name: Control


title: Cardiomyocytes, si-Rbm22

description: Library name: si-Rbm22-CMs

data_processing:
ATAC-seq reads were trimmed from 3' end until the final base had a quality score > 20, using Fastx  (version:0.0.13), discarding reads left with < 20 bp.
ATAC-seq reads were aligned to the  reference  mm10 genome using Bowtie (version:0.12.8). MACS (version 2.2.7.1) was applied to call peaks.
To create ATAC-seq coverage plots, the locations of the mapped ATAC-seq reads were renormalized (to reads per million, rpkm) and reformatted in the bigWig file format.
The bam file and R package DiffBind were used to analyze the differences between the peaks of the specified two samples. The default parameters were set as fold change ≥ 2 or ≤ 1/2, and P value < 0.05. The differences between the obtained peaks were annotated.
The annotation program was the same as the above peak annotation program, including different peak location and annotation information, etc.
Assembly: mm10
Supplementary files format and content: bigWig files

growth_protocol: Hearts from 1-day-old neonatal C57BL/6J mice were harvested. The Neonatal Heart Dissociation Kit, along with the gentleMACS™ Octo Dissociator (Miltenyi Biotec, Teterow, Germany), was used to isolate cardiomyocytes from neonatal hearts. The cardiomyocytes were then incubated in DMEM supplemented with 10% fetal bovine serum overnight at 37 ℃ with 5% CO₂. Cardiomyocytes were stained to confirm the expression of c-TnT. Cells with purity >97.5% were used for subsequent experiments.

extract_protocol:
Cells were trypsinized with 0.25% trypsin-EDTA and resuspended in 1X PBS (calcium and magnesium-free).
For the ATAC-seq library preparation, 5×104 viable cells were used and collected. The cell pellets were resuspended in cold lysis buffer (1 M Tris-HCl, pH 7.4, 5 M NaCl, 1 M MgCl2, IGEPALCA-630) and incubated on ice for 5 min. Then, the cells were collected and resuspended with 50 μl transposition mixtures according to ATAC Kit instructions (Vazyme). Mixtures were incubated for the PCR reaction. Mixtures were purified with VAHTS DNA Clean Beads (Vazyme) and amplified for 15 cycles using TruePrep Index Kit V2 for Illumina (Vazyme). Amplification products were further purified with VAHTS DNA Clean Beads.

treatment_protocol: Neonatal cardiomyocytes in primary culture were transfected with siRNA against Rbm22 (si-Rbm22) or scramble siRNA (si-Control) and cultured for 48 h to prepare samples.

value: postnatal day 1

tag: treatment

value: Rbm22 siRNA transfection


title: HS-02 Heat Stroke T0

description: Gene expression from heatstroke

value: Male


title: Donor 1, Lumbar spinal cord, snRNA sample 17

description: Library name: Donor1_Lumbar_Plate17

tag: tissue


title: HT-16 Control

description: Gene expression from heatstroke

value: Female


title: Donor 1, Lumbar spinal cord, snRNA sample 16

description: Library name: Donor1_Lumbar_Plate16


title: Cardiomyocytes, si-Control

description: Library name: si-Control-CMs

tag: cell type

value: Control siRNA transfection


title: Donor 1, Lumbar spinal cord, snRNA sample 15

description: Library name: Donor1_Lumbar_Plate15


title: Donor 1, Lumbar spinal cord, snRNA sample 14

description: Library name: Donor1_Lumbar_Plate14


title: Cardiomyocytes, si-Rbm22, rep 3

description: Library name: si-Rbm22-3

data_processing:
Illumina Casava1.7 was software used for basecalling.
Raw reads in fastq format were first processed using fastp, and low-quality reads were removed to obtain clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated, and the read counts of each gene were obtained using HTSeq-count.
Differential expression analysis was performed using DESeq2. Q value < 0.05 and fold change > 2 or < 0.5 were set as the thresholds for significantly differentially expressed genes (DEGs).
Assembly: GRCm38
Supplementary files format and content: matrix table with raw gene counts for every gene and every sample

growth_protocol: Hearts from 1-day-old neonatal C57BL/6J mice were harvested. The Neonatal Heart Dissociation Kit, along with the gentleMACS™ Octo Dissociator (Miltenyi Biotech, Teterow, Germany), was used to isolate cardiomyocytes from neonatal hearts. The cardiomyocytes were then incubated in DMEM supplemented with 10% fetal bovine serum overnight at 37 ℃ with 5% CO₂. Cardiomyocytes were stained to confirm the expression of c-TnT. Cells with purity >97.5% were used for subsequent experiments.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit (Vazyme) according to the manufacturer’s instructions.

treatment_protocol: Neonatal mouse cardiomyocytes in primary culture were transfected with siRNA against Rbm22 (si-Rbm22) or scramble siRNA (si-Control) and cultured for 48 h to prepare samples (three biological replicates for each group).

tag: strain


title: HT-17 Control

description: Gene expression from heatstroke


title: HT-15 Control

description: Gene expression from heatstroke


title: Donor 1, Lumbar spinal cord, snRNA sample 12

description: Library name: Donor1_Lumbar_Plate12


title: Donor 1, Lumbar spinal cord, snRNA sample 13

description: Library name: Donor1_Lumbar_Plate13


title: HT-14 Control

description: Gene expression from heatstroke


title: Cardiomyocytes, si-Rbm22, rep 2

description: Library name: si-Rbm22-2


title: Donor 1, Lumbar spinal cord, snRNA sample 10

description: Library name: Donor1_Lumbar_Plate10


title: HT-13 Control

description: Gene expression from heatstroke


title: Cardiomyocytes, si-Rbm22, rep 1

description: Library name: si-Rbm22-1


title: Donor 1, Lumbar spinal cord, snRNA sample 11

description: Library name: Donor1_Lumbar_Plate11


title: Donor 1, Lumbar spinal cord, snRNA sample 7

description: Library name: Donor1_Lumbar_Plate07


title: Donor 1, Lumbar spinal cord, snRNA sample 9

description: Library name: Donor1_Lumbar_Plate09


title: Donor 1, Lumbar spinal cord, snRNA sample 5

description: Library name: Donor1_Lumbar_Plate05


title: Cardiomyocytes, si-Control, rep 2

description: Library name: si-Control-2


title: HT-12 Control

description: Gene expression from heatstroke


title: Donor 1, Lumbar spinal cord, snRNA sample 6

description: Library name: Donor1_Lumbar_Plate06


title: Donor 1, Lumbar spinal cord, snRNA sample 3

description: Library name: Donor1_Lumbar_Plate03


title: HT-10 Control

description: Gene expression from heatstroke


title: Donor 1, Lumbar spinal cord, snRNA sample 8

description: Library name: Donor1_Lumbar_Plate08


title: Donor 1, Lumbar spinal cord, snRNA sample 2

description: Library name: Donor1_Lumbar_Plate02


title: HT-11 Control

description: Gene expression from heatstroke


title: mouse, CD8, ponatinib_3

city: Tsukiji

first: Yuki

last: Okuhiro

state: Tokyo-to

country: Japan

institute: National cancer center research institute

description: Library name: Ponatinib_3

data_processing:
Raw FASTQ files were processed using fastp version 0.19.5, and transcript abundance was quantified using Salmon version 1.5.1 Gene expression was analyzed with normalized count data calculated by DESeq2 version 1.22.1.
Assembly: GRCm38
Supplementary files format and content: Processed data includes TPM-normalized gene expression values for all samples, combined into a single file (tpm_matrix_all_samples.tsv). Rows represent genes and columns represent individual samples. Gene identifiers are Ensembl IDs.

source_name: splenocytes

extract_protocol:
Cells were washed with PBS twice, and total RNA were extracted using a RNeasy Plus Micro Kit (QIAGN, Venlo, Netherland; Cat. #74034).
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina according to the manufacturer’s instructions.

treatment_protocol: Murine naive CD8⁺ T cells, purified from the splenocytes of C57BL/6 mice, were stimulated with anti-CD3 and anti-CD28 monoclonal antibodies in the presence of either DMSO (control) or 10 nM ponatinib. The cells were cultured in RPMI medium supplemented with 10% fetal bovine serum (FBS), L-glutamine, 2-mercaptoethanol, and recombinant mouse IL-2.

value: splenocytes

value: CD8+ T cells

value: Wild type

value: ponatinib


title: Cardiomyocytes, si-Control, rep 3

description: Library name: si-Control-3

value: heart


title: Donor 1, Lumbar spinal cord, snRNA sample 4

description: Library name: Donor1_Lumbar_Plate04


title: Donor 1, Cervical spinal cord, snRNA sample 25

description: Library name: Donor1_Cervical_Plate25


title: Donor 1, Cervical spinal cord, snRNA sample 24

description: Library name: Donor1_Cervical_Plate24


title: mouse, CD8, ponatinib_2

description: Library name: Ponatinib_2


title: Donor 1, Cervical spinal cord, snRNA sample 23

description: Library name: Donor1_Cervical_Plate23


title: Cardiomyocytes, si-Control, rep 1

description: Library name: si-Control-1


title: HT-09 Control

description: Gene expression from heatstroke


title: mouse, CD8, ponatinib_1

description: Library name: Ponatinib_1


title: Donor 1, Cervical spinal cord, snRNA sample 22

description: Library name: Donor1_Cervical_Plate22


title: HT-18 Control

description: Gene expression from heatstroke


title: Donor 1, Cervical spinal cord, snRNA sample 21

description: Library name: Donor1_Cervical_Plate21


title: HT-07 Control

description: Gene expression from heatstroke


title: HT-06 Control

description: Gene expression from heatstroke


title: mouse, CD8, DMSO_3

description: Library name: Control_3

value: DMSO


title: HT-08 Control

description: Gene expression from heatstroke


title: HS-19 Heat Stroke T1

description: Gene expression from heatstroke


title: Donor 1, Cervical spinal cord, snRNA sample 20

description: Library name: Donor1_Cervical_Plate20


title: Donor 1, Cervical spinal cord, snRNA sample 19

description: Library name: Donor1_Cervical_Plate19


title: Donor 1, Cervical spinal cord, snRNA sample 17

description: Library name: Donor1_Cervical_Plate17


title: mouse, CD8, DMSO_2

description: Library name: Control_2


title: Donor 1, Cervical spinal cord, snRNA sample 18

description: Library name: Donor1_Cervical_Plate18


title: Donor 1, Cervical spinal cord, snRNA sample 14

description: Library name: Donor1_Cervical_Plate14


title: Donor 1, Cervical spinal cord, snRNA sample 12

description: Library name: Donor1_Cervical_Plate12


title: Sorted p53KO-emiRFP (K) cells from WT+p53KO mosaic gastruloids 144h rep2

city: Barcelona

first: Joshua

middle: D

last: Frenster

address: Carrer del Doctor Aiguader, 88

institute: Universitat Pompeu Fabra

description: Library name: KK1443

data_processing:
Adapter trimming and low-quality filtering were conducted with TrimGalore (version 0.6.7), removing reads with a Phred score below 20.
The processed sequencing data were aligned to the mouse genome (GRCm38.p6) using Gencode annotation (version 25) and the STAR aligner (version 2.7.11b). Alignments were performed with default settings and uniquely mapped read counts were generated using the --quantMode option in STAR
The final count matrix was created by concatenating the assembled reads in a Python 3 environment.
Assembly: mouse genome (GRCm38.p6) using Gencode annotation (version 25)
Supplementary files format and content: normalized reads, csv file containing all samples

extract_protocol:
Cells were FACS isolated from mosaic gastruloids and RNA was isolated using the Qiagen RNeasy Micro Kit according to the manufacturor protocol.
stranded library preparation with poly A enrichment

tag: cell line

tag: sample group


title: Sorted p53KO-emiRFP (K) cells from WT+p53KO mosaic gastruloids 144h rep3

description: Library name: KK1444

tag: genotype


title: Donor 1, Cervical spinal cord, snRNA sample 15

description: Library name: Donor1_Cervical_Plate15


title: HS-18 Heat Stroke T1

description: Gene expression from heatstroke


title: Donor 1, Cervical spinal cord, snRNA sample 16

description: Library name: Donor1_Cervical_Plate16


title: Donor 1, Cervical spinal cord, snRNA sample 13

description: Library name: Donor1_Cervical_Plate13


title: Donor 1, Lumbar spinal cord, snRNA sample 1

description: Library name: Donor1_Lumbar_Plate01


title: HS-17 Heat Stroke T1

description: Gene expression from heatstroke


title: HT-04 Control

description: Gene expression from heatstroke


title: Sorted p53KO-emiRFP (K) cells from WT+p53KO mosaic gastruloids 144h rep1

description: Library name: KK1442


title: Donor 1, Cervical spinal cord, snRNA sample 10

description: Library name: Donor1_Cervical_Plate10


title: Donor 1, Cervical spinal cord, snRNA sample 11

description: Library name: Donor1_Cervical_Plate11


title: Donor 1, Cervical spinal cord, snRNA sample 9

description: Library name: Donor1_Cervical_Plate09


title: Donor 1, Cervical spinal cord, snRNA sample 6

description: Library name: Donor1_Cervical_Plate06


title: Sorted p53KO-emiRFP (K) cells from WT+p53KO mosaic gastruloids 120h rep2

description: Library name: KK1203


title: Donor 1, Cervical spinal cord, snRNA sample 8

description: Library name: Donor1_Cervical_Plate08


title: Donor 1, Cervical spinal cord, snRNA sample 5

description: Library name: Donor1_Cervical_Plate05


title: HT-03 Control

description: Gene expression from heatstroke


title: Donor 1, Cervical spinal cord, snRNA sample 7

description: Library name: Donor1_Cervical_Plate07


title: Sorted p53KO-emiRFP (K) cells from WT+p53KO mosaic gastruloids 120h rep3

description: Library name: KK1204


title: HT-02 Control

description: Gene expression from heatstroke


title: HT-01 Control

description: Gene expression from heatstroke


title: Donor 1, Cervical spinal cord, snRNA sample 3

description: Library name: Donor1_Cervical_Plate03


title: Sorted p53KO-emiRFP (K) cells from WT+p53KO mosaic gastruloids 96h rep3

description: Library name: KK0964


title: Sorted p53KO-emiRFP (K) cells from WT+p53KO mosaic gastruloids 120h rep1

description: Library name: KK1202


title: Sorted p53KO-emiRFP (K) cells from WT+p53KO mosaic gastruloids 96h rep2

description: Library name: KK0963


title: Donor 3, Thoracic spinal cord, snRNA sample 4

description: Library name: Donor3_Thoracic_Sample4_GEX

data_processing:
Cell Ranger ARC 2.0.2
Assembly: GRCh38
Supplementary files format and content: Donors2-6_GEX_barcodes.tsv.gz nuclei demultiplexing file for each sample
Supplementary files format and content: Donors2-6_GEX_matrix.mtx.gz counts-by-nucleus file for each sample
Supplementary files format and content: Donors2-6_GEX_features.tsv.gz feature annotation file for each sample

extract_protocol:
Spinal cord tissue was surgically resected from Donors 2-6 organ donors during organ donation. Individual nuclei were isolated through homogenization and gradient centrifugation.
snRNA-seq libraries were generated using 10x Chromium Single Cell Multiome ATAC+Gene Expression, following manufacturer's guidelines.


title: Donor 1, Cervical spinal cord, snRNA sample 2

description: Library name: Donor1_Cervical_Plate02


title: Donor 3, Thoracic spinal cord, snRNA sample 3

description: Library name: Donor3_Thoracic_Sample3_GEX


title: HS-15 Heat Stroke T1

description: Gene expression from heatstroke


title: Donor 2, Lumbar spinal cord, snRNA sample 4

description: Library name: Donor2_Lumbar_Sample4_GEX


title: Sorted p53KO-emiRFP (K) cells from WT+p53KO mosaic gastruloids 96h rep1

description: Library name: KK0962


title: Donor 1, Cervical spinal cord, snRNA sample 1

description: Library name: Donor1_Cervical_Plate01


title: Donor 3, Thoracic spinal cord, snRNA sample 2

description: Library name: Donor3_Thoracic_Sample2_GEX


title: HS-12 Heat Stroke T1

description: Gene expression from heatstroke


title: Sorted p53KO-emiRFP (K) cells from WT+p53KO mosaic gastruloids 72h rep3

description: Library name: KK0724


title: Donor 2, Lumbar spinal cord, snRNA sample 3

description: Library name: Donor2_Lumbar_Sample3_GEX


title: Donor 2, Lumbar spinal cord, snRNA sample 2

description: Library name: Donor2_Lumbar_Sample2_GEX


title: Sorted p53KO-emiRFP (K) cells from WT+p53KO mosaic gastruloids 72h rep2

description: Library name: KK0723


title: Donor 3, Thoracic spinal cord, snRNA sample 1

description: Library name: Donor3_Thoracic_Sample1_GEX


title: Sorted p53KO-emiRFP (K) cells from WT+p53KO mosaic gastruloids 72h rep1

description: Library name: KK0722


title: HS-10 Heat Stroke T1

description: Gene expression from heatstroke


title: HS-11 Heat Stroke T1

description: Gene expression from heatstroke


title: HS-13 Heat Stroke T1

description: Gene expression from heatstroke


title: mouse, CD8, DMSO_1

description: Library name: Control_1


title: HS-09 Heat Stroke T1

description: Gene expression from heatstroke


title: Donor 1, Thoracic spinal cord, snATAC sample 6

description: Library name: Donor1_Thoracic_Sample6

library_source: genomic single cell

data_processing:
Bio-Rad ATAC-seq analysis toolkit was used for nuclei demultiplexing
MACS2 v2.2.7.1 was used for peak calling
ChromVAR v1.3.0.1 was used for nucleus-by-peak matrix generation
Assembly: GRCh38
Supplementary files format and content: Donor1_ATAC_Cervical_cells_500.txt: demultiplexing file for all Cervical samples
Supplementary files format and content: Donor1_ATAC_Cervical_count_matrix_500.mtx: fragments-per-nuclei matrix for all Cervical samples
Supplementary files format and content: Donor1_ATAC_Lumbar_cells_500.txt: demultiplexing file for all Lumbar samples
Supplementary files format and content: Donor1_ATAC_Lumbar_count_matrix_500.mtx: fragments-per-nuclei matrix for all Lumbar samples
Supplementary files format and content: Donor1_ATAC_Thoracic_cells_500.txt: demultiplexing file for all Thoracic samples
Supplementary files format and content: Donor1_ATAC_Thoracic_count_matrix_500.mtx: fragments-per-nuclei matrix for all Thoracic samples

extract_protocol:
Spinal cord tissue was surgically resected from a tissue donor. Individual nuclei were isolated through homogenization and gradient centrifugation.
snATAC-seq libraries were generated using BioRad ddSEQ Single-Cell ATAC-seq Library Prep following manufacturer's guidelines


title: Donor 1, Thoracic spinal cord, snATAC sample 7

description: Library name: Donor1_Thoracic_Sample7


title: Donor 1, Thoracic spinal cord, snATAC sample 8

description: Library name: Donor1_Thoracic_Sample8


title: Donor 1, Thoracic spinal cord, snATAC sample 5

description: Library name: Donor1_Thoracic_Sample5


title: Sorted p53KO-emiRFP (K) cells from WT+p53KO mosaic gastruloids 48h rep3

description: Library name: KK0484


title: Donor 2, Lumbar spinal cord, snRNA sample 1

description: Library name: Donor2_Lumbar_Sample1_GEX


title: Donor 1, Thoracic spinal cord, snATAC sample 3

description: Library name: Donor1_Thoracic_Sample3


title: Sorted p53KO-emiRFP (K) cells from WT+p53KO mosaic gastruloids 48h rep2

description: Library name: KK0483


title: HS-08 Heat Stroke T1

description: Gene expression from heatstroke


title: HS-08 Heat Stroke T0

description: Gene expression from heatstroke


title: Donor 1, Thoracic spinal cord, snATAC sample 4

description: Library name: Donor1_Thoracic_Sample4


title: Sorted p53KO-emiRFP (K) cells from WT+p53KO mosaic gastruloids 48h rep1

description: Library name: KK0482


title: Donor 1, Cervical spinal cord, snRNA sample 4

description: Library name: Donor1_Cervical_Plate04


title: Donor 1, Thoracic spinal cord, snATAC sample 2

description: Library name: Donor1_Thoracic_Sample2


title: HS-06 Heat Stroke T1

description: Gene expression from heatstroke


title: HS-07 Heat Stroke T0

description: Gene expression from heatstroke


title: Sorted WT-mCh (F) cells from WT+p53KO mosaic gastruloids 144h rep3

description: Library name: KF1444

value: WT


title: Donor 1, Lumbar spinal cord, snATAC sample 6

description: Library name: Donor1_Lumbar_Sample6


title: Sorted WT-mCh (F) cells from WT+p53KO mosaic gastruloids 144h rep2

description: Library name: KF1443


title: Donor 1, Thoracic spinal cord, snATAC sample 1

description: Library name: Donor1_Thoracic_Sample1


title: Donor 1, Lumbar spinal cord, snATAC sample 5

description: Library name: Donor1_Lumbar_Sample5


title: Sorted WT-mCh (F) cells from WT+p53KO mosaic gastruloids 144h rep1

description: Library name: KF1442


title: Donor 1, Lumbar spinal cord, snATAC sample 2

description: Library name: Donor1_Lumbar_Sample2


title: Donor 1, Lumbar spinal cord, snATAC sample 4

description: Library name: Donor1_Lumbar_Sample4


title: Donor 1, Lumbar spinal cord, snATAC sample 3

description: Library name: Donor1_Lumbar_Sample3


title: HS-06 Heat Stroke T0

description: Gene expression from heatstroke


title: HT-05 Control

description: Gene expression from heatstroke


title: Donor 1, Lumbar spinal cord, snATAC sample 1

description: Library name: Donor1_Lumbar_Sample1


title: Donor 1, Cervical spinal cord, snATAC sample 6

description: Library name: Donor1_Cervical_Sample6


title: HS-16 Heat Stroke T0

description: Gene expression from heatstroke


title: Sorted WT-mCh (F) cells from WT+p53KO mosaic gastruloids 120h rep3

description: Library name: KF1204


title: HS-05 Heat Stroke T0

description: Gene expression from heatstroke


title: Donor 1, Cervical spinal cord, snATAC sample 5

description: Library name: Donor1_Cervical_Sample5


title: HS-15 Heat Stroke T0

description: Gene expression from heatstroke


title: Donor 1, Cervical spinal cord, snATAC sample 4

description: Library name: Donor1_Cervical_Sample4


title: Donor 1, Cervical spinal cord, snATAC sample 3

description: Library name: Donor1_Cervical_Sample3


title: Sorted WT-mCh (F) cells from WT+p53KO mosaic gastruloids 120h rep1

description: Library name: KF1202


title: Donor 1, Cervical spinal cord, snATAC sample 2

description: Library name: Donor1_Cervical_Sample2


title: Sorted WT-mCh (F) cells from WT+p53KO mosaic gastruloids 96h rep3

description: Library name: KF0964


title: Donor 3, Thoracic spinal cord, snATAC sample 3

description: Library name: Donor3_Thoracic_Sample3_ATAC

data_processing:
Cell Ranger ARC 2.0.2
Assembly: GRCh38
Supplementary files format and content: Donors2-6_ATAC_fragments.tsv.gz cell-by-peak counts matrix  for each sample
Supplementary files format and content: Donors2-6_ATAC_peak_annotation.tsv fragment file  for each sample
Supplementary files format and content: .bed annotations file for each sample

extract_protocol:
Spinal cord tissue was surgically resected from organ donors during organ donation. Individual nuclei were isolated through homogenization and gradient centrifugation.
snATAC-seq libraries were generated using 10x Chromium Single Cell Multiome ATAC+Gene Expression, following manufacturer's guidelines.


title: Donor 1, Cervical spinal cord, snATAC sample 1

description: Library name: Donor1_Cervical_Sample1


title: Donor 3, Thoracic spinal cord, snATAC sample 4

description: Library name: Donor3_Thoracic_Sample4_ATAC


title: Donor 3, Thoracic spinal cord, snATAC sample 2

description: Library name: Donor3_Thoracic_Sample2_ATAC


title: Sorted WT-mCh (F) cells from WT+p53KO mosaic gastruloids 96h rep1

description: Library name: KF0962


title: HS-14 Heat Stroke T0

description: Gene expression from heatstroke


title: Donor 3, Thoracic spinal cord, snATAC sample 1

description: Library name: Donor3_Thoracic_Sample1_ATAC


title: PRC2cKO_CT_P6NGO_H3K27ac_rep2

city: Davis

first: Satoshi

last: Namekawa

address: One Shields Avenue

institute: UC Davis

data_processing:
For CUT&Tag data processing, we basically followed the online tutorial posted by Henikoff Lab (https://protocols.io/view/cut-amp-tag-data-processing-and-analysis-tutorial-bjk2kkye.html).
Raw paired-end reads were trimmed by Trim-galore (https://github.com/FelixKrueger/TrimGalore) (version 0.6.10)
Trimmed reads were aligned with the mouse genome (GRCm38/mm10) using Bowtie2 83 (version 2.4.5) with options: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. D. melanogaster DNA delivered by Drosophila S2 cells was used as spike-in DNA for CUT&Tag. For mapping D. melanogaster spike-in fragments, we also use the --no-overlap --no-dovetail options to avoid cross-mapping. PCR duplicates from all mapped bam files were removed using the ‘MarkDuplicates’ command in Picard tools (version 3.0.0) (https://broadinstitute.github.io/picard/ ).
To compare replicates, Pearson correlation coefficients were calculated and plotted by ‘multiBamSummary bins’ and ‘plot correlation’ commands from deepTools 84 (version 3.5.5). Biological replicates were pooled using the ‘merge’ command in samtools for visualization and other analyses after confirming reproducibility (Pearson correlation coefficient > 0.85). Spike-in normalization was implemented using the exogenous scaling factor computed from the dm6 mapping files (scale factors = 10,000 / aligned spike-in reads).
Spike-in normalized genome coverage tracks with 1 bp resolution in BigWig format were generated using ‘bamCoverage’ from deepTools with the parameters ‘--binSize 1 --extendReads --samFlagInclude 64 --normalizeUsing RPKM --scaleFactor $scale_factor’. Track views were visualized and exported from Integrative Genomics Viewer 85 (version 2.14.1).
Assembly: mm10
Supplementary files format and content: bigWig, spike-in normalized tracks
Supplementary files format and content: bed, peaks
Library strategy: CUT&Tag

source_name: ovary

extract_protocol:
CUT&Tag libraries of oocytes were prepared as previously described32,33 with some modifications (a step-by-step protocol https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3 ) using CUTANA™ pAG-Tn5 (Epicypher, 15-1017). To perform quantitative spike-in CUT&Tag, Drosophila S2 cells were added to mouse oocytes at a fixed ratio (e.g. 2000 S2 cells to 1000 mouse oocytes) at the beginning of each reaction.
CUT&Tag libraries were prepared using NEBNext HiFi 2x PCR Master mix (NEB, M0541L) according to the protocol (a step-by-step protocol https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3 ).

value: ovary

value: primary cells

value: P6 non-growing oocytes

value: EedF/-; Ddx4-Cre

tag: reads length


title: HS-11 Heat Stroke T0

description: Gene expression from heatstroke


title: Sorted WT-mCh (F) cells from WT+p53KO mosaic gastruloids 96h rep2

description: Library name: KF0963


title: Donor 2, Lumbar spinal cord, snATAC sample 4

description: Library name: Donor2_Lumbar_Sample4_ATAC

value: spinal cord


title: HS-13 Heat Stroke T0

description: Gene expression from heatstroke


title: Sorted WT-mCh (F) cells from WT+p53KO mosaic gastruloids 72h rep3

description: Library name: KF0724


title: Donor 2, Lumbar spinal cord, snATAC sample 3

description: Library name: Donor2_Lumbar_Sample3_ATAC


title: bovine embryo, ATAC, siCtrl, 16C, rep3

city: hangzhou

first: Hao

last: Jin

address: Nongshenghuan Building E, Zhejiang University, Hangzhou, Zhejiang

institute: Zhejiang University

description: Library name: b_ATAC_siCtrl_16C_rep3

data_processing:
Bulk RNA-Seq data were trimmed and then aligned to the bovine (ARS-UCD1.2) or human (hg19) reference genome by HISAT2 (Version 2.2.1). For scRNA-Seq data, bases 1 - 8 of read 2 were extracted as cell barcodes by UMI-tools (version 1.1.2). Read 1 was trimmed to remove adapter and template switching oligo (TSO) sequences at the 5′ end and poly(A) tails at the 3′ end. Then, aligned reads were split based on their corresponding cell barcodes using Picard (version 2.26.3). The read counts and FPKM values of each gene were calculated by FeatureCounts (version 2.0.1) and StringTie (version 2.1.2).
For CUT&Tag, ChIP-seq, and ATAC-seq data,  Paired end CUT&Tag, ChIP-seq, and ATAC-seq reads were trimmed and then aligned to bovine (ARS-UCD1.2) or human (hg19) genome with Bowtie (version 2.2.5). Low quality reads (MAPQ <20) and PCR duplicated were removed by samtools (version 1.10) and sambamba (version 0.6.6). For downstream analysis, read counts were normalized to RPKM in a 50bp bin by bamCoverage from deepTools (version 3.5.3).
Assembly: bovine (ARS-UCD1.2) or human (hg19)
Supplementary files format and content: excel files include raw counts for scRNA-Seq and FPKM values for bulk RNA-Seq
Supplementary files format and content: bigwig for CUT-Tag, ChIP-Seq and ATAC-Seq signals

organism: Bos taurus

source_name: bovine embryo

extract_protocol:
The zona pellucidae of embryos were removed using 0.5% pronase E (Sigma- Aldrich, 107433). Then the embryos were washed in 0.5% BSA (Sigma- Aldrich, SRE0098) and manually transfer into PCR tubes
For RNA-Seq, library construction were performed according to the protocol described previously (Hu et al., 2024). For ChIP-Seq, library construction were performed according to the protocol described previously (Brind’Amour et.al 2015). For ATAC-Seq, library construction were performed according to the protocol described previously (Wu et al., 2018). For CUT-Tag, library construction were performed according to the protocol of Vazyme TD904 kit.

value: 16-cell bovine embryos

value: wild type

value: siCtrl


title: HS-12 Heat Stroke T0

description: Gene expression from heatstroke

value: Male


title: PRC2ctrl_CT_P6NGO_H3K27ac_rep2

value: EedF/+; Ddx4-Cre


title: Donor 2, Lumbar spinal cord, snATAC sample 1

description: Library name: Donor2_Lumbar_Sample1_ATAC


title: bovine embryo, ATAC, siCtrl, 16C, rep2

description: Library name: b_ATAC_siCtrl_16C_rep2


title: PRC2ctrl_CT_P6NGO_H3K27ac_rep1


title: Sorted WT-mCh (F) cells from WT+p53KO mosaic gastruloids 72h rep2

description: Library name: KF0723


title: bovine embryo, ATAC, siCtrl, 16C, rep1

description: Library name: b_ATAC_siCtrl_16C_rep1


title: HS-10 Heat Stroke T0

description: Gene expression from heatstroke

value: Female


title: Sorted WT-mCh (F) cells from WT+p53KO mosaic gastruloids 72h rep1

description: Library name: KF0722


title: HS-09 Heat Stroke T0

description: Gene expression from heatstroke


title: Donor 2, Lumbar spinal cord, snATAC sample 2

description: Library name: Donor2_Lumbar_Sample2_ATAC


title: Sorted WT-mCh (F) cells from WT+p53KO mosaic gastruloids 48h rep2

description: Library name: KF0483


title: PRC2cKO_CT_P6NGO_H3K4me3_rep2

value: H3K4me3(Active Motif; #39159)


title: bovine embryo, ATAC, siSP1, 16C, rep2

description: Library name: b_ATAC_siSP1_16C_rep2


title: Sorted WT-mCh (F) cells from WT+p53KO mosaic gastruloids 48h rep3

description: Library name: KF0484


title: KPK-Slc33a1-KO cells, complemented empty vector, Tm, replicate 3

city: New York

first: Shanshan

last: Liu

address: 430 East 63rd Street,

institute: The Rockefeller University

description:
Library name: KPK_KO_Tm_rep3
RNA isolated from whole-cell lysate

data_processing:
Raw reads were quality checked using standard Illumina pipeline tools.
Reads were pseudoaligned to the mouse reference genome (mm10) using Salmon.
Transcript-level quantifications were imported into R using tximport.
Data were normalized and differential enrichment analysis was performed using limma-voom.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Tab-delimited text files containing normalized gene-level expression values and differential enrichment statistics. Rows correspond to genes and columns correspond to samples

source_name: KPK

growth_protocol: KPK Cells were cultured in DMEM supplemented with 10% fetal bovine serum and maintained at 37 °C with 5% CO₂. Cells were harvested at approximately 70–80% confluency for ER immunoprecipitation and RNA extraction.

extract_protocol:
KPK cell lysates were extracted using TRIzol reagent according to the manufacturer’s instructions. RNA was precipitated with isopropanol, washed with 70% ethanol, and resuspended in nuclease-free water.
RNA libraries were prepared using an Illumina-compatible RNA-seq library preparation kit according to the manufacturer’s instructions and sequenced on an Illumina platform.

treatment_protocol: Cells were treated with either DMSO as a vehicle control or tunicamycin to induce ER stress. Tunicamycin was used at a concentration of 10 ng/ml for 8 hours prior to RNA extraction. Experiments were performed in Slc33a1 knockout KPK cells expressing either vector control or SLC33A1 cDNA, and biological replicates were collected for RNA sequencing.

value: KPK

value: non-small cell lung cancer

value: Slc33a1 KO+EV

value: Tnunicamycin


title: KPK-Slc33a1-KO cells, complemented empty vector, Tm, replicate 2

description:
Library name: KPK_KO_Tm_rep2
RNA isolated from whole-cell lysate


title: bovine embryo, ATAC, siSP1, 16C, rep3

description: Library name: b_ATAC_siSP1_16C_rep3


title: PRC2cKO_CT_P6NGO_H3K4me3_rep1


title: KPK-Slc33a1-KO cells, complemented empty vector, Tm, replicate 1

description:
Library name: KPK_KO_Tm_rep1
RNA isolated from whole-cell lysate


title: PRC2ctrl_CT_P6NGO_H3K4me3_rep1


title: bovine embryo, ATAC, siSP1, 16C, rep1

description: Library name: b_ATAC_siSP1_16C_rep1


title: Sorted WT-mCh (F) cells from WT+p53KO mosaic gastruloids 48h rep1

description: Library name: KF0482

value: WT


title: KPK-Slc33a1-KO cells, complemented empty vector, DMSO, replicate 3

description:
Library name: KPK_KO_DMSO_rep3
RNA isolated from whole-cell lysate

value: DMSO


title: bovine embryo, H3K27ac, siCtrl, input, 16C, rep1

description: Library name: b_H3k27ac_siCtrl_input_16C_rep1


title: Sorted WT-emiRFP (W)  cells from WT+WT mosaic gastruloids 144h rep1

description: Library name: WW1442


title: PRC1cKO_CT_P6NGO_H3K27ac_rep2

value: ovary

value: primary cells

value: Ring1-/-; Ring1F/-; Ddx4-Cre


title: Sorted WT-emiRFP (W)  cells from WT+WT mosaic gastruloids 144h rep2

description: Library name: WW1443


title: KPK-Slc33a1-KO cells, complemented empty vector, DMSO, replicate 2

description:
Library name: KPK_KO_DMSO_rep2
RNA isolated from whole-cell lysate


title: bovine embryo, H3K27ac, siCtrl, input, 16C, rep2

description: Library name: b_H3k27ac_siCtrl_input_16C_rep2


title: PRC2ctrl_CT_P6NGO_H3K4me3_rep2

value: P6 non-growing oocytes


title: PRC1cKO_CT_P6NGO_H3K27ac_rep1


title: Sorted WT-emiRFP (W)  cells from WT+WT mosaic gastruloids 144h rep3

description: Library name: WW1444


title: bovine embryo, H3K27ac, siSP1, input, 16C, rep2

description: Library name: b_H3k27ac_siSP1_input_16C_rep2

value: 16-cell bovine embryos


title: Sorted WT-emiRFP (W)  cells from WT+WT mosaic gastruloids 120h rep3

description: Library name: WW1204


title: bovine embryo, H3K27ac, siSP1, input, 16C, rep1

description: Library name: b_H3k27ac_siSP1_input_16C_rep1

value: wild type


title: Sorted WT-emiRFP (W)  cells from WT+WT mosaic gastruloids 120h rep2

description: Library name: WW1203


title: KPK-Slc33a1-KO cells, complemented SLC33A1 cDNA, TM, replicate 3

description:
Library name: KPK_AB_Tm_rep3
RNA isolated from whole-cell lysate

value: Slc33a1 KO+cDNA


title: KPK-Slc33a1-KO cells, complemented empty vector, DMSO, replicate 1

description:
Library name: KPK_KO_DMSO_rep1
RNA isolated from whole-cell lysate


title: bovine embryo, H3K27ac, siCtrl, 16C, rep3

description: Library name: b_H3k27ac_siCtrl_16C_rep3

value: siCtrl


title: PRC1ctrl_CT_P6NGO_H3K27ac_rep2

value: Ring1-/-; Rnf2F/+; Ddx4-Cre


title: PRC1ctrl_CT_P6NGO_H3K27ac_rep1


title: Sorted WT-mCh (F) cells from WT+p53KO mosaic gastruloids 120h rep2

description: Library name: KF1203


title: Sorted WT-emiRFP (W)  cells from WT+WT mosaic gastruloids 120h rep1

description: Library name: WW1202


title: PRC1cKO_CT_P6NGO_H3K4me3_rep2


title: KPK-Slc33a1-KO cells, complemented SLC33A1 cDNA, TM, replicate 2

description:
Library name: KPK_AB_Tm_rep2
RNA isolated from whole-cell lysate


title: KPK-Slc33a1-KO cells, complemented SLC33A1 cDNA, TM, replicate 1

description:
Library name: KPK_AB_Tm_rep1
RNA isolated from whole-cell lysate


title: bovine embryo, H3K27ac, siCtrl, 16C, rep2

description: Library name: b_H3k27ac_siCtrl_16C_rep2


title: bovine embryo, H3K27ac, siCtrl, 16C, rep1

description: Library name: b_H3k27ac_siCtrl_16C_rep1


title: PRC1cKO_CT_P6NGO_H3K4me3_rep1


title: PRC1ctrl_CT_P6NGO_H3K4me3_rep2


title: Sorted WT-emiRFP (W)  cells from WT+WT mosaic gastruloids 96h rep3

description: Library name: WW0964


title: PRC2cKO_CT_P6NGO_H3K27ac_rep1

value: EedF/-; Ddx4-Cre


title: KPK-Slc33a1-KO cells, complemented SLC33A1 cDNA, DMSO, replicate 3

description:
Library name: KPK_AB_DMSO_rep3
RNA isolated from whole-cell lysate


title: Sorted WT-emiRFP (W)  cells from WT+WT mosaic gastruloids 96h rep2

description: Library name: WW0963


title: bovine embryo, H3K27ac, siSP1, 16C, rep3

description: Library name: b_H3k27ac_siSP1_16C_rep3


title: PRC1ctrl_CT_P6NGO_H3K4me3_rep1

value: H3K4me3(Active Motif; #39159)


title: KPK-Slc33a1-KO cells, complemented SLC33A1 cDNA, DMSO, replicate 2

description:
Library name: KPK_AB_DMSO_rep2
RNA isolated from whole-cell lysate

value: KPK


title: Sorted WT-emiRFP (W)  cells from WT+WT mosaic gastruloids 96h rep1

description: Library name: WW0962


title: KPK-Slc33a1-KO cells, complemented SLC33A1 cDNA, DMSO, replicate 1

description:
Library name: KPK_AB_DMSO_rep1
RNA isolated from whole-cell lysate

value: non-small cell lung cancer


title: Sorted WT-emiRFP (W)  cells from WT+WT mosaic gastruloids 72h rep3

description: Library name: WW0724


title: WT_CT_P7GO_H3K27ac_rep2

value: P7 growing oocytes


title: Sorted WT-emiRFP (W)  cells from WT+WT mosaic gastruloids 72h rep2

description: Library name: WW0723


title: WT_CT_P7GO_H3K27ac_rep1


title: bovine embryo, H3K27ac, siSP1, 16C, rep1

description: Library name: b_H3k27ac_siSP1_16C_rep1


title: CITE-seq CD64+ Synovial Macrophages from Young Male Mice, ADT

city: Chicago

first: Deborah

middle: R

last: Winter

state: IL

address: 240 E. Huron Street, M300

institute: Northwestern University

description:
Library name: Joint_Mac_Young_Male_ADT
Antibody Derived Tag
Joint_Mac_Young_Male_raw_matrix.h5
Joint_Mac_Young_Male_filtered_matrix.h5

library_source: other

data_processing:
The cellranger v.7.1.0 pipeline was run with the mm10-2020-A reference transcriptome.
AgingJoint_feature_reference.csv was used to assign ADT
Assembly: mm10
Supplementary files format and content: Matrix files with UMI and feature counts for all data (raw)
Supplementary files format and content: Matrix files  with UMI and feature counts after filtering for cells (filtered)
Library strategy: CITE-seq

molecule: protein

source_name: Ankle Joint Synovium

growth_protocol: Male and female C56BL/6 mice were euthanized at approximately 8 (young) or 22 months (old) for this study.

extract_protocol:
Synovial tissue was processed into a single-cell suspension and live CD45+CD11b+Ly6g-SiglecF-Cd64+ cells were sorted
Cellular Indexing of Transcriptome and Epitopes by sequencing (CITE-seq) was performed using the 10x Genomics 3’ GEX v3 and Feature Barcoding kits
Libraries were sequenced on an Illumina NextSeq 2000 targeting 40,000 reads per cell.

value: Ankle Joint Synovium

value: CD64+ Synovial Macrophages

value: young (8 months)

tag: Sex

value: male

tag: samples pooled

tag: library type

value: ADT


title: bovine embryo, CUT&Tag, WT, MO, rep3

description: Library name: b_CUT_Tag_WT_MO_rep3

value: morula bovine embryos


title: bovine embryo, H3K27ac, siSP1, 16C, rep2

description: Library name: b_H3k27ac_siSP1_16C_rep2


title: Sorted WT-emiRFP (W) cells from WT+WT mosaic gastruloids 72h rep1

description: Library name: WW0722

value: WT


title: CITE-seq CD64+ Synovial Macrophages from Old Male Mice, ADT

description:
Library name: Joint_Mac_Old_Male_ADT
Antibody Derived Tag
Joint_Mac_Old_Male_raw_matrix.h5
Joint_Mac_Old_Male_filtered_matrix.h5

value: old (22 months)


title: Sorted WT-emiRFP (W) cells from WT+WT mosaic gastruloids 48h rep3

description: Library name: WW0484


title: WT_CT_P6NGO_H3K27ac_rep1

value: ovary

value: primary cells

value: P6 non-growing oocytes


title: bovine embryo, CUT&Tag, WT, MO, rep1

description: Library name: b_CUT_Tag_WT_MO_rep1

value: wild type


title: bovine embryo, CUT&Tag, WT, MO, rep2

description: Library name: b_CUT_Tag_WT_MO_rep2


title: bovine embryo, CUT&Tag, siSP1, 16C, rep2

description: Library name: b_CUT_Tag_siSP1_16C_rep2

value: 16-cell bovine embryos


title: CITE-seq CD64+ Synovial Macrophages from Young Female Mice, ADT

description:
Library name: Joint_Mac_Young_Female_ADT
Antibody Derived Tag
Joint_Mac_Young_Female_raw_matrix.h5
Joint_Mac_Young_Female_filtered_matrix.h5

value: female


title: Sorted WT-emiRFP (W) cells from WT+WT mosaic gastruloids 48h rep1

description: Library name: WW0482