title: FGO_H3K36me2_rep2

value: FGO


title: MII_H3K36me2_rep1

status: Public on Sep 27 2025

type: SRA

city: Shanghai

first: Yu

last: Zhang

address: 138 Yi Xue Yuan Road

country: China

institute: Fudan university

library_source: genomic

data_processing:
Paired-end reads were first processed by TrimGalore (v.0.6.4) with default parameters to remove adaptor sequences and reads of low quality. The filtered reads were then mapped to the mm9 genome using Bowtie2 (v2.2.5) (Langmead and Salzberg, 2012) with the default parameters. Duplicates were removed with MarkDuplicates.jar. The unique mapped reads were then used to calculate the RPKM (Reads per kilobase per million of sequenced reads), which was further Z-score normalized to minimize the batch and cell type variation. The Pearson correlation was calculated for each sample with two biological replicates (10-kb bin). Replicates with good reproducibility were pooled together for downstream analyses. The UCSC genome browser was used for visualization.
Assembly: mm9
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Mus musculus

source_name: MII

growth_protocol: Serum/Lif (S/L) R1 mESCs were cultured in 0.1% gelatin-coated dishes in Dulbecco’s modified Eagle’s medium (Gibco, 11995065) containing 15% FBS (Gibco, 16000-044), 1000 IU/ml leukemia inhibitory factor (Lif) (Merck Millipore, ESG1107), 100 IU/ml penicillin and 100 μg/ml streptomycin (Merck Millipore, TMS-AB2-C), 2 mM GlutaMAX (Gibco, 35050061), 1% EmbryoMax nucleosides (Merck Millipore, ES-008-D), 0.1 mM nonessential amino acids (Gibco, 25-025-CIR), and 0.1 mM 2-mercaptoethanol (Gibco, 21985023). 2i mESCs were cultured on 0.2% gelatin-coated dishes in 2i/Lif medium (N2B27 medium supplemented with 1 μm PD0325901 (Tocris, 41921), 3 μm CHIR99021 (Tocris, 4423) and 1000 IU/ml Lif). Cells were routinely propagated every 2-3 days. The formative EpiLCs were induced as previously described (Hayashi et al., 2011). Briefly, 1.0×105 2i ESCs were plated in a well of a 12-well plate coated with Matrigel (BD, 356230/356231, diluted at a ratio of 1:100 in N2B27 medium). Cells were cultured in N2B27 medium containing activin A (20 ng/ml), bFGF (12 ng/ml), XAV939 (5 μM), and KSR (1%). EpiLCs were collected for analysis at the indicated time point.Embryos were collected in vivo.

extract_protocol:
Embryos or cells were lysed in lysis buffer and subject to Mnase digestion, antibody immunoprecipitation, and subsequent library preparation.
STAR ChIP-seq was performed as previously described (Zhang et al., 2016) with modifications. Briefly, samples were suspended and lysed followed by chromatin fragmentation by micrococcal nuclease (MNase, Sigma-Aldrich, N3755-200UN) at 37°C for 5 min. After being terminated, the supernatant containing chromatin was incubated with 1 μg of primary antibody (H3K36me2, Active motif, 61019; H3K36me3, Active motif, 61021 or 61902) at 4°C overnight with rotation. The next day, 100 μg of Protein A/G dynabeads (mixed at 1:1, Thermo Fisher Scientific, 10001D for Protein A and 10004D for Protein G) was added to each sample and incubated at 4°C for 3 hours with rotation. The beads were next washed five times with 150 μl of RIPA buffer and once with 150 μl of LiCl buffer. For each sample, beads were resuspended with 28 μl of H2O, 1 μl of 10× Ex Taq buffer (Takara, RR006B), and 1 μl of proteinase K (NEB, P8107S) and incubated at 55°C for 90 min, followed by incubation at 72°C for 40 min to inactivate the proteinase K. Samples were then subjected to TruSeq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). Libraries were sequenced using the Illumina Hiseq X Ten or Novaseq 6000 system according to the manufacturer’s protocol.

tag: tissue

value: MII

tag: chip antibody

value: H3K36me2 (active motif, 61019)

tag: genotype

value: WT

tag: developmental stage

tag: treatment


title: Mouse Skin SCA1+ Fibroblasts, 3dpw, 3

city: Washington

first: Brett

middle: Adam

last: Shook

state: DC

address: 2300 I St NW

department: Biochemistry & Molecular Medicine

country: USA

institute: George Washington University

description: Matrix column name: 3D3

library_source: transcriptomic

data_processing:
Alignment and quantification of gene counts were performed using the default settings of the STAR (https://github.com/alexdobin/STAR), samtools (https://www.htslib.org/), and featureCounts (https://subread.sourceforge.net/featureCounts.html) tools in the Partek Flow software (https://www.nihlibrary.nih.gov/resources/tools/partek-flow). Raw fastq files and a text file with the combined counts outputs for each sample following these processing steps are included in this submission.
Assembly: Mouse mm10
Supplementary files format and content: matrix .txt file

molecule: polyA RNA

source_name: Wounded back skin 3dpw

extract_protocol:
Unwounded and wounded skin samples were minced with scissors and digested in a liberase digestion solution. Cells were passed through 70μm and 40μm strainers. Cells were incubated with an anti-CD45-APC-Cy7, anti-CD31-APC-Cy7, and anti-SCA1-BV650 antibodies and stained with SYTOX Blue viability dye. Live, CD45-, CD31-, SCA1+ cells were sorted from each sample on a Sony SH800 instrument. RNA extraction was immediately performed using the Agilent Absolutely RNA Nanoprep Kit.
RNA Integrity Number scores for all 12 samples were assessed using an Agilent Bioanalyzer RNA 6000 Pico kit (p/n 5067-1513), producing measurements suitable for library preparation using the Takara Bio USA, Inc SMART-Seq® v4 Ultra® Low Input RNA Kit (p/n 634888). Total RNA input ranged from 76-789 ng (average 375 ng), with an minimum RIN score of 7. General requirements and recommendations were followed for full-length cDNA amplification and purification. cDNA were quantified and assessed using an Agilent Bioanalyzer High Sensitivity DNA kit (p/n 5067-4626) and a Thermo Fisher Qubit 3.0 High Sensitivity DNA kit (p/n Q33230). cDNA samples were diluted and 150 pg input was used as input, per sample, in the Illumina Nextera XT Library Preparation kit (p/n FC-131-1024), per recommendations from the Takara SMART-Seq® v4 Ultra® Low Input RNA Kit user manual. Nextera XT libraries were quantified and assessed using an Agilent Bioanalyzer High Sensitivity DNA kit and a Thermo Fisher Qubit 3.0 High Sensitivity DNA kit. Libraries were pooled and sequenced using an Illumina NextSeq 500 High-Output 150 cycle v2.5 kit (p/n 20024907), generating 470 million paired-end reads. FastQ files were generated and demultiplexed, with even read depth across the twelve samples.

value: Wounded back skin 3dpw

tag: strain

tag: cell type

value: SCA1+ Fibroblasts

value: wild type

tag: age

value: 8 weeks

tag: Sex

value: Male


title: Human_500pg_cfDNA_Zymo-Gold_CBS-seq.biol_rep3

city: Chicago

first: Ruitu

last: Lyu

state: IL

address: 929 E 57th Street

department: Chemistry

institute: The University of Chicago

description: Library name: Sample 27

data_processing:
Raw paired-end bisulfite sequencing reads of three methyl conversion methods (UMBS-seq, EM-seq, and CBS-seq) were first trimmed using Trim Galore (v 0.6.10), which removes Illumina adapter sequences and low-quality bases (Phred score <20).
The trimmed reads were then aligned to a bisulfite-converted reference genome using bismark (v0.24.0) with the Bowtie2 aligner. Prior to alignment, the reference genome (e.g., pUC19 DNA, lambda DNA and human genome) was prepared using bismark_genome_preparation, which generates bisulfite-specific indices.
Mapping was performed in paired-end mode with default parameters, and alignment outputs were stored in BAM format for downstream processing. Following alignment, PCR duplicates were removed using deduplicate_bismark in paired-end mode to minimize amplification bias.
To eliminate unconverted clusters in the EM-seq data, reads with more than 5 unconverted C sites or reads with more than one-third of the total C sites being unconverted were also discarded.
Methylation levels were extracted from the deduplicated BAM files using bismark_methylation_extractor with the --cytosine_report, --CX, and --bedGraph options enabled. This step generated methylation calls for cytosines in CpG, CHG, and CHH contexts, as well as genome-wide coverage files and per-base resolution methylation reports. The methylation extraction was performed using a buffer size of 10 G to ensure efficient processing of large files. All downstream data analysis, visualization, and quality control were conducted using custom Python and R scripts.
Assembly: hg19, lambda DNA, and pUC19 genome
Supplementary files format and content: txt, convertion ratios of each cytosine.
Supplementary files format and content: txt, C-to-U conversion report.

organism: Homo sapiens

source_name: cell-free DNA (cfDNA)

extract_protocol:
cfDNA was extracted and purified from pooled human plasma from Innovative Research Inc. using the Qiagen QIAamp Circulating Nucleic Acid kit. Two samples of ~250 ng of unmethylated Lambda genomic DNA (-dcm, -dam) from Thermo Fisher was fragmented with NEB UltraShear fragmentase for 25-30 minutes according to the NEB protocol.
End repair, A-tailing, and ligation of a sequencing adapter were completed with the KAPA EvoPrep Kit. The NEB single molecule Methylated Adapter was used during ligation, and 3 μL of USER enzyme was added to the ligation reaction mixture following ligation and heated at 37 °C for 15 minutes for opening of the NEB Methylated Adapter loop. A final Cytiva beads purification with a 0.8x beads ratio was used to purify the adaptor ligated libraries. A bioanalyzer trace confirmed an appropriate library size of ~340 bp.

treatment_protocol: Both fragmented lambda DNA and cfDNA were treated with UMBS-seq, EM-seq (NEB), and Zymo EZ-Gold Bisulfite methyl conversion methods.

value: cell-free DNA (cfDNA)

tag: sample group


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 26

city: Guangzhou

first: Jinyi

last: Wu

state: Guangdong

address: No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island

institute: Guangzhou Laboratory

library_source: transcriptomic single cell

data_processing:
For bulk RNA seq, we used Fastp (version 0.23.1) (Chen, S. , et al 2018) to perform basic statistics on the quality of the raw reads. The steps of data processing were as follows: (1) Discard a paired reads if either one read contains adapter contamination; (2) Discard a paired reads if more than 10% of bases are uncertain in either one read; (3) Discard a paired reads if the proportion of low quality (Phred quality <5) bases is over 50% in either one read.  Alignment, annotation, and gene expression quantification were performed with STAR software (v.2.7.9a). The second columns of the output ‘ReadsPerGene’ tables were aggregated into a gene count table. Single cell RNA-seq data were trimmed using Trim Galore coupled with FastQC (v.0.11.2) or fastp software with default parameters. Alignment, annotation, PCR duplicate removal and gene expression quantification were subsequently performed using the STARsolo pipeline.
Assembly: Ensembl GRCh38 release 104
Supplementary files format and content: Bulk RNAseq count table: gene by cell expression matrix generated with STAR; scRNAseq count tables: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

extract_protocol:
For scRNA-seq, 120h SACs were dissociated and sorted by flow cytometer for Smart-seq2 library construction. 60h SACs were collected after replating on gelatinized plate for 30min for feeder removal; day6 stEM and e-stEM were manually picked with a cut-tip, washed once with DPBS and then dissociated with TrypLE Express (Gibco) at 37 °C in 20%O2 and 5% CO2 incubator for 45-60 min.
Library construction was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). For NovaSeq 6000 library construction, the process begins with RNA extraction and quality control, followed by mRNA enrichment using polyA selection or rRNA depletion. First and second strand cDNA synthesis is performed, then the cDNA is fragmented and end-repaired. Sequencing adapters are ligated to the cDNA fragments, which are then purified and size-selected. The library is amplified by PCR, assessed for quality, and loaded onto the NovaSeq 6000 for sequencing. For MGISEQ-2000, the protocol similarly starts with RNA extraction and quality control, mRNA enrichment or rRNA depletion, cDNA synthesis, fragmentation, and end-repair. Sequencing adapters are ligated, followed by purification, size selection, and PCR amplification. Unique to MGISEQ-2000 is a circularization step converting the linear library into a circular DNA molecule before loading and sequencing on the MGISEQ-2000 platform.

tag: cell line

value: pluripotent stem cell


title: Mouse Skin SCA1+ Fibroblasts, 3dpw, 2

description: Matrix column name: 3D2


title: Human_500pg_cfDNA_Zymo-Gold_CBS-seq.biol_rep2

description: Library name: Sample 26


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 30


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 24


title: Human_500pg_cfDNA_Zymo-Gold_CBS-seq.biol_rep1

description: Library name: Sample 25


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 23


title: Mouse Skin SCA1+ Fibroblasts, 3dpw, 1

description: Matrix column name: 3D1


title: Human_500pg_cfDNA_UMBS-seq.biol_rep3

description: Library name: Sample 24


title: liver, 6 month old ki mice, 4

city: Split

first: Maria

last: Boskovic

address: Soltanska 2A

department: Laboratory for Cancer Research

country: Croatia

institute: University of Split School of Medicine

data_processing:
Analysis workflow: Original data -> Data Assessment -> Mapping to Reference Genome -> Expression Quantification (-> RNA Seq Correlation) -> Differential Expression Analysis (-> Transcription Factor Analysis) -> GO Enrichment, Protein-Protein Interaction Analysis and KEGG enrichment. The analysis has been done with the support of Novogene bioinformatics core.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

source_name: Liver

extract_protocol:
RNA was harvested using Qiazol reagent. All samples passed through the following steps of quality control (QC) before library construction: RNA purity measured by Nanodrop, tests RNA degradation and potential contamination using Agarose Gel Electrophoresis, RNA integrity checked by Agilent 21000.
After QC procedures, mRNA was enriched using oligo(dT) beads. The mRNA was then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library was ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment. Library QC: Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies), and then diluted to 1 ng/µl before checking insert size on an Agilent 2100 and quantifying to greater accuracy by quantitative PCR (library activity >2 nM).

value: Liver

value: Sprtn knock-in

value: non-tretated


title: FGO_H3K36me2_rep1

source_name: FGO


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 22


title: liver, 6 month old ki mice, 3


title: Mouse Skin SCA1+ Fibroblasts, 1.5dpw, 3

description: Matrix column name: 1_5D3

source_name: Wounded back skin 1.5dpw

value: Wounded back skin 1.5dpw


title: Human_500pg_cfDNA_UMBS-seq.biol_rep2

description: Library name: Sample 23


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 21


title: Mouse Skin SCA1+ Fibroblasts, 1.5dpw, 1

description: Matrix column name: 1_5D1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 20


title: liver, 6 month old ki mice, 1


title: Human_500pg_cfDNA_UMBS-seq.biol_rep1

description: Library name: Sample 22


title: Mouse Skin SCA1+ Fibroblasts, 1.5dpw, 2

description: Matrix column name: 1_5D2


title: liver, 6 month old ki mice, 2


title: Mouse Skin SCA1+ Fibroblasts, 16hpw, 3

description: Matrix column name: 16H3

source_name: Wounded back skin 16hpw

value: Wounded back skin 16hpw


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 19


title: liver, 6 month old wt mice, 2


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 17


title: Mouse Skin SCA1+ Fibroblasts, 16hpw, 1

description: Matrix column name: 16H1


title: Human_500pg_cfDNA_NEB_EM-seq.biol_rep3

description: Library name: Sample 21

data_processing:
Raw paired-end bisulfite sequencing reads of three methyl conversion methods (UMBS-seq, EM-seq, and CBS-seq) were first trimmed using Trim Galore (v 0.6.10), which removes Illumina adapter sequences and low-quality bases (Phred score <20).
The trimmed reads were then aligned to a bisulfite-converted reference genome using bismark (v0.24.0) with the Bowtie2 aligner. Prior to alignment, the reference genome (e.g., pUC19 DNA, lambda DNA and human genome) was prepared using bismark_genome_preparation, which generates bisulfite-specific indices.
Mapping was performed in paired-end mode with default parameters, and alignment outputs were stored in BAM format for downstream processing. Following alignment, PCR duplicates were removed using deduplicate_bismark in paired-end mode to minimize amplification bias.
To eliminate unconverted clusters in the EM-seq data, reads with more than 5 unconverted C sites or reads with more than one-third of the total C sites being unconverted were also discarded.
Methylation levels were extracted from the deduplicated BAM files using bismark_methylation_extractor with the --cytosine_report, --CX, and --bedGraph options enabled. This step generated methylation calls for cytosines in CpG, CHG, and CHH contexts, as well as genome-wide coverage files and per-base resolution methylation reports. The methylation extraction was performed using a buffer size of 10 G to ensure efficient processing of large files. All downstream data analysis, visualization, and quality control were conducted using custom Python and R scripts.
Assembly: hg19, lambda DNA, and pUC19 genome
Supplementary files format and content: txt, convertion ratios of each cytosine.
Supplementary files format and content: txt, C-to-U conversion report.
Library strategy: EM-seq


title: Human_500pg_cfDNA_NEB_EM-seq.biol_rep2

description: Library name: Sample 20


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 18


title: Human_500pg_cfDNA_NEB_EM-seq.biol_rep1

description: Library name: Sample 19


title: liver, 6 month old wt mice, 1


title: liver, 6 month old wt mice, 3


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 16


title: Mouse Skin SCA1+ Fibroblasts, Unwounded, 2

description: Matrix column name: NW2

source_name: Unwounded back skin

value: Unwounded back skin


title: Human_50pg_cfDNA_Zymo-Gold_CBS-seq.biol_rep3

description: Library name: Sample 18


title: Human_50pg_cfDNA_Zymo-Gold_CBS-seq.biol_rep2

description: Library name: Sample 17


title: Mouse Skin SCA1+ Fibroblasts, Unwounded, 3

description: Matrix column name: NW3


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 15


title: B-4-3

city: NanJing

first: Yongquan

last: Yu

state: JiangSu

address: 87 Dingjiaqiao, Gulou District

department: College of Public Health

institute: Southeast University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10

source_name: Brain, the hippocampus

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: Brain, the hippocampus

value: 4 months old

value: 50 mg/kg/day BBP treated


title: B-4-2


title: Mouse Skin SCA1+ Fibroblasts, Unwounded, 1

description: Matrix column name: NW1


title: B-4-1


title: Human_50pg_cfDNA_Zymo-Gold_CBS-seq.biol_rep1

description: Library name: Sample 16


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 14


title: Human_50pg_cfDNA_UMBS-seq.biol_rep3

description: Library name: Sample 15


title: B-1-3

value: corn oil


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 13


title: Mouse Skin SCA1+ Fibroblasts, 16hpw, 2

description: Matrix column name: 16H2


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 12


title: Human_50pg_cfDNA_UMBS-seq.biol_rep2

description: Library name: Sample 14


title: C2C12 cells, pentanoate, 48h, 2

first: Ziyi

last: Cao

address: No. 221, Yan'an West Road, Jing'ansi Street, Jing'an District, Shanghai

institute: Huadong hospital affiliated to Fudan University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: C2C12 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: After C2C12 cells adhered to the wall, they interfered with 750uM butyric acid and 750uM pentanoate respectively, and Intervention lasts for 48 hours

value: myogenous cell

value: WT

value: pentanoate

tag: time

value: Day 2


title: B-1-2

value: wild type


title: Human_50pg_cfDNA_UMBS-seq.biol_rep1

description: Library name: Sample 13

value: cell-free DNA (cfDNA)


title: C2C12 cells, pentanoate, 48h, 1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 11

value: pluripotent stem cell


title: C2C12 cells, control, 3

value: control


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 10


title: B-1-1


title: Human_50pg_cfDNA_NEB_EM-seq.biol_rep3

description: Library name: Sample 12


title: C2C12 cells, control, 2


title: shEno_3

city: Beijing

first: Xiong

last: Shu

address: 31 Xinjiekou East Street, Xicheng District

institute: Beijing Jishuitan Hospital

description: Library name: sample6

data_processing:
quality control with MultiQC
adapter and quality trimming with Cutadapt
transcript quantification with featureCounts
differential expression analysis (p value <0.05 and |log2foldchange| >1)
Assembly: GRCh38
Supplementary files format and content: genes.fpkm.anno.xlsx

growth_protocol: SNU16 cell lines were cultured in Roswell Park Memorial Institute-1640 medium (Gibco, USA), which all supplemented with 10% fetal bovine serum (FBS; Gibco, USA), 1% penicillin, and 1% streptomycin. Cell lines were maintained in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
To silence ENO1, cell lines were infected by lentivirus containing short hairpin RNA (shRNA) targeting ENO1 (Obio Technology, China;). After two days, cell lines stably expressing shENO1 (ENO1-knockdown) were enriched by a 2-day puromycin (Gibco, USA) treatment for selecting positive clones. To achieve transient overexpression of ENO1, cells were transfected with the pRLenti-CMV-ENO1-3FLAG-PGK-Puro plasmid (Obio Technology, China) using the Nucleofector Electroporation System (Lonza, Switzerland). Additionally, a blank pRLenti-CMV-MCS-3FLAG-PGK-Puro plasmid was transfected as a negative control.
TRIzol reagent was used to extract total RNA and purify it to ensure that the quality and concentration of RNA samples met the requirements of subsequent sequencing. Low-quality sequences, such as head sequence, sequence with mass score <20, original reads with N-base ratio >10% and sequence less than 25bp, were removed from the RNA sequencing results.

value: gastric carcinoma cell

tag: shRNA

value: shEno


title: Human_50pg_cfDNA_NEB_EM-seq.biol_rep2

description: Library name: Sample 11


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 9


title: shEno_2

description: Library name: sample5


title: C2C12 cells, butyrate, 48h, 3

value: butyrate treatment


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 8


title: C2C12 cells, pentanoate, 48h, 3


title: shEno_1

description: Library name: sample4


title: Human_10pg_cfDNA_Zymo-Gold_CBS-seq.biol_rep3

description: Library name: Sample 9


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 7


title: C2C12 cells, control, 1


title: Human_50pg_cfDNA_NEB_EM-seq.biol_rep1

description: Library name: Sample 10


title: Human_10pg_cfDNA_Zymo-Gold_CBS-seq.biol_rep2

description: Library name: Sample 8


title: C2C12 cells, butyrate, 48h, 1


title: C2C12 cells, butyrate, 48h, 2


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 6


title: shcon_1

description: Library name: sample1

value: shcon


title: shcon_2

description: Library name: sample2


title: Human_10pg_cfDNA_Zymo-Gold_CBS-seq.biol_rep1

description: Library name: Sample 7


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 5


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 3


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 4


title: Human_10pg_cfDNA_UMBS-seq.biol_rep3

description: Library name: Sample 6


title: rectum, scRNASeq

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

description: 10X Genomics

data_processing:
Raw sequencing reads were generated as 150-bp paired-end FASTQ files, and then aligned to the mm10 mouse reference genome using the Cell Ranger toolkit (v4.0.0) from 10X Genomics
Following droplet barcode selection and filtering, the resulting UMI count matrices of individual cells were imported into the Seurat R package for further analysis. Low-quality cells were filtered out by discarding cells with fewer than 200 detected genes and genes expressed in fewer than three cells.
Assembly: mm10
Supplementary files format and content: CellRanger output files

source_name: Rectum

extract_protocol:
The cell suspension was stained with propidium iodide (PI, 5 μg/ml), and PI-negative single cells were sorted by FACS (BeckMan)
Single cells were captured using the 10X Genomics Chromium Single Cell Solution, and RNA-seq libraries were prepared following the manufacturer’s protocol (10X Genomics). Libraries were subjected to high-throughput sequencing on an Illumina Hiseq X Ten PE150 platform, and 150-bp paired-end reads were generated.

value: Rectum

value: Epithelial cells, Mesenchymal cells, Immune cells


title: TC-71_BEZ235_3

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Count on FAST DB gene annotations (GenoSplice) and normalization using Deseq
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes deseq normalized expression values for each gene and for each sample. Annotations from Human FAST DB v2022_1 were also provided

growth_protocol: Human TC71 cells were maintained in Iscove’s modified Dulbecco’s medium (IMDM, GIBCO), supplemented with 10% fetal bovine serum, penicillin and streptomycin (Gibco), and maintained at 37°C in humidified 5% CO2 atmosphere.

extract_protocol: RNA from three biological replicates of either control or BEZ235 treated TC-71 cells swas purified using RNeasy Mini kit (Qiagen) and digested with DNase RNase free (Qiagen).

treatment_protocol: The BEZ235 inhibitor was purchased from EMD Chemical Inc./Calbiochem and dissolved in dimethyl sulfoxide. TC71 cells were treated either with BEZ235 or DMSO for 16 hours. After treatmnet cells were washed twice with PBS and collected in RLT buffer (Qiagen).

value: Ewing sarcoma cells


title: TC-71_BEZ235_2


title: Human_10pg_cfDNA_UMBS-seq.biol_rep1

description: Library name: Sample 4


title: TC-71_DMSO_3

value: DMSO


title: ileum, scRNASeq

description: 10X Genomics

source_name: Ileum

value: Ileum


title: shcon_3

description: Library name: sample3


title: jejunum, scRNASeq

description: 10X Genomics

source_name: Jejunum

value: Jejunum


title: Human_10pg_cfDNA_NEB_EM-seq.biol_rep2

description: Library name: Sample 2


title: Human_10pg_cfDNA_NEB_EM-seq.biol_rep3

description: Library name: Sample 3


title: TC-71_DMSO_2

value: WT


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 1


title: scRNA-seq (10X) of 60h SAC


title: TC-71_DMSO_1


title: scRNA-seq (10X) of Day 6 stEM


title: Duodenum, scRNASeq

description: 10X Genomics

source_name: Duodenum

value: Duodenum


title: Human_10pg_cfDNA_NEB_EM-seq.biol_rep1

description: Library name: Sample 1


title: mE6_NPC_RNA_PolII_AM Biological repliacate 1

status: Public on Sep 26 2025

city: Stanford

first: Christy

last: Luong

state: CA

address: 269 Campus Dr

department: Department of Dermatology

institute: Stanford University School of Medicine

description:
Library name: mE6_NPC_RNA_PolII_AM_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.

data_processing:
Reads were aligned with Bowtie2 with a custom N-masked genome. Reads were then deduplicated and indexed with samtools. For allele-specific analysis, reads were split based on informative SNPs using SNPSplit.
Assembly: mm10
Supplementary files format and content: BigWig files: created using bamCovarage with normalization using RPGC and bin size of 10 Genome 1 is the 129 allele and genome 2 is the CAST allele.

growth_protocol: NPC were ifferentiated from mESCs from 2i+Lif. NPCs were grown on 0.1% gelatin with N2B27 medium with FGF and EGF. mESCs were grown on 0.1% gelatin with 2i+lif medium.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 mins and lysed with nuclear lysis buffer containing NP-40. Chromtain was then sheared with a Covaris. Sonicated chromatin underwent immunoprecipitation with antibody of choice then DNA was purified.
NEB II Ultra DNA library prep kit was used for library prep with the ChIP DNA.

value: male

value: neuronal progenitor cells

tag: chip-antibody

value: RNA Pol II-RPB1 (Active Motif, AB_2732926)


title: mE6_NPC_input Biological repliacate 1

description:
Library name: mE6_NPC_input_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: TC-71_BEZ235_1


title: mE6_NPC_RNA_PolII_BL Biological repliacate 1

description:
Library name: mE6_NPC_RNA_PolII_BL_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.

value: RNA Pol II-RPB1 (Biolegend, 664906)


title: mE6_NPC_H3K9me3 Biological repliacate 1

description:
Library name: mE6_NPC_H3K9me3_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.

value: H3K9me3 (Abcam, ab8898)


title: Human_10pg_cfDNA_UMBS-seq.biol_rep2

description: Library name: Sample 5

value: cell-free DNA (cfDNA)


title: mE6_NPC_H3K4me3 Biological repliacate 2

description:
Library name: mE6_NPC_H3K4me3_R2
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.

value: H3K4me3 (Active Motif, 39159)


title: mE6_NPC_H3K4me2 Biological repliacate 2

description:
Library name: mE6_NPC_H3K4me2_R2
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.

value: H3K4me2 (Abcam, ab7766)


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 2

value: pluripotent stem cell


title: mE6_NPC_H3K9me3 Biological repliacate 2

description:
Library name: mE6_NPC_H3K9me3_R2
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: colon, scRNASeq

description: 10X Genomics

source_name: Colon

value: Colon


title: mE6_NPC_Tfap2a_Abcam Biological repliacate 1

description:
Library name: mE6_NPC_Tfap2a_Abcam_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.

value: TFAP2a (Abcam, ab108311)


title: mE6_NPC_H3K27me3 Biological repliacate 2

description:
Library name: mE6_NPC_H3K27me3_R2
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.

value: H3K27me3 (Cell Signaling, C36B11)


title: mE6_NPC_H2AK119ub Biological repliacate 1

description:
Library name: mE6_NPC_H2AK119ub_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.

value: H2AK199ub (Cell signaling, D27C4)


title: mE6_NPC_H3K4me2 Biological repliacate 1

description:
Library name: mE6_NPC_H3K4me2_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: mE6_NPC_H3K27ac_Ab Biological repliacate 2

description:
Library name: mE6_NPC_H3K27ac_Ab_R2
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: F123_mESC_Tfap2a_novus Biological repliacate 2

description:
Library name: F123_mESC_Tfap2a_novus_R2
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.

value: embryonic stem cells


title: F123_mESC_Tfap2a_novus Biological repliacate 1

description:
Library name: F123_mESC_Tfap2a_novus_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: mE6_NPC_H3K27me3 Biological repliacate 1

description:
Library name: mE6_NPC_H3K27me3_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: F123_mESC_RNA_PolII_BL Biological repliacate 2

description:
Library name: F123_mESC_RNA_PolII_BL_R2
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: F123_mESC_RNA_PolII_BL Biological repliacate 1

description:
Library name: F123_mESC_RNA_PolII_BL_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: mE6_NPC_Tfap2a_novus Biological repliacate 1

description:
Library name: mE6_NPC_Tfap2a_novus_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: mE6_NPC_input Biological repliacate 2

description:
Library name: mE6_NPC_input_R2
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: F123_mESC_input Biological repliacate 1

description:
Library name: F123_mESC_input_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: F123_mESC_H3K4me3 Biological repliacate 2

description:
Library name: F123_mESC_H3K4me3_R2
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: F123_mESC_H3K4me3 Biological repliacate 1

description:
Library name: F123_mESC_H3K4me3_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: mE6_NPC_H3K4me3 Biological repliacate 1

description:
Library name: mE6_NPC_H3K4me3_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: F123_mESC_H3K4me2 Biological repliacate 1

description:
Library name: F123_mESC_H3K4me2_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: F123_mESC_H3K4me2 Biological repliacate 2

description:
Library name: F123_mESC_H3K4me2_R2
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: F123_mESC_H3K9me3 Biological repliacate 1

description:
Library name: F123_mESC_H3K9me3_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: F123_mESC_H3K27ac_Ab Biological repliacate 1

description:
Library name: F123_mESC_H3K27ac_Ab_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: F123_mESC_H3K27me3 Biological repliacate 1

description:
Library name: F123_mESC_H3K27me3_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: F123_mESC_H2AK119ub Biological repliacate 1

description:
Library name: F123_mESC_H2AK119ub_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Ch8_NPC_Tfap2a_novus Biological repliacate 1

description:
Library name: Ch8_NPC_Tfap2a_novus_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: F123_mESC_H2AK119ub Biological repliacate 2

description:
Library name: F123_mESC_H2AK119ub_R2
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Ch8_NPC_RNA_PolII_BL Biological repliacate 2

description:
Library name: Ch8_NPC_RNA_PolII_BL_R2
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Ch8_NPC_Tfap2a_Abcam Biological repliacate 1

description:
Library name: Ch8_NPC_Tfap2a_Abcam_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Ch8_NPC_RNA_PolII_BL Biological repliacate 1

description:
Library name: Ch8_NPC_RNA_PolII_BL_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Ch8_NPC_input Biological repliacate 2

description:
Library name: Ch8_NPC_input_R2
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Ch8_NPC_input Biological repliacate 1

description:
Library name: Ch8_NPC_input_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Ch8_NPC_H3K9me3 Biological repliacate 2

description:
Library name: Ch8_NPC_H3K9me3_R2
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Ch8_NPC_H3K9me3 Biological repliacate 1

description:
Library name: Ch8_NPC_H3K9me3_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Ch8_NPC_H3K4me3 Biological repliacate 2

description:
Library name: Ch8_NPC_H3K4me3_R2
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: F123_mESC_input Biological repliacate 2

description:
Library name: F123_mESC_input_R2
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Ch8_NPC_H3K4me2 Biological repliacate 2

description:
Library name: Ch8_NPC_H3K4me2_R2
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Ch8_NPC_H3K27me3 Biological repliacate 1

description:
Library name: Ch8_NPC_H3K27me3_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Ch8_NPC_H3K4me2 Biological repliacate 1

description:
Library name: Ch8_NPC_H3K4me2_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Ch1_NPC_RNA_PolII_BL Biological repliacate 1

description:
Library name: Ch1_NPC_RNA_PolII_BL_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Ch1_NPC_Tfap2a_Abcam Biological repliacate 1

description:
Library name: Ch1_NPC_Tfap2a_Abcam_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Ch1_NPC_H3K4me3 Biological repliacate 1

description:
Library name: Ch1_NPC_H3K4me3_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Ch1_NPC_H3K4me2 Biological repliacate 2

description:
Library name: Ch1_NPC_H3K4me2_R2
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Ch8_NPC_H2AK119ub Biological repliacate 2

description:
Library name: Ch8_NPC_H2AK119ub_R2
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Ch1_NPC_input Biological repliacate 1

description:
Library name: Ch1_NPC_input_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Ch1_NPC_H3K9me3 Biological repliacate 2

description:
Library name: Ch1_NPC_H3K9me3_R2
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: F123_mESC_H3K27me3 Biological repliacate 2

description:
Library name: F123_mESC_H3K27me3_R2
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Ch1_NPC_Tfap2a_novus Biological repliacate 1

description:
Library name: Ch1_NPC_Tfap2a_novus_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Ch1_NPC_H3K4me3 Biological repliacate 2

description:
Library name: Ch1_NPC_H3K4me3_R2
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Wdr4^f/f rep2, scRNA

city: Wuhan

first: Minghe

state: Hubei

address: Donghu Road

institute: WuHan University

description: Library name: FL2

data_processing:
Single-cell RNA sequencing (scRNA-seq) data were aligned and quantified using the CellRanger toolkit v8.0.0 against the reference genome GRCm39-2024-A for mouse tumor samples.
Assembly: GRCm39-2024-A
Supplementary files format and content: 10X cellranger v8.0.1 output filtered matrix

source_name: Hepa1-6 orthotopic tumor

extract_protocol:
Tissues were transported on ice in sterile culture dishes containing 10 mL of 1× Dulbecco’s Phosphate-Buffered Saline (DPBS; Thermo Fisher, Cat. no. 14190144) to remove residual tissue storage solution, and then minced on ice. Tissue digestion was performed using 0.25% Trypsin (Thermo Fisher, Cat. no. 25200-072) and 10 µg/mL DNase I (Sigma, Cat. no. 11284932001), dissolved in PBS supplemented with 5% Fetal Bovine Serum (FBS; Thermo Fisher, Cat. no. SV30087.02). The tissues were incubated at 37°C with shaking at 50 r.p.m. for approximately 40 minutes. Dissociated cells were collected every 20 minutes to improve cell yield and viability. Cell suspensions were passed through a 40 µm nylon cell strainer, and red blood cells were removed using 1× Red Blood Cell Lysis Solution (Thermo Fisher, Cat. no. 00-4333-57). The dissociated cells were then washed with 1× DPBS containing 0.4% FBS. Cell viability was assessed using 0.4% AO/PI staining on a Countstar Rigel S2 system (Countstar, Shanghai). Samples were subsequently submitted to Majorbio Bio-Pharm Technology Co., Ltd. (Shanghai, China) for downstream processing.
Beads containing unique molecular identifiers (UMIs) and cell barcodes were loaded at near-saturation levels to ensure that each cell was encapsulated with a bead in a Gel Beads-in-Emulsion (GEM). Upon exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the oligonucleotides on the beads. Beads were then recovered into a single tube for reverse transcription. During cDNA synthesis, each cDNA molecule was tagged at the 3′ end (corresponding to the 5′ end of the mRNA transcript) with both a UMI and a cell-specific barcode to indicate its cell of origin. Subsequently, the beads were subjected to second-strand cDNA synthesis, adaptor ligation, and universal amplification. Sequencing libraries were constructed from randomly fragmented whole-transcriptome amplification products, enriching for the 3′ ends of transcripts that were linked to cell barcodes and UMIs. All remaining procedures, including library construction, were performed following the manufacturer’s protocol for the Chromium Single Cell 3′ v3.1 platform (10x Genomics). Libraries were quantified using the High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). Sequencing was carried out on Illumina NovaSeq X Plus and MGI DNBSEQ-T7 platforms using 2×150 bp paired-end chemistry. All sequencing was performed at Majorbio Bio-Pharm Technology Co., Ltd. (Shanghai, China).

value: Hepa1-6 orthotopic tumor

value: Immune cells from hepa1-6 orthotopic tumor samples

tag: batch

value: 10x Genomics


title: Ch1_NPC_H3K4me2 Biological repliacate 1

description:
Library name: Ch1_NPC_H3K4me2_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.

value: male


title: Ch1_NPC_input Biological repliacate 2

description:
Library name: Ch1_NPC_input_R2
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.

value: neuronal progenitor cells


title: Wdr4^f/f rep1, scRNA

description: Library name: FL1


title: Ch8_NPC_H2AK119ub Biological repliacate 1

description:
Library name: Ch8_NPC_H2AK119ub_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Ch1_NPC_H3K27me3 Biological repliacate 2

description:
Library name: Ch1_NPC_H3K27me3_R2
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Wdr4^cKO rep2, scRNA

description: Library name: cKO2


title: Ch1_NPC_H3K27me3 Biological repliacate 1

description:
Library name: Ch1_NPC_H3K27me3_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Ch1_NPC_RNA_PolII_AM Biological repliacate 1

description:
Library name: Ch1_NPC_RNA_PolII_AM_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.

value: RNA Pol II-RPB1 (Active Motif, AB_2732926)


title: Wdr4^cKO rep1, scRNA

description: Library name: cKO1


title: Ch1_NPC_H2AK119ub Biological repliacate 2

description:
Library name: Ch1_NPC_H2AK119ub_R2
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Ch8_NPC_H3K4me3 Biological repliacate 1

description:
Library name: Ch8_NPC_H3K4me3_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Ch8_NPC_H3K27me3 Biological repliacate 2

description:
Library name: Ch8_NPC_H3K27me3_R2
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Ch1_NPC_H3K9me3 Biological repliacate 1

description:
Library name: Ch1_NPC_H3K9me3_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Ch1_NPC_H2AK119ub Biological repliacate 1

description:
Library name: Ch1_NPC_H2AK119ub_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: d15D92, d15D93, mESC, Mouse

first: Hao

last: Xie

address: No.5 Yiheyuan Road

institute: Peking University

data_processing:
For all cell types, samples with more than 50,000 remaining contacts were retained for downstream analysis. For mESCs (diploid samples), the haplotype of contacts was phased according to SNP sites. Each chromosome in each sample was treated as a polymer chain, evenly divided into 20kb sections, with each section treated as a particle of the polymer chain. The contacts of the sample were used as restraints to search for the optimal x, y, z spatial coordinates of particles using the Force-Directed Graph (FDG) algorithm implemented by “hickit”. To assess the quality of the chromatin 3D structure reconstruction, we generated five replicates using different random seeds and calculated the median RMSD for each combination of three replicates. If the median RMSD of the combination with the lowest value was less than 1.5, the first replicate in that combination was used for downstream analysis.
Assembly: GRCm38
Supplementary files format and content: 3dg file: each line sequentially listing the chromosome name, start position, x, y, and z coordinates, delimited by tab characters
Supplementary files format and content: dip pairs file: A tab-separated file recording allele-specific contacts that conforms to 4DN Consortium standards with chromosomes
Supplementary files format and content: pairs file: A tab-separated file recording contacts that conforms to 4DN Consortium standards with chromosomes

source_name: mESC

extract_protocol:
• Cell lines We utilized a female mouse embryonic stem cell (mESC) line derived from blastocysts at embryonic day 3.5 (E3.5) from crossbred embryos (female C57BL/6J × male CAST/EiJ). The procedures for derivation and culturing followed the methods provided by Arenas et al. (2006). • Cell culture Cells were cultured on flasks coated with 0.1% gelatin in an ES cell medium containing serum. The medium composition included DMEM (Gibco, 10829018), 15% ESC-grade fetal bovine serum (FBS) (VivaCell, C04002-100), 0.1 mM β-mercaptoethanol (Gibco, 21985023), 1% P/S (ThermoFisher, 10378016), NEAA (Sigma, M7145), L-Glutamine (Gibco, 25030-081), nucleotides (Millipore, ES-008-D), and 1000 U/ml leukemia inhibitory factor (LIF) (PeproTech, AF-250-02-25UG). Additionally, the medium was supplemented with 2i: 3 μM Gsk3 inhibitor CT99021 (Selleck, S1263) and 1 μM MEK inhibitor PD0325901 (Selleck, S1036).  • Cell differentiation Differentiation was initiated by withdrawing 2i/LIF in DMEM supplemented with 10% FBS, 1% P/S, NEAA, L-Glutamine, nucleotides, and 0.1 mM β-mercaptoethanol. The cells were plated at a density of 1.5 × 10⁴ cells/cm² on 6 well cell culture plates coated with 10 μg/ml fibronectin (GLPBIO, GP23499).
The single-cell preamplification product was diluted to 5ng/ul and 2 μL of each diluted sample was transposed by the addition of 3 μL Transposition Mixture (1 μL 5 X TTBL, 0.25 μL TTE Mix V50 (Vayme TD501), 1.75 μL water) and incubated at 55 °C for 10 min. Transposition was stopped by adding 1.25 μL 0.2% SDS and then the plate 40 was incubated at room temperature for 10 min. For a slight enrichment of cDNA reads, 2 μL 5 μM i5 unique dual (UD) index and 11.75 ul PCR mixture (4 μL 5X KAPA HiFi GC Buffer, 0.6 μL 10 mM dNTP, 0.2 μL 50 μM RNA-P7 primer, 0.4 μL KAPA HiFi DNA Polymerase (KAPA KK2102) and 6.55 μL water) were added to each well and incubated with the following program: Step 1: 72 °C × 3 min; Step 2: 98 °C × 30 s; Step 3: 98 °C × 15 s, 60 °C × 30 s, 72 °C

value: mESC


title: d15D94, d15D95, mESC, Mouse


title: d15D90, d15D91, mESC, Mouse


title: d15D88, d15D89, mESC, Mouse


title: d15D96, d15D97, mESC, Mouse


title: d15D80, d15D81, mESC, Mouse


title: d15D64, d15D65, mESC, Mouse


title: d15D76, d15D77, mESC, Mouse


title: d15D56, d15D57, mESC, Mouse


title: d15D74, d15D75, mESC, Mouse


title: d15D72, d15D73, mESC, Mouse


title: d15D68, d15D69, mESC, Mouse


title: d15D50, d15D51, mESC, Mouse


title: d15D66, d15D67, mESC, Mouse


title: d15D54, d15D55, mESC, Mouse


title: d15D58, d15D59, mESC, Mouse


title: d15D82, d15D83, mESC, Mouse


title: d15D98, d15D99, mESC, Mouse


title: d15D48, d15D49, mESC, Mouse


title: d15D46, d15D47, mESC, Mouse


title: d15D70, d15D71, mESC, Mouse


title: d15D84, d15D85, mESC, Mouse


title: d15D60, d15D61, mESC, Mouse


title: d15D52, d15D53, mESC, Mouse


title: d15D44, d15D45, mESC, Mouse


title: d15D42, d15D43, mESC, Mouse


title: d15D86, d15D87, mESC, Mouse


title: d15D78, d15D79, mESC, Mouse


title: d15D40, d15D41, mESC, Mouse


title: d15D62, d15D63, mESC, Mouse


title: d15D36, d15D37, mESC, Mouse


title: d15D38, d15D39, mESC, Mouse


title: d15D32, d15D33, mESC, Mouse


title: d15D30, d15D31, mESC, Mouse


title: d15D28, d15D29, mESC, Mouse


title: d15D34, d15D35, mESC, Mouse


title: d15D24, d15D25, mESC, Mouse


title: d15D26, d15D27, mESC, Mouse


title: d15D20, d15D21, mESC, Mouse


title: d15D22, d15D23, mESC, Mouse


title: d15D14, d15D15, mESC, Mouse


title: d15D18, d15D19, mESC, Mouse


title: d15D16, d15D17, mESC, Mouse


title: d4C96, d4C97, mESC, Mouse


title: d4C94, d4C95, mESC, Mouse


title: d4C85, d4C86, mESC, Mouse


title: d4C87, d4C88, mESC, Mouse


title: d4C81, d4C82, mESC, Mouse


title: d4C98, d4C99, mESC, Mouse


title: d4C89, d4C9, mESC, Mouse


title: d4C83, d4C84, mESC, Mouse


title: d4C78, d4C79, mESC, Mouse


title: d4C8, d4C80, mESC, Mouse


title: d4C76, d4C77, mESC, Mouse


title: d4C74, d4C75, mESC, Mouse


title: d4C72, d4C73, mESC, Mouse


title: d4C61, d4C62, mESC, Mouse


title: d4C70, d4C71, mESC, Mouse


title: d4C69, d4C7, mESC, Mouse


title: d4C67, d4C68, mESC, Mouse


title: d4C63, d4C64, mESC, Mouse


title: d4C65, d4C66, mESC, Mouse


title: d4C6, d4C60, mESC, Mouse


title: d4C92, d4C93, mESC, Mouse


title: d4C58, d4C59, mESC, Mouse


title: d15D100, d15D13, mESC, Mouse


title: d4C54, d4C55, mESC, Mouse


title: d4C52, d4C53, mESC, Mouse


title: d4C90, d4C91, mESC, Mouse


title: d4C56, d4C57, mESC, Mouse


title: d4C47, d4C48, mESC, Mouse


title: d4C43, d4C44, mESC, Mouse


title: d4C45, d4C46, mESC, Mouse


title: d4C50, d4C51, mESC, Mouse


title: d4C49, d4C5, mESC, Mouse


title: d4C36, d4C37, mESC, Mouse


title: d4C41, d4C42, mESC, Mouse


title: d4C39, d4C40, mESC, Mouse


title: d4C30, d4C31, mESC, Mouse


title: d4C34, d4C35, mESC, Mouse


title: d4C32, d4C33, mESC, Mouse


title: d4C28, d4C29, mESC, Mouse


title: d4C26, d4C27, mESC, Mouse


title: d4C24, d4C25, mESC, Mouse


title: d4C20, d4C21, mESC, Mouse


title: d4C22, d4C23, mESC, Mouse


title: d4C18, d4C19, mESC, Mouse


title: d4C12, d4C13, mESC, Mouse


title: d4C100, d4C11, mESC, Mouse


title: d3C99, d4C10, mESC, Mouse


title: d4C16, d4C17, mESC, Mouse


title: d4C14, d4C15, mESC, Mouse


title: d3C97, d3C98, mESC, Mouse


title: d3C93, d3C94, mESC, Mouse


title: d3C91, d3C92, mESC, Mouse


title: d3C9, d3C90, mESC, Mouse


title: d3C88, d3C89, mESC, Mouse


title: d3C95, d3C96, mESC, Mouse


title: d3C82, d3C83, mESC, Mouse


title: d3C84, d3C85, mESC, Mouse


title: d3C86, d3C87, mESC, Mouse


title: d3C75, d3C76, mESC, Mouse


title: d3C80, d3C81, mESC, Mouse


title: d3C77, d3C78, mESC, Mouse


title: d3C7, d3C70, mESC, Mouse


title: d3C71, d3C72, mESC, Mouse


title: d3C68, d3C69, mESC, Mouse


title: d3C66, d3C67, mESC, Mouse


title: d3C64, d3C65, mESC, Mouse


title: d3C62, d3C63, mESC, Mouse


title: d3C60, d3C61, mESC, Mouse


title: d3C59, d3C6, mESC, Mouse


title: d3C57, d3C58, mESC, Mouse


title: d3C55, d3C56, mESC, Mouse


title: d3C5, d3C50, mESC, Mouse


title: d3C44, d3C45, mESC, Mouse


title: d3C48, d3C49, mESC, Mouse


title: d3C46, d3C47, mESC, Mouse


title: d3C79, d3C8, mESC, Mouse


title: d3C36, d3C37, mESC, Mouse


title: d3C73, d3C74, mESC, Mouse


title: d3C38, d3C39, mESC, Mouse


title: d3C32, d3C33, mESC, Mouse


title: d3C28, d3C29, mESC, Mouse


title: d3C30, d3C31, mESC, Mouse


title: d3C26, d3C27, mESC, Mouse


title: d3C20, d3C21, mESC, Mouse


title: d3C22, d3C23, mESC, Mouse


title: d3C16, d3C17, mESC, Mouse


title: d3C14, d3C15, mESC, Mouse


title: d3C12, d3C13, mESC, Mouse


title: d2C99, d3C10, mESC, Mouse


title: d3C24, d3C25, mESC, Mouse


title: d3C100, d3C11, mESC, Mouse


title: d2C97, d2C98, mESC, Mouse


title: d3C53, d3C54, mESC, Mouse


title: d3C42, d3C43, mESC, Mouse


title: d2C95, d2C96, mESC, Mouse


title: d3C51, d3C52, mESC, Mouse


title: d2C93, d2C94, mESC, Mouse


title: d3C34, d3C35, mESC, Mouse


title: d2C91, d2C92, mESC, Mouse


title: d2C88, d2C89, mESC, Mouse


title: d3C40, d3C41, mESC, Mouse


title: d2C9, d2C90, mESC, Mouse


title: d2C86, d2C87, mESC, Mouse


title: d2C82, d2C83, mESC, Mouse


title: d2C75, d2C76, mESC, Mouse


title: d2C80, d2C81, mESC, Mouse


title: d2C77, d2C78, mESC, Mouse


title: d2C79, d2C8, mESC, Mouse


title: d2C84, d2C85, mESC, Mouse


title: d3C18, d3C19, mESC, Mouse


title: d2C73, d2C74, mESC, Mouse


title: d2C7, d2C70, mESC, Mouse


title: d2C66, d2C67, mESC, Mouse


title: d2C64, d2C65, mESC, Mouse


title: d2C71, d2C72, mESC, Mouse


title: d2C62, d2C63, mESC, Mouse


title: d2C60, d2C61, mESC, Mouse


title: d2C68, d2C69, mESC, Mouse


title: d2C59, d2C6, mESC, Mouse


title: d2C57, d2C58, mESC, Mouse


title: d2C53, d2C54, mESC, Mouse


title: d2C55, d2C56, mESC, Mouse


title: d2C51, d2C52, mESC, Mouse


title: d2C5, d2C50, mESC, Mouse


title: d2C48, d2C49, mESC, Mouse


title: d2C46, d2C47, mESC, Mouse


title: d2C44, d2C45, mESC, Mouse


title: d2C42, d2C43, mESC, Mouse


title: d2C40, d2C41, mESC, Mouse


title: d2C34, d2C35, mESC, Mouse


title: d2C38, d2C39, mESC, Mouse


title: d2C30, d2C31, mESC, Mouse


title: d2C36, d2C37, mESC, Mouse


title: d2C22, d2C23, mESC, Mouse


title: d2C26, d2C27, mESC, Mouse


title: d2C28, d2C29, mESC, Mouse


title: d2C20, d2C21, mESC, Mouse


title: d2C24, d2C25, mESC, Mouse


title: d2C16, d2C17, mESC, Mouse


title: d2C14, d2C15, mESC, Mouse


title: d2C18, d2C19, mESC, Mouse


title: d2C124, d2C13, mESC, Mouse


title: d2C122, d2C123, mESC, Mouse


title: d2C119, d2C12, mESC, Mouse


title: d2C120, d2C121, mESC, Mouse


title: d2C115, d2C116, mESC, Mouse


title: d2C117, d2C118, mESC, Mouse


title: d2C113, d2C114, mESC, Mouse


title: d2C111, d2C112, mESC, Mouse


title: d2C11, d2C110, mESC, Mouse


title: d2C108, d2C109, mESC, Mouse


title: d2C106, d2C107, mESC, Mouse


title: d2C32, d2C33, mESC, Mouse


title: d2C104, d2C105, mESC, Mouse


title: d2C100, d2C101, mESC, Mouse


title: d2C102, d2C103, mESC, Mouse


title: d1C9, d2C10, mESC, Mouse


title: d1C7, d1C8, mESC, Mouse


title: d1C52, d1C6, mESC, Mouse


title: d1C50, d1C51, mESC, Mouse


title: d1C45, d1C46, mESC, Mouse


title: d1C43, d1C44, mESC, Mouse


title: d1C35, d1C36, mESC, Mouse


title: d1C37, d1C38, mESC, Mouse


title: d1C33, d1C34, mESC, Mouse


title: d1C31, d1C32, mESC, Mouse


title: d1C25, d1C26, mESC, Mouse


title: d1C17, d1C18, mESC, Mouse


title: d1C15, d1C16, mESC, Mouse


title: d1C11, d1C12, mESC, Mouse


title: d1C41, d1C42, mESC, Mouse


title: d0C9, d1C10, mESC, Mouse


title: d1C47, d1C48, mESC, Mouse


title: d1C13, d1C14, mESC, Mouse


title: d1C27, d1C28, mESC, Mouse


title: d1C29, d1C30, mESC, Mouse


title: d0C31, d0C32, mESC, Mouse


title: d0C27, d0C28, mESC, Mouse


title: d1C49, d1C5, mESC, Mouse


title: d1C23, d1C24, mESC, Mouse


title: d1C21, d1C22, mESC, Mouse


title: d0C23, d0C24, mESC, Mouse


title: d0C25, d0C26, mESC, Mouse


title: d0C15, d0C16, mESC, Mouse


title: d0C17, d0C18, mESC, Mouse


title: d0C29, d0C30, mESC, Mouse


title: d0C21, d0C22, mESC, Mouse


title: d0C11, d0C12, mESC, Mouse


title: d1C19, d1C20, mESC, Mouse


title: d4B99, d0C10, mESC, Mouse


title: d4B97, d4B98, mESC, Mouse


title: d4B95, d4B96, mESC, Mouse


title: d4B93, d4B94, mESC, Mouse


title: d0C13, d0C14, mESC, Mouse


title: d0C19, d0C20, mESC, Mouse


title: d4B88, d4B89, mESC, Mouse


title: d4B84, d4B85, mESC, Mouse


title: d4B82, d4B83, mESC, Mouse


title: d4B86, d4B87, mESC, Mouse


title: d4B78, d4B79, mESC, Mouse


title: d4B80, d4B81, mESC, Mouse


title: d4B74, d4B75, mESC, Mouse


title: d4B72, d4B73, mESC, Mouse


title: d4B68, d4B69, mESC, Mouse


title: d4B70, d4B71, mESC, Mouse


title: d4B62, d4B63, mESC, Mouse


title: d4B60, d4B61, mESC, Mouse


title: d4B58, d4B59, mESC, Mouse


title: d4B54, d4B55, mESC, Mouse


title: d4B56, d4B57, mESC, Mouse


title: d4B52, d4B53, mESC, Mouse


title: d4B50, d4B51, mESC, Mouse


title: d4B9, d4B90, mESC, Mouse


title: d4B46, d4B47, mESC, Mouse


title: d4B48, d4B49, mESC, Mouse


title: d4B44, d4B45, mESC, Mouse


title: d4B91, d4B92, mESC, Mouse


title: d4B38, d4B39, mESC, Mouse


title: d4B40, d4B41, mESC, Mouse


title: d4B76, d4B77, mESC, Mouse


title: d4B34, d4B35, mESC, Mouse


title: d4B36, d4B37, mESC, Mouse


title: d4B32, d4B33, mESC, Mouse


title: d4B28, d4B29, mESC, Mouse


title: d4B30, d4B31, mESC, Mouse


title: d4B64, d4B65, mESC, Mouse


title: d4B22, d4B23, mESC, Mouse


title: d4B24, d4B25, mESC, Mouse


title: d4B20, d4B21, mESC, Mouse


title: d4B18, d4B19, mESC, Mouse


title: d4B12, d4B13, mESC, Mouse


title: d4B14, d4B15, mESC, Mouse


title: d4B16, d4B17, mESC, Mouse


title: d4B102, d4B103, mESC, Mouse


title: d4B42, d4B43, mESC, Mouse


title: d3B99, d4B10, mESC, Mouse


title: d4B100, d4B101, mESC, Mouse


title: d3B93, d3B94, mESC, Mouse


title: d3B97, d3B98, mESC, Mouse


title: d3B91, d3B92, mESC, Mouse


title: d3B89, d3B90, mESC, Mouse


title: d3B95, d3B96, mESC, Mouse


title: d3B85, d3B86, mESC, Mouse


title: d4B26, d4B27, mESC, Mouse


title: d3B83, d3B84, mESC, Mouse


title: d3B81, d3B82, mESC, Mouse


title: d3B69, d3B70, mESC, Mouse


title: d3B77, d3B78, mESC, Mouse


title: d3B65, d3B66, mESC, Mouse


title: d3B67, d3B68, mESC, Mouse


title: d4B104, d4B11, mESC, Mouse


title: d3B63, d3B64, mESC, Mouse


title: d3B61, d3B62, mESC, Mouse


title: d3B57, d3B58, mESC, Mouse


title: d3B59, d3B60, mESC, Mouse


title: d4B66, d4B67, mESC, Mouse


title: d3B87, d3B88, mESC, Mouse


title: d3B55, d3B56, mESC, Mouse


title: d3B51, d3B52, mESC, Mouse


title: d3B53, d3B54, mESC, Mouse


title: d3B47, d3B48, mESC, Mouse


title: d3B39, d3B40, mESC, Mouse


title: d3B45, d3B46, mESC, Mouse


title: d3B43, d3B44, mESC, Mouse


title: d3B41, d3B42, mESC, Mouse


title: d3B33, d3B34, mESC, Mouse


title: d3B79, d3B80, mESC, Mouse


title: d3B73, d3B74, mESC, Mouse


title: d3B29, d3B30, mESC, Mouse


title: d3B35, d3B36, mESC, Mouse


title: d3B71, d3B72, mESC, Mouse


title: d3B37, d3B38, mESC, Mouse


title: d3B75, d3B76, mESC, Mouse


title: d3B31, d3B32, mESC, Mouse


title: d3B21, d3B22, mESC, Mouse


title: d3B25, d3B26, mESC, Mouse


title: d3B27, d3B28, mESC, Mouse


title: d3B23, d3B24, mESC, Mouse


title: d3B115, d3B116, mESC, Mouse


title: d3B113, d3B114, mESC, Mouse


title: d3B49, d3B50, mESC, Mouse


title: d3B111, d3B112, mESC, Mouse


title: d3B107, d3B108, mESC, Mouse


title: d3B103, d3B104, mESC, Mouse


title: d2B99, d3B100, mESC, Mouse


title: d3B101, d3B102, mESC, Mouse


title: d2B97, d2B98, mESC, Mouse


title: d2B9, d2B90, mESC, Mouse


title: d2B86, d2B87, mESC, Mouse


title: d2B88, d2B89, mESC, Mouse


title: d2B84, d2B85, mESC, Mouse


title: d2B80, d2B81, mESC, Mouse


title: d2B91, d2B92, mESC, Mouse


title: d2B82, d2B83, mESC, Mouse


title: d2B74, d2B75, mESC, Mouse


title: d2B72, d2B73, mESC, Mouse


title: d2B76, d2B77, mESC, Mouse


title: d2B78, d2B79, mESC, Mouse


title: d3B109, d3B110, mESC, Mouse


title: d2B70, d2B71, mESC, Mouse


title: d2B64, d2B65, mESC, Mouse


title: d2B68, d2B69, mESC, Mouse


title: d2B66, d2B67, mESC, Mouse


title: d3B105, d3B106, mESC, Mouse


title: d2B62, d2B63, mESC, Mouse


title: d2B60, d2B61, mESC, Mouse


title: d2B58, d2B59, mESC, Mouse


title: d2B56, d2B57, mESC, Mouse


title: d2B54, d2B55, mESC, Mouse


title: d2B95, d2B96, mESC, Mouse


title: d2B46, d2B47, mESC, Mouse


title: d2B50, d2B51, mESC, Mouse


title: d2B93, d2B94, mESC, Mouse


title: d2B52, d2B53, mESC, Mouse


title: d2B44, d2B45, mESC, Mouse


title: d2B42, d2B43, mESC, Mouse


title: d2B48, d2B49, mESC, Mouse


title: d2B38, d2B39, mESC, Mouse


title: d2B36, d2B37, mESC, Mouse


title: d2B30, d2B31, mESC, Mouse


title: d2B28, d2B29, mESC, Mouse


title: d2B34, d2B35, mESC, Mouse


title: d2B26, d2B27, mESC, Mouse


title: d2B20, d2B21, mESC, Mouse


title: d2B22, d2B23, mESC, Mouse


title: d1C39, d1C40, mESC, Mouse


title: d2B24, d2B25, mESC, Mouse


title: d2B40, d2B41, mESC, Mouse


title: d2B12, d2B13, mESC, Mouse


title: d2B14, d2B15, mESC, Mouse


title: d2B16, d2B17, mESC, Mouse


title: d2B102, d2B103, mESC, Mouse


title: d2B104, d2B11, mESC, Mouse


title: d2B100, d2B101, mESC, Mouse


title: d1B55, d1B56, mESC, Mouse


title: d1B9, d2B10, mESC, Mouse


title: d1B49, d1B50, mESC, Mouse


title: d1B51, d1B52, mESC, Mouse


title: d1B53, d1B54, mESC, Mouse


title: d1B47, d1B48, mESC, Mouse


title: d2B32, d2B33, mESC, Mouse


title: d1B43, d1B44, mESC, Mouse


title: d1B41, d1B42, mESC, Mouse


title: d1B45, d1B46, mESC, Mouse


title: d1B37, d1B38, mESC, Mouse


title: d1B35, d1B36, mESC, Mouse


title: d1B33, d1B34, mESC, Mouse


title: d2B18, d2B19, mESC, Mouse


title: d1B29, d1B30, mESC, Mouse


title: d1B31, d1B32, mESC, Mouse


title: d1B27, d1B28, mESC, Mouse


title: d1B39, d1B40, mESC, Mouse


title: d1B21, d1B22, mESC, Mouse


title: d1B23, d1B24, mESC, Mouse


title: d1B15, d1B16, mESC, Mouse


title: d1B19, d1B20, mESC, Mouse


title: d1B17, d1B18, mESC, Mouse


title: d1B25, d1B26, mESC, Mouse


title: d1B13, d1B14, mESC, Mouse


title: d0B9, d1B10, mESC, Mouse


title: d1B11, d1B12, mESC, Mouse


title: d0B53, d0B54, mESC, Mouse


title: d0B55, d0B56, mESC, Mouse


title: d0B51, d0B52, mESC, Mouse


title: d0B49, d0B50, mESC, Mouse


title: d0B47, d0B48, mESC, Mouse


title: d0B45, d0B46, mESC, Mouse


title: d0B39, d0B40, mESC, Mouse


title: d0B37, d0B38, mESC, Mouse


title: d0B41, d0B42, mESC, Mouse


title: d0B43, d0B44, mESC, Mouse


title: d0B33, d0B34, mESC, Mouse


title: d0B35, d0B36, mESC, Mouse


title: d0B31, d0B32, mESC, Mouse


title: d0B29, d0B30, mESC, Mouse


title: d0B27, d0B28, mESC, Mouse


title: d0B25, d0B26, mESC, Mouse


title: d0B17, d0B18, mESC, Mouse


title: d0B21, d0B22, mESC, Mouse


title: d0B23, d0B24, mESC, Mouse


title: d0B19, d0B20, mESC, Mouse


title: d3B9, d0B10, mESC, Mouse


title: d3B15, d3B16, mESC, Mouse


title: d3B17, d3B18, mESC, Mouse


title: d3B11, d3B12, mESC, Mouse


title: d3B19, d3B20, mESC, Mouse


title: d3B13, d3B14, mESC, Mouse


title: d0B13, d0B14, mESC, Mouse


title: d0B11, d0B12, mESC, Mouse


title: d4B6, d4B7, mESC, Mouse


title: d4B2, d4B3, mESC, Mouse


title: d4B8, d3B10, mESC, Mouse


title: d3B8, d4B1, mESC, Mouse


title: d2B8, d3B1, mESC, Mouse


title: d3B2, d3B3, mESC, Mouse


title: d2B6, d2B7, mESC, Mouse


title: d2B4, d2B5, mESC, Mouse


title: d2B2, d2B3, mESC, Mouse


title: d0B15, d0B16, mESC, Mouse


title: d1B2, d1B3, mESC, Mouse


title: d1B6, d1B7, mESC, Mouse


title: d1B4, d1B5, mESC, Mouse


title: d0B8, d1B1, mESC, Mouse


title: d0B6, d0B7, mESC, Mouse


title: d4B4, d4B5, mESC, Mouse


title: d0B4, d0B5, mESC, Mouse


title: d0B2, d0B3, mESC, Mouse


title: d4A77, d4A8, mESC, Mouse


title: d4A7, d4A70, mESC, Mouse


title: d4A73, d4A74, mESC, Mouse


title: d4A64, d4A65, mESC, Mouse


title: d4A71, d4A72, mESC, Mouse


title: d4A75, d4A76, mESC, Mouse


title: d4A9, d0B1, mESC, Mouse


title: d3B6, d3B7, mESC, Mouse


title: d4A60, d4A61, mESC, Mouse


title: d3B4, d3B5, mESC, Mouse


title: d4A57, d4A58, mESC, Mouse


title: d4A62, d4A63, mESC, Mouse


title: d1B8, d2B1, mESC, Mouse


title: d4A55, d4A56, mESC, Mouse


title: d4A53, d4A54, mESC, Mouse


title: d4A51, d4A52, mESC, Mouse


title: d4A5, d4A50, mESC, Mouse


title: d4A48, d4A49, mESC, Mouse


title: d4A46, d4A47, mESC, Mouse


title: d4A44, d4A45, mESC, Mouse


title: d4A39, d4A4, mESC, Mouse


title: d4A42, d4A43, mESC, Mouse


title: d4A40, d4A41, mESC, Mouse


title: d4A37, d4A38, mESC, Mouse


title: d4A68, d4A69, mESC, Mouse


title: d4A35, d4A36, mESC, Mouse


title: d4A66, d4A67, mESC, Mouse


title: d4A33, d4A34, mESC, Mouse


title: d4A31, d4A32, mESC, Mouse


title: d4A28, d4A29, mESC, Mouse


title: d4A26, d4A27, mESC, Mouse


title: d4A22, d4A23, mESC, Mouse


title: d4A59, d4A6, mESC, Mouse


title: d4A20, d4A21, mESC, Mouse


title: d4A19, d4A2, mESC, Mouse


title: d4A17, d4A18, mESC, Mouse


title: d4A3, d4A30, mESC, Mouse


title: d4A1, d4A10, mESC, Mouse


title: d4A24, d4A25, mESC, Mouse


title: d4A13, d4A14, mESC, Mouse


title: d3A8, d3A9, mESC, Mouse


title: d4A15, d4A16, mESC, Mouse


title: d4A11, d4A12, mESC, Mouse


title: d3A76, d3A77, mESC, Mouse


title: d3A74, d3A75, mESC, Mouse


title: d3A70, d3A71, mESC, Mouse


title: d3A72, d3A73, mESC, Mouse


title: d3A67, d3A68, mESC, Mouse


title: d3A65, d3A66, mESC, Mouse


title: d3A63, d3A64, mESC, Mouse


title: d3A61, d3A62, mESC, Mouse


title: d3A56, d3A57, mESC, Mouse


title: d3A6, d3A60, mESC, Mouse


title: d3A54, d3A55, mESC, Mouse


title: d3A58, d3A59, mESC, Mouse


title: d3A50, d3A51, mESC, Mouse


title: d3A52, d3A53, mESC, Mouse


title: d3A49, d3A5, mESC, Mouse


title: d3A41, d3A42, mESC, Mouse


title: d3A47, d3A48, mESC, Mouse


title: d3A4, d3A40, mESC, Mouse


title: d3A36, d3A37, mESC, Mouse


title: d3A43, d3A44, mESC, Mouse


title: d3A33, d3A35, mESC, Mouse


title: d3A38, d3A39, mESC, Mouse


title: d3A45, d3A46, mESC, Mouse


title: d3A31, d3A32, mESC, Mouse


title: d3A26, d3A27, mESC, Mouse


title: d3A20, d3A21, mESC, Mouse


title: d3A24, d3A25, mESC, Mouse


title: d3A3, d3A30, mESC, Mouse


title: d3A69, d3A7, mESC, Mouse


title: d3A22, d3A23, mESC, Mouse


title: d3A19, d3A2, mESC, Mouse


title: d3A28, d3A29, mESC, Mouse


title: d3A17, d3A18, mESC, Mouse


title: d3A13, d3A14, mESC, Mouse


title: d2A8, d2A9, mESC, Mouse


title: d2A75, d2A76, mESC, Mouse


title: d3A1, d3A10, mESC, Mouse


title: d2A73, d2A74, mESC, Mouse


title: d2A71, d2A72, mESC, Mouse


title: d2A7, d2A70, mESC, Mouse


title: d2A68, d2A69, mESC, Mouse


title: d2A66, d2A67, mESC, Mouse


title: d2A64, d2A65, mESC, Mouse


title: d2A62, d2A63, mESC, Mouse


title: d2A55, d2A56, mESC, Mouse


title: d2A59, d2A6, mESC, Mouse


title: d2A53, d2A54, mESC, Mouse


title: d2A51, d2A52, mESC, Mouse


title: d2A48, d2A49, mESC, Mouse


title: d2A5, d2A50, mESC, Mouse


title: d2A39, d2A4, mESC, Mouse


title: d2A42, d2A43, mESC, Mouse


title: d3A15, d3A16, mESC, Mouse


title: d2A57, d2A58, mESC, Mouse


title: d2A44, d2A45, mESC, Mouse


title: d2A37, d2A38, mESC, Mouse


title: d3A11, d3A12, mESC, Mouse


title: d2A33, d2A34, mESC, Mouse


title: d2A46, d2A47, mESC, Mouse


title: d2A40, d2A41, mESC, Mouse


title: d2A31, d2A32, mESC, Mouse


title: d2A24, d2A25, mESC, Mouse


title: d2A3, d2A30, mESC, Mouse


title: d2A35, d2A36, mESC, Mouse


title: d2A26, d2A27, mESC, Mouse


title: d2A22, d2A23, mESC, Mouse


title: d2A28, d2A29, mESC, Mouse


title: d2A60, d2A61, mESC, Mouse


title: d2A20, d2A21, mESC, Mouse


title: d2A13, d2A14, mESC, Mouse


title: d2A15, d2A16, mESC, Mouse


title: d2A11, d2A12, mESC, Mouse


title: d1A8, d1A9, mESC, Mouse


title: d1A74, d1A75, mESC, Mouse


title: d1A76, d1A77, mESC, Mouse


title: d1A6, d1A60, mESC, Mouse


title: d1A67, d1A68, mESC, Mouse


title: d1A61, d1A62, mESC, Mouse


title: d1A56, d1A57, mESC, Mouse


title: d1A58, d1A59, mESC, Mouse


title: d1A69, d1A7, mESC, Mouse


title: d1A63, d1A64, mESC, Mouse


title: d1A70, d1A71, mESC, Mouse


title: d1A65, d1A66, mESC, Mouse


title: d1A54, d1A55, mESC, Mouse


title: d1A50, d1A51, mESC, Mouse


title: d1A72, d1A73, mESC, Mouse


title: d1A52, d1A53, mESC, Mouse


title: d1A43, d1A44, mESC, Mouse


title: d1A49, d1A5, mESC, Mouse


title: d2A19, d2A2, mESC, Mouse


title: d1A47, d1A48, mESC, Mouse


title: d2A1, d2A10, mESC, Mouse


title: d1A45, d1A46, mESC, Mouse


title: d1A36, d1A37, mESC, Mouse


title: d1A38, d1A39, mESC, Mouse


title: d1A34, d1A35, mESC, Mouse


title: d1A30, d1A31, mESC, Mouse


title: d1A29, d1A3, mESC, Mouse


title: d1A27, d1A28, mESC, Mouse


title: d1A2, d1A20, mESC, Mouse


title: d2A17, d2A18, mESC, Mouse


title: d1A23, d1A24, mESC, Mouse


title: d1A18, d1A19, mESC, Mouse


title: d1A10, d1A11, mESC, Mouse


title: d1A4, d1A40, mESC, Mouse


title: d0A9, d1A1, mESC, Mouse


title: d1A12, d1A13, mESC, Mouse


title: d0A77, d0A8, mESC, Mouse


title: d1A14, d1A15, mESC, Mouse


title: d1A16, d1A17, mESC, Mouse


title: d0A75, d0A76, mESC, Mouse


title: d1A32, d1A33, mESC, Mouse


title: d0A66, d0A67, mESC, Mouse


title: d0A64, d0A65, mESC, Mouse


title: d0A71, d0A72, mESC, Mouse


title: d0A62, d0A63, mESC, Mouse


title: d0A7, d0A70, mESC, Mouse


title: d0A59, d0A6, mESC, Mouse


title: d0A73, d0A74, mESC, Mouse


title: d0A55, d0A56, mESC, Mouse


title: d0A53, d0A54, mESC, Mouse


title: d0A57, d0A58, mESC, Mouse


title: d1A25, d1A26, mESC, Mouse


title: d1A21, d1A22, mESC, Mouse


title: d0A68, d0A69, mESC, Mouse


title: d0A48, d0A49, mESC, Mouse


title: d0A42, d0A43, mESC, Mouse


title: d0A35, d0A36, mESC, Mouse


title: d0A39, d0A4, mESC, Mouse


title: d0A37, d0A38, mESC, Mouse


title: d0A31, d0A32, mESC, Mouse


title: d0A46, d0A47, mESC, Mouse


title: d0A3, d0A30, mESC, Mouse


title: d0A33, d0A34, mESC, Mouse


title: d0A28, d0A29, mESC, Mouse


title: d0A60, d0A61, mESC, Mouse


title: d0A26, d0A27, mESC, Mouse


title: d0A20, d0A21, mESC, Mouse


title: d0A17, d0A18, mESC, Mouse


title: d0A24, d0A25, mESC, Mouse


title: d0A22, d0A23, mESC, Mouse


title: d0A15, d0A16, mESC, Mouse


title: d0A19, d0A2, mESC, Mouse


title: d0A51, d0A52, mESC, Mouse


title: d0A5, d0A50, mESC, Mouse


title: d0A11, d0A12, mESC, Mouse


title: d0A1, d0A10, mESC, Mouse


title: d0A13, d0A14, mESC, Mouse


title: Male Sample was collected between 6-12 ZT after 5 days of Bloomington Media

city: Institute

first: Gerardo

last: Flores-Iga

state: West Virginia

address: Integrated Research and Extension Building

department: Biology

institute: West Virginia State University

description: Library name: KBMC

data_processing:
Raw single-nucleus RNA-seq (snRNA-seq) files were processed using CellRanger v9.0 (10x Genomics, Pleasanton, CA). Sequencing reads were aligned to the Drosophila melanogaster reference genome Dmel_20221217
Assembly: Dmel_20221217
Supplementary files format and content: *.h5
Supplementary files format and content: Capsaicin_fly.h5ad file contains the output object after annotation and analyses

molecule: nuclear RNA

organism: Drosophila melanogaster

source_name: Brain

growth_protocol: All experiments were conducted under a 12:12 light-dark cycle at 25 °C and 55–65% humidity in incubators using Bloomington Formulation medium. Flies were mated for 48 hours before being sorted into male or female vials at a density of 30 flies per vial, and transferred to new vials every other day.

extract_protocol:
Dissected tissues were cleared of RNAlate before flash-freezing in liquid nitrogen, stored at −80 °C, and shipped on dry ice to SingulOmics Corporation (NY, USA). Tissues were then homogenized and lysed with Triton X-100 in RNase-free water. The nuclei were subsequently purified, centrifuged, and resuspended in PBS containing RNase inhibitor.
Standardized 10× capture and library preparation were performed using the 10x Genomics Chromium GEM-X 3′ Single Cell Reagent Kit v4 (10x Genomics, Pleasanton, CA), targeting the recovery of 10,000–15,000 nuclei per sample and 20-25,000 reads per nucleus. The libraries were sequenced with ~400 million 150 bp paired-end reads on the Illumina NovaSeq X Plus platform (Illumina, San Diego, CA).

treatment_protocol: Capsaicin intervention

value: Brain

value: Berlin-K (8522)

value: Control


title: Male Sample was collected between 6-12 ZT after 5 days of Bloomington Media with Capsaicin

description: Library name: KBMT

value: 2 mM Capsaicin


title: Female Sample was collected between 6-12 ZT after 5 days of Bloomington Media with Capsaicin

description: Library name: KBFT


title: d0A44, d0A45, mESC, Mouse


title: d0A40, d0A41, mESC, Mouse


title: WT24hr_rep2

city: Nijmegen

first: Hendrik

last: Marks

address: Geert Grooteplein Zuid 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

description: Library name: WT24hr_rep2

data_processing:
Sequence reads were processed using the seq2science pipeline (v1.2.2)10. Paired-end reads were trimmed with fastp v0.23.2 with default options. Genome assembly GRCm39 was downloaded with genomepy 0.16.1. Reads were aligned with bwa-mem2 v2.2.1 with options '-M'. Afterwards, duplicate reads were marked with Picard MarkDuplicates v3.0.0. Before peak calling, paired-end info from reads was removed with seq2science so that both mates in a pair get used. Bam files were randomly sampled down to the reads number as the same as the lowest reads sample. Peaks were called with macs2 v2.2.7 with options ' --shift 75 --extsize 200 –nolambda’. Differential peaks were calculated by Diffbind (v3.12.0). Peak tracks and heatmaps were generated by Deeptools (v3.5.5). Peaks were annotated by ChIPseeker v1.38.0.
Assembly: GRCm39
Supplementary files format and content: bw file contains peak data that can be displayed in the Genome Browser

growth_protocol: The mouse embryonic stem cell line v6.5 was obtained from ThermoFisher (MES1402) and cultured in Dulbecco’s modified Eagle Medium (DMEM, ThermoFisher) supplemented with 15% heat-inactivated foetal calf scultured erum (ThermoFisher), 1X Minimal essential amino acids (ThermoFisher), 2 mM L-glutamine, 103 U/ml of LIF (Stemcell Technologies) and 50 µM 2-mercaptoethanol (ThermoFisher). Stem cells were grown on plates coated with 0.1% gelatine, detached using 0.05% Trypsin (ThermoFisher). BV-2 microglial? cells were cultured in Dulbecco’s modified Eagle Medium (DMEM, ThermoFisher) supplemented with 10% heat-inactivated foetal calf serum (ThermoFisher) and 2 mM L-glutamine. Cells were incubated at 5% CO2 at 37°C.

extract_protocol:
The ATAC (mt-remove) protocol was adapted from previously established methods8,9 with modifications. A total of 10,000 cells were collected, washed with 1 mL of ice-cold PBS containing EDTA-free protease inhibitor, and centrifuged at 500 × g for 5 minutes at 4 ℃. The supernatant was completely removed, and the cell pellet was resuspended in 20 μL of transposase reaction mixture (homemade), consisting of 1× TD buffer, 1 μL Tn5 enzyme, and 0.02% digitonin. The transposition reaction was carried out at 37 ℃ for 30 minutes with continuous agitation.
Following transposition, DNA was purified and the ATAC-seq library was constructed using the KAPA HyperPrep Kit (KAPA Biosystems, 07962363001) and barcoded with NEXTflex DNA barcodes (Integrated DNA Technologies).

value: mouse pluripotency stem cells

value: WT


title: WT0hr_rep2

description: Library name: WT0hr_rep2


title: Female Sample was collected between 6-12 ZT after 5 days of Bloomington Media

description: Library name: KBFC


title: WT24hr_rep1

description: Library name: WT24hr_rep1


title: WT0hr_rep1

description: Library name: WT0hr_rep1


title: Mda5OE24hr_rep1

description: Library name: Mda5OE24hr_rep1

value: Mda5 overexpression


title: Mda5OE24hr_rep2

description: Library name: Mda5OE24hr_rep2


title: Mda5OE0hr_rep2

description: Library name: Mda5OE0hr_rep2


title: Brain, TBI-VEGFC, rep6

city: Charlottesville

first: John

last: Lukens

state: VA

address: 409 Lane Road

department: Neuroscience

institute: University of Virginia

description: 10X Genomics

data_processing:
Fastq files were processed with Cell Ranger 7.0.1 using  `cellranger count`  to align reads to the mm10 Mus musculus reference genome (80 GB of memory and 16 cores). Sequencing reads were truncated to 28 bp (read 1) and 98 bp (read 2) for the three-prime chemistry protocol used during library preparation.
Cellranger count output files were read into Scanpy for QC, filtering, and downstream analysis.
Quality control filtering excluded low-quality nuclei with fewer than 1,000 total counts or 500 genes, and removed cells with extreme counts, high mitochondrial or ribosomal content, and doublets identified by Scrublet, followed by normalization and log-transformation in Scanpy.
Assembly: mm10
Supplementary files format and content: Tab-separated values (cell by gene matrix)
Supplementary files format and content: Tab-separated values (cell metadata)

source_name: Brain (Hippocampus)

extract_protocol:
Nuclei extraction was performed using the Miltenyi Nuclei Extraction Buffer (Miltenyi Biotec, Auburn, CA, USA) following manufacturer’s guidelines with gentle MACS Dissociation and C tubes.
Library preparation on isolated nuclei was performed with 10X Genomics Chromium Single Cell 3’ kit v3.1, according to standard manufacturer's specifications.

value: Brain (Hippocampus)

value: Male

value: TBI, AAV-VEGFC

tag: hemisphere

value: Left


title: Mda5OE0hr_rep1

description: Library name: Mda5OE0hr_rep1


title: Brain, TBI-GFP, rep4

description: 10X Genomics

value: TBI, AAV-GFP


title: Brain, TBI-GFP, rep3

description: 10X Genomics

value: Right


title: Brain, Sham-GFP, rep1

description: 10X Genomics

value: Sham, AAV-GFP


title: MDA-MB-231-120h_DP_30uM-B4

city: Barcelona

first: Magdalena

last: Arnal Segura

address: Carrer de Natzaret 113

country: Spain

institute: Vall d'Hebron Institute of Oncology

description: Library name: MDAMB231_120h_DP30_B4

data_processing:
Sequencing reads were aligned using TopHat v2.1.1 aligner and Ensembl reference genome GRCh38. Then, they were quantified with HTSeq-count v0.13.5 (-s reverse option).
Normalization of expression levels was performed using TMM method with calcNormFactors function from edgeR
Assembly: GRCh38
Supplementary files format and content: raw counts (counts.txt)
Supplementary files format and content: TMM norm counts (cpm_matrx.txt)

source_name: breast cancer

growth_protocol: MDA-MB-231 cells were purchased from ATCC (catalogue no. HTB-26) and were maintained in DMEM/F12 (Life Technologies) with 10% FBS.

extract_protocol:
Total RNA extraction of cell-line samples was done by Qiagen RNeasy Mini Kit and quality checked by TapeStation. The extracted RNA was purified with oligo(dT) magnetic beads to capture mRNAs,fragmented and subject to a stranded RT proceeding.
Library preparation protocol from Illumina Stranded mRNA Prep. Library QC included fluorometric quantification (Qubit) and fragment size distribution (TapeStation).

treatment_protocol: For in vitro RNA sequencing, MDA-MB-231 cells were treated with 30μM Omomyc for 120 hours.

value: breast cancer

value: triple negative breast cancer

value: XX


title: Human kidney epithelial cells OSR1+SIX2 double overexpression replicate 1

city: TEL AVIV

first: Naomi

last: Pode-Shakked

address: Weizmann St 6

department: Pediatric Nephrology

country: Israel

institute: Tel Aviv Souraski Medical Center

description:
Library name: 12_AK94P5-Double1
OSR1+SIX2-hKEpCs, donor AK94P5, biological replicate 1

data_processing:
Quality assessment: FastQC v0.11.9
Trimming and filtering: Trimmomatic v0.39 with parameters ILLUMINACLIP:TruSeq3-PE.fa:2:30:10, LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, MINLEN:36
Alignment: STAR aligner v2.7.3a to human reference genome GRCh38/hg38
Gene quantification: featureCounts v2.0.1 using GENCODE v32 annotations
Differential expression: DESeq2 v1.30.0 with Benjamini-Hochberg correction; genes with adjusted p-values <0.05 and |log2FC| >1 considered significant
Assembly: GRCh38/hg38
Supplementary files format and content: All_NormData.csv: Normalized expression matrix containing 13,272 genes across 13 samples. Values represent DESeq2 normalized counts
Supplementary files format and content: LFC files: Differential expression results containing gene names, log2FoldChange, padj, and baseMean values
Supplementary files format and content: DE files: Filtered differential expression results for upregulated (Up), downregulated (Dwn), and all significant genes (Res) with fold change >0.58 and p-value <0.05}

source_name: adult kidney

growth_protocol:
IMDM + 10% FBS + growth factors (50ng/mL bFGF, 50ng/mL EGF, 5ng/mL SCF)
Primary human adult kidney cells were cultured in Iscove's modified Dulbecco's medium (IMDM) supplemented with 10% fetal bovine serum, 1% L-glutamine, 1% penicillin-streptomycin, and growth factors: 50 ng/mL bFGF, 50 ng/mL EGF, and 5 ng/mL SCF (R&D Systems). Cells were maintained at 37'b0C in a humidified atmosphere containing 5% CO2. Cells were passaged using trypsin-EDTA (Gibco) upon reaching 70-80% confluency and used between passages 2-7.

extract_protocol:
Total RNA was extracted from cells at passage 4-6 using RNeasy Mini Kit (Qiagen) with on-column DNase digestion according to manufacturer's instructions. RNA concentration and purity were assessed using NanoDrop spectrophotometer with acceptable 260/280 ratios between 1.8-2.0. RNA integrity was assessed using Agilent 2100 Bioanalyzer with RNA 6000 Nano Kit; only samples with RIN values >8.0 were used.
RNA-Seq libraries were prepared from 1 uc0u956 g total RNA using TruSeq Stranded mRNA Library Prep Kit (Illumina). mRNA was isolated using poly-A selection, fragmented, and reverse transcribed using random hexamer primers. Second-strand cDNA synthesis was performed using dUTP for strand specificity. Following end repair, A-tailing, and adapter ligation, libraries were amplified by PCR for 12-15 cycles. Library quality was assessed using Agilent 2100 Bioanalyzer and quantified by qPCR using KAPA Library Quantification Kit.

treatment_protocol: For lentiviral transduction, hKEpCs were seeded at 5'd710^4 cells per well in 6-well plates and transduced with lentiviral particles at MOI of 5 in the presence of 8 uc0u956 g/mL polybrene. After 24 hours, medium was replaced with fresh REGM containing 10% FBS. Transduced cells were selected with puromycin (2 u956 g/mL) for 7 days. For double transduction, OSR1-expressing cells were additionally transduced with SIX2-encoding virus and selected with puromycin and neomycin.

value: primary adult kidney epithelial cells

tag: genotype/variation

value: OSR1+SIX2 overexpression

tag: transfection

value: lentiviral OSR1-mCherry + lentiviral SIX2

value: puromycin + neomycin selection


title: Human kidney epithelial cells OSR1+SIX2 double overexpression replicate 2

description:
Library name: 14_AK94P5-Double3
OSR1+SIX2-hKEpCs, donor AK94P5, biological replicate 2


title: MDA-MB-231-120h_Vehicle-B4

description: Library name: MDAMB231_120h_veh_B4

tag: tissue

value: vehicle


title: Human kidney epithelial cells OSR1 overexpression replicate 2

description:
Library name: 10_AK94P4-OSR1-N2-RNA
OSR1-hKEpCs, donor AK94P4, biological replicate 2

value: OSR1 overexpression

value: lentiviral OSR1-mCherry

value: puromycin selection


title: MDA-MB-231-120h_Vehicle-B3

description: Library name: MDAMB231_120h_veh_B3

tag: genotype


title: Human kidney epithelial cells OSR1 overexpression replicate 3

description:
Library name: 11_AK94P4-OSR1-P-RNA
OSR1-hKEpCs, donor AK94P4, biological replicate 3


title: MDA-MB-231-120h_DP_30uM-B3

description: Library name: MDAMB231_120h_DP30_B3


title: Human kidney epithelial cells SIX2 overexpression replicate 3

description:
Library name: 8_AK94P5-Six2-RNA3
SIX2-hKEpCs, donor AK94P5, biological replicate 3

value: SIX2 overexpression

value: lentiviral SIX2


title: Human kidney epithelial cells mCherry control replicate 3

description:
Library name: 5_AK94P5-Control3
mCherry control hKEpCs, donor AK94P5, biological replicate 3

value: wild type

value: lentiviral mCherry


title: Human kidney epithelial cells mCherry control replicate 2

description:
Library name: 4_AK94P5-Control2
mCherry control hKEpCs, donor AK94P5, biological replicate 2


title: Human kidney epithelial cells SIX2 overexpression replicate 2

description:
Library name: 7_AK94P5-Six2-RNA2
SIX2-hKEpCs, donor AK94P5, biological replicate 2


title: Human kidney epithelial cells SIX2 overexpression replicate 1

description:
Library name: 6_AK94P5-Six2-RNA1
SIX2-hKEpCs, donor AK94P5, biological replicate 1


title: Human kidney epithelial cells naive replicate 2

description:
Library name: 2_AK94P5-Naive2
Naive hKEpCs, donor AK94P5, biological replicate 2


title: Human kidney epithelial cells naive replicate 1

description:
Library name: 1_AK94P5-Naive1
Naive hKEpCs, donor AK94P5, biological replicate 1


title: Brain, TBI-VEGFC, rep5

description: 10X Genomics

value: Brain (Hippocampus)

value: Male

value: TBI, AAV-VEGFC

value: Right


title: ARPE-19, Meta, macroH2A1, Rep2 (Chip)

city: Minhang

first: deng

last: yongzhuo

state: Shanghai

address: DongchuanoRoad N0.800

institute: Shanghai Jiao Tong University

description: Library name: ARPE-19_Meta_macroH2A1_Chip, Rep2

data_processing:
Utilize TrimGalore to remove sequencing adapter sequences and low-quality bases from your reads (Q<20)
Use Bowtie2 to align the trimmed single reads to human genome
Use Samtools to remove the unknown chromosome segments mapped reads, unmappable reads and multi-mapped reads The mapped reads are converted to bam format, are de-duplicated by Sambamba markdup
mapped reads are used to identidfy macroH2A1 enriched domains  by normR after normalization by the control (input nucleosome DNA). Genome is divided into 2kb bins,regimeR is used for calling peaks,  significant bins identified by Fisher’s test (P < 0.05) are use exportR to output into Bed files and BigWig files
Assembly: Homo_sapiens.GRCh38.114
Supplementary files format and content: BigWig

source_name: cell line

growth_protocol: All cell lines are kept in a humidified incubator at 37°C temperature with a 5% CO2 supply and cultured in DMEM (GIBCO, Carlsbad, CA, USA) with 10% FBS (GIBCO, Carlsbad, CA, USA) and 1% Pen/Strep antibiotin (GIBCO, Carlsbad, CA, USA).

extract_protocol:
In brief, collected cells are lysis in hypotonic buffer. After centrifugation, then resuspend in PA buffer. Cells are homogenized with a Dounce homogenizer for 10min with intermittent pauses. After removing large debris, supernatant is filtered through 10 μm and 5 μm filters. Chromosomes are centrifuged at 1750 × g for 10 min at 4°C and resuspend in MNase buffer.
Sequencing libraries are generated using approximately 1 ng of DNA per sample with the NEBNext® Ultra™ II DNA Library Prep Kit (E7645S, NEB, Ipswich, MA, USA), and sequencing is conducted on the Illumina® NovaSeq 500 platform. Prior to library preparation, the DNA is extracted using phenol-chloroform and ethanol precipitation. To obtain the DNA, either input mono-nucleosomes or ChIP-purified macroH2A1 nucleosomes are treated overnight at 56°C with 1% SDS and 200 μg/mL Proteinase K (Invitrogen, Carlsbad, CA, USA) following a pre-incubation with 100 μg/mL RNase A (Invitrogen, Carlsbad, CA, USA) to eliminate RNA contamination.

treatment_protocol: Culture cells with 100ng/ml colcemid (Sigma-Aldrich, St. Louis, MO, USA) overnight. After the incubation period, collected cells are lysed for purifing mitotic chromosome

value: cell line

value: human retinal pigment epithelial cell line

value: epithelial cells


title: TOV21G. control

city: SUITA

first: WANG

last: YAN

state: OSAKA

address: 2-2 YAMADAOKA

country: Japan

institute: Osaka University

description: Library name: Sample 1

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode. Illumina RTA v3.4.4 software was used for base calling. Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18. Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: hg19
Supplementary files format and content: FPKM values for each sample

source_name: Ovary

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Mini Kit (Qiagen, Venlo, Netherlands).
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).

value: Ovary

value: Ovarian clear cell carcinoma

value: No drugs


title: TOV21G. GSK458_0_1uM

description: Library name: Sample 3


title: TOV21G. Thiostrepton_1uM

description: Library name: Sample 2

value: Thiostrepton 1uM 48h


title: TOV21G. Thiostrepton_1uM_GSK458_0_1uM

description: Library name: Sample 4

value: Thiostrepton 1uM 48 h + GSK458 0.1 uM 48h


title: Brain, Sham-VEGFC, rep2

description: 10X Genomics

value: Sham, AAV-VEGFC


title: KMS20 Control 24H S1

city: Boston

first: Mehmet

middle: Kemal

last: Samur

state: MA

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

description: Library name: K20-CNT-1-24H

data_processing:
RSeQC for  quality control
STAR RNAseq aligner
VIPER pipeline
Assembly: hg38
Supplementary files format and content: txt file with raw read counts

growth_protocol: All myeloma cell lines were cultured in RPMI-1640supplemented with 10% fetal bovine serum, 1% L-glutamine and 1% penicillin/streptomycin.

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 10ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared using Roche Kapa Biosystems RiboErase and RNA HyperPrep sample preparation kits from 100ng of RNA.

treatment_protocol: Control and ID2-overexpressing (ID2-OE) cells were incubated with 0.25 µg/ml doxycycline for 24 hours to induce ID2 expression.

value: WT


title: KMS20 ID2 24H S2

description: Library name: K20-ID2-2-24H

value: ID2 OE


title: KMS20 ID2 24H S1

description: Library name: K20-ID2-1-24H


title: Human kidney epithelial cells OSR1 overexpression replicate 1

description:
Library name: 9_AK94P4-OSR1-N1-RNA
OSR1-hKEpCs, donor AK94P4, biological replicate 1

value: primary adult kidney epithelial cells

value: OSR1 overexpression

value: lentiviral OSR1-mCherry

value: puromycin selection


title: H929 ID2 24H S1

description: Library name: H-ID2-1-24H