title: Infant Blood_CDH_09

description:
Library name: Sample 68
column name in Table8.4_CDH_IBvsCTL_IB.txt:  Infant Blood_CDH_09

data_processing:
The ACGT101-miR program removed adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA), and repeats.
Unique sequences (18–26 nucleotides) were mapped to species-specific precursors in miRBase 22.0 by BLAST search to identify known and novel 3p- and 5p-derived miRNAs. Sequences mapping to mature miRNAs in hairpin arms were identified as known miRNAs, while those mapping to the opposite arm of known precursors were novel candidates. Remaining sequences were mapped to other selected species’ precursors in miRBase 22.0 and further BLASTed against the Homo sapiens genome to determine their genomic locations.
Assembly: hg38
Supplementary files format and content: Raw Counts Text Files

extract_protocol:
Total miRNA was purified using the Qiagen miRNeasy Mini Kit (Qiagen, Valencia, CA, USA) per the manufacturer's protocol. miRNA concentrations were measured using the NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). Quality control analysis and quantification were performed using Agilent Technologies 2100 Bioanalyzer (Agilent, CA, USA), and RNA integrity number >7.0 confirmed sample integrity.
Sequencing was performed by LC Sciences (Houston, Texas, USA). We used 1 µg of total RNA to prepare small RNA libraries with TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA). Single-end 50bp sequencing was conducted on an Illumina Hiseq 2500 system.


title: H1417_TAS1440_300nM_Day7_rep3

status: Public on Jan 20 2026

type: SRA

city: chiba

first: YINGBO

last: GONG

department: Medicine

country: Japan

institute: CHIBA University

library_source: transcriptomic

data_processing:
Deep sequencing was performed on an Illumina NovaSeq 6000 (paired-end reads) according to the manufacturer’s protocols. Sequenced reads from the RNA-seq experiments were aligned using the Bowtie 2 and TopHat (version 1.3.2), and Cufflinks (version 2.0.2) was used for transcriptome assembly. Gene expression levels were expressed as fragments per kilobase of exons per million mapped sequence reads. DEGs were identified using the R software package (version 4.2.0). Heatmaps and dendrograms were generated using R, GraphPad Prism 9.0, or https://www.chiplot.online/. DEG-related and terms of the KEGG were analyzed by gene set enrichment analysis software (GSEA, version 4.2.3).
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: NCI-1417 [H1417] (Cat. No. CRL-5869), NCI-H209 [H209] (HTB-172), SHP-77 (Cat. No. CRL-2195), NCI-H211 (Cat. No. CRL-5824), NCI-H196 (Cat. No. CRL-5823), NCI-H146 (Cat. No. HTB-173), NCI-H187 (Cat. No. CRL-5804), NCI-H69 (Cat. No. HTB-119), NCI-H446 [H446] (Cat. No. HTB-171), DMS 79 (Cat. No. CRL-2049), NCI-H510A [H510A, NCI-H510] (Cat. No. HTB-184), DMS 114 (Cat. No. CRL-2066), DMS 53 (Cat. No. CRL-2062), NCI-H2081 (Cat. No. CRL-5920), NCI-H524 [H524] (Cat. No. CRL-5831), NCI-H128 (Cat. No. HTB-120), NCI-H526 (Cat. No. CRL-5811), and NCI-H1694 (Cat. No. CRL-5888) cell lines were purchased from the American Type Culture Collection. Lu-135 (Cat. No. JCRB0170), COR-L51 (Cat. No. 92031916), CPC-N (Cat. No. ACC 306), and SBC-5 (Cat. No. JCRB0819) cell lines were obtained from the Japanese Collection of Research Bioresources, European Collection of Authenticated Cell Cultures, German Collection of Microorganisms and Cell Cultures GmbH, and Health Science Research Resources Bank, respectively. All of these are small-cell lung cancer cell lines and were cultured in RPMI1640 medium (Cat#: 189-02025, FUJIFILM Wako Pure Chemical Corporation, Osaka, Japan) supplemented with 10% FBS (Cat#: 10270106, GIBCO Thermo Fisher Scientific, San Jose, CA) (NCI-1417, NCI-H209, SHP-77, NCI-H211, NCI-H196, Lu-135, and COR-L51), in conditioned, high-glucose RPMI1640 (Wako, Cat#: 187-02705) with 10% FBS (NCI-H146, NCI-H187, NCI-H69, NCI-H446, NCI-H526, NCI-H524, and DMS 79), in McCoy’s 5A (GIBCO, Cat#: 16600-082) with 10% FBS (CPC-N), in minimum essential medium (Cat#: 21442-25, Nacalai Tesque, Kyoto, Japan) with 10% FBS (SBC-5), in F-12K medium (GIBCO, Cat#: 11765-054) with 10% FBS (NCI-H510A), in Waymouth’s medium (GIBCO, Cat#: 11220-035) with 10% FBS (DMS 114 and DMS 53), in IMDM medium (GIBCO, Cat#: 12440-053) with 20% FBS (NCI-H128), or in HITES medium (GIBCO, 11330-032) with 10% FBS, Insulin (FUJIFILM, Cat#: 093-06351), Transferrin (Cat#: 10652202001, Roche Diagnostics, Rotkreuz, Switzerland), Hydrocortisone (Cat#: H6909-10ML, SIGMA-Aldrich, St. Louis, MO, USA), GlutaMAX (GIBCO, Cat#: 35050-061), Sodium Selenite (FUJIFILM, Cat#: 190-10844), and -Estradiol (SIGMA-Aldrich, Cat#: E2758-250MG) (NCI-H2081 and NCI-H1694). INSM1 knockout NCI-H1417 and NCI-H146 cells were generated using CRISPR‒Cas9 genome editing as previously described (Ochiiwa et al., 2021).

extract_protocol:
SCLC cell lines were treated, for the indicated durations, with different LSD1 inhibitors. Total cellular RNA was extracted using a modified chloroform/phenol procedure (TRIzol™, Invitrogen Thermo Fisher Scientific). RNA integrity and concentration were measured using a 4200 TapeStation system for high-throughput automated electrophoresis (Agilent, Santa Clara, CA, USA)
RNA-Seq libraries were prepared using the NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA) with the SPRIselect reagent (Cat. No. B23318, Beckman Coulter, Indianapolis, IN, USA) following the manufacturers’ protocols.

treatment_protocol: The SCLC cell lines were seeded in plates. The following day, LSD1 inhibitors were serially diluted with DMSO and mixed with the culture medium. The mixtures were then added to each well on the plates. The final concentration of DMSO was set at 0.075 %. Cells were maintained with the inhibitors without any medium change.

tag: cell line

tag: cell type

value: small-cell lung cancer

tag: genotype

value: WT

tag: treatment


title: NCIH661_DPPA2_4_DKO_c14_2

city: Melbourne

first: Janith

last: Seneviratne

state: VIC

address: Peter MacCallum Cancer Centre, 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

description: Library name: NCIH661_DPPA2_4_DKO_c14_2

data_processing:
Reads in fastq files were filtered (for quality (phred score > 20) and length (>20 bases)) and trimmed (Illumina adapters) using TrimGalore (v0.6.6) in single-end mode with the following flags (--phred33 --fastqc --quality 20 --length 20).
Filtered and trimmed reads were then aligned to the human genome (GRCh38.p13) using the STAR aligner (v2.7.5b) with the following flags (--outSAMattributes Standard --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within). A STAR index was generated prior to alignment using gencode v36 gene annotations (--runMode genomeGenerate).
Coordinate sorted binary alignment files (BAM) were indexed and mapping statistics were generated using samtools (v1.9) (index/flagstat).
Read counts in indexed BAM files were then quantified at the gene level using the featureCounts utility from subread (v2.0.6) with default flags using gencode v36 gene annotations.
Raw counts were normalised by total library size and gene length (Transcripts Per Million) using R (v4.0.2).
Assembly: GRCh38 (GRCh38.p13)
Supplementary files format and content: A tab-delimited text file that includes raw gene count values for each sample.
Supplementary files format and content: A tab-delimited text file that includes TPM normalised gene count values for each sample.

molecule: polyA RNA

source_name: lung cancer

growth_protocol: Non-small cell lung cancer cell lines NCI-H661 and NCI-H1299 were cultured in RPMI-1640 (Gibco), A427 and HuTu80 with EMEM (Gibco), DMS114 with Waymouth (Gibco) and Cov318 with DMEM (Gibco) growth medium, all supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 1x penicillin/streptomycin at 37℃, 5% CO2. Cells were routinely passaged to maintain exponential growth, using Trypsin-Low EDTA (LE) Express (Gibco) to detach cells each time. Cells were regularly tested for mycoplasma contamination using the Mycoplasma PCR Detection Kit (abcam, #ab289834). NSCLC cell lines were also STR profiled to ensure authenticity. NCI-H661, NCI-H1299, A427, HuTu80, DMS114 and Cov318 were purchased from ATCC.

extract_protocol:
RNA extraction was performed on cell pellets collected from each cell line, using the Monarch Total RNA miniprep kit (NEB #T2010S) with DNAse I treatment according to the manufacturers instructions. RNA was quantified using the Qubit™ RNA High Sensitivity (HS) Assay Kit (Invitrogen) on a Qubit 3.0 flourometer.
Following RNA quantitation, 1 microgram of RNA was used as input for PolyA+ directional RNA-seq library preparation using the NEBNext Ultra II Directional RNA-seq Kit (#E7765, NEB) with the PolyA mRNA magnetic isolation module (#E7490, NEB) according to the manufacturers instructions. Following adaptor ligation, the final PCR used to incorportate multiplexing oligos for Illumina libraries using the NEBNext Multiplex Oligos for Illumina (Index Primers Set 1-4) was ran for a total of 8 cycles. Individual and pooled libraries were quantified and quality controlled using the dsDNA high sensitivity (HS) Qubit assay (Invitrogen) on the Qubit 3.0 fluorometer (Invitrogen) and D1000 High Sensitivity DNA kit (Agilent) on the TapeStation 2200 (Agilent).The pooled library was sequenced on an Illumina NextSeq 500 or NextSeq 2000 either as single-end 75bp or 100bp configurations respectively.

treatment_protocol: For NCI-H661 CRISPR knockouts, cells were electroporated using Neon™ Transfection System (ThermoFisher) with Cas9 RNP (loaded with a single guide RNA targeted to DPPA2 or DPPA4. Post electroporation, cells were seeded at low density (1 cell/well in a 384-well plate) to isolate monoclonal populations. After 3 weeks in single-cell dilution, populations were screened by PCR and edits identified by Sanger sequencing. Based on sequencing data, clones were selected for further genotype evaluation.Clones with an indel knockout on all alleles were expanded, cryopreserved, and tested for mycoplasma. For NCI-H661 inducible shRNA knockdowns miR30 based shRNAs were expressed using a tetracycline-inducible PiggyBac transposon system (pCLIIPi-iRFP-shRNA-pGK-mVenus), as previously described (Eckersley-Maslin et al. 2020). Established shRNA sequences against either; Renilla luciferase (non-targeting control) (#713), human DPPA2 (#760) or DPPA4 (#1993) were cloned by first annealing complementary oligo’s and ligating them into a digested pMSCV-miR30 backbone3 , followed by PCR, digestion and ligation into the pCLIIPi backbone. Stable cell lines were generated by transfecting NCI-H661 cells with the shRNA vectors along with PiggyBac transposase (pRM1024), waiting for 2 weeks, then sorting mVenus positive cells twice with expansion in between, collecting the top 50% of mVenus positive cells each time as a bulk population for further experiments. The mVenus DPPA4 shRNA construct underwent additional cloning to replace mVenus with tagBFP to allow for selection of cells containing both DPPA2 and DPPA4 inducible shRNA. To generate the double inducible knockdown line, stable shDPPA2 (mVenus+) cells were transfected with the shDPPA4 (tagBFP) vector and selected as above for both mVenus+/tagBFP+ cells. To induce shRNA expression, cells were treated with 2μg/ml doxycycline (Dox) for 7 days. For NCI-H661, A427, HuTu80, DMS114 and Cov318 siRNA knockdowns, 10uL Lipofectamine 2000 (ThermoFisher, #11668027) and 200pmol of non-targeted and DPPA2/4 targeted siRNA twice over 96 hours (first dose at day 0, second dose at day 2, collection on day 4) using SMARTpool siRNA (containing 4 siRNAs per pool) (Horizon/Dharmacon, Non-targeting; #D-001810-10-05, DPPA2; #L-018977-01-0005, DPPA4; #L-020766-01-0005). Lipofectamine 2000 and siRNA complexes were first formed with reduced-serum OptiMEM medium (Gibco) for 20 mins at room temperature, prior to addition to cells grown in complete medium. For the drug treatment experiment, NCI-H661 cells were treated with either a vehicle control (DMSO) or the p300/CBP inhibitor A-485 (10uM) for 24 hours.

tag: tissue

value: lung cancer

value: lung large cell carcinoma

value: DKO clone c14

value: sgDPPA2 + sgDPPA4

tag: batch


title: SD6010-1

city: NEW HAVEN

first: Museog

last: Choe

state: CT

address: 10 Amistad Street, Ste 214J

department: Genetics

country: USA

institute: Yale University

description:
Library name: RNA-seq sample9
truseq stranded mrna library

data_processing:
For RNA-seq, Sequencing reads were first quality-trimmed using fastp (v0.20.1) with adapter detection enabled and a minimum length cutoff of 25 bp. The quality of the trimmed reads was evaluated with FastQC (v0.11.9). Trimmed paired-end reads were aligned to the human reference genome (GRCh38) using STAR (v2.7.9a), with the primary assembly FASTA file and GTF annotations obtained from Ensembl (release 112). The alignment included both transcriptome and gene count quantification modes. Parameters allowed for a maximum of 20 multimapping reads and required a minimum overhang of 8 bp for splice junctions. Aligned reads were sorted and indexed using samtools (v1.10), and transcript quantification was performed with Salmon (v1.5.2) in alignment-based mode using the sorted BAM files, accounting for sequence and GC biases.  For scRNA-seq, The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest/tutorials/cr-tutorial-in)
Assembly: GRCh38
Supplementary files format and content: For RNA-seq, csv file including TPM. For scRNA-seq, matrix, features and barcode files.

source_name: brain organoid

extract_protocol:
for RNAseq, RNA was extracted using RNeasy plus universal mini prep kit (Quiagen). 1 ug total RNA was used for construction of sequencing libraries. For scRNA-seq organoids were dissociated with Papain dissociation system (worthington biochemical). And total 10,000 cells were used for library contruction.
for RNA-seq, Truseq stranded mRNA library prep kit (Illumina) was used following manufacture's protocol. For scRNA-seq, Library prep was performed following 3P standard  v3.1 (Next GEM)  protocol (10X Genomics)

value: brain organoid

tag: disease state

value: Angelman syndrome


title: NCIH661_DPPA2_KO_c40_1

description: Library name: NCIH661_DPPA2_KO_c40_1

value: DPPA2 KO clone c40


title: H1417_ORY-1001_100nM_Day7_rep2


title: scRNA-seq of mice pit: POMC-KO

city: Montreal

first: Kevin

last: Sochodolsky

state: QC

address: 110 Av des Pins O

department: Molecular Genetic

country: Canada

institute: Institut de recherche clinique de Montreal

description: Library name: POMC-KO

data_processing:
Reads were aligned on the mm10 mouse reference genome with 10x Genomics Cell Ranger 5.0.1 using the default parameters. Data analyses, filtering, normalization and scaling, dimensionality reduction, standard unsupervised clustering was performed using the Seurat R package v3.1 (32). Low quality cells were excluded using these parameters: 1500 > nFeature counts > 4000; nCount RNA > 10,000; 5 > mitochondrial DNA > 0.5. The samples were then combined using the merge function in Seurat. Transcript counts were normalized for total read depth. Cell clusters were identified by principal component analysis and visualized by uniform manifold approximation and projection (UMAP) embedding and unsupervised graph-based clustering with the Louvain algorithm with a resolution of 0.8. UMAP identified cell clusters were annotated based on differential expression of key pituitary marker genes.
Assembly: mm10
Supplementary files format and content: normalised.merged.rds ; Contains R object of both normalised samples merged with Feature count per barcode with clustering.

organism: Mus musculus

source_name: Pituitary

extract_protocol:
Dissociated pituitary cells were processed using Chromium Single Cell 3′ v3 Reagent (10x Genomics, Pleasanton, CA) following the manufacturer’s instructions.
8000 cells from two 380 days old animals of each genotype. Pituitary cells were partitioned into gel beads in emulsion for cell lysis and barcoded with oligo-dT priming and reverse transcribed. cDNA libraries were amplified, fragmented and size selected. Samples were controlled at multiple steps during the procedure by running on BioAnalyzer. Resulting libraries were sequenced on Illumina HiSeq 4000 S1 PE28x91 generating ≈3x10^6 reads/sample.

value: Pituitary

value: KO


title: NCIH661_DPPA2_4_DKO_c14_1

description: Library name: NCIH661_DPPA2_4_DKO_c14_1


title: NCIH661_DPPA2_4_DKO_c08_3

description: Library name: NCIH661_DPPA2_4_DKO_c08_3

value: DKO clone c08


title: ECD:huHER2Tg_3c

city: Omaha

first: Vimla

last: Band

state: Nebraska

address: 601 Saddle Creek road

department: Department of Genetics, Cell Biology & Anatomy,

institute: University of Nebraska Medical Center

description:
Library name: SAMPLES 21
Column name in BR_raw_counts.csv: 3c

data_processing:
RNA-seq of tumors: Raw FASTQ reads were trimmed using the Trim Galore v0.6.5 to remove the adapters, terminal unknown bases (Ns), and low-quality regions (Phred score < 33). The reads that passed the quality control were mapped to the mouse genome assembly (mm10) using STAR v2.7 and the gene level values were quantified using RSEM v1.3 based on GENCODE annotation (v35).
RNA-seq of 76NERT cell line transfectants: The RNA-seq reads underwent processing via the nf-core RNA-seq pipeline (version 3.9), accessed through Nextflow (version 22.10.3), and executed with Singularity to ensure reproducibility and portability. Utilizing paired-end sequencing reads, alignment to the human reference genome (GRCh38) was achieved using the Spliced Transcripts Alignment to a Reference (STAR) software (version 2.7.11a), integrating Ensembl gene annotations for precise mapping.
Assembly: mm10 and GRCh38
Supplementary files format and content: tab-delimited text file includes FPKM and TPM values for each Sample of 76NERT cell line
Supplementary files format and content: csv files include TPM values for each tumor Sample

source_name: Mammary Tumor

growth_protocol: 76NTERT cells expressing vector, ECD, ERBB2, and ECD+ERBB2 were cultured in triplicates in DFCI-3 starvation medium for 72 h.

extract_protocol:
Trizol-Chloroform RNA-extraction and RNA clean up using Qiagen Rneasy clean up microkit for both cell lines and tumors
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit v2 (Illumina)

value: Mammary Tumor

value: ECD; huHER2Tg


title: SingleCell Vista KO VDJ TCRseq

city: Cleveland

first: Lily

last: Wang

state: OH

address: 9500 Euclid Ave

institute: Cleveland Clinic

description:
Library name: KO_VJD
5' VDJ
VDJ

data_processing:
Processed files are direct outputs of alignment via uase of CellRanger software.
Seurat object is downstream processed using Seurat V4 includiing those cells used in the study.
Assembly: mouse_mm10-2020-A, vdj_GRCm38_alts_ensembl-5.0.0
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: VDJ (TCR seq)

source_name: tumor tissue

extract_protocol:
B16 melanoma tumors were pooled and digested to obtain single cell suspensions. Tumor infiltrating CD8  and CD4 T cells were stained with anti-CD8 antibody and purified by FACS sorting. 10e4 sorted viable T cells  were loaded into a Chromium Controller (10X Genomics).
Viable sorted T cells were washed three times before being processed using 10X genomics Feature barcoding protocol and workflow with v3.1 3’ technology. The single-cell RNAseq libraries are prepared by the Genomics Core facility at Lerner Research Institute. The single-cell RNAseq libraries are prepared according to the manufacturer’s Chromium Single Cell 3ʹ v3.1 with Feature Barcode technology for Cell Surface Protein (CSP) protocol. Briefly, cDNA for the 3’ gene expression library was initially synthesized from poly-adenylated mRNA, and DNA for the CSP library was synthesized from the cell surface protein feature Barcode. A minimum of 1 nanogram of cDNA was used to begin fragmentation, followed by end-repair, adapter ligation, and sample indexing. Each sequencing library including the CSP library was tagged with a dual index (10-nucleotide long each) sample barcode that identifies from which sample a sequence was derived. In addition, a 12-base unique molecular indexes (UMIs) were introduced to reduce duplicate reads. Constructed libraries are pooled and quantified using a Quantabio Q cycler. NovaSeq 6000 RapidRun flow cells are used to sequence a minimum of 20,000 read pairs per cell for the Gene expression library and a minimum of 5,000 read pairs per cell for the Cell surface protein library using specifications recommended by the manufacturer (10X Genomics, document # CG000317).
Separate feature barcoding libraries sequenced targeting 5,000 reads per cell at 10,000 cells per sample and were mapped to cells using cellranger software. Antibody counts were compiled with gene expression data in Seurat V4.0 software and normalized via CLR normalization methods for plotting.

value: tumor tissue

value: tumor infiltrating T cells

tag: library type

value: RNA


title: H1417_TAS1440_300nM_Day7_rep2

value: small-cell lung cancer


title: scRNA-seq of Mus musculus: skin, UVR and treated with 0.03% 9-cis HPR, rep2

city: Hangzhou

first: Yicheng

last: Xie

address: 3333 Binsheng Rd

country: China

institute: Children’s Hospital Zhejiang University School of Medicine

description: Library name: Low_dose_group_2

library_source: transcriptomic single cell

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software (version2.20).
Sample demultiplexing, barcode processing and single-cell 3’gene counting by using the Cell Ranger pipeline(https://support.10xgenomics.com/single-cell-geneexpression/ software/pipelines/latest/what-is-cell-ranger, version 3.1.0) .
Assembly: mm10
Supplementary files format and content: matrix.mtx file, store the gene expression matrix in sparse format, representing counts of UMIs (unique molecular identifiers) for each gene (row) in each cell barcode (column).
Supplementary files format and content: barcodes.tsv file, list of cell barcodes (columns of matrix)
Supplementary files format and content: features.tsv file, feature annotations (rows of matrix: gene ID, name, type).

source_name: skin

growth_protocol: Ten to twelve-week-old female SKH-1 mice (2311A01051, Charles River Laboratories, USA), weighing between 22 and 25 g, were bred and housed in a controlled environment at the Experimental Animal Center of Zhejiang University. They were maintained on a 12-hour light-dark cycle, with temperatures ranging from 23°C to 27°C and humidity between 40% and 70%, with free access to food and water.

extract_protocol:
The dorsal skin from a consistent area of the female SKH-1 mice was rapidly removed, placed in a container with cold PBS, and cut into small fragments. These fragments were washed three times before being immersed in a digestive mixture containing collagenase I, collagenase II, and Dispase® (all from Sigma, USA). After digestion, the mixture of liquid and tissue was transferred to a centrifuge tube, rinsed with DMEM, and centrifuged at 4°C at 350 g for 7 minutes. Next, 1-2 mL of trypsin was added, and the mixture was incubated at room temperature for 3-5 minutes before resuspension. After digestion, the cell suspension was strained through a 70 µm sieve (Miltenyi, GER). The resulting filtrate was centrifuged at 350 g for 7 minutes at 4°C, and the supernatant was discarded. The pellet was treated with a lysis reagent, resuspended, and chilled on ice for 2-3 minutes. To halt the lysis, 5 mL of DMEM containing 10% FBS was added, followed by centrifugation at 350 g for 7 minutes at 4°C. The pellet was then washed and resuspended according to its volume. Single cells were isolated using the 10× Genomics Chromium Single Cell 3′ Solution (10× Genomics, USA).
Single-cell suspensions were loaded to 10x Chromium to capture single cell according to the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’ kit (V3) .The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150bp) by LC-Bio Technology co.ltd., (HangZhou,China) at a minimum depth of 20,000 reads per cell.

value: skin

value: SKH-1 mice

value: UVR and treated with 0.03% 9-cis HPR


title: scRNA-seq of Mus musculus: skin, UVR and treated with 0.03% 9-cis HPR, rep1

description: Library name: Low_dose_group_1


title: H1417_GSK2879552_3000nM_Day7_rep1

value: WT


title: NCIH661_DPPA2_4_DKO_c14_3

description: Library name: NCIH661_DPPA2_4_DKO_c14_3

value: lung cancer

value: lung large cell carcinoma

value: DKO clone c14

value: sgDPPA2 + sgDPPA4


title: NCIH661_DPPA2_KO_c40_3

description: Library name: NCIH661_DPPA2_KO_c40_3

value: DPPA2 KO clone c40


title: H1417_DMSO_0_Day7_rep3

value: DMSO


title: YO1058-2

description:
Library name: RNA-seq sample6
truseq stranded mrna library

value: brain organoid

value: Angelman syndrome


title: HUTU80_siDPPA2_R3

description: Library name: HUTU80_siDPPA2_R3

source_name: duodenal cancer

value: duodenal cancer

value: Parental

value: siDPPA2 4 days


title: SD6010-2

description:
Library name: RNA-seq sample10
truseq stranded mrna library


title: SingleCell WT VDJ TCRseq

description:
Library name: WT_VDJ
5' VDJ
VDJ

value: tumor tissue

value: tumor infiltrating T cells

value: RNA


title: H1417_ORY-1001_100nM_Day7_rep1

value: small-cell lung cancer


title: YO1058-4

description:
Library name: RNA-seq sample8
truseq stranded mrna library


title: Control-4

description:
Library name: RNA-seq sample4
truseq stranded mrna library

value: healty control (SH2)


title: huHER2Tg_2a

description:
Library name: SAMPLES 16
Column name in BR_raw_counts.csv: 2a

value: Mammary Tumor


title: SingleCell WT gene expression

description:
Library name: WT_gex
5' mRNA library read 1 contains cell barcode and UMI; read 2 contains transcript
poly A RNA


title: H146_GSK2879552_3000nM_Day7_rep3

value: WT


title: HUTU80_siDPPA2_R1

description: Library name: HUTU80_siDPPA2_R1


title: H1417_DMSO_0_Day7_rep2


title: NCIH661_DPPA2_4_DKO_c08_2

description: Library name: NCIH661_DPPA2_4_DKO_c08_2

value: lung cancer

value: lung large cell carcinoma

value: DKO clone c08


title: NCIH661_DPPA2_4_DKO_c08_1

description: Library name: NCIH661_DPPA2_4_DKO_c08_1

value: sgDPPA2 + sgDPPA4


title: YO1058-3

description:
Library name: RNA-seq sample7
truseq stranded mrna library


title: Control-2

description:
Library name: RNA-seq sample2
truseq stranded mrna library


title: huHER2Tg_2c

description:
Library name: SAMPLES 18
Column name in BR_raw_counts.csv: 2c


title: ECD; huHER2Tg_3b

description:
Library name: SAMPLES 20
Column name in BR_raw_counts.csv: 3b

value: ECD; huHER2Tg


title: HUTU80_siCTRL_R3

description: Library name: HUTU80_siCTRL_R3

value: siControl 4 days


title: H1417_TAS1440_300nM_Day7_rep1


title: huHER2Tg_2b

description:
Library name: SAMPLES 17
Column name in BR_raw_counts.csv: 2b


title: Control-3

description:
Library name: RNA-seq sample3
truseq stranded mrna library

value: brain organoid


title: ECD; huHER2Tg_3a

description:
Library name: SAMPLES 19
Column name in BR_raw_counts.csv: 3a


title: H146_GSK2879552_3000nM_Day7_rep2


title: ECDTg_1c

description:
Library name: SAMPLES 15
Column name in BR_raw_counts.csv: 1c

value: ECDTg


title: HUTU80_siCTRL_R1

description: Library name: HUTU80_siCTRL_R1

value: duodenal cancer

value: Parental


title: ECDTg_1b

description:
Library name: SAMPLES 14
Column name in BR_raw_counts.csv: 1b


title: YO1058-1

description:
Library name: RNA-seq sample5
truseq stranded mrna library

value: Angelman syndrome


title: H146_GSK2879552_3000nM_Day7_rep1


title: HUTU80_siDPPA2_R2

description: Library name: HUTU80_siDPPA2_R2

value: siDPPA2 4 days


title: HUTU80_siCTRL_R2

description: Library name: HUTU80_siCTRL_R2


title: ECDTg_1a

description:
Library name: SAMPLES 13
Column name in BR_raw_counts.csv: 1a


title: H146_ORY-1001_100nM_Day7_rep1


title: KA_3ClassV_3_RNA

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota

description: Library name: S35

data_processing:
Raw sequencing reads were first assessed for quality using FastQC. The reads were then trimmed for adaptor sequences and low-quality bases using Trimmomatic. Trimmed reads were aligned to the rn6 rat reference genome using the Hisat2 sequence alignment program. Gene counts were calculated using featureCounts. Count data was normalized using the variance stabilizing transformation (vst) method in DESeq2.
Assembly: rn6
Supplementary files format and content: csv file includes raw count files

organism: Rattus norvegicus

source_name: hippocampal

extract_protocol:
Hippocampi were dissected from each animal following euthanasia and immediately flash-frozen on dry ice. Total RNA was subsequently extracted using the Qiagen AllPrep DNA/RNA Mini Kit. The quality and quantity of the extracted RNA were assessed using a TapeStation system.
RNA-sequencing libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit for Illumina.

value: hippocampal

value: Sprague-Dawley

tag: epileptogenesis model

value: Kainic acid (KA)

tag: group

value: 3 Class V


title: KA_3ClassV_2_RNA

description: Library name: S34


title: Control-1

description:
Library name: RNA-seq sample1
truseq stranded mrna library

value: healty control (SH2)


title: H146_TAS1440_300nM_Day7_rep3

value: small-cell lung cancer

value: WT


title: COV318_siDPPA4_R4

description: Library name: COV318_siDPPA4_R4

source_name: ovarian cancer

value: ovarian cancer

value: siDPPA4 4 days


title: KA_3ClassV_1_RNA

description: Library name: S32


title: COV318_siDPPA4_R2

description: Library name: COV318_siDPPA4_R2


title: KA_Sham_7_RNA

description: Library name: S24

value: Sham


title: Mouse_Kidney_scATAC-Seq

city: Toronto

first: Amin

last: Nooranikhojasteh

state: ON

address: 101 College Street

institute: Princess Margaret Cancer Centre

description:
Library name: Kidney_Sample_scATAC
10x Genomics

library_source: genomic single cell

data_processing:
Raw FASTQ files generated from the sequencing runs were aligned to the mouse genome (mm10) using the STAR aligner. Alignment files were processed using Cell Ranger ATAC-Seq (10x Genomics) to filter high-quality barcodes, remove duplicates, and generate fragment files. The processed data were imported into the ArchR framework for dimensionality reduction, batch correction (Harmony), clustering, and annotation. Marker peaks were identified, and transcription factor motifs were analyzed for enriched accessible regions. Gene activity scores were computed, and pathway enrichment analysis was performed for functional characterization.
Assembly: mm10
Supplementary files format and content: Tab Separated values file and matrix file

molecule: genomic DNA

source_name: Kidney

extract_protocol:
Nuclei were isolated from fresh-frozen tissue samples of nine murine organs using a protocol optimized for each tissue type. The process included tissue homogenization in cold homogenization buffer, filtration through cell strainers, and density gradient centrifugation using OptiPrep solutions. Isolated nuclei were checked for integrity using SYBR Green staining and counted before proceeding to single-cell library preparation.
Single-cell libraries were prepared using the Chromium Single Cell ATAC reagent kit v1.1 (10x Genomics) following the manufacturer’s guidelines. Approximately 10,000 nuclei per sample were subjected to transposition using Tn5 transposase, followed by partitioning into GEMs using the Chromium Controller. After barcoding and amplification of DNA fragments, libraries were purified, indexed, and size-selected for high-throughput sequencing. Quality control was performed using Agilent Bioanalyzer and KAPA Library Quantification kits.

value: Kidney


title: COV318_siCTRL_R4

description: Library name: COV318_siCTRL_R4

value: siControl 4 days


title: Mouse_Pancreas_scATAC-Seq

description:
Library name: Pancreas_Sample_scATAC
10x Genomics

source_name: Pancreas

value: Pancreas


title: KA_Sham_6_RNA

description: Library name: S23


title: COV318_siDPPA4_R3

description: Library name: COV318_siDPPA4_R3


title: H146_TAS1440_300nM_Day7_rep2


title: H146_TAS1440_300nM_Day7_rep1


title: Mouse_Small-Intestine_scATAC-Seq

description:
Library name: Small Intestine_Sample_scATAC
10x Genomics

source_name: Small Intestine

value: Small Intestine


title: KA_Sham_5_RNA

description: Library name: S22


title: H146_ORY-1001_100nM_Day7_rep2


title: Mouse_Spleen_scATAC-Seq

description:
Library name: Spleen_Sample_scATAC
10x Genomics

source_name: Spleen

value: Spleen


title: H1417_DMSO_0_Day7_rep1

value: DMSO


title: COV318_siCTRL_R2

description: Library name: COV318_siCTRL_R2

value: Parental


title: COV318_siCTRL_R3

description: Library name: COV318_siCTRL_R3


title: Mouse_Liver_scATAC-Seq

description:
Library name: Liver_Sample_scATAC
10x Genomics

source_name: Liver

value: Liver


title: KA_Sham_4_RNA

description: Library name: S21

value: hippocampal

value: Sprague-Dawley


title: Mouse_Heart_scATAC-Seq

description:
Library name: Heart_Sample_scATAC
10x Genomics

source_name: Heart

value: Heart


title: H146_DMSO_0_Day7_rep3


title: Mouse_Lung_scATAC-Seq

description:
Library name: Lung_Sample_scATAC
10x Genomics

source_name: Lung

value: Lung


title: H146_DMSO_0_Day7_rep1

value: small-cell lung cancer


title: H146_DMSO_0_Day7_rep2

value: WT


title: KA_Sham_3_RNA

description: Library name: S20

value: Kainic acid (KA)


title: DMS114_siDPPA2_R3

description: Library name: DMS114_siDPPA2_R3

value: lung cancer

value: small cell lung cancer

value: siDPPA2 4 days


title: Mouse_Large-Intestine_scATAC-Seq

description:
Library name: Large Intestine_Sample_scATAC
10x Genomics

source_name: Large Intestine

value: Large Intestine


title: Mouse_Brain_scATAC-Seq

description:
Library name: Brain_Sample_scATAC
10x Genomics

source_name: Brain

value: Brain


title: DMS114_siDPPA2_R1

description: Library name: DMS114_siDPPA2_R1

source_name: lung cancer


title: DMS114_siDPPA2_R2

description: Library name: DMS114_siDPPA2_R2


title: H1417_GSK2879552_3000nM_Day3_rep2


title: KA_Sham_1_RNA

description: Library name: S18

value: Sham


title: H1417_ORY-1001_100nM_Day3_rep3


title: DMS114_siCTRL_R3

description: Library name: DMS114_siCTRL_R3

value: siControl 4 days


title: E0771_KClNS_3

city: CHICAGO

first: Ekrem Emrah

last: Er

state: IL

address: 909 S  WOLCOTT AVE

department: Physiology and Biophysics

institute: The University of Illinois at Chicago

description: Library name: E0771_KClNS_3

data_processing:
Reads were aligned to the GRCm38 genome with STAR
Counts were generated from the BAM files using Feature Counts
Assembly: GRCm38
Supplementary files format and content: raw counts table

extract_protocol:
Qiagen RNeasy
NuGen Universal Plus mRNA

value: breast cancer cells


title: E0771_KClBMS_3

description: Library name: E0771_KClBMS_3


title: KI_3ClassV_3_RNA

description: Library name: S16

value: Kindling (KI)

value: 3 Class V


title: DMS114_siCTRL_R1

description: Library name: DMS114_siCTRL_R1

value: Parental


title: H1417_GSK2879552_3000nM_Day3_rep1


title: DMS114_siCTRL_R2

description: Library name: DMS114_siCTRL_R2


title: H146_ORY-1001_100nM_Day7_rep3


title: E0771_KCl_3

description: Library name: E0771_KCl_3

value: 24hr 40mM KCl


title: KI_3ClassV_4_RNA

description: Library name: S17

value: hippocampal

value: Sprague-Dawley


title: A427_siDPPA2_R3

description: Library name: A427_siDPPA2_R3

value: lung adenocarcinoma


title: KI_3ClassV_2_RNA

description: Library name: S14


title: KI_3ClassV_1_RNA

description: Library name: S13


title: A427_siDPPA2_R2

description: Library name: A427_siDPPA2_R2


title: E0771_NS_3

description: Library name: E0771_NS_3


title: H1417_ORY-1001_100nM_Day3_rep2

value: small-cell lung cancer

value: WT


title: KI_Sham_4_RNA

description: Library name: S6


title: A427_siDPPA2_R1

description: Library name: A427_siDPPA2_R1

value: lung cancer


title: E0771_BMS_3

description: Library name: E0771_BMS_3


title: KI_Sham_3_RNA

description: Library name: S5


title: AT-3_KClBMS_3

description: Library name: AT-3_KClBMS_3


title: A427_siCTRL_R3

description: Library name: A427_siCTRL_R3


title: H1417_GSK2879552_3000nM_Day3_rep3


title: H1417_TAS1440_300nM_Day3_rep3


title: E0771_DMSO_3

description: Library name: E0771_DMSO_3

value: 24hr DMSO


title: A427_siCTRL_R2

description: Library name: A427_siCTRL_R2


title: H1417_DMSO_0_Day3_rep2

value: DMSO


title: KI_Sham_2_RNA

description: Library name: S4


title: A427_siCTRL_R1

description: Library name: A427_siCTRL_R1


title: H1417_TAS1440_300nM_Day3_rep1


title: H1417_DMSO_0_Day3_rep3


title: H1417_TAS1440_300nM_Day3_rep2


title: AT-3_KClNS_3

description: Library name: AT-3_KClNS_3


title: H1417_DMSO_0_Day3_rep1


title: AT-3_BMS_3

description: Library name: AT-3_BMS_3


title: KA_3ClassV_2_RRBS

description: Library name: S34

library_source: genomic

data_processing:
Raw sequencing reads were first assessed for quality using FastQC. The reads were then trimmed for adaptor sequences and low-quality bases using Trim Galore. Trimmed reads were aligned to the in silico bisulfite-converted rn6 rat reference genome using Bismark and Bowtie2. CpG sites on the X and Y chromosomes were excluded from the analysis. Methylation levels at each CpG site were calculated using Bismark. PCA was performed on the most variable 10% of CpG sites to assess sample relationships. Differentially methylated CpGs (DMCs) were identified using methylKit with a significance threshold of adjusted p-value < 0.01. DMCs were then annotated based on gene features (e.g., gene body, promoter regions) using the genomation package.
Assembly: rn6
Supplementary files format and content: tab-delimited file contains beta values

extract_protocol:
Hippocampi were dissected from each animal following euthanasia and immediately flash-frozen on dry ice. Total RNA was subsequently extracted using the Qiagen AllPrep DNA/RNA Mini Kit. The quality and quantity of the extracted DNA were assessed using a Qubit fluorometer and a TapeStation system.
Genomic DNA was digested with Msp1 restriction enzyme and purified using phenol:chloroform extraction and ethanol precipitation. Following Msp1 digestion, genomic DNA underwent blunt-end digestion, phosphorylation, and ligation of adapters with methylated cytosines. Ligated fragments, processed for size selection using agarose gel electrophoresis, were bisulfite converted, amplified by PCR, and then cleaned using AMPure XP beads (Beckman Coulter Life Sciences).

value: Kainic acid (KA)


title: NCIH661_siDPPA24_DKD_R3

description: Library name: NCIH661_siDPPA24_DKD_R3

value: lung large cell carcinoma

value: siDPPA2+siDPPA4 4 days


title: AT-3_NS_3

description: Library name: AT-3_NS_3


title: H146_GSK2879552_3000nM_Day3_rep3


title: KA_Sham_7_RRBS

description: Library name: S24

value: Sham


title: E0771_KClBMS_2

description: Library name: E0771_KClBMS_2

value: breast cancer cells


title: KA_3ClassV_1_RRBS

description: Library name: S32


title: KA_3ClassV_3_RRBS

description: Library name: S35


title: H146_GSK2879552_3000nM_Day3_rep1


title: AT-3_KCl_3

description: Library name: AT-3_KCl_3


title: KA_Sham_2_RNA

description: Library name: S19


title: H1417_ORY-1001_100nM_Day3_rep1


title: AT-3_DMSO_3

description: Library name: AT-3_DMSO_3


title: KA_Sham_5_RRBS

description: Library name: S22


title: NCIH661_siDPPA24_DKD_R1

description: Library name: NCIH661_siDPPA24_DKD_R1


title: KI_Sham_1_RNA

description: Library name: S1

value: Kindling (KI)


title: NCIH661_siDPPA2_R3

description: Library name: NCIH661_siDPPA2_R3

value: siDPPA2 4 days


title: NCIH661_siDPPA4_R3

description: Library name: NCIH661_siDPPA4_R3

value: Parental

value: siDPPA4 4 days


title: E0771_NS_2

description: Library name: E0771_NS_2


title: KA_Sham_4_RRBS

description: Library name: S21

value: hippocampal


title: E0771_BMS_2

description: Library name: E0771_BMS_2


title: H146_ORY-1001_100nM_Day3_rep3


title: H146_GSK2879552_3000nM_Day3_rep2


title: E0771_KCl_2

description: Library name: E0771_KCl_2

value: 24hr 40mM KCl


title: H146_TAS1440_300nM_Day3_rep3


title: NCIH661_siDPPA2_R1

description: Library name: NCIH661_siDPPA2_R1


title: H146_ORY-1001_100nM_Day3_rep2


title: NCIH661_siDPPA4_R2

description: Library name: NCIH661_siDPPA4_R2


title: KA_Sham_6_RRBS

description: Library name: S23

value: Sprague-Dawley


title: E0771_DMSO_2

description: Library name: E0771_DMSO_2


title: KA_Sham_1_RRBS

description: Library name: S18


title: H146_ORY-1001_100nM_Day3_rep1

value: small-cell lung cancer


title: NCIH661_siCTRL_R3

description: Library name: NCIH661_siCTRL_R3

value: siControl 4 days


title: KA_Sham_2_RRBS

description: Library name: S19


title: H146_TAS1440_300nM_Day3_rep2

value: WT


title: NCIH661_siDPPA4_R1

description: Library name: NCIH661_siDPPA4_R1

value: lung cancer


title: NCIH661_siDPPA2_R2

description: Library name: NCIH661_siDPPA2_R2


title: AT-3_KClNS_2

description: Library name: AT-3_KClNS_2


title: H146_DMSO_0_Day3_rep3

value: DMSO


title: E0771_KClNS_2

description: Library name: E0771_KClNS_2


title: NCIH661_siDPPA24_DKD_R2

description: Library name: NCIH661_siDPPA24_DKD_R2


title: AT-3_KCl_2

description: Library name: AT-3_KCl_2


title: H146_DMSO_0_Day3_rep1


title: NCIH661_siCTRL_R2

description: Library name: NCIH661_siCTRL_R2


title: KI_Sham_4_RRBS

description: Library name: S6


title: LUAD,T1N0M0,sample2

city: Xi’an

first: Run-Ze

last: Zhang

address: 569 Xinsi Road

department: Department of thoracic surgery

institute: Tangdu Hospital, Air Force Medical University

description:
Library name: Nor2
10x Genomics

data_processing:
CellRanger software (<https://support.10xgenomics.com/single-cell-vdj>) was used to align and annotate reads against the human genome assembly GRCh38p13, and a count matrix was generated using the genome annotation version Ensemble V105. After alignment, the Seurat R package (version 4.1.0) was used in R (version 3.6.0) to process barcodes associated with cell identifiers and unique molecular identifiers (UMIs). Cells with mitochondrial UMI counts > 25% or fewer than 500 genes detected were identified as low-quality cells and removed. DoubletFinder was used to remove doublets.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
The obtained tissue was transferred to a culture dish pre-added with 1×PBS (free of RNase and Ca, Mg ions) (the culture dish was placed on wet ice), and the tissue was cut into 0.5mm² small pieces. Then, the pieces were repeatedly washed with 1×PBS to remove surface blood stains, grease and other adherents. The washed small pieces of tissue were added with dissociation solution (0.35% collagenase IV, 2 mg/ml papain, 120 Units/ml DNase I), and reacted at 37°C on a water bath shaker (100 rpm) for 20 minutes. Then, 1×PBS (containing 10% fetal bovine serum FBS) was added to terminate the dissociation, and the cells were gently pipetted 5-10 times (with gentle operation to prevent cell death caused by shear force). The cell suspension was filtered through a 70-30um cell sieve, and then centrifuged at 300g for 5 minutes at 4°C. After centrifugation, the cell precipitate was collected and resuspended in 100ul 1×PBS (0.04% BSA) solution. To remove red blood cells, 1ml of red blood cell lysis buffer (MACS 130-094-183, 10×) was added, and the lysis was carried out at room temperature or on wet ice for 2-10 minutes. After lysis, the cells were centrifuged at 300g for 5 minutes at room temperature, and the cell precipitate was collected. Then, 50μl of dead cell removal reagent: Dead Cell Removal MicroBeads (MACS 130-090-101) was added and dead cells were removed using Miltenyi® Dead Cell Removal Kit (MACS 130-090-101). After the reaction, the reagent was removed by centrifugation. Subsequently, the cells were resuspended in 1×PBS (0.04% BSA) and centrifuged at 300g for 3 minutes at 4°C (repeated twice). The candidate cells after tissue dissociation, red blood cell lysis and dead cell removal were resuspended in 50μl 1×PBS (0.04% BSA) to form a cell suspension. Cell viability was detected by trypan blue staining, and the cell viability requirement was >85%. The cell count was determined by hemocytometer or cell automatic counter (Countess II Automated Cell Counter), and the cell concentration requirement was 700-1200 cells/μl.
Add the prepared cell suspension and reaction mixture (Master Mix + Sample), 10× barcode gel beads (VDJ 3' Gel Beads v1.1), and partitioning oil to different wells of the Chromium Next GEM Chip, respectively. A GEM is formed via the microfluidic "single cross" system. Then, dissolve the gel beads and lyse the cells within each GEM. The released oligonucleotides are mixed with the lysed cells and Master Mix (containing RT reagents and RT primers) for reverse transcription to obtain full-length complementary DNA (cDNA) sequences with 10× barcodes. After reverse transcription, destroy the water-in-oil structure using a recovery agent, and purify the cDNA. Subsequently, amplify the cDNA using DNA polymerase. Then fragment the amplified cDNA and select appropriate fragments. After end repair and A-tailing, ligate Read2 sequencing primers, perform PCR, and construct a cDNA library with P5 and P7 adapters.

value: Lung


title: KI_3ClassV_4_RRBS

description: Library name: S17

value: 3 Class V


title: H146_DMSO_0_Day3_rep2


title: AT-3_NS_2

description: Library name: AT-3_NS_2


title: LUAD,T1N0M0,sample3

description:
Library name: Nor3
10x Genomics


title: AT-3_KClBMS_2

description: Library name: AT-3_KClBMS_2


title: AT-3_BMS_2

description: Library name: AT-3_BMS_2


title: NCIH661_siCTRL_R1

description: Library name: NCIH661_siCTRL_R1

value: lung large cell carcinoma


title: KI_Sham_3_RRBS

description: Library name: S5

value: Sham


title: TFRC_input_2

city: Harbin

first: Jiansi

last: Li

address: Xuefu Road No.246

institute: Harbin Medical University

data_processing:
Illumina bcl2fastq software used for basecalling.
Raw reads with ≥ 2-N bases were initially dropped. Following that, a FASTX-Toolkit (Version 0.0.13) was used to remove adaptors and low-quality bases from the raw sequencing reads.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniquely mapped reads were remained. One more reads with the same start and end position, only one is considered.
after the reads were aligned onto the genome with HISAT2 (Kim, Langmead et al. 2015), the unique aligned reads on the genome was finally obtained, with the PCR duplicates being removed. And Piranha and the ABL in silico Random Clustering (ABLIRC) were employed to call peaks. Piranha has been previously described (Uren, Bahrami-Samani et al. 2012). ABLIRC was employed to identify the binding regions of GRCh38 on the genome (Xia, Chen et al. 2017)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include peak information for each group.

source_name: HRMC  cell

growth_protocol: The HRMC cell line were cultured with 5% CO2 at 37℃ in HRMC complete medium  with 100 U/mL penicillin , 10% fetal bovine serum (FBS)  and 100 µg/mL streptomycin

extract_protocol:
HRMCs were UV irradiated (CL-3000, UVP, Germany) once for 400 mJ/cm2, and lysed in ice-cold wash buffer. Cells were lysed in cold wash buffer (1× PBS, 0.1% SDS, 0.5% NP-40 and 0.5% sodium deoxycholate) containing PIC (B14001,bimake, China) and a 200 U/mL RNase inhibitor (2313U, Takara, Japan), and incubated on ice for 30 min. Cell lysate was cleared by centrifugation at 10,000 rpm at 4°C for 10 min. RQ I (1U/μl, M610A, Promega, Madison, WI, USA) was added to a final concentration of 0.05 U/μl and incubated in water bath at 37°C for 40 min. Immediately, DNase was quenched by adding stop solution to the lysate. Subsequently, to remove cell debris, the mixture was subjected to vibration and centrifugation at 13,000 x g at 4℃ for 20 min. RNAs were digested by micrococcal nuclease (MNase) (2910A, Thermo Scientific, USA).
The KAPA RNA Hyper Prep Kit (KK8541, Roche, Switzerland) was used to prepare the cDNA libraries following the manufacturer’s procedure. The libraries were applied to Illumina NovaSeq system for 150 nt paired-end sequencing following the manufacturer's instructions.

value: HRMC  cell

value: HRMC  cell  (input)

tag: rip target

value: none (input)

tag: antibody


title: KA_Sham_3_RRBS

description: Library name: S20

value: Kainic acid (KA)


title: H146_TAS1440_300nM_Day3_rep1


title: TFRC_input_1


title: KI_3ClassV_1_RRBS

description: Library name: S13

value: Kindling (KI)


title: E0771_KClNS_1

description: Library name: E0771_KClNS_1

value: breast cancer cells


title: E0771_KClBMS_1

description: Library name: E0771_KClBMS_1


title: OE_TFRC_3

data_processing:
Illumina bcl2fastq software used for basecalling.
Raw reads with ≥ 2-N bases were initially dropped. Following that, a FASTX-Toolkit (Version 0.0.13) was used to remove adaptors and low-quality bases from the raw sequencing reads.In addition,The short reads ≤ 21nt were discarded.
HISAT2 was used to map the clean reads to the GRCh38 genome (Kim, Langmead et al. 2015) allowing 4 mismatches. Eventually, to calculate gene reads number and fragments per kilobase of transcript per million fragments mapped (FPKM), uniquely mapped reads were used (Trapnell, Williams et al. 2010).
The R Bioconductor package DESeq2 was employed to screen out the DEGs (Love, Huber et al. 2014). The fold change (FC) >2 or < 0.5 and P value <0.05 were set as the cut-off values for identification of DEGs.
the ABLas pipeline was employed to define and quantify the alternative splicing events (ASEs) and regulated alternative splicing events (RASEs) between the samples (Jin, Li et al. 2017, Xia, Chen et al. 2017),Student’s t-test was performed to evaluate the significance of RBP-regulated ASEs’ ratio alteration. Those events at a P-value cutoff corresponding to a false discovery rate (FDR) of 0.05 were considered significant TFRC-regulated ASEs.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: HRMC cells

extract_protocol:
The HRMC cell lines (4200, Sciencell, USA) were cultured with 5% CO2 at 37℃ in HRMC complete medium (4200, Sciencell, USA) with 100 U/mL penicillin (SV30010, Hyclone, USA), 10% fetal bovine serum (FBS) (10091148, Gibco, China) and 100 µg/mL streptomycin
For each sample, the VAHTS Stranded mRNA-seq Library Prep Kit (NR605-02, Vazyme, China) was used to prepare RNA-seq library through 1μg of the total RNA. Polyadenylated mRNAs were subjected to purification and fragmentation. Following that, they were converted into double-strand complementary DNAs (cDNAs). The DNAs were ligated to VAHTS RNA Adapters after end repair and A tailing. The heat-labile uracil-DNA glycocasylase (UDG) was used to digest the adapter-ligated products corresponding to 200-500 bps. Then the single-strand cDNAs were subjected to amplification, purification and quantification. Eventually, they were stored at -80℃ for subsequent sequencing. The libraries were applied to Illumina NovaSeq 6000 system for 150 nt paired-end sequencing following the manufacturer's protocol.

value: HRMC cells

value: TRFC overexpressed  in HRMC cell


title: KI_Sham_1_RRBS

description: Library name: S1

value: hippocampal

value: Sprague-Dawley


title: Lymph Node,T1N2M0,sample3

description:
Library name: Ade3L
10x Genomics

source_name: Lymph Node

value: Lymph Node


title: KI_3ClassV_3_RRBS

description: Library name: S16


title: E0771_NS_1

description: Library name: E0771_NS_1


title: AT-3_DMSO_2

description: Library name: AT-3_DMSO_2

value: 24hr DMSO


title: Lymph Node,T1N2M0,sample2

description:
Library name: Ade2L
10x Genomics


title: LUAD,T1N2M0,sample3

description:
Library name: Ade3
10x Genomics


title: LUAD,T1N0M0,sample1

description:
Library name: Nor1
10x Genomics


title: pxy pxl1 pxl2 er erl2 biol rep 2

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

description: Library name: pf_ef_2

data_processing:
Paired-end reads were mapped to the Arabidopsis TAIR10 genome (EnsemblePlants, release 47) sequence with corresponding gtf file using HISAT2 (v2.0.5) software. The read numbers mapped to each gene were counted using Featurecounts (v1.5.0-p3) software.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include raw count per gene, one file per sample

organism: Arabidopsis thaliana

source_name: Hypocotyls and the upper 5mm of root

growth_protocol: Plants were grown under standard long day conditions for 3 weeks. The Arabidopsis ecotype Columbia-0 (Col-0, referred to as wild type) and previously described pxy-3 pxl1-1 pxl2-1 triple mutant (pxf) (Etchells et al., 2013), er-105 erl2-1 double mutant (er erl2) and pxf er erl2 quintuple mutant lines (Wang et al., 2019), were obtained from laboratory stocks.

extract_protocol:
Total RNA was extracted using Trizol reagent
Libraries were constructed by Novogene. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Hypocotyls and the upper 5mm of root

value: pxy pxl1 pxl2 er erl2


title: E0771_KCl_1

description: Library name: E0771_KCl_1

value: 24hr 40mM KCl


title: pxy pxl1 pxl2 er erl2 biol rep 3

description: Library name: pf_ef_3


title: LUAD,T1N2M0,sample2

description:
Library name: Ade2
10x Genomics

value: Lung


title: NC_3

value: HRMC  cell (control plasmid)


title: pxy pxl1 pxl2 er erl2 biol rep 1

description: Library name: pf_ef_1


title: LUSC1,T1N0M0,sample1

description:
Library name: LUSC1
10x Genomics


title: pxy pxl1 pxl2 biol rep 2

description: Library name: pxf_2

value: pxy pxl1 pxl2


title: pxy pxl1 pxl2 biol rep 3

description: Library name: pxf_3


title: TFRC_IP_1

value: HRMC  cell

value: HRMC  cell  (IP)

value: anti-TFRC

value: anti-FLAG (Proteintech(China), catalog number# 80010-1-RR)


title: OE_TRFC_2


title: KI_Sham_2_RRBS

description: Library name: S4

value: Kindling (KI)

value: Sham


title: E0771_DMSO_1

description: Library name: E0771_DMSO_1

value: breast cancer cells


title: TFRC_IP_2


title: KI_3ClassV_2_RRBS

description: Library name: S14

value: hippocampal

value: 3 Class V


title: NC_2

value: HRMC cells


title: AT-3_KClBMS_1

description: Library name: AT-3_KClBMS_1


title: Lymph Node,T1N2M0,sample1

description:
Library name: Ade1L
10x Genomics

value: Lymph Node


title: E0771_BMS_1

description: Library name: E0771_BMS_1


title: OE_TFRC_1

value: TRFC overexpressed  in HRMC cell


title: AT-3_KClNS_1

description: Library name: AT-3_KClNS_1


title: AT-3_KCl_1

description: Library name: AT-3_KCl_1


title: PFD-008-T0-N

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

country: Spain

institute: IDIBAPS

description:
Library name: PFD-008-T0-N
10x Genomics

data_processing:
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting, and aggregation of multiple sequencing runs were performed using the Cell Ranger analysis pipeline (v3.1.0)
Background and non-cellular barcodes are removed
Assembly: GRCh38
Supplementary files format and content: .tsv: barcodes, genes, .mtx: count matrix

source_name: rectum

extract_protocol:
Tissue digestion with Liberase
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode.

value: rectum

tag: subject status

value: patients with Crohn's Disease (CD) with and without perianal fistulizing disease (PFD)


title: LUAD,T1N2M0,sample1

description:
Library name: Ade1
10x Genomics

value: Lung


title: AT-3_BMS_1

description: Library name: AT-3_BMS_1


title: er erl2 biol rep 2

description: Library name: er_erl_2

value: Hypocotyls and the upper 5mm of root

value: er erl2


title: Lyz2-Cre_INPUT

city: Guangzhou

first: Sijia

last: Liang

address: 74 Zhongshan 2 Rd

department: Pharmacology

institute: Sun Yat-Sen University

description: Library name: Sample 6

data_processing:
Raw sequencing data were quality‑checked with FastQC, and adapters and low‑quality bases were trimmed using Trimmomatic.
Clean reads were aligned to the mouse genome (GRCm38) with Bowtie2 or BWA, and PCR duplicates were removed.
Peak calling was performed with MACS2 by comparing ChIP samples against input or IgG controls, and statistically significant peaks were annotated to nearby genomic features using HOMER.
Assembly: mm10
Supplementary files format and content: bigWig (except for Input samples)

source_name: BMDMs

growth_protocol: Mice were bred in ventilated cages with a 12-h light/dark cycle and access to an enriched environment, water and ad libitum feeding.BMDMs were differentiated from bone marrow cells cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% fetal ovine serum, 1% HEPES, 1% penicillin/streptomycin, and 30% L929-conditioned medium for 7 days.

extract_protocol:
Cells (1 × 10⁷) were cross-linked with 1% formaldehyde at 37°C for 10 minutes, and the reaction was quenched with 125 mmol/L glycine for 5 minutes. Nuclei were isolated using lysis buffer and sonicated using a Bioruptor UCD-300 (Diagenode) for 30 minutes (30 s ON/OFF cycle) to generate chromatin fragments ranging from 200 to 500 bp.
Sequencing libraries were constructed using the NEBNext® Ultra DNA Library Prep Kit for Illumina®, including end‑repair, A‑tailing, adapter ligation, size selection (200–500 bp), and PCR amplification.

value: BMDMs

tag: chip antibody


title: PFD-038-T0-N

description:
Library name: PFD-038-T0-N
10x Genomics


title: Lyz2-Cre_NFATc3

description: Library name: Sample 5

value: NFATc3 (ProteinTech, #18222-1-AP)


title: AT-3_DMSO_1

description: Library name: AT-3_DMSO_1

value: 24hr DMSO


title: Nfatc3-MKI_H3K4me3

description: Library name: Sample 4

value: Nfatc3 macrophage knockin

value: H3K4me3 (Abcam, #ab8580)


title: pxy pxl1 pxl2 biol rep 1

description: Library name: pxf_1

value: pxy pxl1 pxl2


title: Nfatc3-MKI_INPUT

description: Library name: Sample 7


title: PFD-039-T0-N

description:
Library name: PFD-039-T0-N
10x Genomics


title: PFD-036-T0-N

description:
Library name: PFD-036-T0-N
10x Genomics


title: er erl2 biol rep 3

description: Library name: er_erl_3


title: er erl2 biol rep 1

description: Library name: er_erl_1


title: wild type biol rep 1

description: Library name: WT_1

value: wild type


title: PFD-006-T0-N

description:
Library name: PFD-006-T0-N
10x Genomics


title: NC_1

value: HRMC  cell (control plasmid)


title: AT-3_NS_1

description: Library name: AT-3_NS_1

value: breast cancer cells


title: PFD-035-T0-N

description:
Library name: PFD-035-T0-N
10x Genomics


title: JNK inhibitor treatment (control), anti-H3K4Me3 antibody (pos control), biological replicate 2

city: New Haven

first: Mandar

middle: Deepak

last: Muzumdar

address: 333 Cedar Street

data_processing:
Adapter sequences from paired-end sequencing reads were trimmed with Trimmomatic and quality control was performed using FastQC.
Bowtie2 version 2.4.2 was used to align reads to the GRCm38 genome using the –very-sensitive flag and allowing for one mismatch. SAMtools version 1.16 was used to remove unmapped reads, secondary alignment reads, and reads with a Phred score of <30.
Macs2 version 2.2.7.1 was used to call narrow peaks with default peak-calling settings. H3K4me3 and cJun CUT&RUN peaks were called against IgG negative controls. IDR was used to determine significant peaks between the two biological replicates.
Deeptools version 3.5.1 was used for data visualization. To visualize average CUT&RUN signal per sample, Deeptools bamCoverage was used to normalize bigWig signal based on E. coli spike in control DNA.  A scaling factor was calculated based on the percentage of reads mapped to the E. coli K12, MG1655 reference genome.  The following additional bamCoverage flags were used: --extendReads --ignoreDuplicates --samFlagInclude 64.  Differences in read coverage between samples were normalized based on CPM.  In all plots, the mean normalized bigWig signal between two biological replicates is plotted.
Peak intersections were performed using BEDTools v2.30. Enriched motifs were identified using MEME v5.4.1 meme-chip.
Assembly: mm10
Supplementary files format and content: Idr: bed files with significant peaks between the 2 biological reps based on IDR
Supplementary files format and content: Bigwigs: bigWig files normalized by E. Coli spike-in and CPM
Library strategy: CUT&RUN

growth_protocol: Min6 cells were plated (2.5 million) and grown for 3 days prior to treatment.

extract_protocol:
550,000 cells were harvested per reaction and condition.
Cells were processed using the CUTANA ChIC/CUT&RUN Kit (14-1048), JUN/cJun CUTANA CUT&RUN antibody (SKU:13-2019), and positive (anti-H3K4Me3) and negative (IgG) control antibodies from the kit following the manufacturer’s protocol. Library preparation was performed by the Yale Center for Genome Analysis followed by sequencing to a depth of 30 million paired-end 150 bp reads (2x150) per sample on NovaSeq (Illumina).

treatment_protocol: Cells were treated with the JNK inhibitor SP600125 (20 uM, Med Chem Express) or DMSO (control) for 48 hours.

value: Pancreas

value: Min6 cells

value: JNK inhibitor

value: Beta cells

tag: cut&run antibody

value: H3K4me3 Antibody, SNAP-Certified™ for CUT&RUN


title: JNK inhibitor treatment (control), JUN antibody, biological replicate 2

value: JUN/c-Jun CUTANA CUT&RUN antibody


title: PFD-031-T0-N

description:
Library name: PFD-031-T0-N
10x Genomics

value: rectum


title: JNK inhibitor treatment (control), JUN antibody, biological replicate 1


title: wild type biol rep 2

description: Library name: WT_2

value: Hypocotyls and the upper 5mm of root


title: wild type biol rep 3

description: Library name: WT_3


title: ASK1-MKI_3

description: Library name: Sample 28

data_processing:
After library quality control, different libraries were pooled based on the effective concentration and targeted data amount. 5'-end of each library was phosphorylated and cyclized. Subsequently, loop amplification was performed to generate DNA nanoballs. We ultimately loaded these DNA nanoballs into flow cytometry cells with DNBSEQ-T7 or Illumina HiSeq 2000 for 2×150bp paired-end sequencing  following the vendor's recommended protocol.
Quality control.Clean datas were obtained by removing low quality reads with Fastp.
Reads mapping.Clean reads were mapped to mouse reference genome mm10 by hisat2.
Differential expression analysis of two conditions/groups was performed using the feartureCounts.
Assembly: mm10

extract_protocol:
Total RNA extraction was conducted by TRlzol Reagent. RNA detect concentration using qubit (Thermo Fisher Scientific, Q33226). RNA purity was checked using the NanoDrop PR-1(Thermo Fisher Scientific,CHEM-PR1-KIT). RNA integrity was assessed using the Qsep1 system (Qsep1 Technologies, CA, China).
Messenger RNA was purified from total RNA using attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: The metabolic dysfunction-associated steatohepatitis model was established by feeding male mice (8 week-old) with methionine- and choline-deficient diet (A02082002B, Research Diets, Inc., New Brunswick, NJ) for 4 weeks. Subsequently, mouse livers were isolated.

value: BMDMs

value: ASK1 macrophage knockin


title: JNK inhibitor treatment (control), IgG antibody (neg control), biological replicate 1

value: CUTANA™ Rabbit IgG CUT&RUN Negative Control Antibody


title: Lyz2-Cre_H3K4me3

description: Library name: Sample 3


title: MDKO_4

description: Library name: Sample 16

source_name: Livers

value: Livers

value: NFATc3 and ASK1 double knockout

value: MCD feeding


title: Lyz2-Cre_H3k27ac

description: Library name: Sample 1

value: H3K27ac (Abcam, #ab4729)


title: JNK inhibitor treatment (control), IgG antibody (neg control), biological replicate 2


title: JNK inhibitor treatment (control), anti-H3K4Me3 antibody (pos control), biological replicate 1


title: Nfatc3-MKI_H3k27ac

description: Library name: Sample 2

value: Nfatc3 macrophage knockin


title: MDKO_2

description: Library name: Sample 14


title: ASK1-MKI_2

description: Library name: Sample 27


title: PFD-032-T0-N

description:
Library name: PFD-032-T0-N
10x Genomics


title: PFD-028-T0-N

description:
Library name: PFD-028-T0-N
10x Genomics


title: ASK1-MKI_1

description: Library name: Sample 26


title: PFD-029-T0-N

description:
Library name: PFD-029-T0-N
10x Genomics


title: DMSO treatment (control), anti-H3K4Me3 antibody (pos control), biological replicate 1

value: DMSO


title: Control_3 (for ASK1-MKI)

description: Library name: Sample 25


title: DMSO treatment (control), JUN antibody, biological replicate 2

value: Pancreas


title: PFD-030-T0-N

description:
Library name: PFD-030-T0-N
10x Genomics


title: ASK1-MKO_3

description: Library name: Sample 11

value: ASK1 macrophage knockout


title: MDKO_1

description: Library name: Sample 13


title: ASK1-MKO_2

description: Library name: Sample 10


title: PFD-027-T0-N

description:
Library name: PFD-027-T0-N
10x Genomics


title: PFD-034-T0-N

description:
Library name: PFD-034-T0-N
10x Genomics


title: DMSO treatment (control), IgG antibody (neg control), biological replicate 2

value: Min6 cells


title: NFATc3-MKO_4

description: Library name: Sample 8

value: NFATc3 macrophage knockout


title: DMSO treatment (control), anti-H3K4Me3 antibody (pos control), biological replicate 2

value: Beta cells

value: H3K4me3 Antibody, SNAP-Certified™ for CUT&RUN


title: DMSO treatment (control), IgG antibody (neg control), biological replicate 1


title: 5xFAD;Bmp4-cKO mice, cortex, replicate 5

city: Daegu

first: Jaemyung

last: Jang

address: 61, Cheomdan-ro, Dong-gu

country: South Korea

institute: Korea Brain Research Institute

description: inDropTM

data_processing:
The previously published pipeline in Python available at [https://github.com/indrops/indrops] was used to read raw sequencing data under modified settings (Bowtie 1.2.3, m = 200, n = 1, l = 15, e = 1000) and align them to the Ensembl mouse reference genome (GRCm38 release 102) to obtain a cell-gene expression matrix.
Seurat package (version 4.3) (Butler et al., 2018;Stuart et al., 2019;Hao et al., 2021) in R environment (version 4.3.0) were used to filter cells, reduce dimensionality, cluster with Louvain, and project cells with UMAP. We removed cells with low quality (less than 1,000 reads and 500 UMI-filtered mapped read) and doublets using ScDblFinder package (Germain et al., 2021). The G2M phase score, S-phase score, UMI count, and mitochondrial gene proportion were regressed out using the SCTransform wrapper. cells were annotated using the top most significant upregulated cluster-specific genes. Microglia was isolated preferentially expressed markers of microglia or macrophages. The subset of microglia was processed though dimensionality reduction, Louvain clustering, and projection into UMAP.
Assembly: GRCm38 (release 102)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cortex

extract_protocol:
Mice were deeply euthanized by CO2 asphyxiation and subsequently transcardially perfused with ice-cold PBS, pH 7.4. The brain tissues were dissected, and the cortical tissues were collected. The tissues were cut into 1mm slices and then dissociated enzymatically by 1 mg/ml collagenase type II (Worthington, 4176) and 2 mg/ml DNase 1 (Sigma-Aldrich, DN25) in 20 ml neurobasal media (Gibco, 21103049) at 37°C for 30 min.  Tissue slices were pelleted by centrifugation at 300g for 10 min and dissociated once more in a papain solution [1 mg/ml papain (Worthington, LS003119) and 2 mg/ml DNase 1 (Sigma-Aldrich, DN25) in 20 ml neurobasal media (Gibco, 21103049)] at 37°C for 30 min. The enzymes were then inactivated by adding 20 μg/ml ovoicoid protease inhibitor (OIA) (Worthington, 50-592-486). Dissociated cells were filtered through a 70um filter and spun down at 300 g for 10 min.
Single-cell barcoding and complementary DNA (cDNA) library preparation were performed according to the previously published  protocol (Zilionus,R et al.,Nat protoc, 2017.) with following modification. A home-made microfluidic device was connected to the Drop-seq apparatus in the  Korea Brain Research Institute.  Amplified cDNA was not fragmented, and cDNA clean up and size selection was performed using SPRIselect beads (Beckman Coulter, B23317).  Single-cell libraries were sequenced on an Illumina NovaSeq 6000 system though a sequencer company (Macrogen).

value: Cortex

tag: age

tag: strain


title: MDKO_3

description: Library name: Sample 15


title: NFATc3-MKI_1

description: Library name: Sample 20

value: NFATc3 macrophage knockin


title: NFATc3-MKO_2

description: Library name: Sample 6


title: PFD-024-T0-N

description:
Library name: PFD-024-T0-N
10x Genomics

value: rectum


title: PFD-022-T0-N

description:
Library name: PFD-022-T0-N
10x Genomics


title: ASK1-MKO_1

description: Library name: Sample 9


title: NFATc3-MKI_3

description: Library name: Sample 22

value: BMDMs


title: DMSO treatment (control), JUN antibody, biological replicate 1

source_name: Pancreas

tag: cell line

value: JUN/c-Jun CUTANA CUT&RUN antibody


title: PFD-021-T0-N

description:
Library name: PFD-021-T0-N
10x Genomics


title: ASK1-MKO_4

description: Library name: Sample 12

value: Livers


title: Control_2 (for ASK1-MKI)

description: Library name: Sample 24

tag: cell type


title: NFATc3-MKI_2

description: Library name: Sample 21

tag: genotype


title: PFD-023-T0-N

description:
Library name: PFD-023-T0-N
10x Genomics


title: PFD-026-T0-N

description:
Library name: PFD-026-T0-N
10x Genomics


title: Control_1 (for ASK1-MKI)

description: Library name: Sample 23


title: PFD-025-T0-N

description:
Library name: PFD-025-T0-N
10x Genomics


title: 5xFAD;Bmp4-cKO mice, cortex, replicate 3

description: inDropTM


title: Control_2 (for NFATc3-MKI)

description: Library name: Sample 18


title: 5xFAD;Bmp4-cKO mice, cortex, replicate 4

description: inDropTM


title: Lyz2-Cre_4

description: Library name: Sample 4

tag: treatment


title: NFATc3-MKO_3

description: Library name: Sample 7

tag: tissue


title: NFATc3-MKO_1

description: Library name: Sample 5


title: PFD-020-T0-N

description:
Library name: PFD-020-T0-N
10x Genomics


title: #1270, soleus muscles, Cdh5Cre-NOX1CKO, high fat diet

city: Los Angeles

first: hua

last: cai

state: California

address: 450 Hilgard Ave

institute: University of California, Los Angel

description: Library name: 1270

data_processing:
Raw reads were mapped to the mouse UCSC transcriptome (mm10) using Bowtie2 (v2.1.0), gene expression was quantified with RSEM (v1.2.15), normalized using the trimmed mean of M-values (TMM), and differentially expressed genes were identified using edgeR.
Assembly: UCSC mm10 (GRCm38)
Supplementary files format and content: Processed data files are tab-delimited text files containing gene-level count matrices and normalized expression values generated by RSEM, as well as differential expression result tables produced by edgeR with fold changes and statistical significance values.

source_name: soleus muscles

extract_protocol:
Libraries for RNA-Seq were prepared with KAPA Stranded mRNA-Seq Kit
KAPA Stranded RNA-SeqKit was used for preparing the libraries of RNA-Seq according to the manufacturer’s instructions

value: soleus muscles

value: high fat diet


title: Control_1 (for NFATc3-MKI)

description: Library name: Sample 17


title: 5xFAD;Bmp4-cKO mice, cortex, replicate 1

description: inDropTM


title: PFD-015-T0-N

description:
Library name: PFD-015-T0-N
10x Genomics


title: #1185, soleus muscles,  Cdh5cre-WT mice, high fat diet

description: Library name: 1185


title: Lyz2-Cre_1

description: Library name: Sample 1

value: MCD feeding


title: PFD-018-T0-N

description:
Library name: PFD-018-T0-N
10x Genomics


title: #1201, soleus muscles, Cdh5Cre-NOX1CKO, high fat diet

description: Library name: 1201


title: PFD-019-T0-N

description:
Library name: PFD-019-T0-N
10x Genomics


title: #1200, soleus muscles,  Cdh5cre-WT mice, high fat diet

description: Library name: 1200


title: 5xFAD;Bmp4-WT mice, cortex, replicate 6

description: inDropTM


title: PFD-014-T0-N

description:
Library name: PFD-014-T0-N
10x Genomics


title: Lyz2-Cre_3

description: Library name: Sample 3


title: Asynchrous Fucci mESCs, biological replicate 2

city: Kobe

first: Ichiro

last: Hiratani

state: Hyogo prefecture

address: 2-chōme−２−3, Minatojima Minamimachi, Chuo ward

institute: RIKEN BDR

description: Library name: Fucci_ESC_Async_R2

data_processing:
Hi-C reads were processed with the FANC pipeline (v0.95) using iterative mapping (BWA v0.7.17) to the mm9 genome with a quality cutoff of 30 (MAPQ≥30). Aligned reads were converted to valid pairs, and multi-resolution normalized contact matrices (.mcool format) were generated using cooler zoomify (v0.9.3) with iterative balancing. This step outputs normalized contact matrices at 40 kb, 100 kb, 200 kb, 400 kb, 500 kb, and 1 Mb resolution.
A/B compartments (PC1) were called at 200-kb resolution using a custom Python implementation of principal component analysis (PCA) via cooltools (0.3.2). PC1 sign was oriented using mm9 gene density tracks, with positive values defining active (A) and negative values inactive (B) compartments.
Chromatin subcompartments were identified using CALDER2 within a Docker container. Merged multi-replicate .mcool files at 40-kb resolution were converted to .hic format (cooler dump + juicer_tools v1.22.01) for compatibility. Subcompartment hierarchical ranks (0.125–1) were called genome-wide, generating the provided .bed files.
Assembly: mm9
Supplementary files format and content: .mcool - Multi-resolution, balanced Hi-C contact matrices for each sample (resolutions: 40 kb, 100 kb, 200 kb, 400 kb, 500 kb, 1 Mb).
Supplementary files format and content: .bw - BigWig files containing the first principal component (PC1) values for A/B chromatin compartments called at 200-kb resolution.
Supplementary files format and content: .bed - BED files containing CALDER2-assigned hierarchical chromatin subcompartment ranks at 40-kb resolution. The analysis was performed on merged biological replicates; the same file is linked to both individual replicates (R1 and R2)

source_name: R26p-Fucci2 mESC

growth_protocol: Mouse embryonic stem cells were maintained in 2i/LIF medium consisting of NDiff 227 base medium supplemented with the two inhibitors (2i) PD0325901 (1 uM) and CHIR99021 (3 uM), plus leukemia inhibitory factor (LIF; 1000 U/mL), penicillin-streptomycin (0.5 mg/mL) and 2-mercaptoethanol (0.1 mM) on iMatrix-511-coated dishes. Cells were cultured at 37 C with 5% CO2 and passaged every 2-3 days using trypsin/EDTA.

extract_protocol:
Harvested cells were fixed in 1% formaldehyde in PBS for 10 minutes at room temperature (1 mL fixative per 1 million cells) followed by quenching with 0.125 M glycine. Cells were permeabilized with 0.1% saponin and stained with Hoechst33342 (10 µg/mL) for 30 minutes for DNA labeling. Cells were FACS-sorted on a Sony MA900 cell sorter to isolate specific cell-cycle populations based on Hoechst signal. Sorted cell pellets were flash-frozen in liquid nitrogen and stored at –80°C until library preparation.
Hi-C libraries were prepared from 0.5–1 million fixed, sorted cells. Nuclei were isolated and chromatin was digested with DpnII (NEB, R0543). Restriction fragment overhangs were filled with biotin-labeled nucleotides and ligated. After reverse crosslinking and DNA purification, 0.5–1 µg of DNA was sheared to 150–400 bp using a Covaris S220 sonicator. Biotinylated fragments were captured on Streptavidin M‑280 Dynabeads, and libraries were prepared using the NGS LTP Library Preparation Kit (KK8232). Final libraries were quantified and quality-checked before sequencing on a NovaSeq X platform (150 bp paired‑end reads, ~100 M reads per sample).

value: R26p-Fucci2 mESC

value: embryonic stem cells

value: Fixation with 1% formaldehyde followed by FACS sorting


title: Lyz2-Cre_2

description: Library name: Sample 2


title: Control_3 (for NFATc3-MKI)

description: Library name: Sample 19


title: Asynchrous Fucci mESCs, biological replicate 1

description: Library name: Fucci_ESC_Async_R1


title: PFD-013-T0-N

description:
Library name: PFD-013-T0-N
10x Genomics


title: PFD-012-T0-N

description:
Library name: PFD-012-T0-N
10x Genomics


title: #1134, soleus muscles, Cdh5Cre-NOX1CKO, high fat diet

description: Library name: 1134


title: INK128-treated Fucci mESCs (72h), biological replicate 2

description: Library name: Fucci_ESC_Noc_INK_72h_R2

value: mTOR inhibitor INK128 (72 hours), fixation with 1% formaldehyde followed by FACS sorting


title: 3H3PM8

city: Bunkyo-ku

first: Shu

last: Shimada

state: Tokyo

address: 1-5-45 Yushima

department: Department of Molecular Oncology

institute: Tokyo Medical and Dental University

data_processing:
Sequence reads were checked by using FastQC.
Sequence reads were mapped to GRCm38/mm10 by using STAR.
Read count extraction was performed by using RSEM.
Normalization and differential expression analysis were performed by using DESeq2.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text files include expected_count, TPM and FPKM, which were calculated by using RSEM.

growth_protocol: Mouse cell line 3H3 was derived from a liver tumor grown in a C57BL/6 MC4R-KO mouse fed with high-fat diet (Itoh M et al. Am J Pathol 2011) and had HrasQ61L mutation (Akasu M et al. Sci Rep 2021). We introduced Trp53 mutation in the 3H3cells by using the CRISPR/Cas9 system, and confirmed the loss of p53 protein expression and frameshift mutation in Trp53 in the Trp53-knockout 3H3 cells (3H3P) by Western blot analysis and sequencing analysis. We next generated the 3H3P cells ectopically expressing MYC (3H3PM). These 3H3PM cells slowly but steadily grew in nude mice, and nine subclones (3H3PM1-9) were isolated from the transplanted tumors. Cells were cultured in DMEM (Wako) medium containing 10% fetal bovine serum, and 1% penicillin, streptomycin and amphotericin B (Wako), maintained in a humidified incubator at 37 °C in 5% CO2, and harvested with 0.05% trypsin-0.03% EDTA (Wako).

extract_protocol:
Total RNA was extracted from cells by using TRIzol Reagent (Thermo Fisher Scientific). Contaminating DNA was removed by digestion with DNA-free DNA Removal Kit (Thermo Fisher Scientific). The RNA Integrity Number (RIN) of all the samples was confirmed to be greated than 7.0 by using 2100 Bioanalyzer (Agilent Technologies).
RNA libraries for RNA-seq were prepared by using NEBNext Ultra Directional RNA Library Prep Kit for Illumina following manufacturer's protocols.

value: Hepatocellular carcinoma cells

value: Trp53 knockout and MYC overexpression


title: 3H3PM9


title: INK128-treated Fucci mESCs (120h), biological replicate 2

description: Library name: Fucci_ESC_Noc_INK_120h_R2

value: mTOR inhibitor INK128 (120 hours), fixation with 1% formaldehyde followed by FACS sorting


title: 5xFAD;Bmp4-WT mice, cortex, replicate 3

description: inDropTM


title: PFD-004-T0-N

description:
Library name: PFD-004-T0-N
10x Genomics


title: INK128-treated Fucci mESCs (120h), biological replicate 1

description: Library name: Fucci_ESC_Noc_INK_120h_R1


title: PFD-010-T0-N

description:
Library name: PFD-010-T0-N
10x Genomics


title: 3H3PM6


title: PFD-011-T0-N

description:
Library name: PFD-011-T0-N
10x Genomics


title: 5xFAD;Bmp4-WT mice, cortex, replicate 5

description: inDropTM


title: #1009, soleus muscles, Cdh5cre-WT mice, chow diet

description: Library name: 1009

value: chow diet


title: 5xFAD;Bmp4-WT mice, cortex, replicate 4

description: inDropTM

value: Cortex


title: INK128-treated Fucci mESCs (24h), biological replicate 1

description: Library name: Fucci_ESC_Noc_INK_24h_R1

value: mTOR inhibitor INK128 (24 hours), fixation with 1% formaldehyde followed by FACS sorting


title: #1133, soleus muscles, Cdh5cre-WT mice, high fat diet

description: Library name: 1133


title: #970, soleus muscles, Cdh5Cre-NOX1CKO, chow diet

description: Library name: 970


title: #1089, soleus muscles, Cdh5Cre-NOX1CKO, chow diet

description: Library name: 1089


title: #969, soleus muscles, Cdh5Cre-NOX1CKO, chow diet

description: Library name: 969


title: PFD-003-T0-N

description:
Library name: PFD-003-T0-N
10x Genomics

value: rectum


title: #1088, soleus muscles, Cdh5cre-WT mice, chow diet

description: Library name: 1088


title: INK128-treated Fucci mESCs (24h), biological replicate 2

description: Library name: Fucci_ESC_Noc_INK_24h_R2


title: #971, soleus muscles, Cdh5cre-WT mice, chow diet

description: Library name: 971


title: 3H3PM7


title: 3H3PM2


title: Nocodazole-arrested Fucci mESC (10h) released to thymidine (9h), biological replicate 2

description: Library name: Fucci_ESC_Noc_Thy_9h_R2

value: Nocodazole (10 hours), Thymidine (9 hours), fixation with 1% formaldehyde followed by FACS sorting


title: Nocodazole-arrested Fucci mESC (10h) released to thymidine (12h), biological replicate 2

description: Library name: Fucci_ESC_Noc_Thy_12h_R2

value: Nocodazole (10 hours), Thymidine (12 hours), fixation with 1% formaldehyde followed by FACS sorting


title: KO_1_MDA-MB-231 scRNA-Seq

city: Stony Brook

first: Fei

last: Chen

state: New York

address: Lauterbur Drive Stony Brook, NY 11794

institute: Stony Brook Cancer Center

description: 10x Genomics

data_processing:
The sequencing data was processed  using the Cell Ranger software v 6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The data for this project was of high quality for all samples analyzed. Each sample called > 5,000 cells with a median genes per cell > 6,000. The analysis was structured such that for each sample we have performed an individual analysis including dimensionality reduction, clustering, and marker gene detection.
Assembly: hg38 was used as a genome build for alignments
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Breast ( Breast Cancer)

growth_protocol: Cells were cultured in DMEM/ F-12 medium (GIBCO, Grand Island, NY) supplemented with 10% FBS and 1% penicillin-streptomycin (Sigma, St. Louis MO) and grown in 37 °C-humidified incubators in the presence of 5% CO2 (Baker ReCO2ver™).

extract_protocol:
Four million WT or KO MDA-MB-231 cells were collected according to Active Motif's protocol.
Libraries for single cells were generated using the 10x Chromium System (Chromium Next GEM Single Cell 3' Library Kit v3.1).

value: Breast ( Breast Cancer)

value: MDA-MB 231 KO

value: Triple negative breast cancer, mdig knockout

value: cell line


title: KO_2_MDA-MB-231 scRNA-Seq

description: 10x Genomics


title: 3H3PM1


title: kidney, BS, RNA, 1272

city: Sant Joan Despí

first: Maruja

last: Navarro-Díaz

state: Barcelona

address: Oriol Martorell, 12

department: Nephrology

institute: Hospital Sant Joan Despí Moisès Broggi

description: Library name: 1272_kidney_RNA

data_processing:
Quality assessment of RNA using TapeStation 2200 and Bioanalyzer
Removal of genomic DNA using DNase I.
Trimming of adapter sequences from reads using Cutadapt.
Mapping and quantification of transcripts using Salmon and Subread/Rsubread.
Summarization and quantification of small RNA transcripts using annotations from miRBase v22 and Ensembl release 102.
Quality control checks including multi-dimensional scaling plot analysis and Euclidean distances between samples.
Differential expression testing using DESeq2 v1.24.0 Bioconductor’s package.
Cataloging miRNA target sites using multiMiR Bioconductor’s package.
Upregulation/downregulation classification of miRNAs based on adjusted p-value and Log2 fold change.
Assembly: Rnor6.0 genome
Supplementary files format and content: Text files includes raw counts for each sample

source_name: kidney

extract_protocol:
RNA was obtained from frozen tissue blocks using Trizol Reagent (Invitrogen, Thermo Fisher). Genomic DNA was removed by incubation with DNase I for 10 minutes (Invitrogen) and QC was assessed in a TapeStation 2200 (Agilent, Santa Clara, USA). Half of RNA were used for RNA-Seq experiments and the rest were used for qPCR purposes. SmallRNAs from tissue were purified using 1mg of total isolated RNA following an enrichment protocol with SPRIselect beads (Bee Na Lee, Beckman Coulter, California, USA). qPCR validations were done . The urine samples were collected and 500ml (total cell-free and exosomal RNA) used for smallRNA obtention following the instructions of the ZR Urine RNA Isolation Kit (Zymo Research Corp, CA, USA). In both cases, assessment of QC was done in a Bioanalyzer using a High Sensitivity chip (Agilent).
RNA-seq Libraries were prepared from 1mg of total isolated RNA with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, NEB, Massachusetts, USA), run in a HighSeq 2500 System (Illumina, CA, USA) and 40-50M of reads per sample were obtained. The quality of reads was assessed using the FastQC tool and a trimming step was applied to remove the adapters using the Cutadapt tool. Salmon tool was used to map and quantify the aligned transcripts to the Rnor6.0 genome. DESeq2 v1.24.0 Bioconductor’s package has been used for differential expression testing and the analysis of biological significance has been based on Gene Set Enrichment Analysis (GSEA) performed over two annotation databases: Gene Ontology (GO) and the Reactome Pathway Knowledge base. smallRNA libraries were prepared following the instructions of the NebNext Small RNA Library Prep Set for Illumina (NEB). Size selection of fragments was done in a 6% Polyacrylamide Gel (Invitrogen) and QC of libraries in a TapeStation 2200 using a HighSens D1000 screentape (Agilent). Libraries were sequenced in a HighSeq 2500 System (Illumina) and 12-15M reads per sample were obtained and analyzed. The quality of reads was assessed using the FastQC tool and a trimming step was applied to remove the adapters using the Cutadapt tool. The Subread/Rsubread package was used to map and quantify the aligned transcripts to the Rnor6.0 genome. For summarization/quantification step, annotations were obtained from different databases depending on the small RNA class: miRNA precursor and mature annotation was derived from miRBase v22 (http://www.mirbase.org/ftp.shtml), whereas annotations for other non-coding smallRNAs described in rat were derived from Ensembl release 102 (https: //www.ensembl.org/info/data/ftp/index.html). smallRNA libraries were prepared following the instructions of the NebNext Small RNA Library Prep Set for Illumina (NEB). Size selection of fragments was done in a 6% Polyacrylamide Gel (Invitrogen) and QC of libraries in a TapeStation 2200 using a HighSens D1000 screentape (Agilent). Libraries were sequenced in a HighSeq 2500 System (Illumina) and 12-15M reads per sample were obtained and analyzed. The quality of reads was assessed using the FastQC tool and a trimming step was applied to remove the adapters using the Cutadapt tool. The Subread/Rsubread package was used to map and quantify the aligned transcripts to the Rnor6.0 genome. For summarization/quantification step, annotations were obtained from different databases depending on the small RNA class: miRNA precursor and mature annotation was derived from miRBase v22 (http://www.mirbase.org/ftp.shtml), whereas annotations for other non-coding smallRNAs described in rat were derived from Ensembl release 102 (https: //www.ensembl.org/info/data/ftp/index.html). Different types of quality controls were also conducted (multi-dimensional scaling plot analysis, Euclidean distances between samples) to ensure the normalized data are appropriate for the differential expression analysis; as a result, no outliers or batch effects were detected. DESeq2 v1.24.0, a Bioconductor package, was utilized for the differential expression testing. miRNA target sites were cataloged in databases based on experimental validation and computational prediction using the multiMiR Bioconductor package (http://multimir.ucdenver.edu). DESeq2 v1.24.0 Bioconductor’s package was used for differential expression testing. miRNA target sites have been catalogued in databases based on experimental validation and computational prediction using the multiMiR Bioconductor’s package (http://multimir.ucdenver.edu).

value: kidney

value: Wistar rats


title: 3H3PM3


title: 5xFAD;Bmp4-WT mice, cortex, replicate 7

description: inDropTM


title: WT_1_MDA-MB-231 scRNA-Seq

description: 10x Genomics

value: MDA-MB 231 WT

value: Triple negative breast cancer


title: WT_2_MDA-MB-231 scRNA-Seq

description: 10x Genomics


title: Nocodazole-arrested Fucci mESC (10h) released to thymidine (9h), biological replicate 1

description: Library name: Fucci_ESC_Noc_Thy_9h_R1

value: R26p-Fucci2 mESC

value: embryonic stem cells


title: KO_2_MDA-MB-231

data_processing:
Raw reads were mapped to the reference genome using the STAR aligner
Read Mapping :
The paired-end 42 bp or paired-end 150 (full transcript assayssequencing reads generated by Illumina sequencing are mapped to the genome using the STAR algorithm with default settings. Alignment information for each read is stored in the BAM format.
Fragment Assignment:
The number of fragments overlapping predefined genomic features of interest (e.g. genes) are counted.
a. For full transcript assays: only read pairs that have both ends aligned are counted. Read pairs that have their two ends mapping to different chromosomes or mapping to same chromosome but on different strands are discarded. Typically, the gene annotations we use were obtained from Subread package. These annotations were originally from NCBI RefSeq database and then adapted by merging overlapping exons from the same gene to form a set of disjoint exons for each gene. Genes with the same Entrez gene identifiers were also merged into one gene.
b. For DGE assays: aligned reads were quantified at the annotated 3’ end of genes
Differential Analysis:
After obtaining the gene table containing the fragment counts of genes, we perform differential analyses to identify statistically significant differential genes using DESeq2. The following lists the pre-processing steps before differential calling.
a. Data Normalization: DESeq2 expects un-normalized count matrix of sequencing fragments. The DESeq2 model internally corrects for library size using their median-of- ratios method. The gene table obtained from Analysis Step 2) is used as input to perform the DESeq2’s differential test.
b. Filtering before multiple testing adjustment: After a differential test has been applied to each gene except the ones with zero counts, the p-value of each gene is calculated and adjusted to control the number of false positives among all discoveries at a proper level.
c. Differential Calling: differential genes were detected by DESeq2 at 0.1 (or 10%) FDR (i.e. adjusted p-value).
Assembly: h19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Two million WT and two million  KO MDA-MB-231 cells were collected according to Active Motif (Carlsbad, CA) protocol and samples were shipped to Active Motif, CA for RNA sequencing. Total RNA was isolated, and the RNA quality/integrity was assessed using an Agilent Bioanalyzer. Preparation of libraries and RNA sequencing assay were performed by Active Motif based on Illumina platform
RNA was harvested  and was used for the construction of sequencing libraries by Active Motif


title: Bulk Tissue, Sham +3d -6

city: Ulm

first: Bernd

last: Baumann

address: Albert-Einstein-Allee 11

country: Germany

institute: Ulm University

data_processing:
The sequencing reads which containing low-quality, adaptor-polluted and high content of unknown base (N) reads, were removed prior to downstream analyses.
After reads filtering, clean reads were mapped to reference genome using HISAT [1]. On average 94.96% reads are mapped, and the uniformity of the mapping result for each sample suggests that the samples are comparable.
After genome mapping, StringTie was used to reconstruct transcripts, and with genome annotation information we identify novel transcripts by using Cuffcompare(a tool of Cufflinks) and predict the coding ability of those new transcripts using CPC
After novel transcript detection, novel coding transcripts were merged with reference transcripts to get complete reference, clean reads were mapped to it using Bowtie2, then calculate gene expression level for each sample with RSEM \
Assembly: mm10
Supplementary files format and content: tab-delimited document includes FPKM values of all processed samples

source_name: Brain (Cortex, TBI insult area)

extract_protocol:
RNA was harvested using PeqGOLD® TriFast™ kit (peQlab, Darmstadt, Germany)
Library construction and data processing steps were conducted by BGI. The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligoattached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. The PCR yield was quantified by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the BGISEQ-500 platform for the following data analysis study. For this step, the BGISEQ-500 platform combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.

treatment_protocol: Animals were subjected to traumatic brain injury using the closed head injury (CHI) model or sham-treated by skin incision. Three days after operation, the animals were sacrificed and tissue was taken from the insult area for RNA isolation.

value: Brain (Cortex, TBI insult area)

value: Wildtype

value: Sham treatment

tag: time point

value: day 3


title: INK128-treated Fucci mESCs (72h), biological replicate 1

description: Library name: Fucci_ESC_Noc_INK_72h_R1

value: mTOR inhibitor INK128 (72 hours), fixation with 1% formaldehyde followed by FACS sorting


title: PFD-002-T0-N

description:
Library name: PFD-002-T0-N
10x Genomics

value: rectum


title: Nocodazole-arrested Fucci mESC (10h) released to thymidine (6h), biological replicate 1

description: Library name: Fucci_ESC_Noc_Thy_6h_R1

value: Nocodazole (10 hours), Thymidine (6 hours), fixation with 1% formaldehyde followed by FACS sorting


title: kidney, BS, RNA, 1273

description: Library name: 1273_kidney_RNA


title: 3H3P

value: Hepatocellular carcinoma cells

value: Trp53 knockout


title: Nocodazole-arrested Fucci mESC (10h) released to thymidine (3h), biological replicate 1

description: Library name: Fucci_ESC_Noc_Thy_3h_R1

value: Nocodazole (10 hours), Thymidine (3 hours), fixation with 1% formaldehyde followed by FACS sorting


title: Nocodazole-arrested Fucci mESC (10h) released to thymidine (3h), biological replicate 2

description: Library name: Fucci_ESC_Noc_Thy_3h_R2


title: Bulk Tissue, Sham +3d -7


title: Bulk Tissue, Sham +3d -2