title: EAE D18-scRNA-seq

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

description: Library name: EAED18

data_processing:
We utilized CellRanger v6.1.0 and Seurat 4.3.0 software for single-cell RNA sequencing (scRNA-seq) data analysis, with R version 4.1.0, on an Ubuntu 18.04 server. Quality control: After reading the raw data, we initialized a Seurat object using the `CreateSeuratObject` function and employed quality control metrics (QC metrics) to identify and filter out low-quality cells based on their distribution, filtering out cells with UMI counts greater than 1,000 or less than 100,000, as well as cells with a percentage of mitochondrial genes greater than 10% or of red blood cell genes greater than 0.5%. We used the `DoubletFinder` function to identify and remove potential doublets. Normalization: Data normalization is a critical step in scRNA-seq analysis. We employed the `NormalizeData` function in Seurat, which normalizes data to eliminate expression differences between cells, laying the groundwork for subsequent analysis. Feature selection: To identify the most representative genes, we used the `FindVariableFeatures` function. This function helps us recognize genes with the greatest expression variation in the dataset, which are crucial for subsequent clustering and differential expression analysis. Dimension reduction: Dimension reduction is the process of converting high-dimensional data into low-dimensional data for visualization and further analysis. We used the `RunUMAP` function in Seurat, which employs the Uniform Manifold Approximation and Projection (UMAP) algorithm to reduce data dimensions while preserving the original structure of the data as much as possible. Data integration: For datasets from different samples or conditions, we used the `FindIntegrationAnchors` and `IntegrateData` functions for data integration. These functions help us identify shared cell states across datasets and correct technical differences between datasets. Clustering analysis: Clustering is the process of grouping similar cells. We used the `FindClusters` function in Seurat to identify cell populations. This function uses graph-based methods to identify cell populations based on the data after dimension reduction. Differential expression gene analysis: We used the `FindAllMarkers` function to identify differentially expressed genes between different cell populations. The expression patterns of these genes can provide important information about cell functions and states.
Paired-end Cut&Tag reads were aligned to the mm10 genome with the following parameters: --end-to-end --very-sensitive -I 10 -X 2000 --no-mixed --no-discordant by Bowtie2 version 2.4.2. Aligned reads were filtered with a minimum mapping quality of 20 and PCR duplicates were removed. Read coverages over the mm10 genome were estimated by bamCoverage from deepTools v.3.5.1 with parameters --binSize 50 --normalizeUsing RPKM and visualized by UCSC browser. Peaks were called using MACS2 version 2.2.7 with the parameters --nolambda --nomodel. Peaks in all heatmaps were sorted according to peak enrichment in each group. Promoters were defined as ±2.5 kb around the TSS.
Assembly: mm10
Supplementary files format and content: CellRanger output files:mRNA barcodes.tsv.gz, mRNA features.tsv.gz, mRNA matrix.mtx.gz
Supplementary files format and content: CUT&TAG outfile: outfile.bw

source_name: spinal cord

growth_protocol: Mice were housed 4–5 per cage with a 12-h light/dark cycle and food and water ad libitum. All experimental animal procedures were approved by the institutional animal care and use committee of the Beijing Institute of Basic Medical Sciences.

extract_protocol:
EAE mice at different disease stages, including naïve (day 0), priming (day 13), peak (day18), and chronic stages (day 25, day30, and day 35), were deeply anesthetized with pentobarbital sodium and perfused transcardially with ice-cold saline. The whole spinal cord was immediately removed and washed with prechilled PBS. For scRNA-seq, three spinal cords were pooled as one sample and dissociated into single cell suspensions for sequencing. For in situ sequencing, spinal cords were embedded in Tissue-Tek OCT compound (Sakura) and snap-freezing using dry ice. The OCT-embedded spinal cords were then coronally cryosectioned to a thickness of 10 μm using a cryostat (Leica CM3050S). The lumbar sections were collected and layered onto a spatially barcoded array for the subsequent in situ sequencing.
CUT&Tag was performed with CUT&Tag (Cleavage Under Targets and Tagmentation, Hyperactive pA-Tn5 Transposase for CUT&Tag, S603-01, Vazyme) method. In brief, 100,000 cells were collected and bounded to Concanavalin A–coated beads. Isolated MG/Mac were resuspended in antibody buffer and incubated with primary antibodies against H3K18la (PTM-1427RM, PTM BI) or H4K12la (PTM-1411, PTM BIO) and secondary antibodies in order. The samples were incubated with pA-Tn5 transposase. After transposon activation and tagmentation, DNA was isolated, amplified, and purified to construct library. The library for sequencing was constructed with VAHTS Turbo DNA Library Prep Kit for Illumina (Vazyme Biotech) according to manufacturer’s instructions. AMPure XP beads were used for purification steps. The library was quantified with VAHTS Library Quantification Kit for Illumina (Vazyme Biotech) and sequenced on an Illumina novaseq 150PE.

treatment_protocol: Eight-week-old female mice were used to induce the EAE model as we previously described50. Briefly, each mouse was subcutaneously immunized with 150 μg MOG35–55 peptide (ChinaPeptides Co.,Ltd) emulsified in complete Freund’s adjuvant (#F5881, Sigma-Aldrich) containing 4 mg/ml heat-killed Mycobacterium tuberculosis (#231141, BD Bioscience), followed by intraperitoneal injection of 200 ng pertussis toxin (#180, List Biological) on days 0 and 2, respectively. The bodyweight and clinical score were recorded everyday post immunization. Standard for evaluation of EAE clinical score is based on a five-point scale: 0, no disability; 1, loss of tone in the tail; 2, hind limb paresis; 3, hind limb paralysis; 4, tetraplegia; 5, moribund.

value: spinal cord


title: Stellate Ganglion, plate 7

status: Public on Jan 01 2026

type: SRA

city: New York

first: Daniele

last: Neri

state: NY

address: 630 West 168th Street

country: USA

institute: Columbia University Irving Medical Center

description:
Library name: LS007
columns in the processed dataset from this file start with "LS007_"

library_source: transcriptomic single cell

data_processing:
Reads were aligned to mouse genome, GRCm38, gencode version M13 (Ensembl 88) using STAR v2.5.3a. The aligned reads were assigned to genes using featureCounts v1.5.3. Next the bam files were sorted and indexed using Samtools v1.4.1 (http://www.htslib.org/), duplicated reads were removed and a UMI count matrix was generated using umi tools.
Assembly: GRCm38, gencode version M13 (Ensembl 88)
Supplementary files format and content: processed_dataset.csv: Comma separated value file of all the count matrices generated (one for each plate) merged together.
Supplementary files format and content: stellate_combined.rds: Seurat object with the dataset processed according to the information in the manuscript to be uploaded on R.

molecule: total RNA

organism: Mus musculus

source_name: Stellate Ganglion

extract_protocol:
The plates were centrifuged at 200g for 2 min and snap frozen on dry ice. Each well received 7.5 μl of lysis buffer [0.2% Triton X-100 (Sigma), SUPERaseIN (1 U/μl) (Thermo Fisher Scientific), 2 mM deoxyribonucleotides (dNTPs) (Thermo Fisher Scientific), and 2 μM reverse transcriptase (RT) primer (Integrated DNA Technologies)]. Primer annealing was performed at 72°C for 3 min. Reverse transcription was performed by adding 7.5 μl of RT mix to each well [2 M betaine (Affymetrix), 2× Protoscript Buffer (New England Biolabs), 12 mM MgCl2 (Thermo Fisher Scientific), 10 mM dithiothreitol (Thermo Fisher Scientific), 5.3 U of Protoscript II Reverse Transcriptase (New England Biolabs), 0.53 U of SUPERaseIN (Thermo Fisher Scientific), and 2 μM Template Switching Oligo (Integrated DNA Technologies; table S6)]. Reverse transcription was performed at 42°C for 90 min, followed by 10 cycles of 50°C for 2 min, 42°C for 2 min, 70°C for 10 min, followed by a 4°C hold. Excess primers were removed by adding 2 μl of Exonuclease I (Thermo Fisher Scientific) mix to each well (1.875 U of ExoI in water) and incubating at 37°C for 30 min, 85°C for 15 min, 75°C for 30 s, and 4°C hold.
The cDNA was pooled for PCR and library construction. Pooled, 3’-end sequencing libraries were sequenced on an Illumina NextSeq 500/550 platform.

tag: tissue

value: Stellate Ganglion

tag: Sex

value: Male

tag: age

value: 6-8 weeks

tag: genotype

tag: batch

value: Set 2


title: EAE D30-scRNA-seq

city: Beijing

country: China

description: Library name: EAED30


title: TLR5- macrophages_2

city: Nanjing

first: REN

last: DESHAN

state: --- Select One ---

address: 12 Xuefu-Road, Pukou District  Nanjing 210061, China

institute: Nanjing university

library_source: transcriptomic

data_processing:
The sequencing data was filtered with fastp (v0.23.4) to remove reads with sequencing adapter, those with low quality (reads with Qphred<=20 base number accounting for more than 50% of the entire read length) and those with 'N' base (where 'N' represents undetermined base information). Clean reads were obtained and stored in FASTQ format.  The clean reads were aligned to the reference genome of Mus musculus (UCSC mm39) using hisat2 (v2.2.1). Aligned reads were converted and then sorted by samtools (v1.6).  Gene counts were obtained using featureCounts (v2.0.2) on GENCODE vM32 annotations. Fragments Per Kilobase of exon per Million fragments mapped (FPKM) was selected as the gene expression value for RNA sequencing.
Assembly: mm10
Supplementary files format and content: tab-delimited txt file includes raw counts for each Sample
Supplementary files format and content: tab-delimited txt file includes FPKM values for each Sample

source_name: Brain

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen). Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit following manufacturers protocols.

value: Brain

tag: cell type

value: Macrophages

tag: sorted cells

value: TLR5- macrophages


title: Stellate Ganglion, plate 2

description:
Library name: LS002
columns in the processed dataset from this file start with "LS002_"

value: Set 1


title: Stellate Ganglion, plate 1

description:
Library name: LS001
columns in the processed dataset from this file start with "LS001_"


title: EAE D13-scRNA-seq

description: Library name: EAED13


title: Stellate Ganglion, plate 8

description:
Library name: LS008
columns in the processed dataset from this file start with "LS008_"


title: TLR5+ macrophages_1

value: TLR5+ macrophages


title: scRNAseq_HTO_library

city: Pasadena

first: Samantha

middle: J

last: Chang

state: CA

address: 1200 E California Blvd

department: Biology and Biological Engineering

institute: California Institute of Technology

description:
Library name: scRNAseq_HTO_library
Hashtag oligo library

library_source: other

data_processing:
scRNAseq raw reads from cDNA libraries were aligned to the mouse reference genome GRCm38/mm10 using CellRanger and the hashtag oligo (HTO) libraries were quantified and demultiplexed using in-house tools (hashtag tool) as described previously (Zhou et al., 2022 Sci Immunol, PMID: 35594339).
Assembly: GRCm38/mm10
Supplementary files format and content: Cell ranger filterted feature barcode matrix output files (barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz)
Supplementary files format and content: Binarized HTO counts output

molecule: other

source_name: synthetic DNA barcode

growth_protocol:
In vitro HSPC expansion: Lineage- bone marrow cells were cultured in HSPC expansion medium (F12 DMEM , 1 mg/mL of PVA, 1× Insulin–transferrin–selenium–ethanolamine, 10 mM HEPES,  1×  Penicillin–streptomycin–glutamine, 100 ng/mL of recombinant mouse thrombopoietin (TPO) and 10 ng/mL of recombinant mouse stem cell factor (SCF) for 10-14 days, and then enriched for the Sca1+ population using PE-conjugated anti-Sca1 and anti-PE microbeads (Miltenyi Biotec) such that the resulting Lin-Sca1+Kit+ cells could be frozen down in Bam Banker solution (FUJIFILM) for future experimental use.
In vitro early T cell development: after retroviral infection, expanded HSPCs were co-cultured with OP9-Dll1 cells in OP9 medium (alphaMEM, 20% FBS, 1×PSQ, and 50 microM beta-mercaptoethanol ) with human Flt3-ligand (Flt3L) and human IL-7 (10 ng/mL each)

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen #74105) with on-column DNase I treatment (Qiagen #1023460)
Single-cell RNA-seq cDNA libraries were prepared using 10X Chromium 3’ capture v3.1 kit.
Single-cell hashtag oligo library was prepared in accordance with the BioLegend TotalseqA guide.

treatment_protocol:
Expanded HSPCs underwent retroviral infection with either control vectors or Lmo2 KO vectors at day 2 of priming. First, retroviral supernatant was centrifuged on RetroNectin-coated plates at 2000xg for 2 hrs at 32°C (non-TC plates prepared overnight with 50 μg/mL RetroNectin (Takara bio) 1×PBS at 4°C, with unbound RetroNectin removed the following day).  Next, expanded HSPCs were incubated on the retroviral vector-bound plates in HSPC expansion medium at 37°C overnight in a 5% CO2 environment. Finally, the following day, infected HSPCs were harvested and transfered back to CellBIND plates (Corning) for later co-culture with OP9-Dll1 stromal cells. Three different sgRNA expressing vectors targeting Lmo2 were pooled for packaging in Phoenix-Eco cells using Fugene 6 Transfection Reagent (Promega).
Flt3L priming was performed by treating expanded HSPCs with 10 ng/mL of human Flt3L in HSPC expansion media for 4 days, in addition to the 100 ng/mL of TPO and 10ng/mL SCF in normal expansion media. Unprimed cells were only cultured with TPO and SCF.

value: synthetic DNA barcode

tag: treatment


title: Naive D0-scRNA-seq

description: Library name: Naive


title: TLR5+ macrophages_2


title: EAE D35-Spatial Transcriptomics

description: Library name: EAED35-1-C

data_processing:
We utilized CellRanger v6.1.0 and Seurat 4.3.0 software for single-cell RNA sequencing (scRNA-seq) data analysis, with R version 4.1.0, on an Ubuntu 18.04 server. Quality control: After reading the raw data, we initialized a Seurat object using the `CreateSeuratObject` function and employed quality control metrics (QC metrics) to identify and filter out low-quality cells based on their distribution, filtering out cells with UMI counts greater than 1,000 or less than 100,000, as well as cells with a percentage of mitochondrial genes greater than 10% or of red blood cell genes greater than 0.5%. We used the `DoubletFinder` function to identify and remove potential doublets. Normalization: Data normalization is a critical step in scRNA-seq analysis. We employed the `NormalizeData` function in Seurat, which normalizes data to eliminate expression differences between cells, laying the groundwork for subsequent analysis. Feature selection: To identify the most representative genes, we used the `FindVariableFeatures` function. This function helps us recognize genes with the greatest expression variation in the dataset, which are crucial for subsequent clustering and differential expression analysis. Dimension reduction: Dimension reduction is the process of converting high-dimensional data into low-dimensional data for visualization and further analysis. We used the `RunUMAP` function in Seurat, which employs the Uniform Manifold Approximation and Projection (UMAP) algorithm to reduce data dimensions while preserving the original structure of the data as much as possible. Data integration: For datasets from different samples or conditions, we used the `FindIntegrationAnchors` and `IntegrateData` functions for data integration. These functions help us identify shared cell states across datasets and correct technical differences between datasets. Clustering analysis: Clustering is the process of grouping similar cells. We used the `FindClusters` function in Seurat to identify cell populations. This function uses graph-based methods to identify cell populations based on the data after dimension reduction. Differential expression gene analysis: We used the `FindAllMarkers` function to identify differentially expressed genes between different cell populations. The expression patterns of these genes can provide important information about cell functions and states.
Paired-end Cut&Tag reads were aligned to the mm10 genome with the following parameters: --end-to-end --very-sensitive -I 10 -X 2000 --no-mixed --no-discordant by Bowtie2 version 2.4.2. Aligned reads were filtered with a minimum mapping quality of 20 and PCR duplicates were removed. Read coverages over the mm10 genome were estimated by bamCoverage from deepTools v.3.5.1 with parameters --binSize 50 --normalizeUsing RPKM and visualized by UCSC browser. Peaks were called using MACS2 version 2.2.7 with the parameters --nolambda --nomodel. Peaks in all heatmaps were sorted according to peak enrichment in each group. Promoters were defined as ±2.5 kb around the TSS.
Assembly: mm10
Supplementary files format and content: CellRanger output files:mRNA barcodes.tsv.gz, mRNA features.tsv.gz, mRNA matrix.mtx.gz
Supplementary files format and content: CUT&TAG outfile: outfile.bw
Library strategy: Spatial Transcriptomics


title: PCA34, YKL-5-124, resistant-4

city: Boston

first: Ziyue

last: Li

state: Massachusetts

address: 450 Brookline Ave, D718

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
All sequencing, alignment, and count generation was performed by Novogene.
Alignment was performed using STAR (version 2.6.1d) with mismatch parameter set to 2 to GRCh38.
Gene counts were generated using FeatureCounts (version 1.5.0-p3) with default parameters.
The gene counts matrix was then used as input for the analysis and normalization was performed using DESeq2 (version 1.24.0) with shrinkage estimates determined by the ahsr method.
Assembly: GRCh38
Supplementary files format and content: Exel file includes raw counts for each sample

organism: Homo sapiens

source_name: PCA34 tumor

growth_protocol: PCA-34 tumors were implanted in nude mice in pathogen-free animal facility.

extract_protocol:
Total RNA was isolated using RNeasy Plus Kit(Qiagen, # 74136).
The samples were then sent to Novogene (Sacramento, CA) for the remainder of the RNA sequencing experiment.

treatment_protocol: Mice carrying PCA-34 tumors were treated with Vehicle (5%DMSO 95% D5W) or YKL-5-124 (10mg/kg dissolved in 5%DMSO 95% D5W)

value: PCA34 tumor

value: Pancreatic cancer Patient Derived Xenograft (PDX)

value: 10mg/kg YKL-5-124 dissolved in 5%DMSO 95% D5W


title: EAE D25-Spatial Transcriptomics

description: Library name: EAED25-2-C


title: Control_rep1

city: Palo Alto

first: Wenjun

last: Yan

state: California

address: 1651 Page Mill Rd

department: Department of Ophthalmology, Byers Eye Institute, Mary M. and Sash A. Spencer Center for Vision Research, Stanford University School of Medicine

institute: Stanford University

description: 10X Genomics, Chromium Next GEM Single Cell 3’ Kits v3.1

data_processing:
The mouse mm10 reference genome was modified to incorporate the transcript sequences for AAV2tm.Flag-HDAC4 3SA or NT (need to upload the sequence) and used for alignment of corresponding libraries respectively. For mice without AAV injection, transcripts were mapped against the HDAC4 3SA composite reference.  Cell Ranger v6.1.2 (Zheng et al., 2017) was used to build the above reference genomes and for reads alignment/counting.
Assembly: mm10
Supplementary files format and content: Count_mat_RGCs.csv is the count matrix of RGCs in the format of .csv
Supplementary files format and content: tab-separed value files and matrix files

source_name: retina

extract_protocol:
scRNA-seq libraries were generated for AAVsc.Flag-HDAC4 3SA and NT injected C57BL/6J mice, as well as non-injected mice, all mice subjected to either ONC or sham injury, two each for a total of 6 libraries. For each library, 8 retinas were collected 1 day after ONC or shame injury by a modified two-step immunopanning protocol. Briefly, retinas were dissociated into a single-cell suspension using papain and incubated on antibody-coated dishes. After depletion of macrophages with an anti-mouse macrophage antibody (Accurate Chemical, AIA31240), cells were selected with an anti-mouse Thy1.2/CD90 (Bio-Rad, MCA02R). Thy1+ cells were re-suspended in DPBS (Gibco, 14287-080) with 1% BSA (Sigma-Aldrich, A4161-5G) and processed immediately. Cell concentration and viability were determined using trypan blue (Gibco, 15250061) and a Countess FL II Automated Cell Counter (Thermo Fisher).
Cells were loaded in parallel for capture onto the Chromium System using Chromium Next GEM Single Cell 3’ Kits v3.1 (Dual Index, 10X Genomics, PN-1000269). Following capture and lysis, cDNA was synthesized and amplified for 12-14 cycles, as per manufacturer’s protocol (10X Genomics). Amplified cDNA was used to construct Illumina sequencing libraries and sequenced using Nova Seq S1 flow cells and 150 bp paired end sequencing.

value: retina

value: 6 weeks

tag: strain

value: sham


title: scRNAseq_cDNA_library

description:
Library name: scRNAseq_cDNA_library
Single-cell RNA library

source_name: bone-marrow

value: bone-marrow

value: Expanded HSPC either gCont-infected or gLmo2-infected under unprimed or Flt3L-priming conditions, collected at two timepoints:before seeding onto OP9-DLL1 (sorted for live lin- infection+) and after 3 days of co-culture of OP9-DLL1 (sorted for live lin- CD45+ infection+ )

value: Cas9 x Bcl2

value: infection with control vectors and Lmo2-KO vectors, both unprimed and Flt3L-primed (4 day priming period)


title: EAE D13-Spatial Transcriptomics

description: Library name: EAED13-1-C

value: spinal cord


title: EAE D35-scRNA-seq

description: Library name: EAED35


title: PCA34, DMSO-1

value: 5%DMSO 95% D5W


title: HDAC43SA_1dpc_rep2

tag: agent

value: AAVsc.Flag-HDAC4 3SA

value: 1day post optic nerve crush


title: DN1, Lmo2 KO, d5 co-culture, bulkRNA, rep2

description: Library name: lmo2KO_DN1_d5_rep2

data_processing:
Bulk RNAseq was processed using ENCODE pipelines. The adapter trimmed reads were aligned to the mouse reference genome GRCm38/mm10 using STAR (v 2.5.1b), and gene expression was calculated with RSEM(v 1.2.31). Then, significant changes in gene expression were determined using DEseq2 (v 1.46.0).
Assembly: GRCm38/mm10
Supplementary files format and content: Raw counts, TPM, and FPKM values from STAR/RSEM outputs

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen #74105) with on-column DNase I treatment (Qiagen #1023460)
Bulk RNA-seq library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina.

treatment_protocol: Expanded HSPCs, thawed in HSPC expansion media as described in the growth protocol, underwent retroviral infection with either control vectors or Lmo2 KO vectors. First, retroviral supernatant was centrifuged on RetroNectin-coated plates at 2000xg for 2 hrs at 32°C (non-TC plates prepared overnight with 50 μg/mL RetroNectin (Takara bio) 1×PBS at 4°C, with unbound RetroNectin removed the following day).  Next, expanded HSPCs were incubated on the retroviral vector-bound plates in HSPC expansion medium at 37°C overnight in a 5% CO2 environment. Finally, the following day, infected HSPCs were harvested and used for co-culture with OP9-Dll1 stromal cells. Three different sgRNA expressing vectors targeting Lmo2 were pooled for packaging in Phoenix-Eco cells using Fugene 6 Transfection Reagent (Promega).

value: Expanded HSPC-derived DN1 (CD25-) from day5 OP9-Dll1 co-culture

value: infection with Lmo2 KO vectors


title: EAE D25-scRNA-seq

description: Library name: EAED25


title: PCA34, DMSO-3


title: Naive D0-Spatial Transcriptomics

description: Library name: Naive-3-A


title: PATU-8988T, YKL-5-124, 24hr-2

growth_protocol: PATU-8988T were maintained in DMEM media supplemented with 10% fetal bovine serum (FBS) and 1%  Pen-strep (PS) in cell incubator (5% CO2 and 37°C).

treatment_protocol: Final concentration of 0.1% DMSO, 100nM THZ1 and 100nM YKL-5-124 were added to PATU-8988T cells

tag: cell line

value: Pancreatic cancer cells


title: Control_1dpc_rep1


title: HDAC43SA_rep1


title: PCA34, DMSO-2

value: PCA34 tumor


title: PATU-8988T, YKL-5-124, 4hr-3


title: 3_ChIP-seq_T32D_DMSO_K4me1

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

country: South Korea

institute: Yonsei University

description: Library name: Sample 3

library_source: genomic

data_processing:
ChIP-Seq raw reads were mapped to the reference mouse (mm9) genome assembly using Bowtie2 allowing two-mismatches for only unique alignment. To avoid clonal artifacts introduced in the library amplification steps, duplicated mapped reads were further discarded using SAMtools (http://samtools.sourceforge.net). HOMER suite (http://homer.salk.edu/homer/) was used for overall analysis. Details were described in the experimental procedues of this study.
bigWig files were generated using makeBigwig.pl script of HOMER suite.
Assembly: mm9
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: KPC-derived T3-2D cell line

growth_protocol: Above cell lines were cultured in conditions as described in this study.

extract_protocol:
Lysates were prepared from 5-10 millon single cell dissociated of organoid cultures or monolayer cultures. Sonicated nuclei with Bioruptor were further proceeded to ChIP assay with apporiate antibodies.
Libraries were prepared using the NEXTflex ChIP-seq kit (Cat# NOVA-5143-02; PerkinElmer) according to the manufacturer's instructions.

treatment_protocol: Treated with drugs as described in this study.

value: KPC-derived T3-2D cell line

value: Murine pancreatic cancer

value: DMSO

tag: chip antibody

value: H3K4me1 (ab8895, Abcam)


title: DN1, control, d5 co-culture, bulkRNA, rep1

description: Library name: control_DN1_d5_rep1

value: infection with control vectors


title: 5_ChIP-seq_T32D_DMSO_K27ac

description: Library name: Sample 5

value: H3K27ac (ab4729, Abcam)


title: HDAC43SA_rep2

value: retina

value: 6 weeks

value: sham


title: DN2, Lmo2 KO, d5 co-culture, bulkRNA, rep2

description: Library name: lmo2KO_DN2_d5_rep2

value: bone-marrow

value: Expanded HSPC-derived DN2 (CD25+Thy1+) from day5 OP9-Dll1 co-culture

value: Cas9 x Bcl2


title: 2_ChIP-seq_T32D_UZH2_K4me3

description: Library name: Sample 2

value: H3K4me3 (ab8580, Abcam)


title: PATU-8988T, YKL-5-124, 24hr-1


title: 1_ChIP-seq_T32D_DMSO_K4me3

description: Library name: Sample 1


title: 6_ChIP-seq_T32D_UZH2_K27ac

description: Library name: Sample 6


title: DN1, control, d5 co-culture, bulkRNA, rep2

description: Library name: control_DN1_d5_rep2

value: Expanded HSPC-derived DN1 (CD25-) from day5 OP9-Dll1 co-culture


title: PATU-8988T, YKL-5-124, 24hr-3


title: DN2, Lmo2 KO, d5 co-culture, bulkRNA, rep1

description: Library name: lmo2KO_DN2_d5_rep1

value: infection with Lmo2 KO vectors


title: 4_ChIP-seq_T32D_UZH2_K4me1

description: Library name: Sample 4


title: Control_rep2


title: PCA34, YKL-5-124, 3Day-2

value: Pancreatic cancer Patient Derived Xenograft (PDX)

value: 10mg/kg YKL-5-124 dissolved in 5%DMSO 95% D5W


title: HDAC43SA_1dpc_rep1

value: AAVsc.Flag-HDAC4 3SA

value: 1day post optic nerve crush


title: HDAC4NT_1dpc_rep2

value: NT


title: HDAC4NT_rep2


title: PATU-8988T, YKL-5-124, 4hr-1

value: Pancreatic cancer cells


title: 2-1_m6A-seq_T32D_sgMettl3-1_fwd

description: Library name: Sample 2

data_processing:
Raw reads were mapped to the reference mouse (mm10) or human (hg19) genome assembly using HISAT2. HOMER suite (http://homer.salk.edu/homer/) was used for overall analysis. Details were described in the experimental procedues of this study.
bigWig files were generated using makeBigwig.pl script of HOMER suite.
Assembly: mm10 or hg19
Supplementary files format and content: bigWig
Library strategy: MeRIP-Seq

extract_protocol:
From 2-5 million cells, total RNA was extracted using the QIAzol reagent following the manufacturer's instructions. After extraction, 200 ng of total RNA was used to perform ULI-MeRIP using 1 µg of anti-m6A antibody (Cat#E1610S, New England Biolabs) as previously described.
The m6A-modified RNA was immunoprecipitated and used as an input for library construction using the SMARTer® Stranded Total RNA-Seq Kit v2 (Cat#634411, Takara) according to the manufacturer's protocol.

value: KPC-derived T3-2D cell line

value: Murine pancreatic cancer

tag: merip antibody


title: PATU-8988T, THZ1, 24hr-3


title: EAE D18-Spatial Transcriptomics

description: Library name: EAED18-2-C

value: spinal cord


title: HDAC4NT_rep1

value: retina

value: 6 weeks


title: PATU-8988T, THZ1, 24hr-2


title: 1-1_m6A-seq_T32D_sgRosa_fwd

description: Library name: Sample 1

value: sgRosa

value: anti-m6A antibody (Cat#E1610S, New England Biolabs)


title: 12_RNA-Seq_T32D_DMSO_rep2

description: Library name: Sample 12

data_processing:
Raw reads were mapped to the reference genome assembly mm10 or hg19 using HISAT2.
Differentially expressed genes were analyzed using Cufflinks.
Assembly: mm10 or hg19
Supplementary files format and content: Excel

growth_protocol: cell lines were cultured in conditions as described in this study.

extract_protocol:
Total RNAs were extracted from ~ 1 million cells using Qiaizol reagent
Libraries were prepared using the NEXTflex Rapid Directional mRNA-seq kit (Cat# NOVA-5138-11; PerkinElmer) according to the manufacturer's instructions.

value: DMSO

tag: biological replicate

value: replicate 2


title: 4_m6A-seq_T32D_DMSO

description: Library name: Sample 4


title: N2a siPTBP1 1

first: Zhang

last: Mengyu

address: HanKou road 22

data_processing:
RIP-seq:
RIP-seq raw files (fastq, PE150) were aligned to the GRCh38/hg38 version of the human reference genome, using STAR with default parameters. Read counts were imported by FeatureCounts.  Differential PTBP1-binding genomic region was performed with DESeq2 packages from R. Transcripts with an adjusted p-value < 0.05 were considered as differentially PTBP1-binding genomic region.
STAR
Differential PTBP1-binding genomic region was performed with DESeq2 packages
R
Adjusted p-value < 0.05
Assembly: GRCh38/hg38
RNA-Seq:
RNA-seq raw files (fastq, PE150) were aligned to the GRCm38/mm10 version of the mouse reference genome, using TopHat2 with default parameters. Read counts were imported by FeatureCounts.  Differential gene expression was performed with DESeq2 packages from R. Transcripts with an adjusted p-value < 0.05 were considered as differentially expressed genes.
TopHat2
Differential gene expression was performed with DESeq2 packages from R
R
Adjusted p-value < 0.05
Assembly: GRCm38/mm10
Supplementary files format and content: BigWig files contain the gene expression tags counts.
Supplementary files format and content: The differential expression file was further provided (csv file).

molecule: polyA RNA

source_name: brain

growth_protocol:
RIP-Seq: Human HeLa cells were cultured in DMEM (Life Technologies) plus 10% fetal bovine serum (FBS) and penicillin/streptomycin (Life Technologies) at 37 °C in an incubator with 95% humidified air and 5% CO2.
RNA-Seq: Neuro-2a cells (N2a) cells were cultured in DMEM (Life Technologies) plus 10% fetal bovine serum (FBS) and penicillin/streptomycin (Life Technologies) at 37 °C in an incubator with 95% humidified air and 5% CO2

extract_protocol:
RIP-Seq: The cells were collected into 1 ml of a polysome lysis buffer containing 10 mM HEPES (pH7.4), 100 mM KCl, 0.5% Nonidet P-40, 0.1% SDS, 0.5 mM DTT, and a cocktail of Roche EDTA-free protease inhibitors. The lysates were cleaned by centrifugation and used for immunoprecipitation by incubating at 4 °C with the antibody pre-bound to BeyoMag Protein A/G magnetic beads (P2108, Beyotime). The beads were washed with a buffer (50 mM Tris-HCl, pH 7.4, 150 mM NaCl, 1 mM MgCl2, 1 mM DTT) for 5 times and then resuspended for proteinase K treatment (55 °C for 30 min). The supernatants were collected, treated with DNase I at 37 °C for 10 min to remove potential DNA contamination, and then cleaned by phenol-chloroform extraction. The RNA was ethanol precipitated and reverse transcribed into cDNA using HiScript® III SuperMix (Vazyme) and usedfor library construction.
The RNA-seq library preparation was followed by the instructions of genergy bio-technology CO., Ltd.
RNA-Seq: Total cellular RNA was extracted using the RNA Rapid Extraction Kit (Vazyme, Nanjing, China) and total tissue RNA was extracted using Trizol (Vazyme), according to the reagent instructions.

treatment_protocol:
RIP-Seq: HSV-1 infected (MOI = 3, for 12 h) or mock-infected HeLa cells were collected by scraping the cells from 10 cm plates.
RNA-Seq: The oligos of small interfering RNA (siRNA) targeting mouse PTBP1 were synthesized by GenePharma. For gene knockdown experiments, N2a cells were transfected with Lipofectamine-2000 and were used at approximately 48-60 h after transfection or as indicated.

value: brain

value: Neuro 2a

value: Neuroblastoma

value: WT

value: siPTBP1 treatment


title: 13_RNA-Seq_T32D_UZH2_rep1

description: Library name: Sample 13

value: replicate 1


title: PATU-8988T, THZ1, 4hr-2


title: HDAC4NT_1dpc_rep1

value: NT

value: 1day post optic nerve crush


title: 5_RNA-Seq_T32D_sgMettl3-2_rep1

description: Library name: Sample 5

value: KPC-derived T3-2D cell line


title: 4_RNA-Seq_T32D_sgMettl3-1_rep2

description: Library name: Sample 4

value: Murine pancreatic cancer


title: DN1, Lmo2 KO, d5 co-culture, bulkRNA, rep1

description: Library name: lmo2KO_DN1_d5_rep1

value: bone-marrow

value: Expanded HSPC-derived DN1 (CD25-) from day5 OP9-Dll1 co-culture

value: Cas9 x Bcl2

value: infection with Lmo2 KO vectors


title: 3_RNA-Seq_T32D_sgMettl3-1_rep1

description: Library name: Sample 3


title: PATU-8988T, THZ1, 24hr-1

value: Pancreatic cancer cells


title: 14_RNA-Seq_T32D_UZH2_rep2

description: Library name: Sample 14


title: 5_m6A-seq_T32D_UZH2

description: Library name: Sample 5

value: anti-m6A antibody (Cat#E1610S, New England Biolabs)


title: 10_RNA-Seq_T32D_sgMettl14-2_rep2

description: Library name: Sample 10

value: replicate 2


title: PATU-8988T, YKL-5-124, 4hr-2


title: N2a siPTBP1 2

value: brain


title: AISI-H-ST/SC-R4-3

first: Zichun

last: Hua

state: Jiangsu

address: Xianlin Road No.163

department: School of Life Sciences

institute: Nanjing University

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Tumor

growth_protocol: A total of 2×10^5 B16F10 cells were inoculated into C57BL/6 mice (7 weeks old, female) in the right axillary region. Once the tumor volume reached 80-120 mm^3, the mice were randomly divided into groups. Subsequently, the mice were intraperitoneally injected with physiological saline, the respective VNP bacterial strain, or modified strains (1.0×10^6 CFU per mouse). Three days later, tumor tissues were collected. To avoid spatial heterogeneity, the entire tumor was homogenized and thoroughly mixed before RNA extraction from the tissue.The extracted RNA was then subjected to RNA sequencing.

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

treatment_protocol: The mice were intraperitoneally injected with physiological saline, the respective VNP bacterial strain, or modified strains (1.0×10^6 CFU per mouse).

value: Tumor

value: 10^6 CFU AISI-htrA strain


title: 3-1_m6A-seq_T32D_sgMettl3-2_fwd

description: Library name: Sample 3


title: organoid, PA-treated, rep3

city: CAMBRIDGE

first: Qiming

last: Zhang

state: MA

address: 88 Ames Street

institute: Koch institute

description: Library name: PA3

data_processing:
BAM files were processed with Picard MarkDuplicates v2.17.0 (https://broadinstitute.github.io/picard/). BAM files were merged using Samtools v1.5. Peaks were called on the merged BAM using Genrich. Read counts per peak per sample were quantified using BEDTools v2.26.
Normalized BigWig files were generated by DeepTools (v.3.5.1) and merged for visualization by pyGenomeTracks (v.3.6).
Motif analyses for differentially enriched peaks were conducted using HOMER v4.10.
Assembly: UCSC mm9
Supplementary files format and content: BigWig, narrowPeak

source_name: Colon

extract_protocol:
Organoids were dissociated by TrypLE Express for 10 min at 37 °C, passed through a 40 μm filter, and a total of 50,000 cells were centrifuged and washed twice with PBS. Cells were resuspended in 50 μl of buffer with TDE1 enzyme (10 mM Tris-HCl (pH 7.5), 5 mM MgCl2, 30% PBS, 0.1% NP-40 (Sigma-Aldrich, 11332473001), 5% dimethylformamide, and Nextera Tn5 Transposase (Illumina, FC-121-1030) in H2O) and incubated at 37 °C for 30 min with gentle agitation. DNA was isolated using the Qiagen MinElute PCR Purification Kit (QIAGEN, 28004).
ATAC-seq libraries were PCR amplified using NEBNext High-Fidelity 2× PCR Master Mix (New England Biolabs, M0541S) for the appropriate numbers of cycles determined by RT–qPCR as previously described.
The 2×75 paired-end sequencing was performed on an Illumina NextSeq 500.

value: Colon

value: in vitro

value: Male

value: PA


title: AISI-B-ST/SC-R4-3

value: 10^6 CFU AISI-NC strain


title: N2a Control 2

value: Neuro 2a

value: Neuroblastoma

value: WT

value: siControl treatment


title: PATU-8988T, DMSO-3

value: DMSO


title: 6_RNA-Seq_T32D_sgMettl3-2_rep2

description: Library name: Sample 6

value: KPC-derived T3-2D cell line

value: Murine pancreatic cancer


title: PB-ON

city: 北京

first: YU

last: ZHANG

state: non-US Resident

address: XUEYUANLU No.38 Haidian District, PKUHSC Anatomy Building

institute: Peking Univ.

data_processing:
Normal sequence Illumina Novaseq 6000
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCH38 whole genome using hisat2 v2.1.0 with parameters hisat2 -p 8 --dta -x  -1  -2 -S.
Transcript assembly and quantification with StringTie. Analysis of RNA-seq experiments requires accurate reconstructions of all the isoforms expressed from each gene, as well as estimates of the relative abundance of those isoforms. Use parameters as stringtie –e –B -p 8 -G -o.
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using Ballgown from Pertea M et al., Nature Protocols, 2016. In short, differential expression analysis proceeds using a linear model. The FPKM values attached to transcripts are typically highly skewed; thus, to stabilize the variance, Ballgown’s builtin functions apply a log transformation and then fit standard linear models that can be used to test for differential expression.
Assembly: GRCH38
Supplementary files format and content: text files include FPKM values for each Sample

source_name: HeLa

growth_protocol: HeLa cells were maintained at 37℃ and 5% CO2 inDMEM medium supplemented with 10% (v/v) FBS, 100 U/mL penicillin, and 100 mg/mL streptomycin. All cell lines were tested for mycoplasma contamination and authenticated utilizing short tandem repeat profiling.

extract_protocol:
Total RNAs were extracted using Trizol. For the enrichment of biotinylated RNAs, total RNAs were mixed with 20μL of Dynabeads MyOne Streptavidin Beads C1, rotating overnight at 4°C, and eluted as previously described. Eluted RNAs were purified using GeneJet RNA Concentration Kits (ThermoFisher).
RNA libraries were prepared for sequencing using NEBNext UltraTM RNA Library Prep Kit

value: HeLa

value: PlaB treatment sample


title: N2a Control 1

value: brain


title: 8_RNA-Seq_T32D_sgMettl14-1_rep2

description: Library name: Sample 8

value: replicate 2


title: AISI-B-ST/SC-R4-2

value: Tumor


title: 2_RNA-Seq_T32D_sgRosa_rep2

description: Library name: Sample 2

value: sgRosa


title: AISI-H-ST/SC-R4-2

value: 10^6 CFU AISI-htrA strain


title: PB-OFF

value: control


title: PATU-8988T, THZ1, 4hr-3

value: Pancreatic cancer cells


title: 11_RNA-Seq_T32D_DMSO_rep1

description: Library name: Sample 11

value: replicate 1


title: 1_RNA-Seq_T32D_sgRosa_rep1

description: Library name: Sample 1


title: organoid, CD, rep3

description: Library name: CD3

value: Colon

value: in vivo

value: Male

value: CD


title: AISI-H-ST/SC-R4-1


title: Erythroleukemia Cell Line_DNA

city: Detroit

first: Katherine

last: Gurdziel

state: MI

address: 275 E. Hancock

institute: Wayne State University

description: patient sample

data_processing:
For RNA-seq: Trimmomatic followed by STAR alignment to Hg38 with htseq-count for tabulation to gene regions.
For WG-seq: Trimmomatic followed by BWA alignemnt to Hg38 followed by samtools snp calling pipeline.
Assembly: Hg38
Supplementary files format and content: count file
Supplementary files format and content: vcf file
Library strategy: DNA-seq

source_name: Ascites Fluid Cells

growth_protocol: LS-CHM cells were maintained at concentration of 2 - 10 x 10^5/mL  in RPMI 1640 medium supplemented with 20% FBS and 1% Gentamycin at 37℃ with 5% CO2.

extract_protocol:
Zymo Direct-zol DNA/RNA extraction kit
RNA-seq: QIAseq Stranded RNA library kit
DNA-seq: QIAseq FX kit

treatment_protocol: Cells were analyzed obtained from cell culture suspensions

value: Ascites Fluid Cells

value: LS-CHM

value: AML- M6

value: Primary Leukemia Cells


title: organoid, CD, rep2

description: Library name: CD2


title: Saline-2

value: saline


title: organoid, CD, rep1

description: Library name: CD1


title: organoid, Control, rep3

description: Library name: Control3

value: in vitro

value: Control


title: PATU-8988T, DMSO-1

value: DMSO


title: 7_RNA-Seq_T32D_sgMettl14-1_rep1

description: Library name: Sample 7

value: KPC-derived T3-2D cell line

value: Murine pancreatic cancer


title: PRMT2-S12A Hyp

city: Tianjin

first: feng

last: dong

address: Qixiangtai Road 22

institute: Tianjin Medical University

data_processing:
The quality control of each sample was accomplished using FASTQC V0.11.5.
For Cut&tag data, clean reads were aligned to human reference genome (hg38) using Hisat2 version 2.1.0.
Peak calling and annotation were performed using R package exomePeak and ChIPseeker respectively.
SAMtools52 was used to remove PCR duplicate and unmapped reads.
Bigwig files were generated by deepTools V2.4.0
Assembly: hg38
Supplementary files format and content: Bam file for each Sample
Supplementary files format and content: bigwig file for each Sample
Library strategy: Cut&tag

source_name: cell line

extract_protocol:
All cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) and maintained at 37 °C with 5% CO2, but hypoxia experiments were performed inhypoxic incubator with 5% CO2 and 1% O2.
Libraries were prepared according to Hyperactive Universal CUT&Tag Assay Kit for Illumina (TD903-01; vazyme, China).

value: cell line

value: glioblastoma cell line

tag: group


title: HTGTS_Chr6_70Mb_APH03_no_ATRi_replicate_3

city: Heidelberg

first: Pei-Chi

last: Wei

state: Baden-Württemberg

address: Im Neuenheim Feld 280

department: Structural and functional genomics

country: Germany

institute: German Cancer Research Center

data_processing:
LAM-HTGTS: a sigularity package https://github.com/brainbreaks/HTGTS
Repli-seq: a sindularity pacakge https://github.com/brainbreaks/HighRes_RepliSeq
GRO-seq:as described in Wei et al., 2016 Cell (https://doi.org/10.1016/j.cell.2015.12.039)
Assembly: mm10
Supplementary files format and content: tlx files contain LAM-HTGTS bait and prey junction, sequneces, start, end, and direction (Strand).
Supplementary files format and content: Bedgraph: display of continuous-valued data in track format
Library strategy: LAM-HTGTS

source_name: ESC-NPC

growth_protocol: The Xrcc4/p53-deficient mouse embryonic stem cells were cultured in DMEM medium supplemented with 15% ESC-grade fetal bovine serum, 20mM HEPES, non-essential amino acids, 100 U/ml Pen/Strep and glutamine mixture, 0.1mM beta-mercaptoethanol and 1000 U/mL ESGRO recombinant mouse leukemia inhibitory factor (LIF) on a monolayer of confluent irradiated mouse fibroblasts. The CAST x 129 hybrid mouse ES cells were cultured in 2i medium (50% DMEM/F12, 50% NeuralBasal, 0.5X N2 supplement, 0.5X B27 supplement, BSA, 10 mM PD03259010, 10 mM CHIR99021, 200 mM Glutamine, 11.9M Monothioglycerol, and 1x10^6 U/ml LIF). To induce mouse neural progenitor cells, Xrcc4/p53-deficient mouse ES cells were plated on laminine/poly-L-ornithine-coated plates and cultured in N2B27 medium (50% DMEM/F12, 50% NeuralBasal, 1% modified N2 supplement, 2% B27 supplement without RA, 1X Glutamax) for seven days. Cells were then passaged to laminin-coated plates and culture in NBBG medium (NeralBasalA, 2% B27 supplement without RA, 0.5 mM Glutamax, 10ng/ml human EGF, 10ng/ml mouse FGFb) for another five to six days. Neural progenitor cells were then collected for nucleofection, DRIP-seq, or Repli-seq experiments.

extract_protocol:
Genomic DNA for HTGTS: cells were lyzed in proteinase K digestion buffer, and genomic DNA were extraced with a standard phenol/chlorofomr protocol. RNA were removed by treating samples with RNAseA prior phenol/chlroform extraction. Genomic DNA for two fraction Repli-seq: cells were lyzed in proteinase K digestion buffer, and genomic DNA were extraced with a standard phenol/chlorofomr protocol. Nascent RNA for GRO-seq: nuclei were lysed in TriZol reagents. RNA were extraced as manufacture instruction.
We follow the published protocol, as indicated below, to construct the libraries. GRO-seq:https://www.sciencedirect.com/science/article/pii/S0092867415017031?via%3Dihub Repli-seq: https://pubmed.ncbi.nlm.nih.gov/29599440/ HTGTS: https://www.nature.com/articles/nprot.2016.043

treatment_protocol: Cells were treated with indicated concentration of aphidicolin or the veichle control DMSO for the indicated period.

value: ESC-NPC

value: Neural progenitor cells

value: Aphidicolin 0.3 uM 96h


title: 9_RNA-Seq_T32D_sgMettl14-2_rep1

description: Library name: Sample 9

value: replicate 1


title: control-TG02


title: PATU-8988T, DMSO-2

value: Pancreatic cancer cells


title: PATU-8988T, THZ1, 4hr-1


title: HTGTS_Chr6_70Mb_APH03_ATRi_replicate_3

value: Aphidicolin 0.3 uM 96h; ATRi 5 nM 96h


title: organoid, Control, rep2

description: Library name: Control2

value: Colon

value: Male


title: organoid, HFD, rep1

description: Library name: HFD1

value: in vivo

value: HFD


title: organoid, PA-treated, rep1

description: Library name: PA1

value: in vitro

value: PA


title: Erythroleukemia Cell Line_RNA

description: patient sample

data_processing:
For RNA-seq: Trimmomatic followed by STAR alignment to Hg38 with htseq-count for tabulation to gene regions.
For WG-seq: Trimmomatic followed by BWA alignemnt to Hg38 followed by samtools snp calling pipeline.
Assembly: Hg38
Supplementary files format and content: count file
Supplementary files format and content: vcf file

value: Ascites Fluid Cells

value: LS-CHM

value: AML- M6

value: Primary Leukemia Cells


title: organoid, Control, rep1

description: Library name: Control1

value: Control


title: AISI-B-ST/SC-R4-1

value: Tumor

value: 10^6 CFU AISI-NC strain


title: HTGTS_Chr6_70Mb_APH03_ATRi_replicate_1

value: ESC-NPC

value: Neural progenitor cells


title: organoid, HFD, rep2

description: Library name: HFD2


title: Saline-3

value: saline


title: PRMT2-S12A-Hyp

description: PRMT2-S12A over-expression

data_processing:
Raw data were processed using CASAVA V1.6 package
The quality control of each sample was accomplished using FASTQC V0.11.5
Clean  reads were aligned to human reference genome hg38 by HISAT
Assembly: hg38
Supplementary files format and content: Bam file for each Sample
Supplementary files format and content: bigwig file for each Sample

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using NEBNext Ultra RNA library Prep Kit for Illumina.

value: cell line

value: glioblastoma cell line

value: Hypoxia


title: Tert- cell, RT, rep1

city: Stanford

first: Li

last: Guan

address: 269 Campus dr, CCSR, Room 1230

institute: Stanford University, Radiation Oncology

data_processing:
Sequenced reads were trimmed for adapter contamination, uncertain nucleotides constitute more than 10 per cent of either read, and low quanlity nucleotides
Trimmed sequence were performed alignments with HISAT2 to the reference
Assembly: mm10
Supplementary files format and content: tab-delimited data file include raw counts for each smaple

source_name: Submandibular gland

extract_protocol:
RNA was extract using RNAeasy mini plus kit (Qiagen)
1ng of purified RNA was used for preparing the library according to the Dr. Picelli’s protocol.

treatment_protocol: Submandibular gland from adult mice were treated with or wthout 15Gy raidation. TertHigh  (DAPI-EpCAM+tdTomato+) and TertLow (DAPI-EpCAM+tdTomato-) cells were sorted from Submandibular gland

value: Submandibular gland

value: Tert+

value: TertCreERT2/+Rosa26LSL-tdTomato/+ mice

value: Radaition Treatment


title: organoid, PA-treated, rep2

description: Library name: PA2

value: Colon

value: in vitro

value: Male

value: PA


title: HTGTS_CAST.129_hPGK_Chr6_70Mb_APH01_replicate_3

source_name: ESC

value: ESC

value: mouse embryonic stem cells

value: Exogenous hPGK promoter replace the endogenous Ptn at the 129 allele

value: 0.1 uM aphidicolin


title: organoid, HFD, rep3

description: Library name: HFD3

value: in vivo

value: HFD


title: Saline-1

value: Tumor

value: saline


title: PRMT2-WT Hyp

value: cell line

value: glioblastoma cell line


title: Tert+ cell, RT, rep4

value: Submandibular gland

value: Tert-


title: HTGTS_CAST.129_Ptn_Chr6_70Mb_APH01_replicate_6

value: TETTA cassette transgene


title: PRMT2-WT-Hyp

description: PRMT2-WT over-expression

value: Hypoxia


title: HTGTS_CAST.129_TRE_Chr6_70Mb_DMSO_replicate_3

value: TETTA cassette transgene, exogenous TRE promoter replace the endogenous Ptn at the 129 allele

value: DMSO


title: HTGTS_Chr6_70Mb_APH03_no_ATRi_replicate_1

value: ESC-NPC

value: Neural progenitor cells

value: Aphidicolin 0.3 uM 96h


title: HTGTS_CAST.129_Ptn_Chr6_70Mb_APH01_replicate_4

value: ESC

value: mouse embryonic stem cells


title: control-Nor

value: control-Nor


title: HTGTS_CAST.129_hPGK_Chr6_70Mb_APH01_replicate_5

value: Exogenous hPGK promoter replace the endogenous Ptn at the 129 allele

value: 0.1 uM aphidicolin


title: Tert+ cell, RT, rep3

value: TertCreERT2/+Rosa26LSL-tdTomato/+ mice

value: Radaition Treatment


title: HTGTS_Chr6_70Mb_APH03_no_ATRi_replicate_2


title: Tert+ cell, RT, rep2


title: Tert- cell, RT, rep3

value: Tert+


title: HTGTS_Chr6_70Mb_APH03_ATRi_replicate_2

value: Aphidicolin 0.3 uM 96h; ATRi 5 nM 96h


title: HTGTS_CAST.129_hPGK_Chr6_70Mb_APH01_replicate_4


title: Tert+ cell, RT, rep1

value: Submandibular gland

value: Tert-


title: Tert- cell, no RT, rep3

value: NO radiation treatment


title: Tert- cell, RT, rep4


title: HTGTS_CAST.129_TRE_Chr6_70Mb_APH01_dox0125_replicate_3

value: TETTA cassette transgene, exogenous TRE promoter replace the endogenous Ptn at the 129 allele

value: 0.1 uM aphidicolin, 0.125 uM doxycyclin


title: control-Hyp

value: cell line

value: glioblastoma cell line

value: control-Hyp


title: Tert- cell, RT, rep2


title: Total RNA-seq siPYGO2-3

city: Suwon-si

first: Daeho

last: Joe

state: Gyeonggi-do

address: 2066, Seobu-ro

institute: Sungkyunkwan University

data_processing:
For Ribo-seq data, we first trimmed reads following manufacturer’s guide(https://immaginabiotech.com/product/laceseq-12-rxns, LACEseq bioIT guidelines). Reads were processed using Cutadapt(version 2.8) and UMI-tools(version 1.1.4). Reads were trimmed from the 3’ end of each read and only reads longer than X+9 were retrieved. UMIs were moved to the read name and first T at the start of each read were removed. The processed sequences were first mapped to the contaminants using bowtie2 with parameters “—un”, which is composed of PhiX genome (GenBank accession J02482.1), predicted tRNA genes (GtRNAdb, http://gtrnadb.ucsc.edu/genomes/eukaryota/Hsapi38/Hsapi38-seq.html), lncRNA transcripts (Gencode, https://www.gencodegenes.org/human/), rRNA repeat units (GenBank accession U13369.1) and all sequences for ribosomal RNA of human (retrieved from Rfam 11.0 of the Wellcome Trust Sanger Institute). Trimmed riboseq data and raw RNA-seq data were mapped to human genome GRCh38 using STAR (v2.7.10b) following deltaTE Support Protocol. Aligned reads were sorted by samtools(v1.10) followed by quantification using featureCounts(v2.0.0). Obtained count matrices were imported into R for further analysis. DESeq2(v1.38.3) was used for calculating differential translation genes (DTGs) requires the count matrices from Ribo-seq and RNA-seq as previously described.
Assembly: GRCh38 from GENCODE, release 43 was used for analysis
Supplementary files format and content: For both Ribo-seq and RNA-seq, comma seperated values(csv) is attached containing raw countdata.

source_name: HeLa TO cells

extract_protocol:
Ribosome protected fragments (RPF) was acquired using RiboLace kit (Immagina) following manufacturer's protocols. 20 ng of RPF was used for the construction of sequencing libraries.
RNA libraries for Active-Ribo-seq were prepared using LACE-seq kit following manufacturer's protocols.
Active-Ribo-seq

value: HeLa TO cells

value: Cervical carcinoma

value: PYGO2 knockdown

value: Shake-off after treatment of nocodazole for 16 h


title: HTGTS_CAST.129_TRE_Chr6_70Mb_APH01_dox0125_replicate_2

value: ESC

value: mouse embryonic stem cells


title: HTGTS_CAST.129_TRE_Chr6_70Mb_DMSO_replicate_2

value: DMSO


title: Total RNA-seq siPYGO2-2


title: HTGTS_CAST.129_TRE_Chr6_70Mb_APH01_dox025_replicate_2

value: 0.1 uM aphidicolin, 0.25 uM doxycyclin


title: Tert- cell, no RT, rep2

value: Tert+

value: TertCreERT2/+Rosa26LSL-tdTomato/+ mice


title: Tert+ cell, no RT, rep2

value: Submandibular gland

value: Tert-


title: HTGTS_CAST.129_Ptn_Chr6_70Mb_APH01_replicate_5

value: TETTA cassette transgene

value: 0.1 uM aphidicolin


title: HTGTS_CAST.129_TRE_Chr6_70Mb_APH01_dox0125_replicate_1

value: TETTA cassette transgene, exogenous TRE promoter replace the endogenous Ptn at the 129 allele

value: 0.1 uM aphidicolin, 0.125 uM doxycyclin


title: HTGTS_CAST.129_TRE_Chr6_70Mb_APH01_dox025_replicate_1


title: HTGTS_CAST.129_TRE_Chr6_70Mb_APH01_replicate_3


title: Total RNA-seq siCTRL-2

value: WT


title: HTGTS_CAST.129_TRE_Chr6_70Mb_APH01_replicate_2


title: HTGTS_CAST.129_TRE_Chr6_70Mb_APH01_dox025_replicate_3


title: Total RNA-seq siCTRL-3

value: HeLa TO cells


title: HTGTS_CAST.129_TRE_Chr6_70Mb_APH01_dox05_replicate_3

value: 0.1 uM aphidicolin, 0.5 uM doxycyclin


title: DMSO-Hyp

description: DMSO treatment

value: cell line

value: glioblastoma cell line

value: Hypoxia


title: Total RNA-seq siCTRL-1

value: Cervical carcinoma

value: Shake-off after treatment of nocodazole for 16 h


title: Tert+ cell, no RT, rep1

value: NO radiation treatment


title: Repliseq_NXP047_22-5_Nrxn1_allele-B_promoter-A_late_replicate_2

description: 22-5_repliseq_50000_rep2_EL_log2_ratio_scaled_smoothed.bedGraph

data_processing:
LAM-HTGTS: a sigularity package https://github.com/brainbreaks/HTGTS
Repli-seq: a sindularity pacakge https://github.com/brainbreaks/HighRes_RepliSeq
GRO-seq:as described in Wei et al., 2016 Cell (https://doi.org/10.1016/j.cell.2015.12.039)
Assembly: mm10
Supplementary files format and content: tlx files contain LAM-HTGTS bait and prey junction, sequneces, start, end, and direction (Strand).
Supplementary files format and content: Bedgraph: display of continuous-valued data in track format
Library strategy: Repli-seq

value: ESC-NPC

value: Neural progenitor cells

value: Xrcc4-/-::p53-/-; ESC-NPC; NXP047; Neurexin 1 B allele deletion; A allele promoter/enhancer deletion (22-5)


title: Total RNA-seq siPYGO2-1

value: PYGO2 knockdown


title: TG02-Hyp

description: TG20 treatment


title: Tert+ cell, no RT, rep3

value: Submandibular gland

value: Tert-

value: TertCreERT2/+Rosa26LSL-tdTomato/+ mice


title: Tert- cell, no RT, rep1

value: Tert+


title: HTGTS_CAST.129_TRE_Chr6_70Mb_APH01_dox05_replicate_1

value: ESC

value: mouse embryonic stem cells

value: TETTA cassette transgene, exogenous TRE promoter replace the endogenous Ptn at the 129 allele


title: HTGTS_CAST.129_TRE_Chr6_70Mb_APH01_dox05_replicate_2

value: 0.1 uM aphidicolin, 0.5 uM doxycyclin


title: glioblastomaT25

first: Xue

last: Yang

address: No. 119, South Fourth Ring Road West

institute: Beijing Tiantan Hospital Affiliated to the Capital Medical University

data_processing:
Total RNA was used as input material for the RNA sample  preparations. Briefly, mRNA was purified from total RNA using poly-T  oligo-attached magnetic beads. Fragmentation was carried out using  divalent cations under elevated temperature in First Strand Synthesis  Reaction Buffer(5X). First strand cDNA was synthesized using random  hexamer primer and M-MuLV Reverse Transcriptase(RNase H-).  Second strand cDNA synthesis was subsequently performed using  DNA Polymerase I and RNase H. Remaining overhangs were converted  into blunt ends via exonuclease/polymerase activities. After adenylation  of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were  ligated to prepare for hybridization. In order to select cDNA fragments  of preferentially 370~420 bp in length, the library fragments were  purified with AMPure XP system. Then PCR was performed with  Phusion High-Fidelity DNA polymerase, Universal PCR primers and  Index (X) Primer. At last, PCR products were purified (AMPure XP  system) and library quality was assessed on the Agilent Bioanalyzer  2100 system.  The clustering of the index-coded samples was performed on a cBot  Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia)  according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 paired-end reads were generated.
Assembly: Reference HG38 genome
Supplementary files format and content: Tab-delimited text file includes FPKM values for each samples

source_name: glioblastoma

extract_protocol:
Samples from glioblastoma patients who underwent surgical treatment at Tiantan Hospital from January 2022 to December 2023 were collected for transcriptome sequencing.
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of  the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).

value: glioblastoma


title: HTGTS_CAST.129_mPGK_Chr6_70Mb_APH01_replicate_3

value: Exogenous mPGK promoter replace the endogenous Ptn at the 129 allele

value: 0.1 uM aphidicolin


title: glioblastomaT26


title: HTGTS_CAST.129_hPGK_Chr6_70Mb_APH01_replicate_2

value: Exogenous hPGK promoter replace the endogenous Ptn at the 129 allele


title: HTGTS_CAST.129_Ptn_Chr6_70Mb_APH01_replicate_3

value: TETTA cassette transgene


title: HTGTS_CAST.129_TRE_Chr6_70Mb_APH01_replicate_1


title: HTGTS_CAST.129_Ptn_Chr6_70Mb_APH01_replicate_2


title: Repliseq_NXP047_22-5_Nrxn1_allele-B_promoter-A_early_replicate_2

value: ESC-NPC


title: Repliseq_NXP047_22-5_Nrxn1_allele-B_promoter-A_late_replicate_1

description: 22-5_repliseq_50000_rep1_EL_log2_ratio_scaled_smoothed.bedGraph

value: Neural progenitor cells


title: HTGTS_CAST.129_hPGK_Chr6_70Mb_APH01_replicate_1


title: HTGTS_CAST.129_Ptn_Chr6_70Mb_APH01_replicate_1


title: glioblastomaT22


title: GROseq_CAST.129_hPGK_replicate_1

description:
CAST.129_hPGK_GROseq_replicate_1.neg.bw
CAST.129_hPGK_GROseq_replicate_1.pos.bw

data_processing:
LAM-HTGTS: a sigularity package https://github.com/brainbreaks/HTGTS
Repli-seq: a sindularity pacakge https://github.com/brainbreaks/HighRes_RepliSeq
GRO-seq:as described in Wei et al., 2016 Cell (https://doi.org/10.1016/j.cell.2015.12.039)
Assembly: mm10
Supplementary files format and content: tlx files contain LAM-HTGTS bait and prey junction, sequneces, start, end, and direction (Strand).
Supplementary files format and content: Bedgraph: display of continuous-valued data in track format
Library strategy: GRO-seq


title: glioblastomaT21


title: HTGTS_CAST.129_mPGK_Chr6_70Mb_APH01_replicate_2


title: glioblastomaT20


title: GROseq_CAST.129_hPGK_replicate_2

description:
CAST.129_hPGK_GROseq_replicate_2.neg.bw
CAST.129_hPGK_GROseq_replicate_2.pos.bw


title: Repliseq_NXP047_22-37_Nrxn1_allele-B_promoter-A_late_replicate_2

description: 22-37_repliseq_50000_rep2_EL_log2_ratio_scaled_smoothed.bedGraph

value: Xrcc4-/-::p53-/-; ESC-NPC; NXP047; Neurexin 1 B allele deletion; A allele promoter/enhancer deletion (22-37)


title: GROseq_CAST.129_mPGK_replicate_1

description:
CAST.129_mPGK_GROseq_replicate_1.neg.bw
CAST.129_mPGK_GROseq_replicate_1.pos.bw


title: glioblastomaT19


title: glioblastomaT23


title: Repliseq_NXP047_22-37_Nrxn1_allele-B_promoter-A_early_replicate_2


title: GROseq_CAST.129_mPGK_replicate_2

description:
CAST.129_mPGK_GROseq_replicate_2.neg.bw
CAST.129_mPGK_GROseq_replicate_2.pos.bw


title: HTGTS_CAST.129_TRE_Chr6_70Mb_DMSO_replicate_1

value: DMSO


title: GROseq_CAST.129_TETTA_replicate_2

description:
CAST.129_TETTA_GROseq_replicate_2.neg.bw
CAST.129_TETTA_GROseq_replicate_2.pos.bw


title: GROseq_CAST.129_TETTA_replicate_1

description:
CAST.129_TETTA_GROseq_replicate_1.neg.bw
CAST.129_TETTA_GROseq_replicate_1.pos.bw


title: Single-cell RNA-seq day4 cell78

city: Guangzhou

first: Hui

last: Zheng

state: Guangdong

address: No.190 Kaiyuan Avenue, Science Park

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

data_processing:
Fastq files were generated from illumina BCL raw data using bcl2fastq scripts;
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Mapped read counts were calculated using RSEM(1.2.22) with parameters(-p 8 --estimated-rspd --no-bam-output).
Assembly: mm10
Supplementary files format and content: Comma separated values files include counts for each Sample

source_name: Mouse embryonic fibroblasts reprgramming cells

growth_protocol: Reprogramming cells were maintained in iCD1 reprogramming medium.

extract_protocol:
Cells were collected by trypsin digestion. Using the C1 Single-Cell Auto Prep System to Generate mRNA from Single Cells and Libraries for Sequencing (Fluidigm, PN 100-5950 B1).
Single cell libraries were constructed following the protocol of Using the C1 Single-Cell Auto Prep System to Generate mRNA from Single Cells and Libraries for Sequencing (Fluidigm, PN 100-5950 B1).

treatment_protocol: MEF cells were infected with OvSvK for reprogramming.

value: OvSvK single-cell RNA-seq reprogramming day4


title: Repliseq_NXP047_22-37_Nrxn1_allele-B_promoter-A_early_replicate_1

description: 22-37_repliseq_50000_rep1_EL_log2_ratio_scaled_smoothed.bedGraph


title: Repliseq_NXP047_22-5_Nrxn1_allele-B_promoter-A_early_replicate_1

value: Xrcc4-/-::p53-/-; ESC-NPC; NXP047; Neurexin 1 B allele deletion; A allele promoter/enhancer deletion (22-5)


title: Single-cell RNA-seq day4 cell77

value: Mouse embryonic fibroblasts reprgramming cells


title: Repliseq_NXP047_22_Nrxn1_allele-B_late_replicate_2

description: 22_repliseq_50000_rep2_EL_log2_ratio_scaled_smoothed.bedGraph

value: Xrcc4-/-::p53-/-; ESC-NPC; NXP047; Neurexin 1 B allele deletion (22)


title: glioblastomaT17


title: Repliseq_NXP047_22_Nrxn1_allele-B_early_replicate_2


title: Single-cell RNA-seq day4 cell76


title: Single-cell RNA-seq day4 cell79


title: Repliseq_NXP047_22-37_Nrxn1_allele-B_promoter-A_late_replicate_1


title: Single-cell RNA-seq day4 cell73


title: Repliseq_NXP047_22_Nrxn1_allele-B_early_replicate_1

description: 22_repliseq_50000_rep1_EL_log2_ratio_scaled_smoothed.bedGraph


title: Single-cell RNA-seq day4 cell74


title: glioblastomaT14


title: Single-cell RNA-seq day4 cell67


title: Single-cell RNA-seq day4 cell68


title: HTGTS_CAST.129_mPGK_Chr6_70Mb_APH01_replicate_1

value: ESC


title: glioblastomaT24


title: Repliseq_NXP010_47-5_Ctnna2_allele-B_late_replicate_1

description: 47_5_repliseq_50000_rep1_EL_log2_ratio_scaled_smoothed.bedGraph

value: Xrcc4-/-::p53-/-; ESC-NPC; NXP010; Ctnna2 B allele deletion (47-5)


title: Repliseq_NXP010_47-5_Ctnna2_allele-B_early_replicate_2

description: 47_5_repliseq_50000_rep2_EL_log2_ratio_scaled_smoothed.bedGraph


title: Single-cell RNA-seq day4 cell63


title: Single-cell RNA-seq day4 cell70


title: Single-cell RNA-seq day4 cell75


title: glioblastomaT11


title: Single-cell RNA-seq day4 cell62


title: Single-cell RNA-seq day4 cell71


title: glioblastomaT16


title: Single-cell RNA-seq day4 cell72


title: Repliseq_NXP010_47-5_Ctnna2_allele-B_early_replicate_1


title: Single-cell RNA-seq day4 cell61


title: Single-cell RNA-seq day4 cell69


title: Repliseq_NXP047_22_Nrxn1_allele-B_late_replicate_1


title: glioblastomaT15


title: Repliseq_NXP010_38-3_Ctnna2_allele-B_promoter-A_late_replicate_1

description: 38_3_repliseq_50000_rep1_EL_log2_ratio_scaled_smoothed.bedGraph

value: Xrcc4-/-::p53-/-; ESC-NPC; NXP010; Ctnna2 B allele deletion; A allele promoter/enhancer deletion (38-3)


title: glioblastomaT7


title: Single-cell RNA-seq day4 cell56


title: Single-cell RNA-seq day4 cell60


title: glioblastomaT8


title: Repliseq_NXP010_38-3_Ctnna2_allele-B_promoter-A_early_replicate_1


title: glioblastomaT18


title: glioblastomaT6


title: Single-cell RNA-seq day4 cell66


title: Single-cell RNA-seq day4 cell64


title: Single-cell RNA-seq day4 cell54


title: Single-cell RNA-seq day4 cell65


title: Single-cell RNA-seq day4 cell51


title: glioblastomaT13


title: Single-cell RNA-seq day4 cell49


title: Repliseq_NXP010_18-4_Ctnna2_allele-B_promoter-A_early_replicate_2

description: 18_4_repliseq_50000_rep2_EL_log2_ratio_scaled_smoothed.bedGraph

value: Xrcc4-/-::p53-/-; ESC-NPC; NXP010; Ctnna2 b allele deletion; A allele promoter/enhancer deletion (18-4)


title: glioblastomaT3

value: glioblastoma


title: glioblastomaT12


title: glioblastomaT5


title: Single-cell RNA-seq day4 cell46


title: Single-cell RNA-seq day4 cell58


title: Single-cell RNA-seq day4 cell44


title: glioblastomaT10


title: Single-cell RNA-seq day4 cell59


title: Repliseq_NXP010_47-5_Ctnna2_allele-B_late_replicate_2


title: Single-cell RNA-seq day4 cell57


title: Single-cell RNA-seq day4 cell53


title: Single-cell RNA-seq day4 cell45


title: Repliseq_NXP010_38-3_Ctnna2_allele-B_promoter-A_late_replicate_2

description: 38_3_repliseq_50000_rep2_EL_log2_ratio_scaled_smoothed.bedGraph


title: Single-cell RNA-seq day4 cell42


title: Single-cell RNA-seq day4 cell40


title: glioblastomaT9


title: Single-cell RNA-seq day4 cell39


title: Single-cell RNA-seq day4 cell47


title: Single-cell RNA-seq day4 cell55


title: Single-cell RNA-seq day4 cell52


title: Single-cell RNA-seq day4 cell36


title: OvSvK CUT&Tag seq of H3K36me3

data_processing:
Raw CUT&Tag reads were trimmed and ﬁltered for quality control using Trim Galore v0.6.7.
Clean paired-end reads were ﬁrst mapped to mouse geneme mm10 using Bowtie2(v2.4.5)  with parameters  '--very-sensitive -X 2000'.
PCR duplicates were removed with sambamba(V0.6.8).
For histone marks enriched in Narrow domains, the NarrowPeak  representation was used applying following settings : -f BAM --keepdup all -q 0.05 --bdg. For histone marks enriched in broad domains, the broadPeak representation was used applying following settings: -f BAM --keepdup all  -q 0.05 --broad --broad-cutoff 0.01.
bigwig files required for coverage tracks as well as heatmaps were generated using Deeptools v3.3.1
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: Mouse embryonic fibroblasts

extract_protocol:
Cells were collected by trypsin digestion.
Libraries for CUT&Tag were prepared using Hyperactive Universal CUT&Tag Assay Kit for Illumina following manufacturer's protocols.

treatment_protocol: MEF cells were infected with OSK or OvSvK for reprogramming.

value: Mouse embryonic fibroblasts, reprgramming cells

tag: antibody


title: Repliseq_NXP010_38-3_Ctnna2_allele-B_promoter-A_early_replicate_2


title: Repliseq_NXP010_18-4_Ctnna2_allele-B_promoter-A_late_replicate_1

description: 18_4_repliseq_50000_rep1_EL_log2_ratio_scaled_smoothed.bedGraph

value: Xrcc4-/-::p53-/-; ESC-NPC; NXP010; Ctnna2 B allele deletion; A allele promoter/enhancer deletion (18-4)


title: Single-cell RNA-seq day4 cell48


title: Single-cell RNA-seq day4 cell34


title: NPC-4-NC

city: Shenzhen

first: Jianrui

address: No.1120 Lianhua Road, Futian District

institute: Peking University Shenzhen Hospital

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
CUT&Tag reads were aligned to the hg38 genome using BWA（0.7.13-r1126） . Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.2 with the significance cut-off q-value <=0.05
bigWig files were generated using the deeptools. Peak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: nucleus pulposus mesenchymal stem cells

extract_protocol:
CUT&Tag assay was performed as described previously with modifications(Hatice et al., 2019 ). Briefly，100000 cells were washed twice gently with wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail).
To amplify libraries, 21μL DNA was mixed with 2μL of a universal i5 and auniquely barcoded i7 primer. A volume of 25 μL NEBNext HiFi 2× PCR Master mix was added and mixed. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72 °C for 5 min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 30 s; final extension at 72 °C for 1 min and hold at 8 °C. libraried clean-up was performed XP beads (Beckman Counter).

value: nucleus pulposus mesenchymal stem cells

value: WT

value: NC


title: OvSvK CUT&Tag seq of H3K27me3


title: Single-cell RNA-seq day4 cell32


title: Repliseq_NXP010_18-4_Ctnna2_allele-B_promoter-A_late_replicate_2

value: ESC-NPC

value: Neural progenitor cells


title: Single-cell RNA-seq day4 cell31


title: Single-cell RNA-seq day4 cell29


title: glioblastomaT1


title: Single-cell RNA-seq day4 cell28


title: Single-cell RNA-seq day4 cell43


title: Single-cell RNA-seq day4 cell50


title: Repliseq_NXP010_18-4_Ctnna2_allele-B_promoter-A_early_replicate_1


title: glioblastomaT4


title: OSK+Flag+siNC CUT&Tag seq of H3K27me3


title: OSK+Ccne1+siCcnd1+siCdkn2a CUT&Tag seq of H3K27me3


title: glioblastomaT2


title: Single-cell RNA-seq day4 cell27


title: NPC-5-Treat

value: 75 μM tert-butyl hydroperoxide


title: NPC-3-NC

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
RNAseq reads were aligned to the hg38 genome using STAR.
Read counts for individual gene of each sample were produced with HTSeq-count
Assembly: hg38
Supplementary files format and content: txt(gene expression of all sample)

extract_protocol:
RNA was extracted using Trizol following the manufacturer's protocol.
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.


title: Single-cell RNA-seq day4 cell30

value: OvSvK single-cell RNA-seq reprogramming day4


title: Single-cell RNA-seq day4 cell26


title: Single-cell RNA-seq day4 cell25


title: Single-cell RNA-seq day4 cell22


title: NPC-2-Treat


title: Single-cell RNA-seq day4 cell38


title: OSK+Ccne1+siCcnd1+siCdkn2a CUT&Tag seq of H3K4me3

value: H3K4me3(abcam, #ab8580)


title: Single-cell RNA-seq day4 cell24

value: Mouse embryonic fibroblasts reprgramming cells


title: NPC-2-NC


title: NPC-3-Treat.


title: Single-cell RNA-seq day4 cell41


title: OvSvK CUT&Tag seq of H3K9me3

value: H3K9me3 (abcam, #ab8898)


title: Single-cell RNA-seq day4 cell37


title: Single-cell RNA-seq day4 cell33


title: ATAC-seq of mCitrine positive cells of OvSvK reprogramming cells

data_processing:
Raw ATAC-seq reads were trimmed and ﬁltered for quality control using Trim Galore v0.6.7
Clean paired-end reads were ﬁrst mapped to mouse geneme mm10 using Bowtie2(v2.4.5)  with parameters  '--very-sensitive -X 2000'
PCR duplicates were removed with sambamba(V0.6.8)
Peak calling was performed with MACS2 with parameters ‘––keep-dup all -q 0.05 -f BEDPE ’
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Cells at different cell cycle stage were isolated by fluorescence-activated cell sorting (FACS).
Libraries for ATAC-seq were prepared using TruePrepTM DNA Library Prep Kit V2 for Illumina following manufacturer's protocols.

treatment_protocol: MEF cells were infected with hCdt1-mCherry and hGeminin-mCitrine to get Fucci indication and also infected with OSK or OvSvK for reprogramming.

value: Mouse embryonic fibroblasts

value: FACS sorting mCitrine positive cells of OvSvK reprogramming cells


title: NPC-3-NC.


title: NPC-5-NC


title: Single-cell RNA-seq day4 cell35


title: NPC-4-Treat


title: OSK+Flag+siNC CUT&Tag seq of H3K4me3


title: OvSvK CUT&Tag seq of H3K4me3


title: NPC-1-NC


title: OSK CUT&Tag seq of H3K9me3


title: NPC-3-Treat


title: OSK CUT&Tag seq of H3K4me3


title: ATAC-seq of mCherry positive cells of OvSvK reprogramming cells

value: FACS sorting mCherry positive cells of OvSvK reprogramming cells


title: OSK CUT&Tag seq of H3K36me3


title: Single-cell RNA-seq day4 cell15


title: Single-cell RNA-seq day4 cell20


title: Single-cell RNA-seq day4 cell23


title: Single-cell RNA-seq day4 cell21


title: NPC-1-Treat


title: OSK CUT&Tag seq of H3K27me3


title: Single-cell RNA-seq day4 cell19


title: Single-cell RNA-seq day4 cell18


title: ATAC-seq of mCherry/mCitrine double positive cells of OvSvK reprogramming cells

value: FACS sorting mCherry/mCitrine double positive cells of OvSvK reprogramming cells


title: Single-cell RNA-seq day4 cell13


title: Single-cell RNA-seq day4 cell16


title: Single-cell RNA-seq day4 cell11


title: Single-cell RNA-seq day4 cell17


title: G62_treat_H

city: Warsaw

first: Agnieszka

last: Bronisz

address: Pawinskiego 5

country: Poland

institute: Mossakowksi Medical Research Institute

description: GSC cells treated with ferroptosis inducer RSL3 (3uM) incubated for 24h in hypoxic oxygen conditions (1% O2, 5% CO2)

data_processing:
Raw sequences were trimmed according to quality using Trimmomatic (Bolger, Lohse, and Usadel 2014) (version 0.39) using the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:20.
Trimmed sequences were mapped to the human reference genome provided by ENSEMBL, (version grch38_snp_tran) using Hisat2 (Kim, Langmead, and Salzberg 2015) with default parameters.
Optical duplicates were removed using MarkDuplicates tool from GATK (McKenna et al. 2010) package (version 4.2.3.0) with default parameters except OPTICAL_DUPLICATE_PIXEL_DISTANCE set to 12000.
Mapped reads were associated with transcripts from grch38 database (Zerbino et al. 2018) (Ensembl, version 106) using HTSeq-count (Anders, Pyl, and Huber 2015) (version 0.9.1) with default parameters except –stranded set to “reverse”.
Differentially expressed genes were selected using the DESeq2 package (Love, Huber, and Anders 2014) (version1.38.3).
Assembly: grch38 database, Ensembl version 106
Supplementary files format and content: Raw counts are included as a spreadshit in Microsoft Excel file containing: sample names,  ensembl ID, Ensembl gene symbol and gene biotype
Supplementary files format and content: Normalized data from DeSeq2 are included as Microsoft Excel file containing: sample names,  ensembl ID, Ensembl gene symbol and gene biotype

growth_protocol: GSCs were cultured in Neurobasal medium with 1% GlutaMax, B27 minus Vit A and EGF/bFGF (20 ng/ml each) in 5% CO2 incubator. Before experiments single cells suspension was plated on ultra low attachment 6-well plates in concentration 400 000 cells.

extract_protocol:
RNA from snap frozen pellets were isolated with phenol-chloroform method. RNA was precipitated overnight using ice-cold isopraponol at -80C and washed with 70% ethanol. Resuspended in water and frozen in -80C for further analysis.
RNA samples (1000 ng) were treated with KAPA RNA HyperPrep Kit with Riboerase to remove ribosomal RNA. To create libraries adapters KAPA_UDI_Indexes were used. Further fragmentation was performed in 94 C for 5 min. PCR amplification was done for 10 cycles, acording to Kapa Biosystems protocol).

treatment_protocol: Control cells treated with DMSO (0.1% final concentration), and ferroptosis inducer at 3 uM (RSL3 in DMSO) and cultured for 24h in either Normoxia (20% oxygen and 5% CO2) or Hypoxia (1% oxygen, 5% CO2).

value: glioblastoma

value: GSCs

tag: growth condition

value: hypoxia


title: G88_treat_H

tag: tissue


title: Single-cell RNA-seq day4 cell12


title: Single-cell RNA-seq day4 cell14


title: Single-cell RNA-seq day4 cell9


title: ATAC-seq of total OvSvK reprogramming cells

value: total OvSvK reprogramming cells


title: Single-cell RNA-seq day4 cell8


title: ATAC-seq of mCitrine positive cells of OSK reprogramming cells

value: FACS sorting mCitrine positive cells of OSK reprogramming cells


title: ATAC-seq of mCherry/mCitrine double positive cells of OSK reprogramming cells

value: FACS sorting mCherry/mCitrine double positive cells of OSK reprogramming cells


title: ATAC-seq of mCherry positive cells of OSK reprogramming cells

value: FACS sorting mCherry positive cells of OSK reprogramming cells


title: G34_treat_H


title: Single-cell RNA-seq day4 cell10


title: G33_treat_H


title: G816_treat_H


title: Single-cell RNA-seq day4 cell6


title: Single-cell RNA-seq day4 cell7


title: PTP1B KO, Control, biol rep 2

city: Madrid

first: Mónica

last: Ruíz Rosario

state: Madrid

address: 7, Calle Faraday

country: Spain

institute: NIMGenetics

data_processing:
The base call (or BCL) files outputted by the sequencer were demultiplexed to fastq files based on their index sequences using Illumina bcl2fastq conversion software
Quality control check with FastQC
Allignment to a mouse transcriptome reference with the Kallisto algorithm, which provides a matrix of estimated counts per transcript as the output
Assembly: Mus_musculus.GRCm38.cdna.all.fa.gz, ENSEMBL
Supplementary files format and content: HDF5 binary files containing run info, abundance esimates, bootstrap estimates, and transcript length information length for each sample

source_name: Liver

growth_protocol: Animals were maintained at 22-24 ºC and 55 % humidity on 12 h light/dark cycles (starting at 8 am) and fed a regular rodent chow diet (A04, Panlab, Barcelona, Spain) and tap water ad libitum.

extract_protocol:
Animal tissues were isolated in TRIzol. Total RNA was extracted using the PureLink RNA Mini Kit (Life Technologies)
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded RNASeq technology (Illumina, San Diego, CA, USA)

treatment_protocol: Mice received a standard chow diet, or the same diet supplemented with olanzapine or aripiprazole (40 mg/kg chow diet), which corresponds to a dosage of 5.5–6.0mg/kg/day considering the daily food intake.

value: Liver

value: PTP1B KO

tag: Sex

value: male

value: Untreated

tag: time

value: 7 months


title: PTP1B KO, Control, biol rep 1

tag: genotype


title: Single-cell RNA-seq day4 cell5

value: Mouse embryonic fibroblasts reprgramming cells

value: OvSvK single-cell RNA-seq reprogramming day4


title: G157_treat_H


title: ATAC-seq of total OSK reprogramming cells

value: Mouse embryonic fibroblasts

value: total OSK reprogramming cells


title: Single-cell RNA-seq day4 cell4


title: Single-cell RNA-seq day4 cell1


title: Single-cell RNA-seq day3 cell89

value: OvSvK single-cell RNA-seq reprogramming day3


title: G44_treat_H

value: glioblastoma


title: Single-cell RNA-seq day3 cell88


title: Single-cell RNA-seq day4 cell2


title: G88_treat

description: GSC cells treated with ferroptosis inducer RSL3 (3uM) incubated for 24h in normal oxygen conditions (21% O2, 5% CO2)

value: GSCs

value: normoxia


title: Single-cell RNA-seq day3 cell87


title: Single-cell RNA-seq day3 cell86


title: G34_treat


title: PTP1B KO, Olanzapine, biol rep 1

value: Olanzapine


title: G146_treat_H

value: hypoxia


title: G62_treat


title: Single-cell RNA-seq day3 cell84


title: Single-cell RNA-seq day3 cell85


title: Single-cell RNA-seq day4 cell3


title: Single-cell RNA-seq day3 cell81


title: PTP1B KO, Aripiprazole, biol rep 1

value: Aripiprazole


title: G33_treat


title: Single-cell RNA-seq day3 cell80


title: Single-cell RNA-seq day3 cell78


title: WT, Control, biol rep 1

value: WT


title: G157_treat


title: G146_treat


title: Single-cell RNA-seq day3 cell77


title: WT, Control, biol rep 2

value: Liver


title: PTP1B KO, Aripiprazole, biol rep 2

value: PTP1B KO


title: Single-cell RNA-seq day3 cell76


title: PTP1B KO, Olanzapine, biol rep 2

value: male


title: Single-cell RNA-seq day3 cell82


title: G44_treat


title: Single-cell RNA-seq day3 cell74


title: G816_treat


title: WT, Olanzapine, biol rep 1


title: WT, Olanzapine, biol rep 2


title: WT, Aripiprazole, biol rep 1


title: Single-cell RNA-seq day3 cell79


title: G34_ctr_H

description: GSC cells control (with DMSO) incubated for 24h in hypoxic oxygen conditions (1% O2, 5% CO2)

value: control,


title: Single-cell RNA-seq day3 cell72


title: G88_ctr_H


title: Single-cell RNA-seq day3 cell68


title: Single-cell RNA-seq day3 cell67


title: Single-cell RNA-seq day3 cell71


title: Single-cell RNA-seq day3 cell75


title: WT, Aripiprazole, biol rep 2

value: 7 months


title: Single-cell RNA-seq day3 cell83

value: Mouse embryonic fibroblasts reprgramming cells


title: G816_ctr_H


title: G62_ctr_H


title: Single-cell RNA-seq day3 cell65


title: Single-cell RNA-seq day3 cell62


title: Single-cell RNA-seq day3 cell73


title: Single-cell RNA-seq day3 cell69


title: control embryos [C4]

city: Wuhan

first: Jing-Jing

state: Hubei

address: 1 Lion Rock Street

department: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction

institute: Huazhong Agricultural University

data_processing:
All RNA-seq data were aligned to the mouse reference genome mm10 using STAR
Gene FPKM (Fragments per kilobase of transcript per million mapped reads) values were quantified using Stringtie
Gene differential expression analysis using DESeq2 (version 1.30.1) based on the reads count file obtained by featureCounts
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: The fertilized eggs were transferred for cleaning to the preheated G1 culture solution 3 times, after which were transferred to the preheated G1 culture drops and cultured in the incubator with 37°C, 5% CO2,  and saturated humidity

extract_protocol:
Two micrograms of total RNA were used for RNA sample preparation. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA concentration of library was measured using Qubit® RNA Assay Kit in Qubit® 3.0 to preliminary quantify and then dilute to 1 ng/μl. Library quality was assessed using the Agilent Bioanalyzer 2100 system.
cDNA was preamplification for 16-18 cycles by using KAPA HiFi HotStart ReadyMix (KK2601, Roche) and IS PCR primers, followed by PCR purification by AMPure XP beads (A63881, Beckman). Finally, amplified cDNA was fragmented and RNA-seq library was constructed by using TruePrep DNA Library Prep Kit (TD502, Vazyme) according to the manufacturer’s instructions. Paired-end 150-bp sequencing was performed on the Illumina NovaSeq 6000 system.

treatment_protocol: While the TCC treatment group was a G1 medium containing 2 μM, 4 μM, and 6 μM TCC, respectively, the control group was a G1 medium containing the same volume of DMSO

value: embryo

value: DMSO


title: TCC-treated embryos [D3]

value: TCC，6 microΜ


title: Single-cell RNA-seq day3 cell63

value: OvSvK single-cell RNA-seq reprogramming day3


title: G33_ctr_H

value: glioblastoma


title: Single-cell RNA-seq day3 cell66


title: G146_ctr_H

value: GSCs


title: Single-cell RNA-seq day3 cell59


title: Single-cell RNA-seq day3 cell61


title: Single-cell RNA-seq day3 cell64


title: Single-cell RNA-seq day3 cell58


title: Single-cell RNA-seq day3 cell70


title: G157_ctr_H


title: G44_ctr_H

value: control


title: TCC-treated embryos [D2]


title: control embryos [C3]


title: TCC-treated embryos [D1]


title: control embryos [C2]


title: TCC-treated embryos [D4]


title: Single-cell RNA-seq day3 cell57


title: G88_ctr

description: GSC cells control (with DMSO) incubated for 24h in normal oxygen conditions (21% O2, 5% CO2)

value: normoxia


title: Single-cell RNA-seq day3 cell56


title: G34_ctr


title: Single-cell RNA-seq day3 cell55


title: 2-cell embryo, 5um-3

data_processing:
All RNA-seq data were aligned to the mouse reference genome mm10 using STAR
Gene FPKM (Fragments per kilobase of transcript per million mapped reads) values were quantified using Stringtie (version 2.1.4)
Gene differential expression analysis using DESeq2 (version 1.30.1) based on the reads count file obtained by featureCounts (version 1.6.2)
Assembly: mm10
Supplementary files format and content: excel file include reads counts for each sample

source_name: 2-cell embryo

treatment_protocol: For sodium arsenite (Sigma, S7400) treatment, G1-PLUS medium was supplied with 5 μM sodium arsenite.

value: 2-cell embryo

value: 5 uM sodium arsenite treatment


title: G62_ctr


title: Single-cell RNA-seq day3 cell60


title: Single-cell RNA-seq day3 cell52


title: Single-cell RNA-seq day3 cell53


title: Single-cell RNA-seq day3 cell51


title: control embryos [C1]


title: Single-cell RNA-seq day3 cell50


title: Single-cell RNA-seq day3 cell48


title: G33_ctr


title: 2-cell embryo, 5um-1


title: 2-cell embryo, 0um-3


title: Single-cell RNA-seq day3 cell54


title: Single-cell RNA-seq day3 cell49


title: G157_ctr


title: G816_ctr


title: Single-cell RNA-seq day3 cell44


title: Single-cell RNA-seq day3 cell47


title: Huh7_palbo_AR-V825

city: Shanghai

last: Wang

address: Building 5, No.1630 Dongfang Road

institute: Shanghai Cancer Institute

data_processing:
Illumina Casava 1.8.2 software used for basecalling. The quality score encoding is in +Phred 33.
Raw sequencing reads were mapped to the human genome (GRCh38) using STAR (version 2.4.2g1).
Gene-level read counts were generated using featureCounts from the subRead package with default settings.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

extract_protocol:
Total RNA was extracted and purified using the Trizol reagent (Invitrogen)
The library was prepared using TruSeq RNA sample prep kit according to the manufacturer’s protocol (Illumina).

treatment_protocol: We first treated senescent  liver cancer cells with vehicle or ARV-825 for 48 hours. Then, RNA sequencing was conducted to quantify the mRNA expression level of vehicle-treated or ARV-825-treated liver cancer cells. ARV-825-induced expression changes were obtained based on the resultant data.

value: liver cancer cell line


title: G146_ctr


title: Single-cell RNA-seq day3 cell42


title: Single-cell RNA-seq day3 cell46


title: Single-cell RNA-seq day3 cell43


title: Single-cell RNA-seq day3 cell40


title: 2-cell embryo, CTR, input

data_processing:
Trim galore software was used to remove sequencing adapters and low-quality bases, trimmed sequencing data were then mapped to the mouse mm10 genome with Bowtie2 using the “-X 2000” options.
low-quality reads (MAPQ < 30) and PCR duplicates were removed by Samtools software.
RPKM-normalized bigwig files were generated by bamCoverage subcommand in deepTools.
Assembly: mm10
Supplementary files format and content: bigWig (except for Input sample)

extract_protocol:
We performed ultra-low-input native chromatin immunoprecipitation sequencing (ULI-NChIP-seq) using early embryos according to a previous method [39]. Briefly, 150 2-cell embryos were washed three times with wash solution (PBS containing 0.5% BSA), and then the zona pellucida was removed with Tyrode’s solution.  After embryos were dispersed into a single blastomere through pipetting, blastomeres were moved into the nuclear isolation buffer and the chromatin was digested by MNase for 7 min at 25°C. Next, samples were incubated with Dynabeads Protein G, which was pre-incubated with 0.5 μg of H3K27ac antibody (Abcam, ab4729) for 6 h at 4°C. After two washes with low salt wash buffer and high salt wash buffer, DNA was released in elution buffer for 2 h at 65°C, and then extracted using phenolchloroform-isoamyl alcohol (25:24:1).
DNA library was generated using KAPA Hyper Prep Kit (Roche), and sequenced by Illumina NovaSeq 6000 system.


title: 2-cell embryo, 0um-2


title: 2-cell embryo, H3K27ac, CTR, rep2

value: H3K27ac (ab4729, Abcam)


title: G44_ctr


title: Single-cell RNA-seq day3 cell39


title: Single-cell RNA-seq day3 cell37


title: Single-cell RNA-seq day3 cell41


title: 2-cell embryo, 0um-1


title: Single-cell RNA-seq day3 cell45


title: Huh7_ctrl_ARV-825

value: Liver


title: 2-cell embryo, 5um-2


title: Huh7_palbo_control


title: Single-cell RNA-seq day3 cell36


title: Huh7_ctrl_control

value: Control


title: 2-cell embryo, AS, input


title: Single-cell RNA-seq day3 cell38


title: 2-cell embryo, H3K27ac, CTR, rep1


title: Single-cell RNA-seq day3 cell34


title: Single-cell RNA-seq day3 cell35


title: PLC_palbo+KPT330_ARV-825

source_name: PLC


title: Single-cell RNA-seq day3 cell33


title: Single-cell RNA-seq day3 cell32


title: Single-cell RNA-seq day3 cell31


title: PLC_palbo+KPT330_control


title: 2-cell embryo, H3K27ac, AS, rep2


title: PLC_ctrl_ARV-825


title: HCT116 ARID1A knockout replicate 3

first: Changjie

last: Wu

address: 1838 Guangzhou Avenue North, 510515 Guangzhou, Guangdong, China

institute: Southern Medical University

description: Library name: Sample 6

data_processing:
cDNA library was sequenced on an Illumina Hi-Seq (Illumina, San Diego, CA). Quality confirmed RNA-seq reads from each library were aligned and mapped with TopHat 2.1.1 (Center for Computational Biology at Johns Hopkins University). Expression quantification was defined with FPKM (Fragments Per Kilobase of transcript per Million mapped reads) by Cufflinks 2.2.1 (Trapnell-Lab, Github) after mapping.
Assembly: GRCh38
Supplementary files format and content: Excel file includes normalized counts for each Sample

source_name: Colorectal cacner

growth_protocol: HCT116 cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from HCT116 ARID1A-Wild Type (WT) and ARID1A Knockout (KO) cells using the RNeasy Kit (Qiagen, Germany; Cat. No. 74136).
cDNA libraries were constructed using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA, USA; Cat. No. E7760

value: Colorectal cacner

value: Colorectal cancer cell line

value: ARID1A knockout


title: 2-cell embryo, H3K27ac, AS, rep1


title: Single-cell RNA-seq day3 cell30

value: Mouse embryonic fibroblasts reprgramming cells


title: snail ventricle rep2

city: Qingdao

first: Long

last: Zhao

address: 5 Yushan Rd

institute: Ocean University of China

description:
snail_v2
snail_DESeq2_diffgene.csv

data_processing:
Alignment of paired-end clean reads to the reference were built using Hisat2 (2.0.5).
The featureCounts (1.5.0) (Liao et al. 2014) was used to count the read numbers mapped to each gene
TPM of each gene was calculated by StringTie (1.3.3b)
Differential expression analysis of the atrium and ventricle in snails and scallops was performed using the DESeq2 (1.20.0)
Constructing the gene co-expression network using the WGCNA package
Assembly: Taxonomy ID: 2315439 & Taxonomy ID: 6573
Supplementary files format and content: tab-delimited text file include raw counts and log2FoldChange for each sample

organism: Lissachatina fulica

source_name: heart

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100  system (Agilent Technologies, CA, USA). (Refer to RNA quality inspection report for specific instruments)
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using  poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA.Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

value: heart

tag: tissue region

value: ventricle

value: WT


title: Single-cell RNA-seq day3 cell29

tag: cell type

value: OvSvK single-cell RNA-seq reprogramming day3


title: 97H_Combination

treatment_protocol: We treated liver cancer cells with vehicle, CDK4/6 inhibitor, XPO1 inhibitor and the combination. Then, RNA sequencing was conducted to quantify the mRNA expression level of vehicle-treated or CDK4/6 inhibitor, XPO1 inhibitor and the combination treated liver cancer cells. CDK4/6 inhibitor, XPO1 inhibitor and the combination induced expression changes were obtained based on the resultant data.

value: CDK4/6 inhibitor + XPO1 inhibitor


title: Single-cell RNA-seq day3 cell28


title: HCT116 ARID1A knockout replicate 1

description: Library name: Sample 4


title: 97H_KPT330

value: XPO1 inhibitor


title: HCT116 ARID1A wild-type replicate 2

description: Library name: Sample 2


title: HCT116 ARID1A wild-type replicate 1

description: Library name: Sample 1


title: HCT116 ARID1A knockout replicate 2

description: Library name: Sample 5


title: snail atrium rep2

description:
snail_a2
snail_DESeq2_diffgene.csv

value: atrium


title: 97H_CDK46

value: CDK4/6 inhibitor


title: HCT116 ARID1A wild-type replicate 3

description: Library name: Sample 3


title: Single-cell RNA-seq day3 cell26


title: snail ventricle rep1

description:
snail_v1
snail_DESeq2_diffgene.csv


title: PLC_ctrl_control