title: HNRNPF_IP

city: Guangzhou，China

first: Jide

last: Wang

state: Guangdong ，China

address: 11838 Guangzhou Avenue North

department: Department of Digestive Medicine

institute: Nanfang Hospital, Southern Medical University

description: Library name: HNRNPF_IP

data_processing:
Raw sequencing data (RawData) underwent initial quality control assessing error rates, data volume, read length, and base quality metrics (Q20/Q30).
Adapter sequences and low-quality reads were removed to obtain clean data (CleanData). CleanData was further evaluated for quality metrics including error rates, data volume, read length, and base quality. Subsequent bioinformatic analyses were performed on CleanData. Known rRNA sequences were filtered using the RNAcentral database.
Clean reads were aligned to the reference genome using HISAT2.
Binding peaks across the transcriptome were identified using the Piranha software package.
Peak annotation was conducted with HOMER. Motif discovery was performed using STREME and MEME algorithms.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: AGS

growth_protocol: AGS cells were cultured in medium supplemented with 10% fetal bovine serum (FBS) at 37°C in a humidified atmosphere with 5% CO₂.

extract_protocol:
RNA immunoprecipitation (RIP) was performed using the Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit (Merck Millipore, USA) according to the manufacturer’s protocol. Briefly, cell lysates were incubated with magnetic beads conjugated with HNRNPF antibody. RNA was extracted from the immunoprecipitates using phenol:chloroform extraction, followed by ethanol precipitation with 75% ethanol. The purified RNA was resuspended in RNase-free water.
IP-enriched RNA was fragmented, followed by first-strand and second-strand cDNA synthesis and purification. The cDNA underwent end repair and 3' adenylation. Adaptors were then ligated, and fragments were size-selected and purified. PCR amplification and purification completed the library construction. Library quality was assessed using the Agilent 2200 TapeStation. Sequencing was performed on the Illumina platform with paired-end 150 bp reads.

value: AGS

value: Human gastric adenocarcinoma cell

tag: rip antibody

value: HNRNPF(Santa Cruz, #32309)


title: WT_rep6

status: Public on Apr 22 2026

type: SRA

city: East Lansing

first: Yu

last: Zhang

state: MI

address: 567 Wilson Rd, Biomedical and Physical Sciences Building, Rm 5176

department: Microbiology, Genetics and Immunology

country: USA

institute: Michigan State University

description: Library name: Sample 12

library_source: genomic

data_processing:
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively. Reads were mapped to the indicated reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used. We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality. To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, remove bait sequences shorter than 50nt and keep only 1 juction for duplicate junctions with the same bait and prey coordinates and the same bait-prey junction sequence.
Assembly: mm9
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library).

molecule: genomic DNA

organism: Mus musculus

source_name: v-Abl transformed pro-B cell line

growth_protocol: v-Abl pro-B lines were maintained in RPIM1640 medium supplemented with 10% FBS, 50 uM 2-Mercaptoethanol, 100 U/ml Penicillin-Streptomycin and 2 mM L-Glutamine.

extract_protocol:
DNA was lysed overnight at 56 degree in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, precipitated by isopropanol and dissolved in buffer containing 10mM Tris-HCl pH7.5, 0.1mM EDTA
Genomic DNA was extracted from G1 arrested cells. 2 to 4 ug of DNA were sonicated via Diagenode bioruptor (20 sec on, 1 min off, 2 cycles with low energy input) and subjected to linear amplification with a biotinylated primer (PCR with Phusion enzyme: 98o 2min, 1cycle; 95o 30sec, 58o 30sec, 72o 90sec, 80 cycles; 72o 2min, 1 cycle). Single-stranded PCR products were purified via Dynabeads MyOne streptavidin C1 beads and ligated to bridge adaptor (25o 1 hour, 22 o 3 hours, 16 o overnight). Adaptor-ligated Products were amplified via nested PCR with indexed locus-specific primers and adaptor primer (PCR with Phusion enzyme: 95o 5min, 1cycle; 95o 30sec, 60o 30sec, 72o 60sec, 15 cycles; 72o 6 min, 1 cycle). The PCR products were further tagged with P5-I5 and P7-I7 sequences (95o 5min, 1cycle; 95o 30sec, 60o 30sec, 72o 60sec, 12 cycles; 72o 6 min, 1 cycle), size-selected via gel extraction (500-1000 bp) and loaded to Mi-Seq machine (Illumina) with paired-end 300 bp sequencing.

treatment_protocol: RAG complementation and 3 uM STI571 induced G1 arrest for 4 days. For Wapl depeletion, 1 uM 5-Ph-IAA was added 4 hours prior to G1 arrest. For induction of dCas9-blockade, 2 ug/ml doxycycline was added 4 hours prior to G1 arrest.

tag: cell line

value: v-Abl transformed pro-B cell line

tag: genotype

value: Emu-Bcl2+, RAG1(D708A)

tag: treatment

value: RAG1 retrovirally complemented, 3 uM STI-571 treated for 4 days


title: NK1

city: Fukuoka

first: Takanori

last: Shinjo

state: fukuoka

address: Maidashi 3-1-1

department: Section of Periodontology

country: Japan

institute: Kyushu University

description: Library name: Sample 7

library_source: transcriptomic

data_processing:
MGI DNBseq-G400 FAST was used to perform the amplicons deep sequencing following the standard operation protocol. The sequence format was 150bp pair read for all samples.
All sequencing reads were trimmed low-quality bases and adapters with Trimmomatic (v.0.38) .
Raw counts for each gene were estimated in each sample using RSEM version 1.3.0 and Bowtie 2. Calculation of the log fold-change (log FC) and p-value were performed using edgeR.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file. normalized CPM count matrix with GeneSymbol index.

molecule: total RNA

source_name: Epididymal adipose tissue

extract_protocol:
The total RNA was isolated from eWAT using TRIzol Reagent (nitrogen) and purified using PureLink Mini Prep kit (Thermo Scientific) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using MGIEasy rRNA Depletion Kit and MGIEasy RNA Directional Library Prep Set  according protocols

tag: tissue

value: Epididymal adipose tissue

tag: strain

value: ND feeding for 10 weeks


title: NWL2

description: Library name: Sample 5

value: WT

value: ND feeding for 10 weeks, experimental peridontitis for 2weeks


title: HNRNPF_Input

country: China

description: Library name: HNRNPF_Input

organism: Homo sapiens

tag: cell type


title: Sham-operated mouse brain, replicate 3

city: zhanjiang

first: tangming

last: guan

address: No. 57, South Renmin Avenue, Xiashan District

institute: Affiliated Hospital of Guangdong Medical University

description:
Library name: S3
Ischemic hemisphere from Sham-operated mouse, replicate 3

data_processing:
Paired-end 150 bp sequencing was performed on an Illumina platform at Ribobio.
Raw reads were filtered to remove adapters and low-quality reads. Clean reads were aligned to the mouse reference genome.
Gene expression levels were quantified using featureCounts.
Differentially expressed genes (DEGs) were identified using DESeq2 with the thresholds:
Assembly: Mus musculus GRCm39 (mm10)
Supplementary files format and content: The processed data file (gene_count_matrix.txt) contains raw read counts for all genes across 12 samples.

source_name: Brain

growth_protocol: Mice were housed under standard conditions with a 12-hour light/dark cycle, constant temperature (22±1℃), and ad libitum access to food and water.

extract_protocol:
Total RNA was isolated from ischemic hemispheres using Magzol Reagent (Magen) following the manufacturer’s instructions. RNA quantity and quality were assessed using K5500 spectrophotometer (Kaiao) and Agilent 2200 TapeStation.
Poly(A)+ mRNA was enriched using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB), fragmented to ~200 bp, and processed with NEBNext® Ultra™ RNA Library Prep Kit for Illumina. Libraries were validated using Agilent 2200 TapeStation and Qubit (Thermo Fisher).

treatment_protocol: Cerebral ischemia-reperfusion injury was induced by transient middle cerebral artery occlusion (tMCAO). Mice in the LJP group were treated with Laminaria japonica polysaccharide (LJP); vehicle group received saline; sham group underwent sham surgery.

value: Brain

value: Sham surgery

tag: batch


title: NWL3

description: Library name: Sample 6


title: Sham-operated mouse brain, replicate 1

description:
Library name: S1
Ischemic hemisphere from Sham-operated mouse, replicate 1


title: WT_rep4

description: Library name: Sample 10


title: WT_rep5

description: Library name: Sample 11


title: Sham-operated mouse brain, replicate 2

description:
Library name: S2
Ischemic hemisphere from Sham-operated mouse, replicate 2


title: Sham-operated mouse brain, replicate 4

description:
Library name: S4
Ischemic hemisphere from Sham-operated mouse, replicate 4


title: NW3

description: Library name: Sample 3


title: NWL1

description: Library name: Sample 4


title: Treatment, Male, Sample 1011

city: Boulder

first: Pei-San

last: Tsai

state: CO

address: 354 UCB

department: Integrative Physiology

institute: University of Colorado Boulder

description:
Library name: TM1011
Column name in rsub_id.coverage.csv: TM1011.bam

data_processing:
DESeq2 (v1.36.0) for R.
Results of sequencing were received in the form of .fq files representing raw reads. Raw reads had adapters removed (Cutadapt v2.1).
Trimmed reads were then aligned to the NCBI GRCh38 human genome using Hisat2 (v2.1.0) with an average alignment rate of ~76.5%.
Counts were generated from aligned reads using Rsubread (v2.0.1) for R and annotated with the NCBI RefSeq annotation downloaded from (https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/hg38.refGene.gtf.gz) on February 23, 2023.
Sample outlier detection and removal was performed on raw read counts with robust principal component analysis (PCA) using RRcov (v1.7-3) for R; based on this analysis, two samples within the WBH group were identified as outliers and were removed from further analysis.
. DESeq2 (v1.26.0) (Love et al., 2014) for R was used to generate normalized counts, perform differentially expressed gene (DEG) analysis, and generate a ranked-order list for use in Gene Set Enrichment Analysis (GSEA) (v4.3.2). As part of regular due diligence, variables were tested as confounders by PCA. Biological sex was identified as a potential confounder and was controlled for by including it in the final DESeq2 object.
Assembly: NCBI GRCh38
Supplementary files format and content: .csv file includes raw, annotated gene counts for each sample

source_name: Blood

extract_protocol:
Blood was collected and stabilized in Tempus™ Blood RNA Tubes (Cat. No. 4329228, Thermo Fisher Scientific, Waltham, MA, USA) thirty minutes post intervention, then stored at –80 °C. Whole blood samples were then shipped and received at the University of Colorado Boulder on dry ice, then stored at –80 °C before subjecting the samples to whole RNA isolation using a MagMAX™ RNA Isolation Kit (Cat. No. 4452292, Thermo Fisher Scientific) according to the manufacturer’s instructions. In-house quality control was assessed by 260 nm/280 nm absorbance ratio using a NanoDrop™ 2000 spectrophotometer (Thermo Fisher Scientific).
Samples were depleted for eukaryotic and bacteria rRNA, then were constructed into directional RNA libraries by Novogene in Tianjin, China.

treatment_protocol: Participants in a randomized controlled trial of WBH for the treatment of MDD were subjected to a blood draw 30 minutes post-intervention by a WBH or sham WBH condition.

value: Blood

value: Whole-blood

tag: Sex

value: male

value: WBH


title: Treatment, Male, Sample 1009

description:
Library name: TM1009
Column name in rsub_id.coverage.csv: TM1009.bam


title: Treatment, Female, Sample 0023

description:
Library name: TF0023
Column name in rsub_id.coverage.csv: TF0023.bam

value: female


title: NW2

description: Library name: Sample 2


title: Treatment, Male, Sample 1006

description:
Library name: TM1006
Column name in rsub_id.coverage.csv: TM1006.bam


title: Stag2KO_rep3

description: Library name: Sample 9

value: Stag2-/-, Emu-Bcl2+, RAG1(D708A)


title: NW1

description: Library name: Sample 1


title: Stag2KO_rep2

description: Library name: Sample 8


title: Treatment, Female, Sample 0021

description:
Library name: TF0021
Column name in rsub_id.coverage.csv: TF0021.bam


title: Mice colonic tissues,irradiated,CF-2 administered,84 hours,bio rep 2

city: 重庆

first: Qianyi

last: Yao

address: 重庆市渝中区医学院路1号

institute: 重庆医科大学

description: Library name: CF2-2

data_processing:
Raw reads were processed to remove adapters and filter low-quality reads (Q≤25 >60% of read length or N>5%).
Clean reads were aligned to reference genome using HISAT2.
Read counts per gene were obtained with FeatureCounts, and FPKM values were calculated.
Differential expression was performed with DESeq2 (|log2FC|>1, padj<0.05).
GO and KEGG enrichment were analyzed using clusterProfiler (padj<0.05).
Assembly: GRCm38 (mm10)
Supplementary files format and content: Count and FPKM

source_name: colon tissue

extract_protocol:
Total RNA was extracted from colon tissues using TRIzol® Reagent (Magen). RNA quality was assessed by A260/A280 ratio (Nanodrop ND-2000) and RIN (Agilent Bioanalyzer 4150).
Paired-end libraries were prepared using ABclonal mRNA-seq Lib Prep Kit. Briefly, mRNA was purified from 1 μg total RNA with oligo(dT) magnetic beads, fragmented, and reverse transcribed. Double-stranded cDNA was end-repaired, adapter-ligated, and PCR amplified. Library quality was assessed on an Agilent Bioanalyzer 4150.

treatment_protocol: Six-week-old male C57BL/6 mice were divided into three groups (n=3): control (con), irradiation (IR), and IR combined with CF-2 (IR+CF-2). IR and IR+CF-2 groups received 13 Gy total body irradiation. CF-2 (7.5 mg/kg) was administered intraperitoneally once before irradiation and at 24 h, 48 h, and 72 h post‑irradiation (four doses total). Colon tissues were collected at 84 h post‑irradiation

value: colon tissue

value: wild type


title: Stag2KO_rep1

description: Library name: Sample 7

value: v-Abl transformed pro-B cell line


title: Mice colonic tissues,irradiated,CF-2 administered,84 hours,bio rep 3

address: 重庆市渝中区医学院路1号

description: Library name: CF2-3


title: Treatment, Female, Sample 0015

description:
Library name: TF0015
Column name in rsub_id.coverage.csv: TF0015.bam


title: Mice colonic tissues,irradiated,CF-2 administered,84 hours,bio rep 1

address: 重庆市渝中区医学院路1号

description: Library name: CF2-1


title: Stag1KO_rep2

description: Library name: Sample 5

value: Stag1-/-, Emu-Bcl2+, RAG1(D708A)


title: Treatment, Female, Sample 0014

description:
Library name: TF0014
Column name in rsub_id.coverage.csv: TF0014.bam


title: Treatment, Female, Sample 0011

description:
Library name: TF0011
Column name in rsub_id.coverage.csv: TF0011.bam


title: Mice colonic tissues,irradiated,84 hours,bio rep 2

address: 重庆市渝中区医学院路1号

description: Library name: IR-2

value: IR


title: Stag1KO_rep1

description: Library name: Sample 4

value: RAG1 retrovirally complemented, 3 uM STI-571 treated for 4 days


title: LV_MI_R2

type: RNA

city: Durham

first: Walter

middle: J

last: Koch

state: NC

address: 487 CARL Building, 213 Research Drive

department: Surgery

institute: Duke University School of Medicine

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 mL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.  After RNA hybridization, tag-conjugating Alexa Fluor®546 dye was circulated through the microfluidic chip for dye staining.  Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression) (2). (2) Bolstad, B. M., Irizarry, R. A., Astrandand, M., Speed, T. P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinfo. 19, 185-193.

source_name: Left ventricle, MI

label_protocol: Microarray assay was performed using a service provider (LC Sciences).  Total RNA sample (2 µg) were 3’-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.  Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://mirbase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate.  The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry.  (1) (a) Gao, X., Gulari, E., and Zhou, X. (2004) In situ synthesis of oligonucleotide microarrays. Biopolymers 73, 579-596; (b) Zhu, Q., Hong, A., Sheng, N., Zhang, X., Jun, K.-Y., Srivannavit, O., Gulari, E., Gao, X., and Zhou, X. (2007) Microfluidic biochip for nucleic acid and protein analysis. in Methods Mol. Biol. Ed. Rampal, J. B. 382:287-312.

growth_protocol: All animal procedures were carried out according to National Institute of Health Guide for the Care and Use of Laboratory Animals and approved by the Animal Care and Use Committee of Temple University. Adult male C57BL/6J (9-12 weeks) mice purchased from Jackson Laboratory were utilized for all in vivo experiments.

extract_protocol: Total RNA extraction was performed using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: Mice were anesthetized with 2% isoflurane inhalation using an isoflurane vaporizer (Viking Medical) without intubation. While on a heated surface, a small incision was made on the left side of the chest to expose the fourth intercostal space. The heart was gently pushed out of the thoracic cavity, and a slipknot was tied around the left coronary artery (LCA) using a 6-0 silk suture. The heart was placed back with manual evacuation of the pneumothoraxes. The skin was closed by suture. Sham operated animals did not receive LCA occlusion. The mouse was then removed from isoflurane inhalation and closely monitored for recovery.

value: left ventricle


title: Mice colonic tissues,irradiated,84 hours,bio rep 3

address: 重庆市渝中区医学院路1号

description: Library name: IR-3


title: LV_MI_R3


title: Mice colonic tissues,irradiated,84 hours,bio rep 4

address: 重庆市渝中区医学院路1号

description: Library name: IR-4


title: Stag1KO_rep3

description: Library name: Sample 6


title: WT_rep3

description: Library name: Sample 3

value: Emu-Bcl2+, RAG1(D708A)


title: Mice colonic tissues,unirradiated,84 hours,bio rep 4

address: 重庆市渝中区医学院路1号

description: Library name: Con-4

value: PBS


title: Treatment, Female, Sample 0008

description:
Library name: TF0008
Column name in rsub_id.coverage.csv: TF0008.bam


title: LV_MI_R1


title: WT_rep2

description: Library name: Sample 2


title: Treatment, Female, Sample 0006

description:
Library name: TF0006
Column name in rsub_id.coverage.csv: TF0006.bam


title: Treatment, Female, Sample 0005

description:
Library name: TF0005
Column name in rsub_id.coverage.csv: TF0005.bam


title: WT_rep1

description: Library name: Sample 1


title: LV_Sham_R3

source_name: Left ventricle, sham


title: Mice colonic tissues,unirradiated,84 hours,bio rep 3

address: 重庆市渝中区医学院路1号

description: Library name: Con-3


title: LV_Sham_R1


title: Sham, Male, Sample 1008

description:
Library name: SM1008
Column name in rsub_id.coverage.csv: SM1008.bam

value: Sham WBH


title: Sham, Male, Sample 1010

description:
Library name: SM1010
Column name in rsub_id.coverage.csv: SM1010.bam


title: 3C_Stag2KO_CTCF-Nm_rep2

description: Library name: Sample 17

data_processing:
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively. Reads were mapped to the indicated reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used. We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality. To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, remove bait sequences shorter than 50nt and keep only 1 juction for duplicate junctions with the same bait and prey coordinates. Additionally, we filtered reads aligned to telomeric and satellite repeat regions to avoid potential PCR artifacts. We also removed bait region reads to minimize the impact of self-ligation on quantitative analysis.
Assembly: mm9
Supplementary files format and content: bedGraph including peak information for samples.

extract_protocol:
10 million cells were cross-linked with 2% formaldehyde at room temperature for 10 minutes, quenched by glycine (final 0.125M), and then lysed with cold cell lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100, one tablet of protease inhibitor in 50 ml) on ice for 10 min. Nuclei were subjected to 0.3% SDS treatment (37 o, 1 hour) and 1.8% Triton X-100 treatment (37 o, 1 hour) successively, followed by overnight NalIII (700 units) digestion at 37 o .  DpnII was inactivated at 65 o for 20 min and samples were subjected to ligation under dilute condition with T4 DNA ligase (100 units). Ligated chromatin was de-crosslinked with Proteinase K (56 o, ON) and treated with RNaseA (37 o, 1 hour). DNA was purified via phenol/chloroform extraction and resuspended in 200ul 1XTE buffer.
10 ug of DNA were sonicated via Diagenode bioruptor (20 sec on, 1 min off, 2 cycles with low energy input) and subjected to linear amplification with a biotinylated primer (PCR with Phusion enzyme: 98o 2min, 1cycle; 95o 30sec, 58o 30sec, 72o 90sec, 80 cycles; 72o 2min, 1 cycle). Single-stranded PCR products were purified via Dynabeads MyOne streptavidin C1 beads and ligated to bridge adaptor (25o 1 hour, 22 o 3 hours, 16 o overnight). Adaptor-ligated Products were amplified via nested PCR with indexed locus-specific primers and adaptor primer (PCR with Phusion enzyme: 95o 5min, 1cycle; 95o 30sec, 60o 30sec, 72o 60sec, 15 cycles; 72o 6 min, 1 cycle). The PCR products were further tagged with P5-I5 and P7-I7 sequences (95o 5min, 1cycle; 95o 30sec, 60o 30sec, 72o 60sec, 12 cycles; 72o 6 min, 1 cycle), size-selected via gel extraction (500-1000 bp) and loaded to Mi-Seq machine (Illumina) with paired-end 300 bp sequencing.

treatment_protocol: 3 uM STI571 induced G1 arrest for 4 days. For Wapl depeletion, 1 uM 5-Ph-IAA was added 4 hours prior to G1 arrest. For induction of dCas9-blockade, 2 ug/ml doxycycline was added 4 hours prior to G1 arrest.

value: 3 uM STI-571 treated for 4 days


title: Blood, 5 DPI, replicate G

city: Galveston

first: Jacquelyn

last: Turcinovic

state: TX

address: Galveston National Laboratory, 301 University Blvd.

department: Microbiology and Immunology

institute: University of Texas Medical Branch

hyb_protocol: Overnight hybridization according to standard NanoString protocol

scan_protocol: Scanned and quantified via nCounter SPRINT profiler according to standard protocol

data_processing: Raw RCC files were background-thresholded using the NSolver v4.0 default parameters to generate the sample matrix. Downstream normalization and differential expression analyses were performed via limma.

organism: Chlorocebus sabaeus

source_name: African green monkey, whole blood, 5 DPI

extract_protocol: Total RNA extracted from AVL spiked with carrier RNA via the QIAgen Viral RNA Kit

tag: dpi


title: 3C_Stag2KO_CTCF-Nm_rep1

description: Library name: Sample 16


title: LV_Sham_R2


title: HIL6_5

city: Cologne

first: Dietmar

last: Fischer

address: Paul-Schallück-Straße 8

department: Pharmacology

country: Germany

institute: University Hospital of Cologne

description:
Library name: HIL6_5
Column name in FPKMs.xlsx: HIL6_5

data_processing:
Processed using kallisto, tximport, and DESeq2 in R with batch-corrected group model.
Assembly: mm10
Supplementary files format and content: xlsx file including FPKM values for each sample

molecule: polyA RNA

source_name: medullary brainstem

extract_protocol:
Tissue punches containing the raphe nuclei were obtained from mice that received intracortical injections of AAV2-HIL6 or AAV2-GFP and placed in RNAlater™ Stabilization Solution (Invitrogen). Tissue was lysed and homogenized using a 16-gauge needle attached to a sterile syringe. RNA was isolated using the Qiagen RNeasy Kit
Illumina Stranded mRNA Prep

value: medullary brainstem

value: wt


title: Blood, 5 DPI, replicate F


title: 3C_Stag2KO_rep5

description: Library name: Sample 15


title: HIL6_3

description:
Library name: HIL6_3
Column name in FPKMs.xlsx: HIL6_3


title: Sham, Male, Sample 1007

description:
Library name: SM1007
Column name in rsub_id.coverage.csv: SM1007.bam

value: Blood

value: Whole-blood

value: male


title: Sham, Male, Sample 1004

description:
Library name: SM1004
Column name in rsub_id.coverage.csv: SM1004.bam


title: Sham, Male, Sample 1005

description:
Library name: SM1005
Column name in rsub_id.coverage.csv: SM1005.bam


title: 3C_Stag2KO_rep4

description: Library name: Sample 14

value: Stag2-/-, Emu-Bcl2+, RAG1(D708A)


title: Mice colonic tissues,unirradiated,84 hours,bio rep 2

address: 重庆市渝中区医学院路1号

description: Library name: Con-2

value: colon tissue


title: Blood, 5 DPI, replicate E


title: 3C_CTCF-Nm_rep2

description: Library name: Sample 13


title: Blood, 5 DPI, replicate D


title: HIL6_2

description:
Library name: HIL6_2
Column name in FPKMs.xlsx: HIL6_2


title: Sham, Female, Sample 0022

description:
Library name: SF0022
Column name in rsub_id.coverage.csv: SF0022.bam

value: female


title: HIL6_4

description:
Library name: HIL6_4
Column name in FPKMs.xlsx: HIL6_4


title: HIL6_1

description:
Library name: HIL6_1
Column name in FPKMs.xlsx: HIL6_1


title: Blood, 5 DPI, replicate C


title: Blood, 5 DPI, replicate B


title: 3C_CTCF-Nm_rep1

description: Library name: Sample 12

value: v-Abl transformed pro-B cell line


title: GFP_4

description:
Library name: GFP_4
Column name in FPKMs.xlsx: GFP_4


title: Sham, Female, Sample 0018

description:
Library name: SF0018
Column name in rsub_id.coverage.csv: SF0018.bam


title: GFP_2

description:
Library name: GFP_2
Column name in FPKMs.xlsx: GFP_2


title: GFP_3

description:
Library name: GFP_3
Column name in FPKMs.xlsx: GFP_3


title: 3C_WT_rep5

description: Library name: Sample 11


title: 3C_WT_rep4

description: Library name: Sample 10


title: Sham, Female, Sample 0016

description:
Library name: SF0016
Column name in rsub_id.coverage.csv: SF0016.bam


title: Blood, 5 DPI, replicate A


title: Sham, Female, Sample 0012

description:
Library name: SF0012
Column name in rsub_id.coverage.csv: SF0012.bam


title: Blood, 4 DPI, replicate P

source_name: African green monkey, whole blood, 4 DPI


title: BMDM, iNOS KO, Stimulated, RepC

city: Madison

first: Jing

last: Fan

state: WI

address: 330 N. Orchard St.

institute: Morgridge Institute for Research

description:
Library name: BMDM_iNOSKO_M148C
BMDM_iNOSKO_M148C
BMDM_gene_count.txt

data_processing:
Quality control was commenced with base recognition using CASAVA, followed by error rate assessment and GC content analysis.
The data were then subjected to stringent filtration, removing adapter contamination, reads with over 10% uncertain nucleotides, and reads where low-quality bases exceeded 50% of the sequence.
Post-filtration, the data were aligned to the mm10 mouse genome using the STAR software.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: bone marrow-derived macrophage

growth_protocol: Murine bone marrow-derived macrophages were isolated from wildtype or iNOS KO C57BL/6J mice. Bone marrow cells were isolated and differentiated from 6–12-week-old males or females. WT or iNOS KO BMDMs and WT or Akr1a1 KO RAW cells were cultured in RPMI 1640 with 10% fetal bovine serum, 25mM HEPES, 2mM glutamine, 1% antibiotics (penicillin, streptomycin) at 37°C and 5% CO2. BMDM were cultured with 20 ng/mL M-CSF

extract_protocol:
For RNA collection, cells were washed twice with DPBS and then lysed with RNA STAT 60. Chloroform was used for phase separation. RNA was precipitated with isopropanol, washed with 75% ethanol, and solubilized in DEPC H2O.
mRNA library preparation was performed by Novogene using poly A enrichment

treatment_protocol: To stimulate BMDMs, cells were incubated with 50ng/mL LPS and 30ng/mL recombinant mouse IFNγ for 48 hours. To stimulated RAW264.7 cells, cells were incubated with 50ng/mL LPS and 10ng/mL recombinant mouse IFNγ for 48 hours. Stimuli then were removed, cells were washed with DPBS, and cell culture was continued in fresh media without stimuli for the remaining timecourse.

value: bone marrow-derived macrophage

value: murine macrophage

value: iNOS knockout


title: BMDM, iNOS KO, Stimulated, RepB

description:
Library name: BMDM_iNOSKO_M148B
BMDM_iNOSKO_M148B
BMDM_gene_count.txt


title: 3C_Stag2KO_rep2

description: Library name: Sample 8


title: Blood, 4 DPI, replicate O


title: HLF cells cultured under Mix-Embed condition, replicate 2

city: Hangzhou

first: Shuting

last: Xue

state: zhejiang

address: 866 Yuhangtang Road

institute: Zhejiang University

description: Library name: HLF_Embed_2

data_processing:
Raw reads were quality-checked using FastQC. Adapters and low-quality bases were trimmed using Trimmomatic. Reads were aligned to the Homo sapiens reference genome (GRCh38/hg38) using STAR (v2.7.9a). Gene-level quantification was performed using featureCounts. FPKM values were calculated based on gene length and total mapped reads.
Assembly: Reads were aligned to the human reference genome (GRCh38/hg38) using STAR (v2.7.9a).
Supplementary files format and content: csv files include include raw counts for each sample (gene_count_Huh7_HLF_2D_Inject_Embed.csv)
Supplementary files format and content: csv files include FPKM values for each Sample (gene_fpkm_Huh7_HLF_2D_Inject_Embed.csv)

source_name: HLF

growth_protocol: Huh7 and HLF cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics at 37°C in a humidified incubator with 5% CO₂. Cells were maintained under standard conditions for 2D culture or prepared for 3D cultures as described.

extract_protocol:
Total RNA was extracted using TRIzol RNA isolation Reagents (Invitrogen) following the manufacturer’s instructions.
Messenger RNA (mRNA) was purified from total RNA using poly-T oligo-attached magnetic beads. The purified mRNA was fragmented, and first-strand cDNA synthesis was performed using random hexamer primers. Subsequently, second-strand cDNA synthesis was conducted, followed by end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Final libraries were checked for concentration and quality using Bioanalyzer 2100 (Agilent Technologies, CA, USA). Libraries that passed quality control were pooled based on effective concentration and target data output, and sequencing was performed on the Illumina NovaSeq 6000 platform using paired-end 150 bp reads.

treatment_protocol: 3D cultures were established using Inject-Embed and Mix-Embed methods: Mix-Embed 3D culture: Matrigel (Cat# 354234, Corning) was thawed overnight at 4°C and gently aspirated, then mixed 1:1 with culture medium to achieve a final concentration of 4–6 mg/ml. The mixture was distributed into 96-well plates at 50 μl per well and incubated at 37°C for 15–30 min to facilitate gelation. A cell suspension was then prepared, containing Huh7 cells (20,000 cells per well) or HLF cells (10,000 cells per well), and mixed with an equal volume of undiluted Matrigel. This mixture (50 μl per well) was dispensed onto the pre-solidified gel, followed by a 30-min incubation at 37°C. After incubation, 100 μl of complete medium was added to each well and refreshed every other day. Inject-Embed 3D culture: 100 μl of 50% diluted Matrigel was added to each well of a 96-well plate and incubated at 37°C for 30 min. A cell suspension containing Huh7 cells (4,000 cells per well) or HLF cells (2,000 cells per well) was gently injected into the center of the gel using a 10 μl pipette tip positioned at the appropriate depth. The injection was performed slowly and steadily to ensure proper embedding. After a 30-min incubation at 37°C, 100 μl of complete medium was added to each well and refreshed every other day. 2D cultures were maintained under standard conditions and harvested after 2 days (approximately 90% confluency). 3D cultures were harvested after 6–8 days.

value: HLF

value: hepatocellular carcinoma cell line

value: wild-type

value: Mix-Embed Culture


title: GFP_1

description:
Library name: GFP_1
Column name in FPKMs.xlsx: GFP_1


title: 3C_Stag2KO_rep3

description: Library name: Sample 9

value: 3 uM STI-571 treated for 4 days


title: HLF cells cultured under Mix-Embed condition, replicate 1

description: Library name: HLF_Embed_1


title: Huh7 cells cultured under Mix-Embed condition, replicate 2

description: Library name: Huh7_Embed_2


title: 3C_Stag2KO_rep1

description: Library name: Sample 7


title: Blood, 4 DPI, replicate M


title: Blood, 4 DPI, replicate N


title: 3C_Stag1KO_rep3

description: Library name: Sample 6

value: Stag1-/-, Emu-Bcl2+, RAG1(D708A)


title: 3C_Stag1KO_rep2

description: Library name: Sample 5


title: BMDM, iNOS KO, Stimulated, RepA

description:
Library name: BMDM_iNOSKO_M148A
BMDM_iNOSKO_M148A
BMDM_gene_count.txt


title: Huh7 cells cultured under Mix-Embed condition, replicate 1

description: Library name: Huh7_Embed_1


title: Blood, 4 DPI, replicate L


title: BMDM, iNOS KO, Unstimulated, RepC

description:
Library name: BMDM_iNOSKO_M0C
BMDM_iNOSKO_M0C
BMDM_gene_count.txt

value: Unstimulated


title: HLF cells cultured under Inject-Embed condition, replicate 2

description: Library name: HLF_Inject_2

value: Inject-Embed Culture


title: HLF cells cultured under Inject-Embed condition, replicate 1

description: Library name: HLF_Inject_1


title: 3C_WT_rep3

description: Library name: Sample 3

value: Emu-Bcl2+, RAG1(D708A)


title: 3C_Stag1KO_rep1

description: Library name: Sample 4


title: BMDM, iNOS KO, Unstimulated, RepA

description:
Library name: BMDM_iNOSKO_M0A
BMDM_iNOSKO_M0A
BMDM_gene_count.txt


title: Huh7 cells cultured under Inject-Embed condition, replicate 2

description: Library name: Huh7_Inject_2


title: Blood, 4 DPI, replicate K


title: BMDM, iNOS KO, Unstimulated, RepB

description:
Library name: BMDM_iNOSKO_M0B
BMDM_iNOSKO_M0B
BMDM_gene_count.txt


title: Blood, 4 DPI, replicate J


title: BMDM, WT, Stimulated, RepC

description:
Library name: BMDM_WT_M148C
BMDM_WT_M148C
BMDM_gene_count.txt


title: Huh7 cells cultured under Inject-Embed condition, replicate 1

description: Library name: Huh7_Inject_1


title: BMDM, WT, Stimulated, RepB

description:
Library name: BMDM_WT_M148B
BMDM_WT_M148B
BMDM_gene_count.txt


title: HLF cells cultured under 2D condition, replicate 2

description: Library name: HLF_2D_2

value: 2D Culture


title: human, IPF, lung, rep3

city: Chengdu

first: Ruijie

last: Hou

address: Renmin South Road

institute: State Key Laboratory of Biotherapy

description: Library name: IPF_3

library_source: transcriptomic single cell

data_processing:
The cellranger pipeline (version 3.1.0, 10X Genomics) was used to process raw sequencing output.
Assembly: hg38
Supplementary files format and content: Cell Ranger software output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: lung

extract_protocol:
The homogenized lung tissues were suspended in DMEM medium (C11995500BT, GIBCO) containing 1 mg/mL type I collagenase (C8140，Solarbio), 1 mg/mL type IV collagenase (C8160，Solarbio), 1 mg/mL Dispase II (D6430，Solarbio), and 0.2 mg/mL DNAase (D8071, Solarbio) at 37°C for 30 min. The digested lung tissues were filtered through a 70 μm filter membrane (BS-70-XBS, biosharp), and the filtrate was centrifuged and treated with red blood cell lysis buffer (R1010, Solarbio) for 10 min, centrifuged again under the same conditions, the pellet was washed once with sterile PBS (C10010500BT, GIBCO), and centrifuged again under the same conditions. Cell pellet was resuspended again with MACS mixture (2 mM EDTA, 0.1% BSA, 1% penicillin/streptomycin/antimitotic in DPBS) to obtain lung single cell suspension.
Single-nucleus RNA sequencing (snRNA-seq) was performed using the 10X Chromium 3′ v3 kit (10X Genomics, Pleasanton, CA) according to the manufacturer's instructions.

value: lung


title: human, IPF, lung, rep2

description: Library name: IPF_2


title: Blood, 4 DPI, replicate H


title: Blood, 4 DPI, replicate I


title: BMDM, WT, Unstimulated, RepC

description:
Library name: BMDM_WT_M0C
BMDM_WT_M0C
BMDM_gene_count.txt


title: 3C_WT_rep2

description: Library name: Sample 2


title: Huh7 cells cultured under 2D condition, replicate 2

description: Library name: Huh7_2D_2


title: BMDM, WT, Unstimulated, RepB

description:
Library name: BMDM_WT_M0B
BMDM_WT_M0B
BMDM_gene_count.txt


title: human, normal, lung, rep5

description: Library name: Normal_5


title: Blood, 4 DPI, replicate E


title: BMDM, WT, Stimulated, RepA

description:
Library name: BMDM_WT_M148A
BMDM_WT_M148A
BMDM_gene_count.txt


title: 3C_WT_rep1

description: Library name: Sample 1


title: Huh7 cells cultured under 2D condition, replicate 1

description: Library name: Huh7_2D_1


title: human, normal, lung, rep4

description: Library name: Normal_4


title: HLF cells cultured under 2D condition, replicate 1

description: Library name: HLF_2D_1


title: Blood, 4 DPI, replicate C


title: Blood, 4 DPI, replicate F


title: BMDM, WT, Unstimulated, RepA

description:
Library name: BMDM_WT_M0A
BMDM_WT_M0A
BMDM_gene_count.txt


title: Blood, 4 DPI, replicate G


title: Blood, 4 DPI, replicate D


title: BJ/HRAS-ER RPA70-GFP, IP gammaH2AX, Rep 4 Day 2

city: Udine

first: Raffaella

last: Picco

address: P.le Kolbe 4

department: Department of Medicine

country: Italy

institute: University of Udine

description: Library name: L8_repB

data_processing:
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2 version 2.3.5.1 with default configuration
Duplicate reads were flagged using samtools but no duplicates were removed
peaks were called using MACS2 version 2.2.9.1
Assembly: GRCh38
Supplementary files format and content: Coverage tracks were generated using the bamCoverage (deepTools) tool, taking an alignment of reads as input (BAM file) and generating a coverage track (bigWig) as output, applying the following parameters: --outFileFormat bigwig --binSize 50 -p 6 --normalizeUsing RPKM

source_name: BJ-hTERT

growth_protocol: BJ/hTERT fibroblasts were grown in Earle’s salts Minimal Essential medium (MEM) (Euroclone), supplemented with Non-Essential Amino Acids (NEAA) (Euroclone). All culture media were enriched with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/mL penicillin (Euroclone) and 100 μg/mL streptomycin (Euroclone). Regular testing for Mycoplasma contamination was performed on all cell lines

extract_protocol:
Chromatin was extracted from BJ/hTERT, BJ/hTERT/HRASG12V-ER, BJ-hTERT/HRASG12V-ER/HDAC4-FLAG, BJ-hTERT/HRASG12V-ER/RPA70-GFP and BJ-hTERT/HRASG12V-ER/H2B-GFP cells and immunoprecipitated with 3 μg of BRCA1, 6 μg of IgG, and 3μg of RNA Pol II Ser5, 3μg RPA32 or phosphoRPA32, 2 μg  γH2AX antibodies. For each ChIP, approximately 3x106 BJ cells were used. Cells were treated as indicated and DNA-protein complexes were crosslinked with 1% formaldehyde (Sigma-Aldrich) for 15 minutes at room temperature. Following quenching with PBS/glycine (125 mM) and two PBS washes, the cells were harvested, centrifuged, and then lysed on ice for 10 minutes using Swelling buffer (20 mM Tris-HCl pH 8, 85 mM KCl, 0.5% NP-40) containing freshly added PIC and PMSF. The samples were centrifuged and the resulting pellets were resuspended in Nuclei lysis buffer (10 mM Tris-HCl pH 7.5, 1% NP-40, 0.5% Na deoxycholate, 0.1% SDS) and incubated on ice for 10 minutes. Following this, the samples were sonicated at 4°C using a Bioruptor Plus (Diagenode) with 30-second pulses for 30 minutes, yielding genomic DNA fragments with an average size of approximately 300 bp. After centrifugation, the supernatants were precleared with magnetic Dynabeads protein A or G (Thermo Fisher Scientific). 1/100 of the samples were taken as input and the remainder was immunoprecipitated overnight at 4°C on a rotating system with the previously mentioned antibodies in the presence of 8 µl of magnetic Dynabeads protein G (Thermo Fisher Scientific) in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 16.7 mM Tris-HCl pH 8, 167 mM NaCl) and Nuclei lysis buffer in a 1:1 ratio. Immunoprecipitated complexes were washed three times with Low Salt Immune Complex Wash Buffer (0.1% SDS, 1% Triton X-100, 20 mM Tris-HCl pH 8, 150 mM NaCl), twice with High Salt Immune Complex Wash Buffer (0.1% SDS, 1% Triton X-100, 20 mM Tris-HCl pH 8, 2 mM EDTA, 500 mM NaCl) and once with LiCl Immune Complex Wash Buffer (250 mM LiCl, 1% NP-40, 0.2% Na-deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8) at 4°C with rotation. A final wash with TE (10 mM Tris-HCl pH 8, 1 mM EDTA) was performed. 100 µl of TE/RNase A (0.2 mg/ml, Ambion) were added to immunocomplexes and inputs, and samples were incubated for 30 minutes at 37°C. Input and beads were resuspended in a 1:1 mixture of TES (50 mM Tris-HCl pH 8, 10 mM EDTA, 2% SDS) and Reverse Crosslinking buffer (250 mM Tris-HCl pH 7.5, 62.5 mM EDTA, 1.25 M NaCl) with 0.27 mg/ml Proteinase K (ITW Reagents). Crosslinking was reversed using the following protocol in a thermocycler: 5 hours at 37°C, 10 hours at 68°C and 1 hour at 10°C. Genomic DNA was purified using the ChIP DNA Clean & Concentrator kit (Zymo Research), eluted in 30 µl water and chromatin was quantified using a Qubit Fluorometer. For DRIP-seq (IP with S9.6), cells were treated as indicated, and DNA-protein complexes were crosslinked with 1% formaldehyde (Sigma-Aldrich) for 10 minutes at room temperature. After quenching with PBS/glycine (125 mM) for 5 minutes at room temperature and two washes in PBS, cells were collected, centrifuged and then lysed for 10 minutes on ice with SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH 8.0) supplemented with PIC and PMSF. Cells were sonicated at 4°C using Bioruptor Plus (Diagenode) with 30-second pulses for 30 minutes, resulting in an average fragment size of ~300 bp for genomic DNA. Samples were centrifuged and the supernatants were diluted with binding buffer solution (10 mM NaPO4, 140 mM NaCl, 0.05% Triton X-100) before preclearing with magnetic Dynabeads protein A or G (Thermo Fisher Scientific) for at least 1 hour at 4°C with rotation. Supernatants were collected using a magnetic bead system. 1/50 of the sample was taken as input, which was split equally for genomic DNA extraction and RNA extraction using Tri-Reagent (Sigma-Aldrich, Germany). The remaining samples were immunoprecipitated overnight at 4°C on a rotating wheel with 6 µg of S9.6 antibody, 6 µg of IgG, and 8 µl of magnetic Dynabeads protein G (Thermo Fisher Scientific). Immunoprecipitated complexes were washed three times with binding buffer and then inputs and beads were resuspended in 100 µl TES (50 mM Tris-HCl pH 8, 10 mM EDTA, 2% SDS) and Reverse Crosslinking salt mixture (250 mM Tris-HCl pH 7.5, 62.5 mM EDTA, 1.25 M NaCl, 0.27 mg/ml Proteinase K (ITW Reagents)). After incubation in a thermocycler (5 hours at 37°C, 10 hours at 68°C, 1 hour at 10°C), nucleic acids were purified with ChIP DNA Clean & Concentrator kit (Zymo Research), eluted in 30 µl water and quantified using a Qubit Fluorometer. dsRNA were removed prior to library preparation by treating samples with 10u RNAseIII (Ambion).
DNA SMART ChIP-Seq Kit (Takara) was used for library generation of samples subjected to Illumina sequencing. To generate ChIP-seq libraries with the DNA SMART ChIP-Seq Kit, a priming site was added to the 3’ end of the DNA template using the Terminal Deoxynucleotidyl Transferase. This was followed by annealing of a Poly(dA) Primer, which anneals to the T-tail. This primer was then used by the SMARTScribe RT to copy the DNA strand. Sequencing libraries were then generated by PCR-mediated addition of Illumina adapters. DNA nanoball (DNB) technology was applied for library preparation of samples subjected to BGI-seq 500 sequencing following manifacturer (Roche)

treatment_protocol: 4-OHT (Merck, Germany) was used to induce HRAS expression (HRAS G12V is Era fused) at 1µM; were indicated 4-OHT was used for 2 days (proliferative phase) or 8 days to reach senescence

value: BJ-hTERT

value: fibroblasts

value: diploid

value: 4-OHT 1mM


title: human, normal, lung, rep2

description: Library name: Normal_2


title: WT3

city: La Jolla

first: Dwayne

middle: G

last: Stupack

state: CA

address: 3855 Health Sciences

department: Obstetrics and Gynecology

institute: UC San Diego Moores Cancer Center

description: Library name: Sample 5

data_processing:
Clean reads (>95%) were aligned to the reference genome using HISAT2. Novogene data pipeline used ClusterProfiler software for enrichment analysis, including GO Enrichment, DO Enrichment, KEGG and Reactome database enrichment to analyze and visualize functional profiles of genomic coordinates, genes and gene clusters.
Novogene performed differential expression analysis of two conditions/groups by using the DESeq2-R software. Clustering and grouping analyses used transcripts with FPKM values > 1and an adjusted p value <0.05. Each dataset was subject to Gene Set Enrichment Analysis (GSEA)
Further differential expression analysis and visualization were performed using Python tools: Expression data were imported from spreadsheets using Pandas, and DEG were filtered based on log2 fold change (log2FC) and p-values. Thresholds were set at log2FC > 0.5 and p < 0.05. Volcano plots were generated using matplotlib, with selected genes of interest highlighted and annotated to enhance biological interpretation. AdjustText was used to improve label clarity where necessary. A heatmap comparing WT and KO samples was created using Matplotlib with Seaborn, with custom color gradient via Matplotlib.colors.
Assembly: mm10
Supplementary files format and content: csv

source_name: peritoneal lavage

growth_protocol: Tumor cells (KT13 FAK KO or KT13 KO rescued with FAK) are grown 48h and supernatant harvested and heat treated (56C x 30 minutes) to inactivate cytokine activity..

extract_protocol:
RNA was extracted using the PureLink RNA Purification Kit (Invitrogen, 12183018A) following the manufacturer’s protocol.
RNA library preparation and sequencing was performed by Novogene Inc. (Beijing, China). RNA library preparation was performed using Abclonal mRNA-seq Lib Prep Kit for Illumina (RK20302) and samples were paired-end 150-bp sequenced using NovaSeq X Plus Series (PE150) platform generating >50 million reads per sample.

treatment_protocol: Macrophage are harvested from the peritoneal cavity of C57bl/76 mice by peritoneal lavage and placed in tissue culture (RPMI, 10% FBS, 1% Pen Strep)  50% Cell supernatant.

value: peritoneal lavage

value: peritoneal macrophage

value: FAK WT Supernatant


title: Blood, 4 DPI, replicate A


title: BJ/HRAS-ER not induced H2B-GFP, IP RPA32, Rep 4 Day 2

description: Library name: L9_repB

value: Untreated


title: WT2

description: Library name: Sample 4


title: A498 cells, siBPGM vorinostat 5

city: Berlin

first: Robert

last: Labes

address: Charitéplatz 1

department: Institute of Translational Physiology

institute: Charité - Universitätsmedizin Berlin

description: Library name: C6

data_processing:
CLC Genomics Workbench v 21.0.4 with default settings
Reads are annotated with their UMI and are then trimmed for poly(A) and adapter sequences, minimum read length (15 nucleotides), read quality, and ambiguous nucleotides (maximum of 2).
They are then deduplicated using their UMI. Reads are grouped into UMI groups when they (1) start at the same position based on the end of the read to which the UMI is ligated (i.e., Read2 for paired data), (2) are from the same strand, and (3) have identical UMIs.
Groups that contain only one read (singletons) are merged into non-singleton groups if the singleton's UMI can be converted to a UMI of a non-singleton group by introducing an SNP (the biggest group is chosen).
Trimmed reads were then mapped to the Mouse genome GRCm38 v. 80 and annotated using the ENSEMBL GRCm38 v. 86 gene annotation.
Assembly: GRCm38 v. 80
Supplementary files format and content: xlsx files containing counts, TPM and RPKM values

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

extract_protocol:
QIAzol Lysis Reagent according to the manufacturer's protocol
QIAseq UPX 3’ Transcriptome Kit (QIAGEN) according to the manufacturers instruction

treatment_protocol: Gene knockdown was achieved by transfecting cells with target-specific small interfering RNAs (siRNAs). SMARTpool siRNAs (comprising four distinct siRNAs per target gene; ON-TARGETplus Mouse Nfat5 siRNA: #L-058868-01-0020; ON-TARGETplus Non-targeting Pool: #D-001810-10-20) were used at a final concentration of 25 nM. Transfections were performed using DharmaFECT 1 reagent according to the manufacturer’s protocol.

value: kidney cancer cell

value: BPGM knockdown

value: Vorinostat


title: A498 cells, siBPGM vorinostat 6

description: Library name: C18


title: KO3

description: Library name: Sample 3

value: FAK KO Tumor Supernatant


title: KO2

description: Library name: Sample 2


title: A498 cells, siBPGM vorinostat 4

description: Library name: C89


title: Blood, 3 DPI, replicate L

source_name: African green monkey, whole blood, 3 DPI


title: BJ/HRAS-ER, Input, Rep 4 Day 8

description: Library name: L5_repB

value: input


title: BJ/HRAS-ER H2B-GFP, IP gammaH2AX, Rep 4 Day 2

description: Library name: L7_repB


title: A498 cells, siBPGM vorinostat 3

description: Library name: C77


title: KO1

description: Library name: Sample 1


title: BJ/HRAS-ER, Input, Rep 4 Day 2

description: Library name: L4_repB


title: Blood, 4 DPI, replicate B


title: Blood, 3 DPI, replicate K


title: Blood, 3 DPI, replicate J


title: BJ/HRAS-ER not induced H2B-GFP, IP gammaH2AX, Rep 4 Day 2

description: Library name: L6_repB


title: BJ/HRAS-ER H2B-GFP, IP RNaseH1, Rep 4 Day 2

description: Library name: L2_repB


title: A498 cells, siBPGM vorinostat 2

description: Library name: C65


title: BJ/HRAS-ER RPA70-GFP, IP RNaseH1, Rep 4 Day 2

description: Library name: L3_repB


title: Hepa1-6 cells, treated with 37 μg/ml Tiamulin 2 days, sample2

city: Shanghai

first: mingshan

last: zhou

address: Xizu Road Street

institute: Shanghai Cancer Institute

description: Library name: Tiamulin2

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

growth_protocol: Cells were cultured in DMEM medium with the supplementation of 10% fetal bovine serum and 1% .penicillin-streptomycin., 5% CO2, 37 ℃

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: Lefamulin or Tiamulin were diluted with DMEM to 37 μg/ml, and then treated Hepa1-6 cells for 2 days. No  manipulation was performed in control group

value: Murine Hepatoma Cell Line

value: 37 μg/ml Tiamulin


title: A498 cells, siBPGM control 6

description: Library name: C41

value: control


title: Hepa1-6 cells, treated with 37 μg/ml Tiamulin 2 days, sample1

description: Library name: Tiamulin1


title: Hepa1-6 cells, treated with 37 μg/ml Tiamulin 2 days, sample3

description: Library name: Tiamulin3


title: A498 cells, siBPGM control 5

description: Library name: C29


title: Blood, 3 DPI, replicate H


title: Hepa1-6 cells, treated with 37 μg/ml Lefamulin 2 days, sample3

description: Library name: Lefamulin3

value: 37 μg/ml Lefamulin


title: A498 cells, siBPGM vorinostat 1

description: Library name: C53


title: BJ/HRAS-ER RPA70-GFP, IP RPA32, Rep 4 Day 2

description: Library name: L11_repB

value: BJ-hTERT


title: Blood, 3 DPI, replicate I


title: BJ/HRAS-ER not induced H2B-GFP, IP RNaseH1, Rep 4 Day 2

description: Library name: L1_repB

value: fibroblasts


title: Hepa1-6 cells, treated with 37 μg/ml Lefamulin 2 days, sample2

description: Library name: Lefamulin2


title: Hepa1-6 cells, treated with 37 μg/ml Lefamulin 2 days, sample1

description: Library name: Lefamulin1


title: A498 cells, siBPGM control 3

description: Library name: C5


title: Blood, 3 DPI, replicate F


title: BJ/HRAS-ER H2B-GFP, IP RPA32, Rep 4 Day 2

description: Library name: L10_repB

value: diploid


title: A498 cells, siBPGM control 4

description: Library name: C17


title: BJ/HRAS-ER, Input, Rep 2 Day 2

description:
Library name: B410P_repB
pulled input of Rep 4 Day 2


title: Blood, 3 DPI, replicate G


title: Blood, 3 DPI, replicate E


title: A498 cells, siBPGM control 2

description: Library name: C88


title: Hepa1-6 cells, control group, sample3

description: Library name: control3

value: no treatment


title: Blood, 3 DPI, replicate D


title: BJ/HRAS-ER not induced H2B-GFP, IP S9.6, Rep 2 Day 2

description: Library name: B401_repB


title: A498 cells, mock vorinostat 6

description: Library name: C64

value: WT


title: BJ/HRAS-ER H2B-GFP, IP S9.6, Rep 2 Day 2

description: Library name: B407_repB

value: 4-OHT 1mM


title: BJ/HRAS-ER RPA70-GFP, IP S9.6, Rep 2 Day 2

description: Library name: B404_repB


title: Hepa1-6 cells, control group, sample1

description: Library name: control1


title: NODctrl

city: Wuhan

first: feng

last: zhang

address: jiefang avenue no.1277

department: neurology

institute: wuhan union hospital

description: Library name: 240923A_NODctrl

data_processing:
The reads were aligned to the mm10 reference genome using sCelluFluMatrix (version 2.0.0) to generate unique molecular identifier (UMI) counts (named as feature-barcode matix) for each gene per cell. Then, Seurat (version 4.2.0) were used for clustering. All samples were assessed for doublet content using DoubletFinder version 2.0.3, and cells called as doublets were removed before further analysis. Meanwhile, cells with fewer than 200 genes, cells with mitochondrial gene context exceeding 25%, and genes expressed in less than 3 cells were filtered out. Data were normalized and scaled, and then principal component analysis (PCA) was calculated utilizing the top 2,000 variable genes. Clusters were identified using the standard k-nearest neighbor method based on 30 dimensions with a 0.6 resolution.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lumbar spinal cord

extract_protocol:
The tissue were washed twice with 1× PBS and minced into approximately 1 mm3 fragments with sharp scissors and digested with enzyme mixtures including collagenase and DNase I at 37℃. Then, the single cell suspensions were collected through a 40 μm strainer (MACS® SmartStrainer 40μm, Miltenyi Biotec, Germany), and centrifuged at 300 g for 5 min, the supernatant was completely removed and cells were resuspended with 1ml 1× PBS containing 0.04% BSA. Finally, the cell number and viability were assessed by an automatic cell counter.
The cells were loaded into microfluidic chip of Chip A Single Cell Kit v2.0 (MobiDrop, cat. no. S050100201) to generate droplets with MobiNova-100(MobiDrop, cat. no.A1A40001). Each cell/nuclus was involved into a droplet which contained a gel bead linked with up to millions oligos (cell unique barcode). After encapsulation, droplets suffer light cut by MobiNovaSP-100(MobiDrop, cat. no.A2A40001) while oligos diffuse into reaction mix. The mRNAs were captured by gel beads containing oligo(dT) in droplets. Following reverse transcription, cDNAs with barcodes were amplified, and a library was constructed using the High Throughput Single Cell 3’RNA-Seq Kit v2.0 (MobiDrop (Zhejiang) Co., Ltd., cat. no. S050200201) and the 3' Single Index Kit( MobiDrop (Zhejiang) Co., Ltd., cat. no. S050300201). The resulting libraries were sequenced on an Illumina NovaSeq 6000 System.

value: Lumbar spinal cord


title: A498 cells, mock vorinostat 4

description: Library name: C40


title: BJ/HRAS-ER not induced H2B-GFP, IP RPA32, Rep 3 Day 2

description: Library name: L9_repA

value: Untreated


title: Hepa1-6 cells, control group, sample2

description: Library name: control2


title: NODEAE

description: Library name: 240923A_NODEAE


title: A498 cells, siBPGM control 1

description: Library name: C76

value: kidney cancer cell


title: Blood, 3 DPI, replicate C


title: A498 cells, mock vorinostat 5

description: Library name: C52


title: Blood, 3 DPI, replicate A


title: Blood, baseline, replicate W

source_name: African green monkey, whole blood, 0 DPI


title: C57ctrl

description: Library name: 240923A_C57ctrl


title: BJ/HRAS-ER H2B-GFP, IP gammaH2AX, Rep 3 Day 2

description: Library name: L7_repA


title: A498 cells, mock vorinostat 3

description: Library name: C28


title: A498 cells, mock vorinostat 2

description: Library name: C16


title: C57EAE

description: Library name: 240923A_C57EAE


title: Blood, 3 DPI, replicate B


title: Blood, baseline, replicate V


title: Blood, baseline, replicate U


title: BJ/HRAS-ER RPA70-GFP, IP gammaH2AX, Rep 3 Day 2

description: Library name: L8_repA


title: A498 cells, mock vorinostat 1

description: Library name: C4


title: BJ/HRAS-ER not induced H2B-GFP, IP gammaH2AX, Rep 3 Day 2

description: Library name: L6_repA


title: BJ/HRAS-ER, Input, Rep 3+4 Day 8

description:
Library name: L5_repA
pulled input of Rep 3+4


title: IP_STAG1_Stag2KO_rep2

description: Library name: Sample6

data_processing:
Reads were aligned using bowtie 2.2.8 with --non-deterministic flag.
Samples were deduplicated using Picard, normalized and converted to bigWig files using bamCoverage with the --SPMR flag.
Assembly: mm9
Supplementary files format and content: bigWig including peak information for samples.

source_name: v-Abl transformed pro-B cell line

extract_protocol:
20 million cells were crosslinked in 37o prewarmed culture medium with 1% formaldehyde for 10 min at RT. Cells were then treated with cell lysis buffer (5mM PIPES pH 8, 85mM KCl, 0.5% NP-40) for 10 min on ice, followed by treatment with nuclei lysis buffer (50mM TrisCl pH 8.1, 10mM EDTA, 1% SDS) for 10 min at RT. Chromatin was subjected to sonication with Diagenode Bioruptor at 4o to achieve an average size of 200-300 bp (30 sec on, 30 sec off, 20 cycles with high energy input). Chromatin were then precleared with Dynabeads Protein A at 4o for 2 hours. 1/30 lysates were kept as input and the rest incubated with 2.5ug SMC3 antibody or CTCF antibody overnight at 4o. IP samples were then captured by Dynabeads Protein A at 4o for at least 2 hours, followed by bead washing and elution. IP and Input DNA were then de-crosslinked at 65o overnight and purified via Qiagen PCR purification columns.
Purified DNA was subjected to ChIP-Seq library preparation with the NEBNext Ultra II DNA Library Prep Kit for Illumina from New England Biolabs and sequenced via paired end 150-bp sequencing on a Illumina NovoSeq 6000 machine.

treatment_protocol: 3 uM STI571 induced G1 arrest for 4 days.

value: v-Abl transformed pro-B cell line

value: Stag2KO, Emu-Bcl2+, RAG1(D708A)

value: 3 uM STI-571 treated for 4 days


title: A498 cells, mock control 6

description: Library name: C87


title: Blood, baseline, replicate R


title: IP_STAG1_Stag2KO_rep3

description: Library name: Sample31


title: Blood, baseline, replicate S


title: BJ/HRAS-ER, Input, Rep 3 Day 2

description:
Library name: L4_repA
pulled input of Rep 3 Day 2

value: input


title: Blood, baseline, replicate T


title: A498 cells, mock control 5

description: Library name: C75


title: IP_STAG1_Stag1KO_rep2

description: Library name: Sample4

value: Stag1KO, Emu-Bcl2+, RAG1(D708A)


title: BJ/HRAS-ER RPA70-GFP, IP RNaseH1, Rep 3 Day 2

description: Library name: L3_repA


title: IP_STAG1_Stag2KO_rep1

description: Library name: Sample5


title: BJ/HRAS-ER H2B-GFP, IP RNaseH1, Rep 3 Day 2

description: Library name: L2_repA


title: A498 cells, mock control 4

description: Library name: C63


title: A498 cells, mock control 3

description: Library name: C51


title: Blood, baseline, replicate P


title: IP_STAG1_WT_rep2

description: Library name: Sample2

value: Emu-Bcl2+, RAG1(D708A)


title: IP_STAG1_Stag1KO_rep1

description: Library name: Sample3


title: BJ/HRAS-ER not induced H2B-GFP, IP RNaseH1, Rep 3 Day 2

description: Library name: L1_repA


title: A498 cells, mock control 1

description: Library name: C27

value: control


title: A498 cells, mock control 2

description: Library name: C39


title: Blood, baseline, replicate O


title: IP_STAG1_WT_rep1

description: Library name: Sample1


title: BJ/HRAS-ER RPA70-GFP, IP RPA32, Rep 3 Day 2

description: Library name: L11_repA


title: Blood, baseline, replicate Q


title: BJ/HRAS-ER H2B-GFP, IP RPA32, Rep 3 Day 2

description: Library name: L10_repA


title: EGCG 40μM + Resveratrol 15 μM, replicate6

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

description:
Library name: Combination6
paired-end

data_processing:
Raw reads were imported using bcl2fastq2 v2.17.1.14
Trimmed to remove adapter content and low-quality base calls, with reads trimmed to a length of less than 25 bases removed from further analysis using Trimmomatic v0.36.
Quality of reads was assessed before and after trimming using FastQC v0.11.5
Reads were aligned to the human reference genome GRCh38 using HISAT2 v2.0.4
Resulting bam files were sorted and indexed using SAMtools v 1.3.1.
Gene counts were computed using the bioconductor package GenomicAlignments version 1.16.0
DESeq2 version 1.20.0 was used to identify differentially expressed genes (DEG) with a False Discovery Rate (FDR) threshold of 0.1.
Assembly: GRCh38
Supplementary files format and content: raw_counts.csv contains RNA fragment counts per gene per sample
Supplementary files format and content: normalized_counts.csv contains read counts per gene per sample normalized according to DESeq2
Supplementary files format and content: fpkm.csv contains FPKM values per gene per sample, computed using DESeq2

growth_protocol: MDA686TU cells were maintained in DMEM/F12 supplemented with 10% FBS in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNAEasy Mini Kit (Qiagen)
Libraries were prepared from 1 μg of total RNA per sample using the TruSeq stranded mRNA kit (Illumina, Inc., San Diego, CA)

treatment_protocol: Treated with the compounds for 24 h

value: Head and neck cancer

tag: egcg

tag: resveratrol


title: BJ/HRAS-ER, Input, Rep 1 Day 2

description: Library name: B410P_repA

value: BJ-hTERT


title: Blood, baseline, replicate L


title: Blood, baseline, replicate M


title: BJ/HRAS-ER H2B-GFP, IP S9.6, Rep 1 Day 2

description: Library name: B407_repA

value: fibroblasts


title: Blood, baseline, replicate N


title: V-AM

city: Taipei city

first: Ting-Chieh

last: Huang

state: Taipei City (TPE)

address: 8F., No. 161, Sec. 6, Minquan E. Rd., Neihu Dist.

department: Graduate Institute of Microbiology and Immunology

country: Taiwan

institute: National Defense Medical University

description:
Library name: Sample3
Column name in raw_count_AM.txt: V_AM

data_processing:
Sequencing reads were trimmed for adaptor sequence and low quality sequence using fastp (v0.20.0) (bases with quality score Phred less than 30 were trimmed from both ends)
Assembly: Assembly: Mus_musculus.GRCm38.99
Supplementary files format and content: tab-delimited text file includes raw count for each sample

source_name: Lung

extract_protocol:
After WT mice were euthanized, BALF was collected by flushing the airways 10 times with 10 ml of sterile PBS (37 °C) containing 0.5% FBS (HyClone™, Cytiva) and 2 mM EDTA using a 1 ml syringe. Cells were pelleted, subjected to red blood lysis, and total RNA was extracted using REzol reagent (Protech) followed by purification with the Direct-zol RNA Microprep Kits (Zymo), according to the manufacturer's instructions.
The purified RNA was used for the preparation of the sequencing library by TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) following the manufacturer’s recommendations.

treatment_protocol: Intratracheal (i.t.) PBS (55 μl) or vancomycin (10 μg/55 μl PBS once daily, Sigma-Aldrich) treatment per day for 1 week to disturb lung commensal microflora. In the last of 4 consecutive days, mice were intranasal (i.n.) administered with K. pneumoniae-derived LPS (2 μg / 55 μl PBS once daily, Sigma-Aldrich) to induce acute lung inflammation.

value: Lung

value: Alveolar Macrophage

value: i.t. Van + i.n. LPS


title: EGCG 40μM + Resveratrol 15 μM, replicate4

description:
Library name: Combination4
paired-end


title: C1-AM

description:
Library name: Sample2
Column name in raw_count_AM.txt: C1_AM

value: WT

value: i.t. PBS + i.n. LPS


title: EGCG 40μM + Resveratrol 15 μM, replicate3

description:
Library name: Combination3
paired-end


title: Blood, baseline, replicate K


title: Blood, baseline, replicate J


title: AFFN1_iLS_Day14_3

city: Suita

first: Masaki

last: Nomura

state: Osaka

address: 2-2, Yamadaoka

department: Department of Cancer Pathology

institute: Graduate School of Medicine, The University of Osaka

description:
Library name: Smaple 18
0802_AFF1

data_processing:
The FASTQ-sequenced reads were mapped to the mm10 genome using STAR.
Raw gene counts were calculated by RSEM.
Batch corrected data counts by ComBat were normalized and differentially expressed genes were identified with Adjusted p value < 0.05 by DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

source_name: Bone marrow

extract_protocol:
FACS sorted cells were proceeded to RNA extraction using RNeasy columns (Qiagen).
RNA libraries were prepared using TruSeq Stranded mRNA Library Prep Kit.

value: Bone marrow

value: CD45.2+ bone marrow cells


title: V1-AM

description:
Library name: Sample4
Column name in raw_count_AM.txt: V1_AM


title: C-AM

description:
Library name: Sample1
Column name in raw_count_AM.txt: C_AM


title: EGCG 40μM + Resveratrol 15 μM, replicate5

description:
Library name: Combination5
paired-end


title: BJ/HRAS-ER not induced H2B-GFP, IP S9.6, Rep 1 Day 2

description: Library name: B401_repA

value: diploid

value: Untreated


title: THP1-shUCP2#3

first: Innocent

middle: Okohi

last: AGIDA

state: Shanghai

address: Building 7, 277 South Chongqing Road, Shanghai Jiao Tong University, School of Medicine. Shanghai, China.

department: Biochemistry and Molecular Cell Biology

description:
Library name: sample 3
THP1-sh3_L1

data_processing:
Data analysis  Quality Control:  In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.  Alignment:  Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1).  Expression analysis  In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.  Differential expression analysis  Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <= 0.05 to detect differential expressed ones.  GO and KEGG enrichment analysis GOSeq(v1.34.1) was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant padj less and equal than 0.05. And topGO was used to plot DAG. KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances (http://en.wikipedia.org/wiki/KEGG). We used scripts in house to enrich significant differential expression gene in KEGG pathways.  Novel transcripts prediction  After assembling a transcriptome from one or more samples, Cuffcompare, a tool of Cufflinks v2.2.1, compared assembly to known transcripts. Then, novel transcripts can be predicted via results of Cuffcompare.  Alternative splicing analysis  Asprofile v1.0 is a suite of programs for extracting, quantifying and comparing alternative splicing (AS) events from RNA-seq data. It took a GTF transcript file created by Cufflinks as its input.  SNV analysis  Samtools v0.1.19 with command mpileup and Bcftools v0.1.19 were used to do SNV calling.  Differential exon usage  By differential exon usage (DEU), we mean changes in the relative usage of exons caused by the experimental condition. The relative usage of an exon is defined as number of transcripts from the gene that contain this exonnumber of all transcripts from the gene The basic concept can be summarized as follows. For each exon (or part of an exon) and each sample, we count how many reads map to this exon and how many reads map to any of the other exons of the same gene. We consider the ratio of these two counts, and how it changes across conditions, to infer changes in the relative exon usage. In the case of an inner exon, a change in relative exon usage is typically due to a change in the rate with which this exon is spliced into transcripts (alternative splicing). Note, however, that DEU is a more general concept than alternative splicing, since it also includes changes in the usage of alternative transcript start sites and polyadenylation sites, which can cause differential usage of exons at the 5’ and 3’ boundary of transcripts. To analysis DEU, we used Bioconductor package DEXSeq (V 1.21.1).  Principal component analysis  This is another way to visualize sample-to-sample distances. In this ordination method, the data points (here, the samples) are projected onto the 2D plane such that they spread out in the two directions that explain most of the differences. The x-axis is the direction that separates the data points the most. The values of the samples in this direction are written PC1. The y-axis is a direction (it must be orthogonal to the first direction) that separates the data the second most. The values of the samples in this direction are written PC2. The percent of the total variance that is contained in the direction is printed in the axis label. Note that these percentages do not add to 100%, because there are more dimensions that contain the remaining variance (although each of these remaining dimensions will explain less than the two that we see). This analysis has been dealt with R language with FPKM value as the input.
Assembly: GRCh38.107
Supplementary files format and content: counts, FPKM values for each sample

growth_protocol: THP1 cells were cultured in RPM 1640I supplemented with 20% Fetal Bovine Serum (FBS) and 100g/mL penicillin/streptomycin.

extract_protocol:
THP1 cell suspension were washed twice with ice cold PBS and DNA was extracted using DNeasy Blood & Tissue Kit (#69504, Qiagen) per instruction manual DNA samples were end-repaired, A tailed, and adaptor ligated using TruSeq Nano DNA Sample Prep Kit (#FC-121-4002, Illumina)
Sequencing library was prepared by converting 10 ng DNA of each sample to phosphorylated blunt-end fragment. An ‘A’ base was added to the 3' end of the blunt phosphorylated DNA fragments, and Illumina's genomic adapters were ligated to the A tailed DNA fragments prior to subject to PCR amplification to enrich ligated fragments. The enriched product of ~200-1500 bp was size selected using AMPure XP beads. The library was denatured with 0.1M NaOH to generate single-stranded DNA molecules, and loaded onto channels of the flow cell at 8pM concentration, amplified in situ using Cluster Kit.

treatment_protocol: UCP2 was knocked down with the UCP2 shRNA with a vector control using the lenti virus systems. After 72hrs positive cells were selected and cutured with 20% FBS alongside 1% PS in 1640 RPMI medium. At a growth rate of 80 to 90% confluence the cells were harvested, washed and was prepared for RNA sequence following the manufactural protocol for RNA extraction

value: human AML cells

value: UCP2 knockdown


title: AFFN1_iLS_Day14_2

description:
Library name: Smaple 17
0730_AFF1


title: BJ/HRAS-ER RPA70-GFP, IP S9.6, Rep 1 Day 2

description: Library name: B404_repA

value: 4-OHT 1mM


title: Resveratrol 15μM, replicate6

description:
Library name: Resveratrol6
paired-end


title: EGCG 40μM + Resveratrol 15 μM, replicate2

description:
Library name: Combination2
paired-end


title: Blood, baseline, replicate G


title: Blood, baseline, replicate I


title: AFFN1_iLS_Day14_1

description:
Library name: Smaple 16
0716_AFF1


title: Blood, baseline, replicate H


title: EGCG 40μM + Resveratrol 15 μM, replicate1

description:
Library name: Combination1
paired-end


title: THP1-shUCP2#2

institute: Shanghai Jiao Tong University, School of Medicine

description:
Library name: sample 2
THP1-sh2_L1


title: Resveratrol 15μM, replicate5

description:
Library name: Resveratrol5
paired-end


title: THP1- NC

description:
Library name: sample 1
THP1-NC_L1


title: KG1-shUCP2#3

first: JIAO

last: MA

address: Huangpu District

institute: Shanghai Jiao Tong University School of Medicine

description: Library name: sample 3

data_processing:
Data analysis  Quality Control:  In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.  Alignment:  Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1).  Expression analysis  In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.  Differential expression analysis  Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <= 0.05 to detect differential expressed ones.  GO and KEGG enrichment analysis GOSeq(v1.34.1) was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant padj less and equal than 0.05. And topGO was used to plot DAG. KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances (http://en.wikipedia.org/wiki/KEGG). We used scripts in house to enrich significant differential expression gene in KEGG pathways.  Novel transcripts prediction  After assembling a transcriptome from one or more samples, Cuffcompare, a tool of Cufflinks v2.2.1, compared assembly to known transcripts. Then, novel transcripts can be predicted via results of Cuffcompare.  Alternative splicing analysis  Asprofile v1.0 is a suite of programs for extracting, quantifying and comparing alternative splicing (AS) events from RNA-seq data. It took a GTF transcript file created by Cufflinks as its input.  SNV analysis  Samtools v0.1.19 with command mpileup and Bcftools v0.1.19 were used to do SNV calling.  Differential exon usage  By differential exon usage (DEU), we mean changes in the relative usage of exons caused by the experimental condition. The relative usage of an exon is defined as number of transcripts from the gene that contain this exonnumber of all transcripts from the gene The basic concept can be summarized as follows. For each exon (or part of an exon) and each sample, we count how many reads map to this exon and how many reads map to any of the other exons of the same gene. We consider the ratio of these two counts, and how it changes across conditions, to infer changes in the relative exon usage. In the case of an inner exon, a change in relative exon usage is typically due to a change in the rate with which this exon is spliced into transcripts (alternative splicing). Note, however, that DEU is a more general concept than alternative splicing, since it also includes changes in the usage of alternative transcript start sites and polyadenylation sites, which can cause differential usage of exons at the 5’ and 3’ boundary of transcripts. To analysis DEU, we used Bioconductor package DEXSeq (V 1.21.1).  Principal component analysis  This is another way to visualize sample-to-sample distances. In this ordination method, the data points (here, the samples) are projected onto the 2D plane such that they spread out in the two directions that explain most of the differences. The x-axis is the direction that separates the data points the most. The values of the samples in this direction are written PC1. The y-axis is a direction (it must be orthogonal to the first direction) that separates the data the second most. The values of the samples in this direction are written PC2. The percent of the total variance that is contained in the direction is printed in the axis label. Note that these percentages do not add to 100%, because there are more dimensions that contain the remaining variance (although each of these remaining dimensions will explain less than the two that we see). This analysis has been dealt with R language with FPKM value as the input.
Assembly: GRCh38.107
Supplementary files format and content: csv files include FPKM values for each sample

growth_protocol: KG1 cells were cultured in RPM 1640I supplemented with 20% Fetal Bovine Serum (FBS) and 100g/mL penicillin/streptomycin.

extract_protocol:
KG1 cell suspension were washed twice with ice cold PBS and DNA was extracted using DNeasy Blood & Tissue Kit (#69504, Qiagen) per instruction manual DNA samples were end-repaired, A tailed, and adaptor ligated using TruSeq Nano DNA Sample Prep Kit (#FC-121-4002, Illumina)
Sequencing library was prepared by converting 10 ng DNA of each sample to phosphorylated blunt-end fragment. An ‘A’ base was added to the 3' end of the blunt phosphorylated DNA fragments, and Illumina's genomic adapters were ligated to the A tailed DNA fragments prior to subject to PCR amplification to enrich ligated fragments. The enriched product of ~200-1500 bp was size selected using AMPure XP beads. The library was denatured with 0.1M NaOH to generate single-stranded DNA molecules, and loaded onto channels of the flow cell at 8pM concentration, amplified in situ using Cluster Kit.


title: Resveratrol 15μM, replicate4

description:
Library name: Resveratrol4
paired-end


title: BN1_iLS_Day14_2

description:
Library name: Smaple 14
0730_BRD9


title: KG1-shUCP2#2

description: Library name: sample 2


title: Resveratrol 15μM, replicate3

description:
Library name: Resveratrol3
paired-end


title: BN1_iLS_Day14_3

description:
Library name: Smaple 15
0802_BRD9


title: KG1- NC

description: Library name: sample 1


title: Blood, baseline, replicate F


title: Blood, baseline, replicate E


title: control_iLS_Day14_3

description:
Library name: Smaple 12
0802_Cont


title: Blood, baseline, replicate C


title: Blood, baseline, replicate D


title: Resveratrol 15μM, replicate2

description:
Library name: Resveratrol2
paired-end


title: HK2725

city: Philadelphia

first: Jonathan

last: Levinsohn

state: PA

address: 3400 Civic Center Blvd, Smilow 12-188

institute: University of Pennsylvania

data_processing:
Demultiplexing, barcode processing and transcript quantificatin was performed with CellRanger (v7.2.0)
Assembly: hg38
Supplementary files format and content: tab separated values and matrix files

source_name: Fetal Kidney

extract_protocol:
Fresh human kidneys were collected in RPMI media and using a razor blade were cut into small pieces 2-4 mm in diameter. Tissue was furthered dissociated with gentleMACS C tube (Miltenyi, #130-110-201) using program Multi_B. Tissue was digested with Enzyme D, Enzyme R and Enzyme A in RPMI at 37C for 30 minutes. A second homogenizination with gentleMacs using the Multi_B program was then performed. The resultant solution was strained through a 70 um filter, and then centrifuged at 600g for 7 minutes. The cell pellet was incubated in RBC lysis buffer for 3 minutes on ice, followed by addition of 10 mL of PBS and centrifuged again for 5 minutes at 500g. Supernatent was removed and the pellet was resuspended in PBS. Cell number and cell viability was examined using the Countess AutoCounter (Invitrogen, C10227), and manual examination.
An estimated 20,000 cells, based on AutoCounter results, were loaded into the Chromium Controller (10X Genomics, PN-120223) in a Chromium Next GEM chip G (10X Genomics, Single Cell Kit PN-1000120). The cDNA and gene expression library were made using the Chromium Next GEM Single Cell 3′ GEM Kit v3.1 (10X Genomics, PN-1000121) and Single Index Kit T Set A (10X Genomics, PN-120262) according to the manufacturer’s protocol.

value: Fetal Kidney

tag: gestational age

tag: additional clinical_info


title: rat TS cells, control shRNA  treated, replicate 3

city: Ames

first: Geetu

last: Tuteja

state: IA

address: 2106 Molecular Biology Building

department: Genetics, Development and Cell Biology

institute: Iowa State University

data_processing:
Raw data obtained from the sequencing facility was converted to fastq format using bcl2fastq (v2.20.0.422) and data quality was inspected using FastQC (v0.11.9)
Read mapping was performed by using the STAR’s (v2.7.10b) alignReads subcommand and was optimized for short reads with the options --outFilterScoreMinOverLread 0.3 and --outFilterMatchNminOverLread 0.3
featureCounts from the subread package to generate a combined count file
The raw count files were imported into R (v4.2.2) and analyzed to obtain differentially expressed genes by using DESeq2 (v1.38.3)
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text files include raw counts values for each Sample (each column represent the condition and each row represents the gene)

organism: Rattus norvegicus

source_name: rat trophoblast stem cells

growth_protocol: Rat Triophoblast Stem cells  were grown and differentiated in the dish for 15 days

extract_protocol:
Total RNA was isolated using the Trizol reagent according to the manufacturer’s instructions (Thermo-Fisher)
Extracted RNA was used as template for cDNA isolation with the High Capacity cDNA Reverse Transcription kit (Applied Biosystems). cDNA libraries were prepared and sequenced using a NovaSeq 6000 by the KUMC Genomics Core

treatment_protocol: Rat Triophoblast Stem cells  were treated with control shRNA or PLAC1 shRNA before differentiation

value: rat trophoblast stem cells

value: Trophoblast

value: Control shRNA


title: control_iLS_Day14_2

description:
Library name: Smaple 11
0730_Cont


title: HK2722


title: HK2716


title: Blood, baseline, replicate A

first: Jacquelyn

last: Turcinovic

address: Galveston National Laboratory, 301 University Blvd.

institute: University of Texas Medical Branch

data_processing: Raw RCC files were background-thresholded using the NSolver v4.0 default parameters to generate the sample matrix. Downstream normalization and differential expression analyses were performed via limma.

extract_protocol: Total RNA extracted from AVL spiked with carrier RNA via the QIAgen Viral RNA Kit


title: EGCG 40μM, replicate6

description:
Library name: EGCG6
paired-end

value: Head and neck cancer


title: Resveratrol 15μM, replicate1

description:
Library name: Resveratrol1
paired-end


title: AFFN1_iLS_Day6_3

description:
Library name: Smaple 9
iLS_D6_AFFN1_3


title: control_iLS_Day14_1

description:
Library name: Smaple 10
0716_Cont


title: rat TS cells, control shRNA  treated, replicate 2


title: rat TS cells, control shRNA  treated, replicate 1


title: Blood, baseline, replicate B


title: HK2723


title: AFFN1_iLS_Day6_2

description:
Library name: Smaple 8
iLS_D6_AFFN1_2


title: EGCG 40μM, replicate5

description:
Library name: EGCG5
paired-end


title: HK2718


title: rat TS cells, PLAC1 shRNA treated, replicate 3

value: PLAC1 shRNA


title: EGCG 40μM, replicate3

description:
Library name: EGCG3
paired-end


title: EGCG 40μM, replicate4

description:
Library name: EGCG4
paired-end


title: rat TS cells, PLAC1 shRNA treated, replicate 2


title: SHSMU-DIPG-01-inputforK27M

first: Rui

last: Guo

address: 131 DongAn Road

institute: Institutes of Biomedical Sciences, Fudan University

data_processing:
ChIP-seq reads were trimmed using trim_galore
Trimmed ChIP-seq reads  were aligned to hg19.Duplicated reads were removed prior to further anlysis.
Peaks were called using MACS2
Assembly: hg19
Supplementary files format and content: bw(except for input sample)

source_name: Brain

growth_protocol: Neurobasal-A Medium (1X), 500ml;D-MEM/F-12 (1X), 1:1,500ml;HEPES Buffer Solution (1M),10ml;MEM Sodium Pyruvate Solution 100mM (100X), 10ml;MEM Non-Essential Amino Acids Solution 10mM (100X),10ml;GlutaMAX-I Supplement,10ml;Antibiotic-Antimycotic (100X), 10ml；B-27 Supplement Minus Vitamin A (50X),20ml;H-EGF,20μg;H-FGF-basic,20μg;H-PDGF-AA,10μg;H-PDGF-BB,10μg; 0.2%Heparin Solution,1ml.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature and stopped with 125 mM glycine. The cell pellets were lysed  in a lysis buffer containing 50 mM HEPES pH7.5, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.05% SDS, 1 mM PMSF, 1 mM DTT and protease inhibitor cocktail. The lysate was sonicated to achieve an average DNA fragment length of 300-500 bp (Qsconica).
ChIP-seq libraries were prepared using VAHTS Universal DNA Library Prep Kit for Illumina® V3 Kits (Vazyme.ND607).

value: Brain

value: DIPG

tag: chip antibody


title: rat TS cells, PLAC1 shRNA treated, replicate 1


title: BN1_iLS_Day6_3

description:
Library name: Smaple 6
iLS_D6_BN1_3


title: SHSMU-DIPG-01-inputforCBFA2T2


title: BN1_iLS_Day6_2

description:
Library name: Smaple 5
iLS_D6_BN1_2


title: gd 13.5 placental tissue from wild type rats, replicate 5

source_name: Placenta

treatment_protocol: Placentas were removed at gestational age 13.5, flash frozen on dry ice,

value: Placenta

value: Holtzman Sprague-Dawley

tag: developmental stage

value: gestation day 13.5

value: PLAC1 Wild type


title: SHSMU-DIPG-01-K27M-ChIP


title: No treatment Control, replicate6

description:
Library name: NT-6
paired-end


title: SHSMU-DIPG-01-CBFA2T2-ChIP

value: CBFA2T2 (Bethyl,A302-089A)


title: gd 13.5 placental tissue from Plac1 mutant rats, replicate 5

value: PLAC1 Null


title: No treatment Control, replicate5

description:
Library name: NT-5
paired-end


title: control_iLS_Day6_3

description:
Library name: Smaple 3
iLS_D6_Mock_3

value: Bone marrow

value: CD45.2+ bone marrow cells


title: AFFN1_iLS_Day6_1

description:
Library name: Smaple 7
iLS_D6_AFFN1_1


title: H9,SIRT1 KO, day 6 of differentiation, scRNAseq

city: Mexico City

first: Alejandro

middle: Alarcón

last: Del Carmen

state: Mexico City

address: Circuito Mario de la Cueva

department: Cell Biology

country: Mexico

institute: Instituto de Investigaciones Biomédicas

data_processing:
The demultiplexing, barcode identification, gene counting and aggegation were made using Cell Ranger version 6.1.2.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: H9 (WA09, WiCell Research Institute Inc.)

growth_protocol: hESCs from the H9 cell line (WA09, WiCell Research Institute Inc.) were cultured on a layer of Geltrex hESC-Qualified at 10% (S15696-01-50mL, Gibco) at 37 °C with 5% CO2. The maintenance culture medium used was mTeSR1 (StemCell Technologies, #05850) supplemented with mTeSR1 5X (StemCell Technologies #05851).

extract_protocol:
hESCs from the H9 cell line were detached using TrypLE Expres directly in the culture plate, the plates were then incubated for 5 minutes at 37°C. Subsequently, 1 ml of mTeSR1 medium was added to each well to recover the cells into a 15 ml Falcon tube. The cells were centrifuged at 1000 rpm for 4 minutes, and the supernatant was removed. The cell pellet was gently resuspended in 1 ml of 1x PBS, followed by a second centrifugation under the same parameters. After removing the supernatant, the cells were resuspended in 500 μl of mTeSR1 medium and filtered using a 5 ml Falcon tube with a 35 μm cell strainer.
The library was performed using the 10x Chromium Next GEM Single Cell 3’ Reagents kit protocol (Document number. CG000204).

value: Human embryonic stem cell (hESC)

tag: genetic modification

value: Sirtuin 1 deletion

value: Day 6 of differentiation protocol towards Dopaminergic Neurons


title: BN1_iLS_Day6_1

description:
Library name: Smaple 4
iLS_D6_BN1_1


title: No treatment Control, replicate4

description:
Library name: NT-4
paired-end


title: gd 13.5 placental tissue from Plac1 mutant rats, replicate 4


title: No treatment Control, replicate3

description:
Library name: NT-3
paired-end


title: H9,Wild Type, day 6 of differentiation, scRNAseq

value: H9 (WA09, WiCell Research Institute Inc.)

value: Wild Type


title: control_iLS_Day6_2

description:
Library name: Smaple 2
iLS_D6_Mock_2


title: No treatment Control, replicate2

description:
Library name: NT-2
paired-end

value: Head and neck cancer


title: gd 13.5 placental tissue from wild type rats, replicate 4


title: EGCG 40μM, replicate1

description:
Library name: EGCG1
paired-end


title: H9,SIRT1 KO, day 0 of differentiation, scRNAseq

value: Day 0 of differentiation protocol towards Dopaminergic Neurons


title: EGCG 40μM, replicate2

description:
Library name: EGCG2
paired-end


title: gd 13.5 placental tissue from Plac1 mutant rats, replicate 3


title: No treatment Control, replicate1

description:
Library name: NT-1
paired-end


title: Prm2 heterozygous testis

city: New Haven

first: Bluma

last: Lesch

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

description: Library name: P2het

data_processing:
Raw count matrices were generated using CellRanger (10X Genomics) and imported to Seurat 4.1.0 (Hao et al., 2021) and combined into one Seurat object. Reads were filtered to exclude doublets (nCount_RNA < mean + one standard deviation), dead or dying cells (nFeature_RNA > mean – one standard deviation) or high mitochondrial content (present.mt < mean + standard deviation). This filtered subset was log normalized and scaled. A linear dimensional reduction was performed using principal component analysis (PCA). Clusters were identified at a resolution of 0.5, and the “RunUMAP()” function was used to further investigate the dataset.
Assembly: mm10
Supplementary files format and content: index (.tsv), feature (.tsv), and matrix (.mtx) files

source_name: whole testis

extract_protocol:
A polypropylene collection tube was coated with 3 ml Collection Buffer (20% FBS in 1X PBS) for 2 hours at RT with end-over-end mixing. Seminiferous tubules were mechanically isolated from the tunica and transferred to a 15ml conical tube containing 5ml Digestion Solution I [0.75 mg/ml collagenase type IV (Gibco, 17104-019) in Dulbecco’s modified Eagle’s media (DMEM, Gibco, 11965092) supplemented with 1:1000 with 1 mg/ml DNase I (StemCell Technologies, 07900)] warmed to 37 °C, followed by incubation at 37 °C for 10 mins with end-over-end rotation. 5ml of cold DMEM was added and tubules allowed to settle on ice. The supernatant was discarded and the tubules were washed again with 5ml cold DMEM to deplete Leydig cells. 5ml of DMEM was added followed by centrifugation at 500xg for 5 mins at 4°C. The supernatant was removed and 5ml of Digestion Solution II [Accutase (Gibco, A1110501) supplemented with 1 mg/ml DNase I at 1:1000 at room temperature)] was added to the tubules followed by incubation with end-over-end rotation for 10 mins at RT with gentle pipetting after 5 mins to disperse the tubules. 5ml of cold Complete Media (10% FBS in DMEM) was added and the sample was centrifuged at 500 xg for 5 mins at 4 °C. The cell pellet was then resuspended in 5 ml of cold Complete Medium, filtered through a 100 μm strainer, and the cell suspension was transferred to a fresh 15 ml conical tube and centrifuged at 500 xg for 5 mins at 4 °C.
15,000 dissociated testis cells were processed using a Chromium Next GEM Single Cell 3’ v3.1 kit (10X Genomics) and sequenced using an Illumina NovaSeq machine with 150 base pair paired-end reads at a depth of 250 million reads.

value: whole testis

value: mixed testicular cells


title: H9,Wild Type, day 0 of differentiation, scRNAseq