title: IgG-CUT&Tag of HBM_mut_LRM_Del E14TG2a cells repeat 2

city: changsha

first: shen

last: yunfan

state: hunan

address: xiangya road

institute: central south university

data_processing:
For CUT&Tag analysis, the CUT&Tag Fastq read files were aligned to the mm10 reference genome using Bowtie2, utilizing the default parameters. To identify Dek-wt peaks, biological replicates were merged, and peak calling was carried out using MACS2 (version 2.2.6) with specific settings (--keep-dup all -g mm -P-value ≤ 1e–5) against the IgG data. The generation of CUT&Tag bedgraph files involved the subtraction of IgG signals from the experimental group signals using Deeptools' bamCompare, with the inclusion of --skipNAs and --scaleFactorsMethod readCount options. The CUT&Tag bedgraph files were then subjected to normalization by calculating the reads per million (RPM), and the resulting bigwig files were generated using bedGraphToBigWig.
Assembly: mm10
Supplementary files format and content: bigWig files were generated using bamCoverage.
Library strategy: CUT&Tag

growth_protocol: Mouse E14TG2a ESCs (a kind gift from M. Zhang’s laboratory, Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China) were cultured on gelatin-coated dishes in DMEM (High Glucose, with Sodium Pyruvate, with L-Alanyl-L-Glutamine) (Vivacell) supplemented with 15% fetal bovine serum (Vistech), 1× non-essential amino acids (Gibco), 100 μM β-mercaptoethanol (Sigma), and 1000 U/mL of leukemia inhibitory factor (LIF) (Millipore). The cells were incubated at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
The CUT&Tag was performed following the protocol provided by the Hieff NGS® G-Type In-Situ DNA Binding Profiling Library Prep Kit (Yeasen). A total of 50,000 cells were harvested and subjected to two rounds of washing using washing buffer (composed of 20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, and 1× Protease inhibitor cocktail). Subsequently, the cells were incubated with activated Concanavalin A coated magnetic beads. To this, 0.5 μg of primary antibody was added and allowed to incubate on a rotating platform at 4 °C for a duration of 16 hours. Following this, 0.5 μL of secondary antibody was introduced and incubated for an additional hour. After a thorough washing step, the cells were treated with pA/G-Tn5 transposase at 37°C for 1 hour. Subsequently, DNA extraction was carried out by DNA selection beads
To amplify libraries, 16 μL CUT&Tag DNA was mixed with 1 μL of a uniquely barcoded i5, 1 μL a uniquely barcoded i7 primer, using a different barcode for each sample, 7 μL ddH2O, and 25 μL 2× Ultima Amplification Mix, and run the following cycling conditions with lid heat on: 72 °C for 3 min; 95 °C for 30 s; 12 cycles of 95 °C for 10 s, 55 °C for 30 s and 72 °C for 30 s; final extension at 72 °C for 5 min and hold at 4 °C. Post-PCR clean-up was performed by adding 1.2× volume of DNA selection beads (60 μL), and libraries were incubated with beads for 5 min at RT, washed twice gently in 80% ethanol, and eluted in 20 μL EB buffer.

value: mouse embryonic stem cell

value: Dek-KO

tag: antibody

value: IgG CUT&Tag antibody


title: sclera.FDM.3

status: Public on Jan 02 2025

type: SRA

city: Shanghai

first: Jibo

last: Zhou

address: Quxi road NO.500, Huangpu district

country: China

institute: NINTH PEOPLE'S HOSPITAL SHANGHAI JIAO TONG UNIVERSITY SCHOOL OF MEDICINE

description: Library name: Sample3

library_source: transcriptomic

data_processing:
Trimmomatic software were used to remove adapter and low quality reads. [Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20.]
STAR is used to align clean reads to reference genome. STAR outperforms other aligners by a factor of >50 in mapping speed, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. [Dobin A1, Davis CA, Schlesinger F, Drenkow J, et.al. STAR: ultrafast universal RNA-seq aligner.Bioinformatics. 2013 Jan;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25.]
Read counts for individual transcripts of each sample were produced with HTSeq-count. [Anders S, Pyl PT, Huber W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31:166–169.]
After perfoming the PCA on the expression of genes from all samples, plotPCA will sort the principal components according to the amount of variability of the data that they explain. Based on this, you will obtain a plot which is the eigenvalues of the top two principal components
Assembly: mCavPor4.1
Supplementary files format and content: All.HTSeq.counts xlsx includes raw counts for each sample

molecule: total RNA

organism: Cavia porcellus

source_name: sclera

extract_protocol:
Samples were subjected to RNA extraction with Trizol (Thermo Fisher Scientific, 15596018 ).
Library construction was performed with the NEBNext UltraTM RNA Library Prep Kit (NEB #E7490) and libraries were purified with beads (AMPure XP system).

tag: tissue

value: sclera

tag: treatment

value: form-deprived


title: H3K27me3-CUT&Tag of HBM_mut_LRM_Del E14TG2a cells repeat 1

status: Public on Jan 01 2025

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell line

tag: cell type

tag: genotype

value: H3K27me3 CUT&Tag antibody


title: Cow_1 [SP380441]

city: Cambridge

first: wenzhong

last: xiao

state: ma

address: 38 sidney st, suite 161

country: USA

institute: massachusetts general hospital

data_processing:
Sequencing quality was assessed additionally using FASTQC (v0.11.9). Transcriptome annotations of each species were downloaded from Ensembl (https://www.ensembl.org, v90). For each sample, firstly, reads were aligned to human genome hg38 using STAR in the established bulk-RNA sequencing workflow of Bcbio (v1.2.1).  Secondly, the abundance of the annotated genes of the species was estimated from the RNA-seq reads as Transcripts per Million (TPM) using Sailfish. Thirdly, to compare the gene expression between species, the abundance of the genes in each species was then translated to that of the corresponding human orthologues. Here, only genes in a non-human species that had known orthologous human genes (Ensembl v90) were considered in further analysis. When m genes in a non-human species had n orthologous genes in human (m>=0, n>=1), the abundance of each of the human orthologues is assumed to be the sum of the abundance of the m genes divided by n.
Assembly: hg38 Ensembl v90
Supplementary files format and content: TPM matrix

organism: Bos taurus

source_name: blood

extract_protocol:
After incubation, blood in TruCulture tubes was separated according to the manufacturer’s instructions with additional centrifugation at 800 ×g for 10 minutes.  Supernatants were saved and frozen at −80 °C for cytokine analysis.  The cell pellets were lysed using red blood cell lysis solution for 10 min followed by centrifugation at 2,000 ×g for 3 minutes, and remaining white blood cells were lysed in Qiazol and frozen at −80 °C until library construction (Qiagen).
RNA isolated from white blood cells (Qiazol, Qiagen) was quality controlled using A260/A280 ratio, 28S/18S rRNA ratio, and an RNA integrity summary score (Agilent RIN). Total RNA samples (250ngs, RIN>=7.0) were enriched for mRNA, fragmented, and converted into indexed cDNA libraries according to Illumina TruSeq Stranded mRNA protocol and quantity controlled using Agilent TapeStation. Samples were sequenced to at least 25M of 2 x 50bp paired-end reads and assessed using in-house QA/QC metric (Q2Solutions Expression Analysis).

treatment_protocol: Blood was collected into heparin tubes using meticulous pyrogen-free conditions. TruCulture tubes (Myriad RBM) containing either cell culture media only (“control”) or cell culture media plus 10 ng, 100 ng, or 1 μg/mL E. coli0113 US national reference strain LPS were prepared in advance, stored at -20 °C or below, and thawed at room temperature immediately prior to use. 1 mL blood was added to each tube and samples were incubated for 2, 6 and 24 h at 37 °C with 5% CO2.

value: blood

tag: subject

value: LPS

tag: time

tag: timeunit

value: Hour

tag: dose

tag: doseunit

value: ng/mL

tag: group

value: S (sensitive)


title: H3K27me3-CUT&Tag of HBM_mut_LRM_Del E14TG2a cells repeat 2


title: IgG-CUT&Tag of HBM_mut_LRM_Del E14TG2a cells repeat 1


title: sclera.FDM.1

description: Library name: Sample1


title: Suz12-CUT&Tag of HBM_mut_LRM_Del E14TG2a cells repeat 2

value: Suz12 CUT&Tag antibody


title: H3K27me3-CUT&Tag of DEKKO_wtOE E14TG2a cells repeat 1


title: IgG-CUT&Tag of DEKKO_wtOE E14TG2a cells repeat 1


title: H3K27me3-CUT&Tag of DEKKO_wtOE E14TG2a cells repeat 2


title: Suz12-CUT&Tag of DEKKO_wtOE E14TG2a cells repeat 2


title: Suz12-CUT&Tag of HBM_mut_LRM_Del E14TG2a cells repeat 1


title: IgG-CUT&Tag of DEKKO_wtOE E14TG2a cells repeat 2


title: H3K4me3-CUT&Tag of DEKKO E14TG2a cells repeat 2

value: H3K4me3 CUT&Tag antibody


title: H3K4me3-CUT&Tag of DEKKO E14TG2a cells repeat 1


title: Suz12-CUT&Tag of DEKKO E14TG2a cells repeat 1


title: RKO cells, OECtrl (MCS) rep1

city: Jining

first: Wenzhi

last: Shen

address: No. 133 Hehua Road

institute: Jining Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Hisat2 tools soft were used to map with reference genome.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Differential expression analysis of two conditions/groups was performed using the DESeq2.
Assembly: mm10
Supplementary files format and content: TXT files include FPKM values for each Sample
Supplementary files format and content: TXT files include count values for each Sample

organism: Homo sapiens

source_name: RKO cells

growth_protocol: RKO cells were cultured in DMEM medium (HyClone) supplemented with 10% FBS, 1% sodium pyruvate (Gibco), 1.5g/L NaHCO3 (Gibco) and 1% NEAA (Gibco).

extract_protocol:
The total RNA was extracted according to the instruction manual of the TRlzol Reagent (Life technologies, California, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample..

treatment_protocol: N/A.

value: RKO cells

value: Cancer cells

value: OECtrl


title: Suz12-CUT&Tag of Parental E14TG2a cells repeat 2

value: Dek-WT


title: Suz12-CUT&Tag of DEKKO_wtOE E14TG2a cells repeat 1

value: mouse embryonic stem cell


title: Suz12-CUT&Tag of Parental E14TG2a cells repeat 1


title: (ctlr-1)cells after transfection with buffer

city: Columbia

first: Davis

last: Noblitt

state: SC

address: 631 Sumpter Street

department: IBS

institute: University of South Carolina

description:
Library name: Jurkat-ctrl-1
RNA sequencing of RNA samples (not derived from blood) from Homo Sapiens using 2x150 bp, 30 million paired-end reads per sample

data_processing:
FASTQ files containing raw paired-end sequencing reads were processed using the CLC Genomics Workbench 24.0.2. The ATF group was renamed from "ATF2" to "ATF3" after sequencing to ensure clarity with unrelated ATF datasets, all raw file names still contain ATF2 nomenclature, but should be taken as ATF3. Quality trimming steps included the removal of adapter sequences detected in reads. Reads with more than two ambiguous nucleotides were trimmed, and sequences shorter than six nucleotides were discarded. Trimming also addressed low-quality sequences with a quality limit of 0.05. As a result of this, the trimmed reads maintained an average length between 144.83 and 147.29 bases across samples. Approximately 13.9% of read pairs were trimmed due to adapter contamination. The final number of genes seen in the expression profile of all samples was 24,493.
Differential expression analysis was performed using the DESeq2 package.
Assembly: hg19 Ensembl v110
Supplementary files format and content: The RawExpresionData file contains counts, TCM, TPM, and RPKM data in a CSV format.
Supplementary files format and content: The Deseq2Results file contains the differential analysis results in CSV format. It specifically include the basemean, Log2FoldChange, Wald "stat", SE, P, and Padj values.

source_name: Lymphocyte

growth_protocol: Human Jurkat cells (ATCC, TIB-152) were cultured in Roswell Park Memorial Institute Medium (RPMI) containing GlutaMax supplemented with 10% v/v fetal bovine serum (FBS, Gibco) and penicillin/streptomycin (Cytiva) at 37 °C in 5% v/v CO2 (g).

extract_protocol:
The total RNA was harvested using an Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using PolyA selection for mRNA species (eukaryotic). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA)

treatment_protocol: Cells suspensions in RPMI (10% FBS + Pen/Strep) were transfected with plasmids using a Bio-Rad Gene Pulser Xcell Electroporator. To a 2 mm MicroPulser cuvette (Bio-Rad, cat. no. 1652086) was added 1x10^6 Jurkat cells and 100 µg of plasmid in RPMI media at a total volume of 200 µL. The transfection was performed using an exponential decay pulse; capacitance = 1000 µF and voltage = 140 V. After equilibrating the cells for 2 h, the media was supplemented with zinc chloride, PMA/Ionomycin, and Brefeldin A.

value: Lymphocyte

value: Jurkat

value: T Lymphocyte

value: WT

value: Shock

tag: batch


title: H3K4me3-CUT&Tag of Parental E14TG2a cells repeat 2


title: G1E-ER4, Control, Replicate1

city: Sydney

first: Charles

last: Bailey

state: NSW

address: Missenden Rd, Building 93

country: Australia

institute: Centenary Institute

description: mRNA-Seq

data_processing:
The first 15 base pairs of each FASTQ read were trimmed using Cutadapt to remove low-quality sequences and adapters. The trimmed reads were then aligned to the Ensembl mouse genome (GRCm38, release 86) using the STAR aligner (version 2.7.10a). The resulting BAM files were processed with Bedtools and UCSC's bedGraphToBigWig tool to generate BigWig files for data visualization. Gene expression levels were quantified by generating a count matrix using the FeatureCounts command from the Rsubread package, and differential expression analysis was performed using the DESeq2 package in R.
Assembly: GRCm38, release 86
Supplementary files format and content: tab-delimited text file includes raw read counts for each sample
Supplementary files format and content: tab-delimited excel file includes deseq2 identified differentially expressed genes in CHD4-APR sample compared to Control sample

molecule: polyA RNA

growth_protocol: G1E-ER4 is an erythroid progenitor cell line derived from murine embryonic stem cells that stably expresses a fusion protein combining GATA-1 fused to the estradiol receptor ligand binding domain. Addition of tamoxifen (4-OHT Sigma, 100 nM) to the cell culture medium results in the transcriptional activation of GATA-1 in the nucleus, triggering erythroid differentiation in 1-2 days. G1E-ER4 cells were cultured in Iscove's Modified Dulbecco's Medium (500 mL), supplemented with 15% FBS, glutamine, penicillin/streptomycin, CHO Kit ligand-conditioned medium (3 mL, generated in-house from CHO-KLS cells), 1-Thioglycerol (6.2 uL, M6145, Sigma) and mouse erythropoietin (EPO, carrier-free, 2 U/mL, #587608, BioLegend).

extract_protocol:
Cell pellets were lysed in 1 mL of TRIzol™ Reagent (Invitrogen). After a 5-minute incubation at room temperature, 200 μL of RNase-free chloroform (Sigma-Aldrich) was added followed by vigorous mixing. The samples were further incubated for 15 minutes at room temperature and then centrifuged at 14,000 g for 15 minutes at 4°C to separate the phases. The uppermost aqueous layer was carefully transferred to sterile 1.5 mL Eppendorf tubes, and 500 μL of isopropanol (Sigma-Aldrich) and 1 μL of glycogen (Sigma-Aldrich) were added and gently mixed by inversion. The RNA samples were then incubated overnight at -20°C. On the next day, the samples were thawed and centrifuged at 12,000 g for 20 minutes at 4°C. The supernatant was discarded, and the RNA pellet was washed with 1 mL of 75% (v/v) ethanol. After further centrifugation at 12,000 g for 5 minutes at 4°C, the supernatant was removed, and the RNA pellet was allowed to air-dry. Finally, 30 μL of RNase-free, UltraPureTM distilled water (Gibco) was added, and the RNA samples were stored at -80°C.
Total RNA (1-3μg/sample) extracted were submitted to the Australian Genome Research Facility Core Facility for quality control analysis. The RNA quality was assessed using the Agilent 2100 Bioanalyzer, and the RNA integrity number for all samples measured >9. The poly(A)-RNA was captured using oligo-dT beads and used for cDNA library preparation using the standard TruSeq RNA Sample Prep Kit v2 protocol (Illumina, CA, USA). Briefly, total RNA was poly-A selected and then fragmented. The cDNA was synthesized using random hexamers, end-repaired and ligated with appropriate adaptors for sequencing. The library then underwent size selection and purification using AMPure XP beads (Beckman Coulter, CA, USA). The appropriate Illumina recommended 6 bp barcode bases are introduced at one end of the adaptors during PCR amplification step. The size and concentration of the RNAseq libraried was measured by Bioanalyzer and Oubit fluorometry (Life Technologies, NY, USA) before loading onto the sequencer. The mRNA libraries were sequenced on the Illumina HiSeq 2000 System with 100 nucleotide paired-end reads, according to the standard manufacturer’s protocol (Illumina, CA, USA).

value: immature erythroblasts

tag: strain

value: Mouse G1E cells Transfected with a GATA-1-ER construct (Gata1 fused to the ligand-binding domains of ESR1)

value: Tamoxifen


title: G1E-ER4,CHD4-APR, Replicate2

description: mRNA-Seq


title: G1E-ER4,CHD4-APR, Replicate3

description: mRNA-Seq


title: H3K4me3-CUT&Tag of Parental E14TG2a cells repeat 1


title: Suz12-CUT&Tag of DEKKO E14TG2a cells repeat 2

value: Dek-KO


title: primary hepatocyte, shAR, gluc 8h-rep-2

city: Hangzhou

first: Chen

last: Jie

state: Zhejiang

address: Dunyu Road No.300

department: School of Life Science

institute: Westlake University

data_processing:
Sequencing reads were demultiplexed (bcl2fastq) and quantified with kallisto 0.46.0 with default parameters to the Mouse GRCm38.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes count values for each Sample

source_name: primary hepatocyte

growth_protocol: Isloated primary hepatocytes were seeded on the collagen coated plates at 2.5×10^5 cells/ml(or each samples) with 7.5%FBS M199(100nM dex), after 4h attachment, the medium was replaced with fresh 7.5%FBS medium with dex and add adenovirus of shScr and shAr to infect cells for 42h,then change to serum free M199(100nM dex) medium, 2h later, treat cells with 100 nM glucagon/Veh for 8hrs and added Trizol to collect the samples

extract_protocol:
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities.
After adenylation of  3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300  bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter,Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: Sex

value: female

value: primary hepatocyte

value: shAR

value: gluc 8h


title: primary hepatocyte, shAR, gluc 8h-rep-3


title: mESC input

city: shanghai

first: Xu

last: Chu

address: Dong'an Road

institute: Fudan University Shanghai Cancer Center

data_processing:
The SPEED datasets in this study were generated in paired-end format. Read 1 contains one segment of barcode in the 5’terminal (barcode 1) and following genomic DNA fragment. Read 2 carries three barcode segments from the 5’terminal sequentially (barcode 3/ barcode 2/ barcode 1). The data processing pipeline was modified from previous study14.
1). Data pre-processing. Sequencing quality of raw read was examined by FastQC (v0.11.9). Raw SPEED data reads were subjected to FastQC (v0.11.9) for checking sequencing quality and trimmed adaptors by Trimmomatic (v 0.38) under PE mode (-phred33 ILLUMINACLIP: TruSeq3-PE-2. fa: 2:30:10 TRAILING:3 SLIDINGWINDOW: 4:20 MINLEN:50).
2). Barcode identification and removal. Each full-length barcode was composed of 3 segments (barcode 1/ barcode 2/ barcode 3). To ensure the completeness, both read 1 and read 2 were used in barcode identification by BarcodeIdentification_v1.2.0.jar with the default parameters 2 and the barcode was added behind the read name. Finally, reads contain all the three barcode segments were filter for following analyses. In generally, around 75% reads were labeled by full-length barcode. To prevent the inclusion of extra barcode sequences at the 3' end of read 1, the second-round barcode-removing was performed by cutadapt (v 1.18) with parameters ‘-j 15 -m 50 -a "file: Split-Pool-jx_3barcode_rev. fa"’.
3). Mapping to genome and PCR duplicates removal. For mESC, mouse cerebral and cerebellar cortex SPEED data, read 1 in each SPEED library underwent two round barcode-removing (described above) were mapped on mm10 reference genome using Bowtie2 (v 2.3.5), and parameter ‘--trim5 11’ was set to remove barcodes on 5’terminal. Uniquely mapped reads were filtered and sorted by genome coordinates using samtools (v 1.9). The barcode strings on read names were stored in bam file tag ‘CB: Z:’. PCR duplicates were marked by the same start/end position and the same barcode and were removed in the following analysis. In analysis of mESC and hSC mixed library, reads were simultaneously mapped to both hg38 and mm10, and the aforementioned analyses were repeated. Subsequently, reads mapped to hg38 and mm10 were counted separately from deduplicated BAM files for each barcode to verify the single-nuclei labeling validity of SPEED library.
4).5hmC peak calling. The 5hmC-enriched regions in each sample were identified as peaks via MACS2 (v 2.1.2) with parameters ‘-f BAM -g mm -q 0.01 --nomodel --extsize 400 --max-gap 500 --keep-dup all’. The peaks in mouse brain and cerebellum are combined for DHMR analyses. The peaks were annotated by ‘annotatePeaks.pl’ in HOMER (v 4.10) with the default parameter.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: mESC

extract_protocol:
1) Nuclei isolation or extraction Cells or purified nuclei were crosslinked with formaldehyde and lysised with lysis buffer.
2) DNA fragmentation SDS and Triton X-100 were used to isolate and permeabilize nuclei. DNA fragmentation was performed by HpyCH4V in 0.1% Triton, 0.2% Tween-20, 0.2% NP-40, and PBS in to get the DNA fragment size range with 200-500bp.
3) DNA End-repair The dA-tailing process was initiated by adding dA tailing buffer to the nuclei, composed of nuclease-free H2O, dA-tail reaction buffer, and Klenow fragment.
4) Barcode in nuclei ligation The isolated nuclei, DPM barcoded tag and ligation mix ( 2 × Instant Sticky-end Ligase Master Mix, 5 × Quick Ligase Buffer, and 1,2-propanediol) were loaded into each well of a 96-well plate. The 96 well plate was subjected to meticulous mixing at 20 °C, allowing the ligation reaction to progress over a duration of 2 hour. After incubation, the in-nuclei DNA ligation was stopped. The contents of each well were transferred into new tube and washed.The nuclei were next performed second and third rounds of ODD and TERMINAL barcode ligation.
5) DNA reverse crosslinking The ligated-nuclei were reverse crosslinked  with 5 × Proteinase K Buffer and Proteinase K. Then, ligated-DNA was purified by DNA clean & concentrator kit.
6) 5hmC labeling and library construction 5hmC labeling and enrichment procedures follow the published protocols13, 14. Following the reaction, DNA substrates were purified by using the DNA Clean & Concentrator Kit and subsequently reconstituted in H2O.
Library construction was performed according to manufacturer’s recommendations for NEBNext® Ultra™ II DNA Library Prep Kit for Illumina.

value: mESC


title: primary hepatocyte, shAR, veh 0h-rep-3

value: veh


title: G1E-ER4, Control, Replicate3

description: mRNA-Seq


title: primary hepatocyte, shscr, gluc 8h-rep-2

value: shscr


title: primary hepatocyte, shAR, gluc 8h-rep-1


title: G1E-ER4, Control, Replicate2

description: mRNA-Seq


title: G1E-ER4,CHD4-APR, Replicate1

description: mRNA-Seq


title: primary hepatocyte, shscr, gluc 8h-rep-3


title: mESC 5hmC

source_name: mESC(mouse embryonic stem cell)

value: mESC(mouse embryonic stem cell)


title: primary hepatocyte, shAR, veh 0h-rep-2


title: mES-HSC-mixed-input

source_name: mES

value: mES


title: primary hepatocyte, shscr, gluc 8h-rep-1


title: primary hepatocyte, shscr, veh-rep-2


title: primary hepatocyte, shscr, veh-rep-1


title: CIPC-scko

city: suzhou

first: zheng

middle: ji

last: qing

address: renairoad

institute: szdx

data_processing:
Illumina Casava  bcl2fastqv2.19 software used for basecalling.
Filter the Raw Reads obtained by sequencing to obtain clean Reads that can be used for data analysis, and apply Seqtk to filter. The main steps are as follows: 1. Remove the linker sequence contained in the reads; 2. Remove the 3'end quality Q less than 20 Bases, that is, the base error rate is less than 0.01, where Q=-10logerror_ratio; 3. Removal of reads less than 25 in length; 4. Removal of ribosome RNA reads of the species.
Use Hisat2 (version: 2.0.4) split mapping algorithm to perform Genome mapping on the preprocessed reads. This algorithm allows the splitting of reads that cannot be matched to the full length to be mapped, and is more suitable for eukaryotic (with intron inter-regions). ) Transcriptome sequencing data; default parameters are used.
In transcriptome sequencing, we can estimate the level of gene expression by mapping the number of reads to the gene region, but the number of reads is not only proportional to the level of gene expression, but also related to the length of the gene itself and the amount of sequencing data. In order to make the gene expression levels of different genes and different samples comparable, the reads were converted into FPKM (Fragments Per Kilobase of exon model per Million mapped reads) to standardize the gene expression levels.
We first use Stringtie (version: 1.3.0) to count the number of Fragments of each gene after Hisat2 comparison, then use the TMM (trimmed mean of M values) method to normalize, and finally use the perl script to calculate each gene FPKM value.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Gastrocnemius muscle

extract_protocol:
Gastrocnemius muscle was isolated from CIPC-scko mice and CIPC-flox/flox mice. Total RNA was extracted using the RNAsimple total RNA Kit per manufacturer’s instructions. The quality of the total RNA was inspected by Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA). Qualified total RNA was further purified by RNAClean XP Kit (Cat# A63987, Beckman Coulter, Inc, Brea, CA). The cDNA library was generated using a VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (Cat# NR604-02, Vazyme, Nanjing, China) and sequenced on an Illumina system (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Gastrocnemius muscle

value: CIPC-scko

tag: age

value: 8 week-old


title: CIPC-flox

value: CIPC-flox/flox


title: primary hepatocyte, shAR, veh 0h-rep-1


title: vitamin A sufficient VAS operated SHAM daily ip injection vehicle VEH 5430261039_E

type: RNA

city: Groningen

first: vincent

last: bloks

department: Pediatrics

country: Netherlands

institute: UMCG

description: Biological replicate3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data where normalized using Quantile normalisation strategies using the  MADMAX analysis pipeline Wageningen, pmid: 21778530

label: Biotin

organism: Rattus norvegicus

source_name: liver

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit ( Applied Biosystems)

extract_protocol: RNA was extracted with TriReagent ( Sigma). Quality control was performed with Biorad Experion analyser

treatment_protocol: 4-5 rats per group where operated ( Sham or  BileDuctLigated ) , half of the groups where VitaminA deficient before operation , the treatment was Vitamin A supplementation  or vehicle

tag: treatment 2

value: operated SHAM

tag: treatment 1

value: vitamin A sufficient VAS

tag: treatment 3

value: daily ip injection vehicle VEH

value: liver

tag: gender

value: male

value: Wistar


title: vitamin A sufficient VAS Bile Duct Ligation BDL daily ip injection vehicle VEH 5457261015_D

description: Biological replicate5

value: Bile Duct Ligation BDL

tag: tissue


title: vitamin A sufficient VAS operated SHAM daily IP injections with retinyl-palmitate VITA  5430261037_I

description: Biological replicate2


title: vitamin A sufficient VAS Bile Duct Ligation BDL daily ip injection vehicle VEH  5430261039_H

description: Biological replicate3


title: vitamin A sufficient VAS Bile Duct Ligation BDL daily ip injection vehicle VEH  5430261037_C

description: Biological replicate1


title: vitamin A sufficient VAS operated SHAM daily ip injection vehicle VEH 5430261037_H

description: Biological replicate2


title: primary hepatocyte, shscr, veh-rep-3

value: female

tag: cell type

value: primary hepatocyte

tag: treatment


title: vitamin A sufficient VAS Bile Duct Ligation BDL daily IP injections with retinyl-palmitate VITA  5457261015_E

description: Biological replicate3


title: vitamin A sufficient VAS operated SHAM daily IP injections with retinyl-palmitate VITA  5457261015_A

description: Biological replicate4


title: vitamin A sufficient VAS operated SHAM daily IP injections with retinyl-palmitate VITA  5430261039_J

description: Biological replicate3


title: Vitamin A deficient VAD operated SHAM daily ip injection vehicle VEH   5457261015_K

description: Biological replicate4

value: Vitamin A deficient VAD


title: vitamin A sufficient VAS Bile Duct Ligation BDL daily ip injection vehicle VEH  5430261037_F

description: Biological replicate2


title: vitamin A sufficient VAS Bile Duct Ligation BDL daily IP injections with retinyl-palmitate VITA  5457261015_J

description: Biological replicate5


title: vitamin A sufficient VAS operated SHAM daily ip injection vehicle VEH 5457261015_B

description: Biological replicate4


title: vitamin A sufficient VAS Bile Duct Ligation BDL daily ip injection vehicle VEH  5430261039_I

description: Biological replicate4


title: vitamin A sufficient VAS Bile Duct Ligation BDL daily IP injections with retinyl-palmitate VITA  5457261015_G

description: Biological replicate4


title: Vitamin A deficient VAD operated SHAM daily ip injection vehicle VEH  5430261037_J

description: Biological replicate2


title: vitamin A sufficient VAS operated SHAM daily ip injection vehicle VEH  5430261037_A

description: Biological replicate1


title: vitamin A sufficient VAS Bile Duct Ligation BDL daily IP injections with retinyl-palmitate VITA  5430261039_F

description: Biological replicate2


title: Vitamin A deficient VAD operated SHAM daily IP injections with retinyl-palmitate VITA  5457261015_C

description: Biological replicate4


title: Vitamin A deficient VAD operated SHAM daily IP injections with retinyl-palmitate VITA  5430261039_L

description: Biological replicate3


title: Vitamin A deficient VAD operated SHAM daily ip injection vehicle VEH   5430261037_E

description: Biological replicate1


title: vitamin A sufficient VAS operated SHAM daily IP injections with retinyl-palmitate VITA  5430261037_G

description: Biological replicate1


title: Vitamin A deficient VAD operated SHAM daily IP injections with retinyl-palmitate VITA  5430261039_G

description: Biological replicate2


title: vitamin A sufficient VAS Bile Duct Ligation BDL daily IP injections with retinyl-palmitate VITA  5430261039_A

description: Biological replicate1


title: Vitamin A deficient VAD Bile Duct Ligation BDL daily ip injection vehicle VEH  5430261039_D

description: Biological replicate3


title: Vitamin A deficient VAD Bile Duct Ligation BDL daily ip injection vehicle VEH  5457261015_I

description: Biological replicate5


title: Vitamin A deficient VAD operated SHAM daily ip injection vehicle VEH   5457261015_F

description: Biological replicate3


title: Vitamin A deficient VAD Bile Duct Ligation BDL daily ip injection vehicle VEH  5457261015_H

description: Biological replicate4


title: Vitamin A deficient VAD operated SHAM daily IP injections with retinyl-palmitate VITA  5430261037_B

description: Biological replicate1


title: Vitamin A deficient VAD Bile Duct Ligation BDL daily IP injections with retinyl-palmitate VITA  5457261015_L

description: Biological replicate5


title: Neuropathology 5xFAD Plcg2 KO+/- M #46

city: Stanford

first: Andy

middle: P

last: Tsai

state: California

address: 290 Jane Stanford Way E365

institute: Stanford University

description: nCounter® Neuropathology Panels

hyb_protocol: standard NanoString protocol

scan_protocol: standard NanoString protocol

data_processing: Data were processed and normalized using NanoString nSolver 4.0 analysis software

label: NanoString

source_name: mouse cortex

label_protocol: standard NanoString protocol

extract_protocol: Total RNAs were prepared with Purelink RNA Mini Kit and subjected to NanoString analysis

tag: sample type

value: Male, 5xFAD PLCG2 KO HET mice, brain

value: Male


title: Neuropathology 5xFAD Plcg2 KO+/- M #11

description: nCounter® Neuropathology Panels


title: Neuropathology 5xFAD Plcg2 KO+/- M #13

description: nCounter® Neuropathology Panels


title: Neuropathology 5xFAD Plcg2 KO+/- M #10

description: nCounter® Neuropathology Panels


title: Neuropathology 5xFAD Plcg2 KO+/- M #3

description: nCounter® Neuropathology Panels


title: Neuropathology 5xFAD Plcg2 KO+/- M #48

description: nCounter® Neuropathology Panels


title: Neuropathology 5xFAD M # 1177

description: nCounter® Neuropathology Panels

value: Male, 5xFAD mice, brain


title: Neuropathology 5xFAD M # 1181

description: nCounter® Neuropathology Panels


title: Neuropathology 5xFAD M # 1268

description: nCounter® Neuropathology Panels


title: Neuropathology 5xFAD M # 1269

description: nCounter® Neuropathology Panels


title: Neuropathology 5xFAD Plcg2 KO+/- F #12

description: nCounter® Neuropathology Panels

value: Female, 5xFAD PLCG2 KO HET mice, brain

value: Female


title: Neuropathology 5xFAD F # 1249

description: nCounter® Neuropathology Panels

value: Female, 5xFAD mice, brain


title: Neuropathology 5xFAD Plcg2 KO+/- F #14

description: nCounter® Neuropathology Panels


title: Neuropathology 5xFAD Plcg2 KO+/- F #8

description: nCounter® Neuropathology Panels


title: Vitamin A deficient VAD Bile Duct Ligation BDL daily IP injections with retinyl-palmitate VITA  5430261039_K

description: Biological replicate4


title: Vitamin A deficient VAD Bile Duct Ligation BDL daily ip injection vehicle VEH  5430261037_L

description: Biological replicate1


title: Neuropathology 5xFAD M # 1182

description: nCounter® Neuropathology Panels


title: Neuropathology 5xFAD F # 1253

description: nCounter® Neuropathology Panels


title: Vitamin A deficient VAD Bile Duct Ligation BDL daily IP injections with retinyl-palmitate VITA  5430261039_C

description: Biological replicate3


title: Vitamin A deficient VAD Bile Duct Ligation BDL daily ip injection vehicle VEH 5430261039_B

description: Biological replicate2


title: Vitamin A deficient VAD Bile Duct Ligation BDL daily IP injections with retinyl-palmitate VITA  5430261037_K

description: Biological replicate2


title: Vitamin A deficient VAD Bile Duct Ligation BDL daily IP injections with retinyl-palmitate VITA  5430261037_D

description: Biological replicate1


title: Neuropathology 5xFAD M # 1270

description: nCounter® Neuropathology Panels


title: Neuropathology 5xFAD F # 1190

description: nCounter® Neuropathology Panels


title: Neuropathology 5xFAD Plcg2 KO+/- F #51

description: nCounter® Neuropathology Panels


title: Neuropathology 5xFAD F # 1248

description: nCounter® Neuropathology Panels


title: Neuropathology 5xFAD F # 1180

description: nCounter® Neuropathology Panels


title: Neuropathology 5xFAD Plcg2 KO+/- F #18

description: nCounter® Neuropathology Panels


title: Neuropathology 5xFAD Plcg2 KO+/- F #19

description: nCounter® Neuropathology Panels


title: MCF10A, vehicle (PBS plus DMSO), replicate 3

type: genomic

city: Chicago

first: Mariana

last: Bustamante Eduardo

state: il

address: 303 E Superior St.

department: Department of Surgery

institute: Northwestern University

hyb_protocol: DNA was treated with sodium bisulphite using the EZ DNA methylation kit (Zymo Research, # D5001) and and Genome-wide DNA methylation profiling was performed using the Illumina Infinium Methylation EPIC Beadchip array.

scan_protocol: Arrays were imaged using Illumina iScan scanner

data_processing:
Raw IDAT files were processed using the GenomeStudio software V2011.1.
Average Beta

label: Cy3 and Cy5

label_protocol: Standard Illumina protocol

growth_protocol: MCF-10A cells were seeded in biological triplicate in complete MEBM media.

extract_protocol: DNA was extracted using Qiagen AllPrep DNA/RNA/Protein Mini Kit (Qiagen # 80004).

treatment_protocol: MCF-10A cells were exposed to vehicle (PBS or PBS plus DMSO), 5mM OA and 5mM OA plus 30uM CBR-5884 for 24 hours

tag: cell line

value: Normal breast epithelial cell

value: PBS plus DMSO


title: MCF10A, Octanoic Acid plus CBR-5884, replicate 2

value: Octanoic Acid plus CBR-5884


title: MCF10A, Octanoic Acid plus CBR-5884, replicate 3


title: MCF10A, Octanoic Acid, replicate 3

value: MCF10A, Octanoic Acid, replicate 3

value: Octanoic Acid


title: MCF10A, Octanoic Acid, replicate 1

value: MCF10A, Octanoic Acid, replicate 1


title: MCF10A, vehicle (PBS), replicate 2

value: MCF10A, vehicle (PBS), replicate 2

value: PBS


title: MCF10A, Octanoic Acid, replicate 1, technical replicate


title: iHO-2D-1

city: Suita

first: Jumpei

last: Inui

address: Yamadaoka 1-6

country: Japan

institute: Osaka University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic.
Trimmed sequence reads were mapped to GRCh38 using HISAT2.
Read count extraction and nomalization were performed using samtools and featureCounts.
Supplementary files format and content: tab-delimited text file includes raw conuts for each Sample.

source_name: human iPS cell-derived hepatic organoid in 2D culture

extract_protocol:
RNA was extracted using RNeasy Mini Kit.
According to the manufacturer's instructions, library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA). Libraries were converted to libraries for DNBSEQ using MGIEasy Universal Library Conversion Kit (App-A).

value: cultured cell

value: differentiation by 2D culture


title: iHO-2D-3

value: human iPS cell-derived hepatic organoid in 2D culture

value: differentiation by 4D culture


title: MCF10A, Octanoic Acid plus CBR-5884, replicate 1


title: iHO-2D-2

value: differentiation by 3D culture


title: MCF10A, vehicle (PBS plus DMSO), replicate 1


title: HLC-2

source_name: human iPS cell-derived hepatocyte like cells


title: MCF10A, Octanoic Acid, replicate 2

value: MCF10A, Octanoic Acid, replicate 2


title: MCF10A, vehicle (PBS), replicate 1

value: MCF10A, vehicle (PBS), replicate 1


title: MCF10A, vehicle (PBS), replicate 3

value: MCF10A, vehicle (PBS), replicate 3


title: HLC-1

value: human iPS cell-derived hepatocyte like cells


title: MCF10A, vehicle (PBS), replicate 1, technical replicate

value: Normal breast epithelial cell


title: iHO-2

source_name: human iPS cell-derived hepatic organoid

value: human iPS cell-derived hepatic organoid


title: iHO-3


title: HLC-3


title: iHO-1


title: Neuropathology 5xFAD F # 1189

description: nCounter® Neuropathology Panels

value: Female, 5xFAD mice, brain

value: Female


title: HCT116NC3

city: Zunyi

first: lin

last: Wang

state: 贵州省遵义市新蒲新区

address: 贵州省遵义市新蒲新区学府西路6号

institute: Zunyi Medical University

description: Library name: HCT116NC3

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads Count for each gene in each sample was counted by HISAT v2.1.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: Homo_sapiens.ENSEMBL.GRCh38.109.chr
Supplementary files format and content: tab-delimited text files include FPKM values for each samples.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Colorectal cancer cell

value: Control


title: LoVoSH1

address: 贵州省遵义市新蒲新区学府西路6号

description: Library name: LoVoSH1

source_name: LoVo

value: LoVo

value: SLERT KD


title: LoVoSH3

address: 贵州省遵义市新蒲新区学府西路6号

description: Library name: LoVoSH3


title: HCT116OE3

address: 贵州省遵义市新蒲新区学府西路6号

description: Library name: HCT116OE3

value: SLERT OE


title: LoVoNC3

address: 贵州省遵义市新蒲新区学府西路6号

description: Library name: LoVoNC3


title: LoVoNC1

address: 贵州省遵义市新蒲新区学府西路6号

description: Library name: LoVoNC1


title: MCF10A, vehicle (PBS plus DMSO), replicate 2

value: PBS plus DMSO


title: LoVoNC2

address: 贵州省遵义市新蒲新区学府西路6号

description: Library name: LoVoNC2


title: HCT116OE1

address: 贵州省遵义市新蒲新区学府西路6号

description: Library name: HCT116OE1


title: HCT116OE2

address: 贵州省遵义市新蒲新区学府西路6号

description: Library name: HCT116OE2


title: Donor 1, Octanoic Acid

description: Library name: 1B

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using CellRanger version 7.0.1.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Normal Breast

growth_protocol: Breast microstructures were resuspended in Human Plasma Like media with H14 media additives.

extract_protocol:
Breast microstructures were centrifuged, washed with HBSS containing 0.1% BSA, and incubated with pre-warmed TrypLE for 15 minutes. The dissociation mixture was pipetted, followed by the addition of complete HPLM media. After centrifugation, cells were treated with RBC lysis buffer, washed, and resuspended in HPLM media with Dispase II and DNase I for further dissociation. Cells were passed through an 18G needle, filtered, and washed again before being suspended in HBSS with 0.04%BSA.
All the procedures were done using Chromium Next GEM Single Cell 3’ Reagent kits v3.1, dual indexing; following the 10x Genomics user guide # CG000315

treatment_protocol: Breast microstrctures were exposed to 5mM OA or vehicle (PBS) for 24 hours.

value: Normal Breast

value: Octanoic Acid

tag: menopausal status

value: Premenopausal


title: LoVoSH2

address: 贵州省遵义市新蒲新区学府西路6号

description: Library name: LoVoSH2


title: HCT116NC2

address: 贵州省遵义市新蒲新区学府西路6号

description: Library name: HCT116NC2


title: Octanoic Acid, H3K4me3, replicate 3

description: Library name: OA H3K4me3 biolrep 3

data_processing:
MACS2 v2.2.7.1 was used to call H3K4me3 narrow peaks and SICER2 was used to call H3K27me3 broad peaks.
Differential binding regions were identified using DiffBind v3.9.
ChIPseeker 1.8.6 was used to annotate the differential peaks identified by DiffBind
Assembly: hg38
Supplementary files format and content: narrowPeak (H3K4me3)
Supplementary files format and content: broadPeak (H3K27me3)
Library strategy: CUT&RUN

extract_protocol:
Aproximately 900’000 cells were processed using the CUTANA kit (Epicypher, #14-1048).
CUT&RUN Libraries were prepared using the NEBNext Ultra II Library Prep Kit for Illumina (New England BioLabs, #E7645S) using unique dual index primer pairs (NEBNext Multiplex Oligos for Illumina from New England BioLabs, # E6440S)

treatment_protocol: MCF-10A cells were exposed to 5mM OA or vehicle (PBS) for 24 hours.

tag: cut&run antibody

value: H3K4me3 Antibody (Epicypher, #13-0041)

value: OA


title: Vehicle, H3K27me3, replicate 3

description: Library name: Vehicle H3K27me3 biolrep 3

value: H3K27me3 antibody (Cell Signaling, #9733)

value: PBS


title: Vehicle, H3K4me3, replicate 1

description: Library name: Vehicle H3K4me3 biolrep 1

value: Normal breast epithelial cell


title: Donor 2, vehicle

description: Library name: 2A


title: Donor 1, vehicle

description: Library name: 1A


title: Octanoic Acid, H3K27me3, replicate 2

description: Library name: OA H3K27me3 biolrep 2


title: Octanoic Acid, H3K27me3, replicate 1

description: Library name: OA H3K27me3 biolrep 1


title: Octanoic Acid, H3K4me3, replicate 2

description: Library name: OA H3K4me3 biolrep 2


title: Donor 2, Octanoic Acid

description: Library name: 2B


title: Octanoic Acid, H3K4me3, replicate 1

description: Library name: OA H3K4me3 biolrep 1


title: Vehicle, H3K27me3, replicate 2

description: Library name: Vehicle H3K27me3 biolrep 2


title: Vehicle, H3K27me3, replicate 1

description: Library name: Vehicle H3K27me3 biolrep 1


title: Vehicle, H3K4me3, replicate 3

description: Library name: Vehicle H3K4me3 biolrep 3


title: Vehicle, H3K4me3, replicate 2

description: Library name: Vehicle H3K4me3 biolrep 2


title: hTERT A41hWAT-SVF,KO2

city: Beijing

first: Hui

last: Yang

address: 7 Panjiayuan Nanli, Room314

department: Department of Toxicology

institute: China National Center for Food Safety Risk Assessment (CFSA)

description:
Library name: sample5
hTERT A41hWAT-SVF,APP KO2

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software.
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.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: WAT

growth_protocol: Human white adipose tissue (WAT) progenitor cell line hTERT A41hWAT-SVF (CRL-3386) was obtained from ATCC. Cells were maintained in Dulbecco’s Modified Eagle Medium with 10%(vol/vol) FBS and 1% (vol/vol) penicillin/streptomycin. Cells were maintained in an atmosphere of 37°C, 5% carbon dioxide(CO2), and 95% humidity.

extract_protocol:
Total RNA was extracted from  cultured cells withTRIzol reagent.mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: CRISPR-Cas9 system was used for gene knockout. Specific guide RNA (gRNA) sequences targeting the APP gene were designed and synthesized.

value: WAT

tag: genotype

value: hTERT A41hWAT-SVF,APP KO2

value: APP Knockout


title: Positive ctrl, replicate 1

description: Library name: Positive ctrl biolrep 1

value: untreated


title: Octanoic Acid, H3K27me3, replicate 3

description: Library name: OA H3K27me3 biolrep 3


title: hTERT A41hWAT-SVF,KO3

description:
Library name: sample6
hTERT A41hWAT-SVF,APP KO3

value: Human white adipose tissue (WAT) progenitor cell line

value: hTERT A41hWAT-SVF,APP KO3


title: Negative ctrl, replicate 1

description: Library name: Negative ctrl biolrep 1

value: Rabbit IgG Negative Control Antibody (Epicypher, #13-0042)


title: hTERT A41hWAT-SVF,WT2

description:
Library name: sample2
hTERT A41hWAT-SVF,WT

value: hTERT A41hWAT-SVF,WT2


title: HCT116NC1

address: 贵州省遵义市新蒲新区学府西路6号

description: Library name: HCT116NC1

value: Colorectal cancer cell

value: Control


title: hTERT A41hWAT-SVF,WT3

description:
Library name: sample3
hTERT A41hWAT-SVF,WT3

value: hTERT A41hWAT-SVF,WT3


title: Positive ctrl, replicate 2

description: Library name: Positive ctrl biolrep 2


title: P10,tumor,HBV-po

city: Shenzhen

first: Zhao

last: Shizheng

address: Shenzhen

department: LIFS

institute: Undefined

description:
Library name: Patient-HCC010-HCC-tumor
SeekOneDD

data_processing:
The Seeksoultools analysis pipeline set was used with default parameters. Briefly, binary base call files were demultiplexed into FASTQ files by cellranger mkfastq using the respective sample sheet with utilized Seekgene barcodes. The seeksoultools count pipeline was used to align read data to the reference genome provided by 10x Genomics (human reference dataset refdata-gex-GRCh38-2020-A), counting aligned reads per gene with intronic reads included in the count matrix, and calculating the clustering and summary statistics. Outputs from the seeksoulgene count of all samples were aggregated, normalized to the same sequencing depth and then the feature-barcode matrices were recomputed by seeksoultools package (1.2.2).
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-seperated value files and matrix

extract_protocol:
Six patients who underwent liver resection and were pathologically diagnosed with HCC between 2022 and 2024 were enrolled in this study. None of the patients had received anti-tumor treatments prior to surgery. Fresh tumor tissues and corresponding para-cancerous tissues were collected from each patient.
Single-cell RNA sequencing (scRNA-seq) libraries were prepared using SeekOne® Digital Droplet Single Cell 3’ library preparation kit (Cat# K00202, SeekGene). Library sequencing was performed on an Illumina NovaSeq 6000 with PE150 read length.

value: liver

value: hepatocyte

tag: disease state

value: hepatocellular carcinoma


title: Negative ctrl, replicate 2

description: Library name: Negative ctrl biolrep 2


title: hTERT A41hWAT-SVF,KO1

description:
Library name: sample4
hTERT A41hWAT-SVF,APP KO1

value: hTERT A41hWAT-SVF,APP KO1


title: P10,adjacent,HBV-po

description:
Library name: Patient-HCC010-HCC-adjacent
SeekOneDD


title: hTERT A41hWAT-SVF,WT1

description:
Library name: sample1
hTERT A41hWAT-SVF,WT1

value: hTERT A41hWAT-SVF,WT1


title: P11,adjacent,HBV-ne

description:
Library name: Patient-HCC011-HCC-adjacent
SeekOneDD


title: P11,tumor,HBV-ne

description:
Library name: Patient-HCC011-HCC-tumor
SeekOneDD


title: P12,adjacent,HBV-po

description:
Library name: Patient-HCC012-HCC-adjacent
SeekOneDD


title: P15,tumor,HBV-ne

description:
Library name: Patient-HCC015-HCC-tumor
SeekOneDD


title: CAYA4T

first: KAI

last: GUO

state: Shanghai

address: Pujian Road, NO. 160, Pudong New Area

institute: Renji Hospital, School of Medicine, Shanghai Jiaotong University

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software 6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: thyroid

extract_protocol:
Tissue samples are stored in MACS Tissue Storage Solution immediately after surgically removed. Tissue samples were processed as described below. Briefly, the tissues were taken in sterile petri dishes and cleaned with DPBS pre-cooled at 4℃. Then, use sterile scissors and tweezers to cut the tissue into small pieces below 1mm3 on ice. Collagenase Type II were added and transferred to 15mL centrifuge tube, vibrated in 37℃ water bath for 30 minutes. The cell suspensions were filtered using 70um nylon meshes filter, resuspended in DPBS and then appropriate amount of RBC lysis buffer were added to remove erythrocytes. Stained using 0.4% trypan blue, mix well and then placed to the Countess II Automated Cell Counter for cell count and cell viability measurements.
The gene Gene Expression libraries were contructed accoding to the manufactuerer's protocol for the 3-prime v3 kit from 10X Genomics. The single cell TCR libraries were contructed accoding to the manufactuerer's protocol for the 5-prime v2 kit from 10X Genomics.

value: thyroid

tag: tissue region

value: T


title: CAYA1P

description: 10X Genomics

value: P


title: CAYA1T

description: 10X Genomics


title: P12,tumor,HBV-po

description:
Library name: Patient-HCC012-HCC-tumor
SeekOneDD


title: P14,adjacent,HBV-ne

description:
Library name: Patient-HCC014-HCC-adjacent
SeekOneDD


title: P13,tumor,HBV-po

description:
Library name: Patient-HCC013-HCC-tumor
SeekOneDD


title: P13,adjacent,HBV-po

description:
Library name: Patient-HCC013-HCC-adjacent
SeekOneDD


title: HFF cells, IgG, rep1

city: Freiburg

first: Florian

last: Full

address: Hermann-Herder-Str. 11

country: Germany

institute: institute of Virology, University Medical Center Freiburg

data_processing:
Sequence reads were mapping to hg38 by STAR or bowtie2
counts files were generated by featurecounts or TEcounts and bigwig files were generated by deeptools
Assembly: hg38
Library strategy: CUT&RUN

source_name: cell line

extract_protocol:
Cells were resuspended in Trizol (Invitrogen) and RNA extracted from Trizol.
RNA-sequencing libraries were constructed using commercial kits (New England Biolabs) total RNA-seq with rRNA depletion as indicated; CUT&RUN was performed according to the CUT&RUN: Targeted in situ genome-wide profiling with high efficiency for low cell numbers V.3 protocol.

value: cell line

value: HFF

value: HFF cells

value: WT


title: HFF cells, KAP1, HSV1, 14hpi, rep2


title: P14,tumor,HBV-ne

description:
Library name: Patient-HCC014-HCC-tumor
SeekOneDD


title: HFF cells, KAP1, HSV1, 6hpi, rep1


title: HFF cells, KAP1, mock, rep1

value: mock


title: 293T cells, DUX4, 12h, rep2

data_processing:
Sequence reads were mapping to hg38 by STAR or bowtie2
counts files were generated by featurecounts or TEcounts and bigwig files were generated by deeptools
Assembly: hg38

value: HEK 293T cells

value: dox


title: P15,adjacent,HBV-ne

description:
Library name: Patient-HCC015-HCC-adjacent
SeekOneDD


title: CAYA5P

description: 10X Genomics


title: CAYA3P

description: 10X Genomics


title: CAYA5T

description: 10X Genomics


title: CAYA2P

description: 10X Genomics


title: CAYA3T

description: 10X Genomics


title: CAYA4P

description: 10X Genomics


title: 293T cells, DUX4, 8h, rep2


title: 293T cells, DUX4, 12h, rep1


title: ADULT1T

description: 10X Genomics


title: CAYA2T

description: 10X Genomics


title: 293T cells, DUX4, mock, rep1


title: ADULT1P

description: 10X Genomics


title: HFF cells, DUX4, 8h, rep1


title: HFF cells, DUX4, 8h, rep2


title: SLK endothelial cells, KSHV, 72h, rep1

value: SLK endothelial cells


title: HFF cells, IgG, rep2


title: HFF cells, KAP1, HSV1, 14hpi, rep1


title: SLK endothelial cells, KSHV, 24h,, rep2


title: 293T cells, DUX4, 8h, rep1


title: SLK endothelial cells, KSHV, 48h, rep1


title: 293T cells, DUX4, mock, rep2


title: HFF cells, HCMV(BAC2), 72h, rep2


title: SLK endothelial cells, mock, rep2


title: HFF cells, DUX4, mock, rep2


title: HFF cells, KAP1, HSV1, 6hpi, rep2


title: SLK endothelial cells, mock, rep1


title: HFF cells, HCMV(BAC2), 36h, rep1


title: HFF cells, DUX4, mock, rep1


title: HFF cells, mock, rep2


title: HFF cells, DUX4, 24h, rep1


title: SW480, shPcyt2_2_2

city: 四川省

first: SU

last: ZHANG

address: 四川省成都市武侯区人民南路三段17号

institute: 四川大学

description: Knockdown PCYT2 in SW480 by using shPCYT2#2 lentiviral vector

data_processing:
CLC Genomics orkbench v11.0.1
Sequence reads were trimmed for adaptor sequence / low-quality sequence using CLC genomic benchwork ( parameter-quality limit:0.05)
Trimmed sequence reads were mapped to GRCM38/ mm10 using CLC genomic benchwork (parameters-mismath cost:2 insertion cost : 3 deletion cost :3 length fraction : 0.8 similarity fraction :0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCh38
Supplementary files format and content: tab-delimited txt files include RPKM values for each Sample

extract_protocol:
RNA was harvested using NEBNext Ultra™RNA Library Prep Kit for Illumina.1.5 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-SEQ were prepared using SMARTER MRNA-SEQ Library Prep Kit following manufacturers protocols

value: Human colorectal cancer (CRC) cell line


title: SLK endothelial cells, KSHV, 72h, rep2


title: SW480, shPcyt2_2_1

address: 四川省成都市武侯区人民南路三段17号


title: HFF cells, DUX4, 24h, rep2


title: HFF cells, KAP1, mock, rep2


title: SLK endothelial cells, KSHV, 48h, rep2


title: input_siNTC

city: Boston

first: Steven

last: Balk

state: MA

address: 3 Blackfan Circle

department: Hematology/Oncology

institute: Harvard Medical School

data_processing:
Adapters were trimmed with trimmomatic/0.36. Fastq files were aligned to hg19 reference genome using bwa mem aligner (0.7.8). Picard/2.8.0 was used to sort and mark duplicates. Samtools/1.9 was used for indexing and removing low quality reads.
MACS2 (2.1.1) was used to call peaks
Deeptools/3.0.2 was used to generate bigwig files
Assembly: hg19
Supplementary files format and content: bigwig files contain genome-wide signal data for each sample, narrowPeak.bed files contain genomic regions for each sample,

source_name: Prostate

growth_protocol: Enzalutamide-resistant VCaP (VCaP16) cells were cultured in DMEM (10% FBS) with 16uM enzalutamide.

extract_protocol:
Cells were crosslinked with double fixation. Cells were first crosslinked in 2 mM fresh disuccinimidyl glutarate for 35 minutes, followed by 1% FA for an additional 10 minutes. The samples were sonicated using the Covaris E220 in sarkosyl lysis buffer.
ChIP-seq libraries were generated using the SimpleChIP ChIP-seq Multiplex Oligos for Illumina with Dual Index Primers (Cell Signaling Technology, cat# 47538) according to the manufacturer’s instructions. Libraries were pooled and sequenced using a NovaSeq 6000 Sequencing System.

treatment_protocol: VCaP16 were treated with siRNA for both NFIB and NFIX (siNFIB/X) and siRNA for non-targeted control (siNTC).

value: Prostate

value: ENZ-resistant VCaP

value: prostate cancer


title: ARv7_siNTC_VC16 rep3


title: SLK endothelial cells, KSHV, 24h, rep1


title: HFF cells, HCMV(BAC2), 36h, rep2


title: HFF cells, HCMV(BAC2), 72h, rep1


title: HFF cells, HCMV(BAC2), 12h, rep2


title: ARv7_siNTC_VC16 rep1


title: ARv7_siNFIBX_VC16 rep4


title: ARv7_siNFIBX_VC16 rep3


title: HFF cells, HCMV(BAC2), 12h, rep1


title: ARfl siNFIBX VC16 rep3

value: ARfl C-terminal SP242 abcam (AB227678)


title: HFF cells, mock, rep1


title: ARfl siNFIBX VC16 rep2


title: ARfl siNFIBX VC16 rep1


title: 1411H-FOXA2_III

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Moorenstr. 5

department: Dep. of Urology

institute: Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University

description: 1411H ChIP FOXA2 III

data_processing:
For data analysis, raw reads of fastq format were processed using the ‘fastp’ software (v 0.19.11). Subsequently, clean reads were generated by removing reads containing adapter, reads containing ploy-N, and low-quality reads. Next, high-quality and clean reads were aligned to the ‘Ensembl 110 Homo sapiens GRCh38 (hg38)’ reference genome using ‘BWA mem’ (v 0.7.12). Afterwards, the ‘MACS2’ peak calling software (v 2.1.0) was used to identify enriched regions of the IP compared to the background (q-value < 0.05). Next, the ‘Homer’ software was used to detect de novo sequence motifs, while the ‘ChIPseeker’ allowed to retrieve and annotate peak-related genes.
SOX17- / FOXA2-ChIP data has been normalized to related input controls. Average data of both cell lines and technical replicates has been calculated (see 'SOX17-ChIP avg.' and 'FOXA2-ChIP avg.)
Assembly: Alignment of reads to the Homo sapiens (GRCh38) genome sequence.
Supplementary files format and content: For data analysis, raw reads of fastq format were processed using the ‘fastp’ software (v 0.19.11). Subsequently, clean reads were generated by removing reads containing adapter, reads containing ploy-N, and low-quality reads. Next, high-quality and clean reads were aligned to the ‘Ensembl 110 Homo sapiens GRCh38 (hg38)’ reference genome using ‘BWA mem’ (v 0.7.12). Afterwards, the ‘MACS2’ peak calling software (v 2.1.0) was used to identify enriched regions of the IP compared to the background (q-value < 0.05). Next, the ‘Homer’ software was used to detect de novo sequence motifs, while the ‘ChIPseeker’ allowed to retrieve and annotate peak-related genes.

growth_protocol: GCT72 / 1411H cells were cultured in DMEM-GlutaMaX including 10& FBS (Thermo Fisher Scientific), 0.5 % penicillin/streptomycin  and 200 mMl-glutamine.

extract_protocol:
Upon two washing steps with PBS, DNA-protein-crosslinking was performed by adding 80 µl of ‘ChIP cross-link Gold’ (Diagenode, Seraing, Belgium) to 20 ml PBS containing 1 mM MgCl2 for 30 min. Subsequently, cells were washed twice with PBS before continuing the ChIP with another crosslinking-step using formaldehyde (Sigma-Aldrich, Taufkirchen, Germany) and using the ‘SimpleChIP Plus Enzymatic Chromatin IP Kit’ (Cell Signaling Technology, Leiden, The Netherlands) according to the manufacturers protocol. To digest and fragmentize the chromatin, 0.5 µl micrococcal nuclease per IP was added and the samples were sonicated three times for 20 sec followed by a pause of 30 sec at an amplitude of 80 %. At that step, one IP of the quadruplicates was used to purify DNA and to validate the chromatin digestion and concentration as a quality control. Upon successful digestion and fragmentation, 2 % of input control was extracted and the ChIP was continued according to the manufacturers protocol by incubating 10 µg of antibody / IP over night at 4°C on a Hula mixer at 20 rpm. Upon immunoprecipitation using ‘Protein G’ magnetic beads, the chromatin was eluted and reversed cross-linked before purification of DNA using spin columns. ChIP-seq was performed of IP samples (GCT72, 1411H; each n = 3) and input controls (n = 2) according to the standard procedure at Novogene Corporation (Munich, Germany). Briefly, the quantity and quality of purified DNA was measured by using the ‘Qubit DNA Assay Kit’ in Qubit 3.0 Fluorometer (Life Technologies, CA, USA) and the NanoPhotometer spectrophotometer (IMPLEN, CA, USA), respectively. All samples required a minimum of 5 ng purified DNA, which indicated main peaks between 100 and 500 bp on an agarose gel.
The library was constructed by Novogene Corporation and its quality was monitored on the Agilent Bioanalyzer 2100 system before being pair-end sequenced on an Illumina platform (Illumina, CA, USA).

treatment_protocol: For ChIP, 1 x 107 cells (GCT72, 1411H) per immunoprecipitation (IP) were seeded into 15 cm dishes in quadruplicates.

value: yolk-sac tumor, germ cell tumor


title: SW480, shNT_2

address: 四川省成都市武侯区人民南路三段17号

description: Control

value: shNT


title: SW480, shPcyt2_1_1

address: 四川省成都市武侯区人民南路三段17号

description: Knockdown PCYT2 in SW480 by using shPCYT2#1 lentiviral vector


title: SW480, shPcyt2_1_2

address: 四川省成都市武侯区人民南路三段17号


title: 1411H-SOX17_I

description: 1411H ChIP SOX17 I


title: GCT72-FOXA2_III

description: GCT72 ChIP FOXA2 III


title: input_siNFBX


title: SW480, shNT_1

address: 四川省成都市武侯区人民南路三段17号

description: Control


title: GCT72-SOX17_II

description: GCT72 ChIP SOX17 II


title: GCT72-input_II

description: GCT72 input II

value: input control


title: ARv7_siNFIBX_VC16 rep2


title: ARfl_siNTC_VC16 rep4


title: ARfl_siNTC_VC16 rep2


title: ARv7_siNFIBX_VC16 rep1


title: ARfl_siNTC_VC16 rep1


title: ARfl_siNTC_VC16 rep3


title: 1411H-FOXA2_II

description: 1411H ChIP FOXA2 II


title: Patient 76, Timepoint 2, Chromium gene expression

city: Charlestown

first: Masashi

last: Nomura

address: 149 13th street

department: Pathology

institute: Massachusetts General Hospital

data_processing:
Cellranger v3.1.0 pipeline was used to generate count matrices from Illumina base calls. FASTQ files were aligned to GRCh38 release 93.
Assembly: GRCh38 for Homo sapiens
Supplementary files format and content: RDS

source_name: GBM single-nucleus, SN10, 2nd Recurrent

extract_protocol:
Protocol 1 (Laboratory 1 and laboratory 2 for the cohorts from Duke University, MDACC, Tokyo University Hospital, St. Michael’s Hospital and Pitié-Salpêtrière Hospital): Nuclei from frozen tumor tissue were isolated as previously described. Tissue was thawed and mechanically dissociated in ST buffer (10mM Tris-HCL pH7.5, 146mM NaCl, 1mM CaCl2, 21mM MgCl2) with 0.49% CHAPS (Millipore). Single-nuclei suspensions were filtered using a 40 μm strainer, centrifuged at 500g for 5min, and resuspended in ST buffer supplemented with 0.01% BSA (Sigma). Nuclear suspensions were inspected by microscope, counted using a hemocytometer, and used for 10x Genomics workflow.Protocol 2 (Laboratory 3 for the cohorts from NorLux and SNU cohorts): Tissue samples were thawed and mechanically dissociated in Nuclei EZ lysis buffer (Millipore Sigma) via dounce homogenization.  The solutions were incubated on ice for 5 minutes and mixed 1-2 times during incubation. Single-nuclei suspensions were filtered through a 70 μm strainer and centrifuged at 500g for 5 minutes at 4 C, resuspended in Nuclei EZ Lysis Buffer and incubated on ice for 5 minutes. The solutions were centrifuged at 500g for 5 minutes at 4 C and resuspended in 1% BSA/0.2 UμL RNase Inhibitor/PBS buffer (three times). For the final resuspension, the DAPI was added to the buffer, the solution was filtered through a 40 μm strainer, cells were counted on a Countess II automated cell counter (Thermo Fisher Scientific), and nuclei were taken into the 10x Genomics workflow.
10x Chromium Single Cell 3’ Reagent Kit v3 (10x Genomics) was used according to manufacturer's protocol. In brief, nuclei were loaded on the Chromium Chip (10x Genomics) with a target cell recovery of 6,000-8,000 nuclei and processed in the Chromium Controller. Single-nuclei were partitioned into Gel Beads-in-emulsion (GEMs), followed by RNA reverse transcription with barcoding. Libraries were created by breaking GEMs and pooling barcoded fractions, cDNA amplification, fragmentation and attachment of sample index and adapter, and sequenced on  Novaseq (Illumina).

value: GBM single-nucleus, SN10, 2nd Recurrent

tag: protocol number

value: Protocol 2


title: 1411H-FOXA2_I

description: 1411H ChIP FOXA2 I


title: GCT72-SOX17_III

description: GCT72 ChIP SOX17 III


title: Patient 74, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, SN08, 1st Recurrent

value: GBM single-nucleus, SN08, 1st Recurrent


title: 1411H-SOX17_III

description: 1411H ChIP SOX17 III


title: 1411H-SOX17_II

description: 1411H ChIP SOX17 II


title: 1411H-input_II

description: 1411H input II


title: ARv7_siNTC_VC16 rep2


title: 1411H-input_I

description: 1411H input I


title: Patient 72, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, SN06, 1st Recurrent

value: GBM single-nucleus, SN06, 1st Recurrent


title: GCT72-FOXA2_II

description: GCT72 ChIP FOXA2 II


title: Patient 70, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, SN04, Primary

value: GBM single-nucleus, SN04, Primary


title: GCT72-SOX17_I

description: GCT72 ChIP SOX17 I


title: GCT72-FOXA2_I

description: GCT72 ChIP FOXA2 I


title: Patient 69, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, SN03, Primary

value: GBM single-nucleus, SN03, Primary


title: GCT72-input_I

description: GCT72 input I


title: Patient 78, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, SN12, 1st Recurrent

value: GBM single-nucleus, SN12, 1st Recurrent


title: GBM single-nucleus, Smart-seq2

description: The file All_cells_metadata.xlsx includes information for all individual nuclei analyzed in this study.

data_processing:
We processed Smart-seq2 data from raw reads to gene expression matrices as previously described in Neftel et al, 2019. We used bcl2fastq to generate demultiplexed FASTQ files, and aligned the resulting paired-end scRNA-seq reads to the reference transcriptome using Bowtie (v0.12.7).
Assembly: GRCh38 for Homo sapiens
Supplementary files format and content: rds

source_name: This sample represents a collection of more than 14K single-nuclei from glioblastoma cells.

extract_protocol:
Nuclear suspension was stained by Vybrant DyeCycle Ruby Stain (Thermo Fisher Scientific) immediately before FACS-sorting. Single-nucleus sorting was performed on a FACS Aria Fusion sorter (Becton Dickinson) using 640nm laser (Ruby, 670/14 filter). After doublet discrimination, intact nuclei were selected with ruby positive and were sorted into 96-well plates containing TCL buffer (Qiagen) with 1% beta-mercaptoethanol. Plates were frozen on dry ice immediately after sorting and stored at -80℃ prior to whole transcriptome amplification, library preparation and sequencing.
Whole transcriptome amplification, library construction and sequencing were performed as previously published with slight modification for nucleus as follow4,18. Briefly, on 96-well plates, RNA derived from single-nuclei was first purified with Agencourt RNAClean XP beads (Beckman Coulter). Then, Oligo-dT primed reverse transcription was performed using Maxima H Minus reverse transcriptase (Thermo Fisher Scientific) and locked TSO oligonucleotide (Qiagen). This was followed by PCR amplification (22 cycles for snRNA-seq) using KAPA HiFi HotStart ReadyMix (KAPA Biosystems) with subsequent Agencourt AMPure XP bead purification. Libraries were tagmented using the Nextera XT Library Prep kit (Illumina) with custom barcode adapters. Libraries from 768 cells with unique barcodes were pooled and sequenced on Illumina sequencer.

value: GBM single-nucleus

tag: number of cells

value: glioblastoma

tag: protocol


title: Patient 78, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, SN12, Primary

value: GBM single-nucleus, SN12, Primary


title: Patient 77, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, SN11, 2nd Recurrent

value: GBM single-nucleus, SN11, 2nd Recurrent


title: Patient 77, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, SN11, Primary

value: GBM single-nucleus, SN11, Primary


title: Patient 66, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, NL10, 1st Recurrent

value: GBM single-nucleus, NL10, 1st Recurrent


title: Patient 76, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, SN10, Primary

value: GBM single-nucleus, SN10, Primary


title: Patient 65, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, NL09, 1st Recurrent

value: GBM single-nucleus, NL09, 1st Recurrent


title: Patient 64, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, NL08, 1st Recurrent

value: GBM single-nucleus, NL08, 1st Recurrent


title: Patient 74, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, SN08, Primary

value: GBM single-nucleus, SN08, Primary


title: Patient 72, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, SN06, Primary

value: GBM single-nucleus, SN06, Primary


title: Patient 63, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, NL07, Primary

value: GBM single-nucleus, NL07, Primary

value: Protocol 2


title: Patient 62, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, NL06, 1st Recurrent

value: GBM single-nucleus, NL06, 1st Recurrent


title: Patient 68, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, SN02, 1st Recurrent

value: GBM single-nucleus, SN02, 1st Recurrent


title: Patient 69, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, SN03, 1st Recurrent

value: GBM single-nucleus, SN03, 1st Recurrent


title: Patient 62, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, NL06, Primary

value: GBM single-nucleus, NL06, Primary


title: Patient 75, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, SN09, 1st Recurrent

value: GBM single-nucleus, SN09, 1st Recurrent


title: Patient 63, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, NL07, 1st Recurrent

value: GBM single-nucleus, NL07, 1st Recurrent


title: Patient 70, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, SN04, 1st Recurrent

value: GBM single-nucleus, SN04, 1st Recurrent


title: Patient 75, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, SN09, Primary

value: GBM single-nucleus, SN09, Primary


title: Patient 67, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, SN01, 1st Recurrent

value: GBM single-nucleus, SN01, 1st Recurrent


title: Patient 67, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, SN01, Primary

value: GBM single-nucleus, SN01, Primary


title: Patient 66, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, NL10, Primary

value: GBM single-nucleus, NL10, Primary


title: Patient 56, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, FR16, 1st Recurrent

value: GBM single-nucleus, FR16, 1st Recurrent

value: Protocol 1


title: Patient 64, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, NL08, 2nd Recurrent

value: GBM single-nucleus, NL08, 2nd Recurrent


title: Patient 55, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, FR15, 1st Recurrent

value: GBM single-nucleus, FR15, 1st Recurrent


title: Patient 54, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, FR14, 1st Recurrent

value: GBM single-nucleus, FR14, 1st Recurrent


title: Patient 56, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, FR16, Primary

value: GBM single-nucleus, FR16, Primary


title: Patient 58, Timepoint 3, Chromium gene expression

source_name: GBM single-nucleus, NL02, 2nd Recurrent

value: GBM single-nucleus, NL02, 2nd Recurrent

value: Protocol 2


title: Patient 53, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, FR13, 1st Recurrent

value: GBM single-nucleus, FR13, 1st Recurrent


title: Patient 58, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, NL02, 1st Recurrent

value: GBM single-nucleus, NL02, 1st Recurrent


title: Patient 55, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, FR15, 2nd Recurrent

value: GBM single-nucleus, FR15, 2nd Recurrent


title: Patient 58, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, NL02, Primary

value: GBM single-nucleus, NL02, Primary


title: Patient 52, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, FR12, Primary

value: GBM single-nucleus, FR12, Primary


title: Patient 53, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, FR13, 2nd Recurrent

value: GBM single-nucleus, FR13, 2nd Recurrent


title: Patient 52, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, FR12, 1st Recurrent

value: GBM single-nucleus, FR12, 1st Recurrent


title: Patient 51, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, FR11, 1st Recurrent

value: GBM single-nucleus, FR11, 1st Recurrent


title: Patient 65, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, NL09, Primary

value: GBM single-nucleus, NL09, Primary


title: Patient 51, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, FR11, Primary

value: GBM single-nucleus, FR11, Primary


title: Patient 50, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, FR10, Primary

value: GBM single-nucleus, FR10, Primary

value: Protocol 1


title: Patient 49, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, FR09, Primary

value: GBM single-nucleus, FR09, Primary


title: Patient 68, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, SN02, Primary

value: GBM single-nucleus, SN02, Primary


title: Patient 47, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, FR07, Primary

value: GBM single-nucleus, FR07, Primary


title: Patient 45, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, FR05, 1st Recurrent

value: GBM single-nucleus, FR05, 1st Recurrent


title: Patient 48, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, FR08, Primary

value: GBM single-nucleus, FR08, Primary


title: Patient 48, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, FR08, 1st Recurrent

value: GBM single-nucleus, FR08, 1st Recurrent


title: Patient 47, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, FR07, 1st Recurrent

value: GBM single-nucleus, FR07, 1st Recurrent


title: Patient 42, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, FR02, Primary

value: GBM single-nucleus, FR02, Primary


title: Patient 41, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, FR01, Primary

value: GBM single-nucleus, FR01, Primary


title: Patient 43, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, FR03, 2nd Recurrent

value: GBM single-nucleus, FR03, 2nd Recurrent


title: Patient 54, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, FR14, Primary

value: GBM single-nucleus, FR14, Primary


title: Patient 40, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, SM07, 1st Recurrent

value: GBM single-nucleus, SM07, 1st Recurrent


title: Patient 39, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, SM06, 1st Recurrent

value: GBM single-nucleus, SM06, 1st Recurrent


title: Patient 40, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, SM07, Primary

value: GBM single-nucleus, SM07, Primary


title: Patient 39, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, SM06, Primary

value: GBM single-nucleus, SM06, Primary


title: Patient 43, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, FR03, Primary

value: GBM single-nucleus, FR03, Primary


title: Patient 49, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, FR09, 1st Recurrent

value: GBM single-nucleus, FR09, 1st Recurrent

value: Protocol 1


title: Patient 38, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, SM05, Primary

value: GBM single-nucleus, SM05, Primary


title: Patient 37, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, SM04, 2nd Recurrent

value: GBM single-nucleus, SM04, 2nd Recurrent


title: Patient 36, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, SM03, Primary

value: GBM single-nucleus, SM03, Primary


title: Patient 36, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, SM03, 1st Recurrent

value: GBM single-nucleus, SM03, 1st Recurrent


title: Patient 38, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, SM05, 1st Recurrent

value: GBM single-nucleus, SM05, 1st Recurrent


title: Patient 50, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, FR10, 1st Recurrent

value: GBM single-nucleus, FR10, 1st Recurrent


title: Patient 37, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, SM04, Primary

value: GBM single-nucleus, SM04, Primary


title: Patient 34, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, SM01, 1st Recurrent

value: GBM single-nucleus, SM01, 1st Recurrent


title: Patient 34, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, SM01, Primary

value: GBM single-nucleus, SM01, Primary


title: Patient 35, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, SM02, 1st Recurrent

value: GBM single-nucleus, SM02, 1st Recurrent


title: Patient 45, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, FR05, Primary

value: GBM single-nucleus, FR05, Primary


title: Patient 33, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, TK14, 1st Recurrent

value: GBM single-nucleus, TK14, 1st Recurrent


title: Patient 33, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, TK14, Primary

value: GBM single-nucleus, TK14, Primary


title: Patient 42, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, FR02, 1st Recurrent

value: GBM single-nucleus, FR02, 1st Recurrent


title: Patient 32, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, TK13, 1st Recurrent

value: GBM single-nucleus, TK13, 1st Recurrent


title: Patient 41, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, FR01, 1st Recurrent

value: GBM single-nucleus, FR01, 1st Recurrent


title: Patient 31, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, TK12, 1st Recurrent

value: GBM single-nucleus, TK12, 1st Recurrent

value: Protocol 1


title: Patient 32, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, TK13, Primary

value: GBM single-nucleus, TK13, Primary


title: Patient 31, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, TK12, Primary

value: GBM single-nucleus, TK12, Primary


title: Patient 30, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, TK11, Primary

value: GBM single-nucleus, TK11, Primary


title: Patient 30, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, TK11, 1st Recurrent

value: GBM single-nucleus, TK11, 1st Recurrent


title: Patient 29, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, TK10, Primary

value: GBM single-nucleus, TK10, Primary


title: Patient 29, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, TK10, 1st Recurrent

value: GBM single-nucleus, TK10, 1st Recurrent


title: Patient 27, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, TK08, 1st Recurrent

value: GBM single-nucleus, TK08, 1st Recurrent


title: Patient 27, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, TK08, Primary

value: GBM single-nucleus, TK08, Primary


title: Patient 35, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, SM02, Primary

value: GBM single-nucleus, SM02, Primary


title: Patient 25, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, TK06, Primary

value: GBM single-nucleus, TK06, Primary


title: Patient 26, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, TK07, Primary

value: GBM single-nucleus, TK07, Primary


title: Patient 24, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, TK05, Primary

value: GBM single-nucleus, TK05, Primary


title: Patient 24, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, TK05, 1st Recurrent

value: GBM single-nucleus, TK05, 1st Recurrent


title: Patient 23, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, TK04, 1st Recurrent

value: GBM single-nucleus, TK04, 1st Recurrent


title: Patient 26, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, TK07, 1st Recurrent

value: GBM single-nucleus, TK07, 1st Recurrent


title: Patient 25, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, TK06, 1st Recurrent

value: GBM single-nucleus, TK06, 1st Recurrent


title: Patient 22, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, TK03, 1st Recurrent

value: GBM single-nucleus, TK03, 1st Recurrent

value: Protocol 1


title: Patient 23, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, TK04, Primary

value: GBM single-nucleus, TK04, Primary


title: Patient 21, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, TK02, Primary

value: GBM single-nucleus, TK02, Primary


title: Patient 21, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, TK02, 1st Recurrent

value: GBM single-nucleus, TK02, 1st Recurrent


title: Patient 22, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, TK03, Primary

value: GBM single-nucleus, TK03, Primary


title: Patient 20, Timepoint 3, Chromium gene expression

source_name: GBM single-nucleus, TK01, 2nd Recurrent

value: GBM single-nucleus, TK01, 2nd Recurrent


title: Patient 32, Timepoint 3, Chromium gene expression

source_name: GBM single-nucleus, TK13, 2nd Recurrent

value: GBM single-nucleus, TK13, 2nd Recurrent


title: Patient 20, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, TK01, Primary

value: GBM single-nucleus, TK01, Primary


title: Patient 9, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, MD02, Primary

value: GBM single-nucleus, MD02, Primary


title: Patient 9, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, MD02, 1st Recurrent

value: GBM single-nucleus, MD02, 1st Recurrent


title: Patient 8, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, MD01, 1st Recurrent

value: GBM single-nucleus, MD01, 1st Recurrent


title: Patient 6, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, DU06, Primary

value: GBM single-nucleus, DU06, Primary


title: Patient 8, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, MD01, Primary

value: GBM single-nucleus, MD01, Primary


title: Patient 5, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, DU05, 1st Recurrent

value: GBM single-nucleus, DU05, 1st Recurrent


title: Patient 28, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, TK09, 1st Recurrent

value: GBM single-nucleus, TK09, 1st Recurrent


title: Patient 6, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, DU06, 1st Recurrent

value: GBM single-nucleus, DU06, 1st Recurrent


title: Patient 28, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, TK09, Primary

value: GBM single-nucleus, TK09, Primary


title: Patient 5, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, DU05, Primary

value: GBM single-nucleus, DU05, Primary

value: Protocol 1


title: Patient 4, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, DU04, 1st Recurrent

value: GBM single-nucleus, DU04, 1st Recurrent


title: Patient 4, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, DU04, Primary

value: GBM single-nucleus, DU04, Primary


title: Patient 3, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, DU03, 1st Recurrent

value: GBM single-nucleus, DU03, 1st Recurrent


title: Patient 3, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, DU03, Primary

value: GBM single-nucleus, DU03, Primary


title: Patient 2, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, DU02, 1st Recurrent

value: GBM single-nucleus, DU02, 1st Recurrent


title: Patient 2, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, DU02, Primary

value: GBM single-nucleus, DU02, Primary


title: Patient 1, Timepoint 1, Chromium gene expression

source_name: GBM single-nucleus, DU01, Primary

value: GBM single-nucleus, DU01, Primary


title: Patient 1, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, DU01, 1st Recurrent

value: GBM single-nucleus, DU01, 1st Recurrent


title: vehicle control, rep 1

city: Daejeon

first: Soontag

last: Jung

address: 141 Gajeong-ro, Yuseong-gu

department: Developmental and reproductive toxicology

country: South Korea

institute: Korea Institute of Toxicology

data_processing:
Raw reads underwent adapter and low-quality sequence removal using Trimmomatic v0.38, followed by quality checks with FastQC before and after trimming.
Trimmed reads were aligned to the GRCh38 reference genome using HISAT2 v2.1.0.
Mapped reads were then assembled individually for each gene using StringTie v2.1.3b.
Assembled read counts were normalized using the trimmed mean of M-values method via the EdgeR v4.0.9 within R v4.3.2.
Assembly: GRCh38
Supplementary files format and content: Comma separated value file includes raw count for each sample

source_name: Rencell VM

growth_protocol: ReNcell VM (Merck Millipore, Darmstadt, Germany), an immortalized human neural progenitor cell line, was employed as a substitute for primary human neural progenitor cells. Before ReNcell VM seeding, all tissue culture plastic ware was coated with DMEM/F-12 supplemented with GlutaMAX™ (Gibco) and 20 μg/mL laminin (Gibco) at 37 °C for 4 h. ReNcell VM were maintained in growth medium consisting of ReNcell® NSC Maintenance Media (Merck Millipore) supplemented with 20 ng/mL epidermal growth factor (EGF, Merck Millipore), 20 ng/mL basic fibroblast growth factor (bFGF, Merck Millipore), and 1% penicillin/streptomycin (Thermo Fisher Scientific, Waltham, MA). Cells were cultured in a humidified incubator at 37 °C with 5% CO2, and the growth medium was changed every two days. Neurospheres were prepared using round bottom ultra-low attachment 384-well spheroid microplates (ULA plate, Corning, Tewksbury, MA). Briefly, ReNcell VM cells that reached confluency were detached with Accutase (Innovative Cell Technologies, San Diego, CA) and seeded on ULA plates at 8000 cells/well in 40 μL of growth medium. Neurospheres were cultured in a humidified incubator at 37 °C with 5% CO2 for 4 days without replacing the medium.

extract_protocol:
Total RNA was extracted by pooling six neurospheres using the Maxwell® RSC simplyRNA Cells Kit (Promega, Madison, WI) following the manufacturer's instructions.
cDNA libraries for RNA-seq were prepared using SureSelect RNA Direct Human Library Preparation kit following manufacturer's protocols.

treatment_protocol: Neurospheres were transferred to a laminin-coated 48-well plate and then cultured in differentiation medium containing N-2 Supplement (Gibco) in DMEM/F-12 supplemented with GlutaMAX™ (Gibco), treated with test substances at concentrations ranging from 0.3 to 100 μM. . The neurospheres were cultured for 6   days, with the differentiation medium and test substances replaced every 2 days.

value: Rencell VM

value: Neurosphere

value: DMSO 0.1%


title: vehicle control, rep 2


title: Mix 100 μM, rep 2

value: Mix 100 uM


title: DProP 100 μM, rep 1

value: DProP 100 uM


title: DProP 100 μM, rep 2


title: DEP 100 μM, rep 2

value: DEP 100 uM


title: DPP 100 μM, rep 2

value: DPP 100 uM


title: DPP 100 μM, rep 1


title: Patient 20, Timepoint 2, Chromium gene expression

source_name: GBM single-nucleus, TK01, 1st Recurrent

value: GBM single-nucleus, TK01, 1st Recurrent


title: HUVEC, 240 min TNFa, ATAC

city: Heidelberg

first: Isabelle

last: Seufert

address: Im Neuenheimer Feld 280

institute: DKFZ

description: 10x Genomics

data_processing:
Demultiplexing, barcode processing, genome mapping, gene counting (including introns) and aggregation were conducted using the Cell Ranger ARC software v1.0.1 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc).
Assembly: GRCh38-2020-A
Supplementary files format and content: h5 single cell count matrix of RNA genes and ATAC peaks, tab-separated ATAC fragment file, comma-separated RNA and ATAC cell barcode info file
Library strategy: Multiome snRNA-/snATAC-seq

source_name: Umbilical vein endothelial cells

growth_protocol: HUVECs from pooled donors (Lonza, cat. #00191027, lot #18TL232828) were cultured in endothelial basal medium (EBM-2) with supplements (Lonza, cat. #CC-3162). Low passage number cells were seeded in 18-well slides (Ibidi) and starved for 20-24 h in EBM + 0.5% FBS prior to treatment.

extract_protocol:
For harvesting, cells were treated with trypsin and resuspended in EBM + 0.5% FBS. After centrifugation, the cell pellet was resuspended in PBS/BSA.
Libraries were prepared according to the Chromium Single Cell Multiome ATAC and Gene Expression protocol v1 from 10x Genomics (Pleasanton, USA).

treatment_protocol: HUVECs were treated with 10 ng/mL human TNFα (PeproTech, cat. #300-01A) for 0, 30 and 240 min.

value: Umbilical vein endothelial cells

tag: time point

value: 240 min

value: TNFa


title: DEP 100 μM, rep 1


title: HUVEC, 240 min TNFa, RNA

description: 10x Genomics

molecule: nuclear RNA


title: HUVEC, 30 min TNFa, ATAC

description: 10x Genomics

value: 30 min


title: HUVEC, 30 min TNFa, RNA

description: 10x Genomics


title: HUVEC, 240 min TNFa, replicate 3 [snATAC-seq]

description: 10x Genomics, TurboATAC protocol

data_processing:
Demultiplexing, barcode processing, genome mapping and aggregation were conducted using the Cell Ranger ATAC software v2.1.0 (https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac).
Assembly: GRCh38-2020-A-2.0.0
Supplementary files format and content: h5 single cell peak count matrix, tab-separated fragment file, comma-separated single cell info file
Library strategy: snATAC-seq

extract_protocol:
For harvesting, cells were treated with trypsin and resuspended in EBM + 0.5% FBS. After centrifugation, the cell pellet was resuspended in PBS/BSA.
Libraries were prepared using our improved TurboATAC protocol that provides an increased Tn5 integration efficiency (I Seufert et al. 2023, Front Epigenet Epigenom; doi: 10.3389/freae.2023.1245879) with the Chromium Next GEM Single Cell ATAC kit v2 from 10x Genomics (Pleasanton, USA).


title: HUVEC, 0 min TNFa, RNA

description: 10x Genomics

value: 0 min


title: HUVEC, 240 min TNFa, replicate 2 [snATAC-seq]

description: 10x Genomics, TurboATAC protocol


title: HUVEC, 0 min TNFa, ATAC

description: 10x Genomics


title: HUVEC, 30 min TNFa, replicate 3 [snATAC-seq]

description: 10x Genomics, TurboATAC protocol


title: HUVEC, 0 min TNFa, replicate 2 [snATAC-seq]

description: 10x Genomics, TurboATAC protocol


title: HUVEC, 30 min TNFa, replicate 2 [snATAC-seq]

description: 10x Genomics, TurboATAC protocol


title: HUVEC, 240 min TNFa, replicate 1 [snATAC-seq]

description: 10x Genomics, TurboATAC protocol


title: HUVEC, 30 min TNFa, replicate 1 [snATAC-seq]

description: 10x Genomics, TurboATAC protocol


title: HUVEC, 0 min TNFa, replicate 1 [snATAC-seq]

description: 10x Genomics, TurboATAC protocol


title: HUVEC, 240 min TNFa, replicate 3

description: 10x Genomics

data_processing:
Demultiplexing, barcode processing, genome mapping, gene counting (including introns) and aggregation were conducted using the Cell Ranger software v7.1.0 (support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38-2020-A-2.0.0
Supplementary files format and content: h5 single cell count matrix of features

extract_protocol:
For harvesting, cells were treated with trypsin and resuspended in EBM + 0.5% FBS. After centrifugation, the cell pellet was resuspended in PBS/BSA.
Libraries were prepared according to the Chromium Next GEM Single Cell 5' (dual index) protocol v2 from 10x Genomics (Pleasanton, USA).


title: HUVEC, 30 min TNFa, replicate 3

description: 10x Genomics