title: DbmDMSO DbmD2

first: Chengguo

last: Wei

address: 1468 Madison Ave, Annenberg 23-16

description: DbmDMSO

data_processing:
The RNA-seq data were analyzed by following the procedure described below.
Briefly,  after sequence quality filtering at a cut-off of a minimum quality score Q20 in at least 90%  bases for the paired-end 150bp FASTQ sequencing data, the good-quality reads aligned  to Reads were processed and aligned to the University of California Santa Cruz (UCSC)  Mus musculus reference genome and transcriptome (build mm10) using the Burrows-  Wheeler Aligner (bwa). The reads that are uniquely aligned to the exon and splicing  junction sites for each transcript were combined to calculate an expression level for a  corresponding transcript and further normalized based on reads per kilobase per million  reads to compare transcription levels among samples.
The transcripts with a low raw  read count <100 in all the samples were excluded for downstream analysis. Gene  expression value was transformed to the log 2 base scale. Principle Component Analysis  (PCA) was first performed to assess the sample correlations using the expression data  of all the genes. The differentially expressed genes in NASH mice compared with control  mice were identified by the R package limma test. A specific gene was considered  differentially expressed if the P-value was ≤0.05.
The Gene Ontology and pathway  analysis for the differentially expressed genes were then performed with a fold change cutoff of ≥1.5 using INGENUITY© IPA (www.ingenuity.com/products/ipa) and the online  tool Enrichr. The read coverage of gene functional elements was also visualized by the  Integrative Genome Viewer tool (www.broadinstitute.org/igv/) from the genome alignment  file. Heatmap analysis was performed for the top 50 differentially expressed genes after  the median center was transformed using Multi-Experiment Viewer software.
Genome_build: mm10

source_name: Kidney glomerular

extract_protocol:
Mice glomeruli were isolated as previously reported. Total RNA was extracted from glomeruli using Trizol method. Purified RNA underwent DNA digestion using RNase-free DNase set (79254, Qiagen). RNA sequencing was performed at Beijing Genomics Institute.
Purifed RNA underwent DNA digestion using RNase-free DNase  set (79254, Qiagen, Germantown, MD). Only samples with an RNA  integrity value of > 7.5 were used for mRNA sequencing at the CLC Genomics and  Epigenomics Core Facility at Weil Cornell Medical College for library construction and sequencing.

treatment_protocol: Male db/db homozygous mice of 8 weeks old on BKS background were purchased from The Jackson Laboratory (Bar Habor, ME). The sex- and age-matched littermate db/m mice were used as controls. The mice at 10 weeks of age were given puerarin (Sigma-Aldrich, Saint Louis MO) dissolved in 5% DMSO by oral gavage at a dose of 20mg/kg body weight/day, or 5% DMSO vehicle as control, for 6 weeks. Blood glucose was monitored every week and blood and urine samples were collected when the mice were sacrificed. All experimental methods were performed in accordance with the approved guidelines as described in the Guide for the Care and Use of Laboratory Animals 38. All animal studies were approved by the Institutional Animal Care and Use Committee at the Icahn School of Medicine at Mount Sinai, New York, NY.

value: C57BL/6J mice

tag: treatment

value: Dbm DMSO control


title: DbDbPue DbDbPue2

status: Public on Feb 15 2022

type: SRA

city: New York

state: NY

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: DbDbPue

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

value: DbDb Puerarin


title: DbDbPue DbDbPue3

description: DbDbPue


title: DbDbDMSO DbDbD1

description: DbDbDMSO

value: DbDb DMSO control


title: DbDbDMSO DbDbD3

description: DbDbDMSO


title: DbmDMSO DbmD3

description: DbmDMSO


title: DbDbDMSO S153

description: DbDbDMSO


title: DbmDMSO S185

description: DbmDMSO


title: pADamID_PT_newAntibody_24h_Dam_r2

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

description: Dam control in E14TG2a (with OsTir1), after 24h of IAA

library_source: genomic

data_processing:
Library strategy: pA-DamID
The full protocol is described in the corresponding manuscript.
The constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts.
Remaining sequences were mapped to the mouse genome (mm10) using bwa mem 0.7.17.
Reads overlapping GATC fragments were counted in 10kb bins and normalized to 1 million reads, after which a log2-ratio was calculated of LaminB1 over the Dam control using custom R scripts. Finally, samples were z-scale normalized to account for different in dynamic range between replicates and experiments.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files of "raw" log2-normalized LaminB1 pADamID scores for 10kb genomic bins; tsv files with genomic coordinates and all z-scores per replicate / average scores per condition.

molecule: genomic DNA

growth_protocol: E14Tg2a mouse embryonic stem cells (mESCs) and derived cell lines were cultured in serum-free DMEM/F12 (Gibco) and Neurobasal (Gibco) medium (1:1) supplemented with N-2 (Gibco), B-27 (Gibco), BSA (0.05%; Gibco), 104 U of leukemia inhibitory factor (LIF; Millipore), the MEK inhibitor PD0325901 (1 μM; Selleckchem), the GSK-3β inhibitor CHIR99021 (3 μM; Cayman Chemical) and 1-thioglycerol (1.5 × 10−4 M; Sigma-Aldrich) on 0.1% gelatin-coated plates. The cell lines were passaged every two days.

extract_protocol:
1 million permeabilized cells were processed with pA-DamID (van Schaik, 2020) with a LaminB1 antibody and for a Dam control condition, to specifically deposit m6A marks at peripherally positioned chromatin. Genomic DNA was isolated using the Bioline Isolate II Genomic DNA Kit.
The full protocol is described in Leemans, 2019, except that the DpnII digestion is omitted. 500 ng of genomic DNA was digested at Dam-methylated GATC sequences with DpnI and ligated to adapters. DNA fragments were amplified with 15-19 PCR cycles. Amplified fragments were further processed with end-repair, 3A-overhang tailing and Y-shaped adapter ligation, before a final round of 10-12 PCR cycles with illumina index adapters.

treatment_protocol: Protein depletion was induced by addition of auxin (IAA) with a final concentration of 500 μM (I5148-10G, Sigma-Aldrich). Protein degradation was induced at different time points and all samples were collected at the end of the time course.

tag: cell type

value: Embyonic stem cell

tag: library type

value: pA-DamID

tag: genetic modification

tag: time point


title: DbmDMSO S184

description: DbmDMSO


title: pADamID_PT_newAntibody_24h_Dam_r1


title: pADamID_PT_newAntibody_0h_Dam_r1

description: Dam control in E14TG2a (with OsTir1), after 0h of IAA


title: DbDbDMSO S152

description: DbDbDMSO


title: DbDbPue S144

description: DbDbPue


title: pADamID_PT_newAntibody_24h_r2

description: LaminB1 pA-DamID in E14TG2a (with OsTir1), after 24h of IAA; new lot of LaminB1 antibody


title: pADamID_PT_newAntibody_0h_r2

description: LaminB1 pA-DamID in E14TG2a (with OsTir1), after 0h of IAA; new lot of LaminB1 antibody


title: pADamID_PT_newAntibody_0h_r1


title: pADamID_PT_newAntibody_24h_r1


title: F1-1A6_S6 SCC Bulk RNAseq SCC098

city: Seattle

first: Martin

last: Prlic

state: WA

address: 1100 Fairview Ave, Mail stop E5-110

institute: Fred Hutch

data_processing:
Bulk RNAseq samples were processed using Galaxy, alighed with STARaligner
Genome_build: GRCh38
Supplementary_files_format_and_content: comma separated values with abundance measurements for each target.

organism: Homo sapiens

source_name: SCC-derived Treg Cells

extract_protocol:
RNA was extracted using SMART-Seq v4 Ultra Low Input RNA kit protocols for bulk RNA-seq
RNA was constructed using NexteraXT DNA sample preperation protocol for bulk RNA-seq

treatment_protocol: Tregs were sorted and cultured with either no stimulation, stimulation with anti-CD3/CD28/CD2 beads,  or stimulation with anti-CD3/CD28/CD2 beads and IL-1b for 1, 2, or 3 days.

tag: phenotype

tag: donors

tag: stimulation

tag: timepoint

value: Day 1

tag: tissue

value: Squamous Cell Carcinoma


title: WT_CDC1_4

city: Parkville

first: Nagaraj

middle: Sundara

last: Moily

state: Victoria

address: Bio21 Institute, The University of Melbourne,

department: Biochemistry and Molecular Biology

country: Australia

institute: The University of Melbourne

data_processing:
Base calling was performed with Illumina Control Software and Illumina CASAVA. FastQC was used to perform quality control of the sequencing
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38/mm10 whole genome using STAR aligner as per default parameters
All 100-base-pair single-end reads were mapped to the reference mouse genome (GRCm38/mm10) using STAR aligner, and gene-wise counts were obtained using Subread package.Counts of samples run on two lanes were averaged and differential expression analysis of RNA sequencing data was carried out using the edgeR  and voom- limma packages in bioconductor.
Genome_build: GRCm38.dna.toplevel.fa
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: txt file for all samples for every gene. There are two count files on every sample record, one for each sequencing run performed in a different lane.

extract_protocol:
Total RNA extracted using theRNeasy mini Kit (Qiagen) as per manufacturer's protocols
RNA libraries were prepared for sequencing using standard Illumina Truseq protocols

treatment_protocol: Splenic cDC1s, B cells and CD11cintCD24+CD8int cells were sorted (95 to 99% purity) with the Influx™ Cell Sorter (BD Biosciences)

value: Spleen

tag: age

value: post natal day 21

tag: genotype

value: wild type


title: M1_CDC1_4


title: WT_CDC1_1


title: WT_Bcell_3

source_name: B Cells

value: B Cells


title: WT_Bcell_2


title: WT_CDC1_3


title: WT_Bcell_4


title: M1_CDC1_3


title: WT_Bcell_1


title: M1_CDC1_1


title: M1_CD11cCD24CD8_4

source_name: CD11cintCD24+CD8int cells

value: CD11cintCD24+CD8int cells


title: M1_CDC1_2


title: M1_CD11cCD24CD8_3


title: M1_CD11cCD24CD8_2


title: M1_CD11cCD24CD8_1


title: pADamID_PT_newAntibody_0h_Dam_r2


title: PRWT_WT2

city: Adelaide

first: Thao

last: Dinh

state: South Australia

address: North Terrace

institute: University of Adelaide

data_processing:
Sequence reads were trimmed for adaptor sequence, filtered for reads with quality >=30, then mapped to mm10 whole genome using bowtie2 with parameters -I 0 -X 500 --fr --dovetail
Aligned reads were filtered for MAPQ >=30, non-mitochondrial reads and de-duplicated
Peak calling was through MACS2 with parameters --format BAMPE --gsize '1870000000' --qvalue '1e-10' --nomodel --extsize '100' --shift '50'
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak bed file including peak information, generated using MACS2
Supplementary_files_format_and_content: bigwig file for visualisation, generated from MACS2 bedgraph

source_name: pre-ovulatory granulosa cells

growth_protocol: 21 days old mice

extract_protocol:
Fresh cells were cytoplasmically lysed then tagmentation using Tn5 enzyme was performed.
Tagmented DNA was purified, then library was amplified and repurified. DNA fragments between 200-600bp in size were selected using magnetic beads. Libraries were quantified and sequenced on Illumina HiSeq 2500 (150bp read, paired-end).

treatment_protocol: mice were injected with 5 IU eCG, after 46 hours mice were either humanely killed (0h treatment) or injected with 5 IU hCG. hCG-injected mice were humanely killed 6 h post-treatment. All mice were then dissected and ovaries were punctured for granulosa cell collection.

value: 6h post-hCG

value: wildtype

value: granulosa cells

value: 21 days


title: M1_Bcell_3


title: WT_CDC1_2


title: M1_Bcell_1


title: PRKO_KO1

value: PR knockout


title: M1_Bcell_2


title: PRKO_KO2


title: LH_PMSG1

value: CBA x C57BL/6 F1


title: LH_PMSG2


title: LH_hCG2

source_name: peri-ovulatory granulosa cells

value: 0h post-hCG


title: LH_hCG1


title: HSB2.dRNAseq.infected.B

city: Würzburg

first: Florian

last: Erhard

address: Versbacher Str. 7

department: Institut für Virologie und Immunbiologie

country: Germany

institute: Julius-Maximilians-Universität Würzburg

data_processing:
Reads that passed the chastity filter on the NextSeq 500 were subject to de-multiplexing and trimming of TriLink adapter residuals using Illumina’s bcl2fastq v2 software (v2.19.1). To refine the output, read quality was checked with FastQC software (v0.11.5) and reads shorter 10 bases or longer 25 bases or containing “N” as a base call, were discarded.
STAR_2.5.3a was used to map all reads against a combined index prepared for the human genome (Ensembl 90) and the HHV6A genome (genbank accession X83413). The following parameters were used: --alignIntronMax 1 --outFilterMismatchNmax 1 --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 10 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 16.
TSS were called with iTiSS version 1.2
Details of dRNA sequencing data analysis is previously published by us (Whisnant et al., 2020).
Genome_build: hg38, X83413

source_name: HSB2 cells (HHV-6 Foundation, USA)

growth_protocol: HSB2 cells were grown in RPMI1640 media in presence of Streptomycin and Penicilin.

extract_protocol:
RNA was extracted using TRI-reagent (SIGMA) following manufacturer's instructions.
Custom
HSB-2 cells were obtained from HHV-6 Foundation, USA and were maintained in RPMI 1640 media with 200 units of Penicilin and Streptomycin. HSB2 cells were infected with HHV-6A atan MOI of 5-10. 3 days post infection, total RNA was prepared using TRI-reagent (SIGMA). Two biological replicates were prepared on two different days. Transcription start site profiling dataset using dRNA-seq was prepared according to the published protocol (Sharma and Vogel, 2014) with some modifications by the Core Unit Systems Medicine (Würzburg). In brief, total RNA was extracted from HHV-6A and mock infected HSB-2 cells. For each sample 3 µg of DNase-digested RNA was treated with T4 Polynucleotide Kinase (NEB) for 1 h at 37 °C. RNA was purified with Oligo Clean & Concentrator columns (Zymo) and each sample was split into an Xrn1 (+Xrn1) and a mock (−Xrn1) sample. The samples were treated with 1.5 U Xrn1 (NEB; +Xrn1) or water (−Xrn1) for 1 h at 37 °C. Digest efficiency was checked on a 2100 Bioanalyzer (Agilent) and 5′ caps were removed by incubation with 20 U of RppH (NEB) for 1 h at 37 °C. Afterwards, RNA was purified and eluted in 7 µL and 6 µL were used as input material for the NEBNext Multiplex Small RNA Library Prep Set for Illumina. Library preparation was performed according to the manufacturer’s instruction with the following modifications: 3′ adapter, SR RT primer and 5′ adapter were diluted 1:2, 13 cycles of PCR were performed with 30 sec of elongation time, and no size selection was performed at the end of library preparation. Concentrations of libraries were determined using the Qubit 3.0 (Thermo Scientific) and their fragment sizes were determined using the Bioanalyzer. Libraries were pooled equimolar. Sequencing of 75 bp single-end reads was performed on a NextSeq 500 (Illumina) at the Core Unit Systems Medicine in Würzburg (dRNA-seq).

treatment_protocol: HSB2 cells were infected with HHV-6A at an mOI of 5-10

tag: cell line

value: HSB2 cells (HHV-6 Foundation, USA)

value: Childhood T acute lymphoblastic leukemia cells

tag: infection

value: HHV-6A infection; Replicate 2

tag: fraction

value: Total RNA used for dRNA-seq


title: HSB2.dRNAseq.infected.A

value: HHV-6A infection; Replicate 1


title: HSB2.dRNAseq.mock.B

value: No infection; Replicate 2


title: HSB2.dRNAseq.mock.A

value: No infection; Replicate 1


title: AGO.uninf.B (lytic)

data_processing:
Reads that passed the chastity filter on the NextSeq 500 were subject to de-multiplexing and trimming of TriLink adapter residuals using Illumina’s bcl2fastq v2 software (v2.19.1). To refine the output, read quality was checked with FastQC software (v0.11.5) and reads shorter 10 bases or longer 25 bases or containing “N” as a base call, were discarded.
STAR_2.5.3a was used to map all reads against a combined index prepared for the human genome (Ensembl 90) and the HHV6A genome (genbank accession X83413). The following parameters were used: --alignIntronMax 1 --outFilterMismatchNmax 1 --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 10 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 16.
Reads were counted using Gedi 1.0.3.
Genome_build: hg38, X83413
Supplementary_files_format_and_content: HSB2.counts.tsv.gz

extract_protocol:
RNA was extracted using TRI-reagent (SIGMA) following manufacturer's instructions.
NEXTflex Small RNA-seq kit v3 (Bioo Scientific, Germany)
HSB-2 cells were obtained from HHV-6 Foundation, USA and were maintained in RPMI 1640 media. For HHV-6A infecttion, cells were seeded into 6-well plates and were infected with cell free virus at a MOI of 5-10. Virus infection was allowed to proceed for 72 h. Afterwards, cells were washed once with PBS and total RNA was extracted using TRI reagent. To study Argonaut bound miRNAs, Ago2 immunoprecipitation was carried out using a previously published protocol (Hauptmann et al., 2015) with minor modifications. 5 million HSB-2 cells were infected with HHV-6A for 3 days as described above. Afterwards, native protein lysates were prepared from mock infected and HHV-6A infected cells using lysis buffer (50 mM Hepes, pH 7,5; 150 mM NaCl; 0.5% NP-40; 1 mM NaF; 10% Glycerol, 2.5 mM MgCl2; protease inhibitor (Roche), 0.5 mM DTT; 10 units/ml RNAse inhibitor (NEB, M0314L)). Anti-flag magnetic beads were washed with PBS and were incubated with TNR6B-flag peptide (Hauptmann et al., 2015) for overnight at 4 C on a head over tail rotor. Next day, beads were washed once with PBS and once with lysis buffer. Afterwards half of the beads were incubated with the protein lysate for overnight at 4C on a head over tail rotor. Rest of the beads were stored at 4 degree C.   Next day, beads were separated from the lysate on a magnet. Collected protein lysate was then mixed with remaining TNR6B-flag beads and were allowed to incubate for another overnight at 4 degree C on a head over tail rotor for further protein-antibody binding. Collected beads were washed 4 times with wash buffer (50 mM Hepes, pH 7,5; 150 mM NaCl; 1 mM NaF; 10% Glycerol, 2.5 mM MgCl2; protease inhibitor (Roche), 0.5 mM DTT; 10 units/ml RNAse inhibitor (NEB, M0314L)). Finally, beads were resuspended in PBS containing 0.5 mM MgCl2. A small fraction of these beads were used for denatured protein lysate preparation (eluate 1) for immunoblotting. Remaining beads were lysed in TRI-reagent and RNA was extracted. Next day, re-incubated beads were processed as described above to get the eluate 2 and the second batch of Ago2-bound RNA. Total RNA from both the batches were pooled together and processed for miRNA sequencing. miRNA sequencing was carried out at CeGaT GmbH, Tübingen usint NEXTflex Small RNA-seq kit v3 (Bioo Scientific, Germany).

value: Ago-bound RNA were used for small RNA-seq


title: AGO.HHV6A.B (lytic)


title: AGO.uninf.A (lytic)


title: mir.uninf.C (lytic)

value: No infection; Replicate 3

value: Total RNA used for small RNA-seq


title: M1_Bcell_4

value: Spleen

value: B Cells

value: post natal day 21


title: mir.HHV6A.B (lytic)


title: Elf CNTL EB-Flag -Dox

first: Hannele

last: Ruohola-Baker

address: 850 Republican Street

institute: Institute for Stem Cell and Regenerative Medicine

data_processing:
Reads were trimmed and aligned to hg19 using bowtie2, and bigWig coverage files were generated using UCSC tools.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

extract_protocol:
Protocol used for ATAC-seq is described in  Corces et al., 2017. Briefly frozen cell pellets were thawed and permeabilized on ice. Tagmentation occurred in the same tube followed by quenching and phenol:chloroform:isoamyl alcohol DNA purification and PCR. Exact temperatures, times, buffer composition were identical to Corces et al., 2017.
PMID: 28846090

value: hESC Elf1


title: Elf CNTL EB-Flag+Dox

value: Dox for 3 days


title: PRWT_WT1

value: 6h post-hCG

value: wildtype

value: granulosa cells

value: 21 days


title: mir.HHV6A.A (lytic)

value: HSB2 cells (HHV-6 Foundation, USA)

value: Childhood T acute lymphoblastic leukemia cells


title: U2OS.-HHV6A.+TSA.B (latent)

description:
small RNA between 10-25 nt length
U2OS.counts.tsv.gz

data_processing:
Reads that passed the chastity filter on the NextSeq 500 were subject to de-multiplexing and trimming of TriLink adapter residuals using Illumina’s bcl2fastq v2 software (v2.19.1). To refine the output, read quality was checked with FastQC software (v0.11.5) and reads shorter 10 bases or longer 25 bases or containing “N” as a base call, were discarded.
STAR_2.5.3a was used to map all reads against a combined index prepared for the human genome (Ensembl 90) and the HHV6A genome (genbank accession X83413). The following parameters were used: --alignIntronMax 1 --outFilterMismatchNmax 1 --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 10 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 16.
Reads were counted using Gedi 1.0.3.
Reads that passed the chastity filter on the NextSeq 500 were subject to de-multiplexing and trimming of TriLink adapter residuals using Illumina’s bcl2fastq v2 software (v2.19.1). Read quality was checked with FastQC software (v0.11.5). Reads shorter than 18 bases were discarded. All reads were mapped to combined index of the human genome (HG38) and the HHV-6A genome (X83413), with the trailing repeat region masked by N. Read mapping was performed using STAR (v2.5.3a) using the parameters suggested by the Encode project for sRNA-seq. Reads were then annotated to mature miRNAs if 5’ end perfectly matched (miRBase 22.1). The raw counts were then normalized and analyzed for differential miRNA expression with the DESeq2 (v1.18.1) package. Statistically significantly differentially regulated genes were called by a Wald test for the interaction of the presence of HHV-6A (or the sncRNA) and activation by TPA (or Dox) with FDR 1% (Benjamini-Hochberg corrected p-value).
Genome_build: hg38, X83413
Supplementary_files_format_and_content: U2OS.counts.tsv.gz

growth_protocol: Cells were grown in RPMI1640 media with 10% FCS without any antibiotics.

extract_protocol:
Cells were washed once with PBS and total cellular RNA was extracted using Qiagen RNeasy mini kit.
RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina) using both, Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad). For sequencing, samples were diluted and pooled into NGS libraries in equimolar amounts and were sequenced using NextSeq 500.
U2-OS cells were purchased from ATCC and were cultured in McCoy5A medium supplemented with 10% (v/v) FBS and 200 units/ml penicillin-streptomycin. U2-OS cells ccarrying latent HHV-6A were reactivated by treating the cells with 80 ng/ml of TSA for 48 h. To generate small RNA sequencing libraries, total cellular RNA was isolated using Qiagen miRNeasy kit and checked for signs of RNA degradation on a 2100 Bioanalyzer instrument (Agilent). Small RNA stranded libraries were prepared using the CleanTag Ligation Kit (TriLink BioTechnologies) starting with 1µg of total RNA per library. For quality control, all final libraries were analyzed by Bioanalyzer to check for the expected miRNA fragment peak at 141 bp. Subsequently, a Pippin Prep instrument (Sage Science) was used to isolated fragments between 10 and 35 bp in size. Library concentrations were measured by PicoGreen on an infinite F200 instrument (Tecan). Libraries were then sequenced on a NextSeq 500 platform (Illumina) using high-output v2 kits with 75 cycles aiming for about 40 million single-end reads per sample.

treatment_protocol: Cells were washed with PBS just before the treatment and then were replaced with freash media containing Ethanol/DMSO/Doxycycline/TSA.

value: Human Osteosarcoma cells carrying no HHV-6A

tag: time

value: TSA (80 ng/ml)


title: U2OS.-HHV6A.+TSA.A (latent)

tag: treatment


title: U2OS.-HHV6A.-TSA.A (latent)

value: DMSO (solvent control)


title: U2OS.-HHV6A.-TSA.B (latent)


title: JK153_gen3

city: Vancouver

first: Marco

middle: A

last: Marra

state: BC

address: 675 W 10th Ave, 7th Floor

country: Canada

institute: Canada's Michael Smith Genome Sciences Centre

data_processing:
Raw sequencing data were demultiplexed using bcl2fastq
Alignment, filtering, barcode counting, and UMI counting were done using the CellRanger software (cellranger count with default parameters except --expect-cells set to 5000; v6.2.1). The CellRanger GRCh38-1.2.0 reference was used for alignment.
Identification of cell-containing barcodes was done in R from raw matrices output by CellRanger using the method described in CellRanger v2.1.1, with an expected cell number of 5,000 for each sample
Additional cell and gene filtering were performed in R on the filtered count matrices using the scater package (v1.10.0). Outlier cells were identified as those with >3 median absolute deviations (MADs) below the median total UMI counts or total number of genes detected, or with >3 MADs above the median percent of counts from mitochondrial genes (per sample). Genes detected (UMI >0) in at least 10 cells with at least 20 UMIs were retained. Normalization was applied on remaining cells/genes using the scran package (v1.10.1). Putative doublets were identified using the doubletCells frunction from the scran package (k = 30) and cells with outlier doublet scores (>3 MADs above the sample median) were discarded. Gene filtering and normalization were performed again on the final dataset.
Genome_build: GRCh38
Supplementary_files_format_and_content: scRNAseq_multigen_all_cells_counts.mtx is a sparse matrix of raw UMI counts from all cells. scRNAseq_multigen_all_cells_barcodes.tsv and scRNAseq_multigen_all_cells_genes.tsv contain associated barcode (column) and gene (row) names. scRNAseq_multigen_all_cells_metadata.csv contains associated cell metadata.
Supplementary_files_format_and_content: scRNAseq_multigen_filtered_cells_norm_counts.mtx is a sparse matrix of normalized UMI counts from QC-filtered cells. scRNAseq_multigen_filtered_cells_barcodes.tsv and scRNAseq_multigen_filtered_cells_genes.tsv contain associated barcode (column) and gene (row) names. scRNAseq_multigen_filtered_cells_metadata.csv contains associated cell metadata.

molecule: polyA RNA

source_name: glioblastoma

growth_protocol: Small sections (~1mm3) of freshly resected tumour tissue were rinsed and placed into small Matrigel forms. Organoids were then cultured in neural stem cell media (NeuroCult) supplemented with EGF, FGF-2, and heparin sulfate. Media was changed or added every 2-3 days until the cells originating from the tumor sections had grown out into the surrounding Matrigel, at which point the organoids were either cryopreserved in 10% (v/v) DMSO or passaged by cutting the explant into smaller pieces (typically 10) and re-implanting these into fresh Matrigel.

extract_protocol: Single-cell 3’ RNA-seq libraries were generated using the Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 (10X Genomics) following the manufacturer’s protocol. Briefly, the provided targeted cell recovery table was used to determine the volume of cell suspension added to the Single Cell Master Mix prior to loading onto the Single Cell A chip (aiming for 5,000 cells). Following gel beads in emulsion (GEM) generation on the Chromium Controller, the GEM-RT reaction was performed, the GEMs were broken, and cDNA cleanup was performed using Dynabeads MyOne Silane beads. Samples that underwent evident clogs or wetting failures at the GEM generation step were not further processed. cDNA amplification was performed with 12 amplification cycles, and reaction cleanup was then performed using the SPRIselect reagent kit (Beckman Coulter). Total cDNA quantification was performed using the Agilent High Sensitivity DNA Kit. Enzymatic fragmentation, library construction, and additional SPRIselect clean-ups were then performed to generate the final indexed libraries. The number of sample index PCR cycles was determined based on the total cDNA yield and ranged from 10-14 cycles. Library quality was assessed using the Agilent High Sensitivity DNA kit and libraries were quantified using the Qubit dsDNA HS Assay kit (Thermo Fisher Scientific). Libraries were pooled and sequenced on an Illumina NovaSeq S4 flow cell using paired-end 150 bp sequencing, aiming for 3 billion reads in total.

treatment_protocol: Cryopreserved organoids were rapidly thawed in a 37oC water bath, dissociated by tituration, and incubated for another 10 min at 37oC. Dissociated cells were then washed twice in Hank’s balanced salt solution (HBSS; Thermo Fisher Scientific) and resuspended in phosphate-buffered saline (PBS; Thermo Fisher Scientific) with 0.04% (w/v) bovine serum albumin (BSA; Thermo Fisher Scientific). Additional HBSS washes were performed in samples with high debris and/or Matrigel content (up to four washes). Single-cell suspensions were filtered through 40 μm FlowMi tip filters (Bel-Art SP Scienceware), and final cell concentrations were determined using the Countess automated cell counter (Thermo Fisher Scientific).

tag: sample type

value: organoid

tag: tumour type

value: primary

tag: patient id

tag: organoid generation


title: JK153_gen2


title: U2OS.+HHV6A.+TSA.B (latent)

tag: cell type

value: Human Osteosarcoma cells carrying latent HHV-6A


title: U2OS.+HHV6A.+TSA.A (latent)


title: mir.HHV6A.C (lytic)

value: HHV-6A infection; Replicate 3

value: Total RNA used for small RNA-seq


title: U2OS.+HHV6A.-TSA.B (latent)


title: JK153_gen1


title: AGO.HHV6A.A (lytic)

value: HHV-6A infection; Replicate 1

value: Ago-bound RNA were used for small RNA-seq


title: JK142_gen1


title: JK142_gen2


title: JK125_gen3


title: U2OS.+HHV6A.-TSA.A (latent)


title: mir.uninf.B (lytic)

value: No infection; Replicate 2


title: mir.uninf.A (lytic)

value: No infection; Replicate 1


title: Parental replicate 1 (RNA-seq)

city: LEBANON

first: Diwakar

middle: Pattabiraman

last: Pattabiraman

state: NH

address: 1 Medical Center Drive

department: Molecular and Systems Biology

institute: Geisel School of Medicine at Dartmouth

data_processing:
FASTQ files were generated using bcl2fastq v2.20.0.422 from Illumina Inc.
Raw reads were trimmed with Cutadapt (v2.4) and aligned to hg38 using STAR (2.7.2b) with parameters “--outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 10 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 –alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1”
Gene-level abundance estimates were generated using RSEM (v1.3.2) using the rsem-calculate-expression command with the parameters “--strandedness reverse --fragment-length-mean 313 --fragment-length-sd 91”.
Genome_build: hg38
Supplementary_files_format_and_content: txt files, RSEM output for each sample. Gene Identifers are from ENSEMBL v97

source_name: Parental

growth_protocol: Grown according to ATCC recommendations

extract_protocol: RNA extraction performed by Rneasy Plus kit acording to directions

treatment_protocol: No treatment

value: ER-/PR- IBC

tag: cell line origin


title: Parental replicate 3 (RNA-seq)


title: JK142_gen3


title: Clone M2 replicate 2 (RNA-seq)

source_name: Clone M2


title: Clone M2 replicate 3 (RNA-seq)


title: JK153_reg2_org

data_processing:
Raw sequencing data were demultiplexed using the CellRanger-dna software (10X Genomics; cellranger-dna mkfastq with default parameters; v1.1)
Alignment, filtering, barcode counting, and UMI counting were done using the CellRanger-dna software (cellranger-dna cnv with default parameters; v1.1). The CellRanger-dna GRCh38-1.0.0 reference was used for alignment.
Data preprocessing was performed in R using the imputed CNV calls output by CellRanger-dna. Cells with at least 50 effective reads per Mb were retained for further analysis. To minimize the effect of noise, we calculated bin sizes that would have on average 200 reads/bin across samples (as recommended by 10X) for each patient and took the mean copy number across these coarse-grained bins.
Genome_build: GRCh38
Supplementary_files_format_and_content:
scWGS_all_cells_cn.tsv is a collated matrix of copy number counts output by CellRanger-dna. scWGS_all_cells_metadata.csv contains associated metadata, including cell-specific summary metrics output by CellRanger-dna.
scWGS_JK136_coarse_cn.tsv is a matrix of coarse-grained copy number counts for all JK136 QC-filtered cells. scWGS_JK136_metadata.csv contains associated cell metadata, including cell-specific summary metrics output by CellRanger-dna.
scWGS_JK142_coarse_cn.tsv is a matrix of coarse-grained copy number counts for all JK142 QC-filtered cells. scWGS_JK142_metadata.csv contains associated cell metadata, including cell-specific summary metrics output by CellRanger-dna.
scWGS_JK153_coarse_cn.tsv is a matrix of coarse-grained copy number counts for all JK153 QC-filtered cells. scWGS_JK153_metadata.csv contains associated cell metadata, including cell-specific summary metrics output by CellRanger-dna.

growth_protocol: Small sections (~1mm3) of freshly resected tumour tissue were rinsed and placed into small Matrigel forms. Organoids were then cultured in neural stem cell media (NeuroCult) supplemented with EGF, FGF-2, and heparin sulfate.

extract_protocol: Single-cell DNA libraries were generated using the Chromium Single Cell DNA Reagent Kit (10X Genomics) following the manufacturer’s protocol. Briefly, targeted cell recovery (250 cells) was used to determine the volume of cell suspension added to the Single Cell Bead Mix prior to loading onto the Chromium Chip C alongside the CB polymer. The generated cell beads were then shaken on a thermomixer overnight. The encapsulated cells were then lysed and the genomic DNA (gDNA) was denatured. The reaction mix, cell beads (containing the denatured DNA), and gel beads were loaded onto the Chromium D Chip to generate GEMs on the Chromium Controller. Following GEM generation, an isothermal incubation was performed, the GEMs were broken, and DNA cleanup was performed using Dynabeads MyOne Silane beads followed by a SPRIselect reaction cleanup. Total DNA quantification was performed using the Agilent High Sensitivity DNA Kit. Library construction and additional SPRIselect clean-ups were then performed to generate the final indexed libraries, using 12 sample index PCR cycles. Library quality was assessed using the Agilent High Sensitivity DNA kit and libraries were quantified using the Qubit dsDNA HS Assay kit. All libraries were pooled together and initially sequenced on four lanes of an Illumina  HiSeqX flow cell using v2.5 chemistry and paired-end sequencing with single indexing following Illumina protocols and 10X sequencing parameters (100 bp read 1, 100 bp read 2, and 8 bp i7 index). Following preliminary analysis of recovered cells per sample, libraries were pooled and further sequenced to reach a median depth of ~750,000 reads/cell.

treatment_protocol: Nuclei isolation was performed following the Isolation of Nuclei for Single Cell DNA Sequencing Demonstrated Protocol (CG000167) from 10X Genomics. Briefly, a small piece (~3-5 mm3) of flash-frozen tissue was cut from larger samples and immediately placed into a 1.5ml Eppendorf tube. Ice-cold lysis buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, and 0.1% NP-40) was added and the tissue homogenized through an 18-gauge syringe followed by a 20-gauge syringe. The sample was briefly centrifuged (300 rcf) and the nuclei-containing supernatant was transferred to a fresh Eppendorf tube. The supernatant was further centrifuged (850 rcf) for 5 min to pellet the nuclei, and the nuclei were washed twice and then resuspended in ice-cold Nuclei Wash & Resuspension buffer (0.04% [w/v] BSA in PBS). Final nuclei concentrations were determined by DAPI staining and counting using the Countess automated cell counter or through manual hemocytometer counts. Cryopreserved organoids were directly placed into 1.5ml Eppendorf tubes and lysed as per tissue sections (4-5 organoids combined).


title: JK153_reg2_tis

value: tissue


title: JK125_gen1


title: JK153_reg1_tis


title: JK124_gen2


title: Clone M2 replicate 1 (RNA-seq)


title: JK124_gen1


title: Clone M1 replicate 1 (RNA-seq)

source_name: Clone M1


title: JK196_tis

value: recurrent


title: JK142_reg2_org


title: Clone EM3 replicate 2 (RNA-seq)

source_name: Clone EM3


title: Clone EM3 replicate 1 (RNA-seq)


title: JK153_reg1_org


title: Clone M1 replicate 3 (RNA-seq)


title: Parental replicate 2 (RNA-seq)


title: Clone M1 replicate 2 (RNA-seq)


title: JK196_org


title: Clone EM3 replicate 3 (RNA-seq)


title: JK125_gen2


title: Clone EM1 replicate 3 (RNA-seq)

source_name: Clone EM1


title: JK142_reg1_org


title: Clone EM1 replicate 1 (RNA-seq)


title: JK142_reg2_tis


title: Clone EM1 replicate 2 (RNA-seq)


title: JK136_reg2_org


title: JK142_reg1_tis


title: Clone E replicate 2 (RNA-seq)

source_name: Clone E


title: JK136_reg1_tis


title: JK202_org


title: Clone EM2 replicate 2 (RNA-seq)

source_name: Clone EM2


title: JK136_reg1_org


title: Parental replicate 2 (ATAC-seq)

description:
Tn5 fragmented genomic DNA
Parental_rep2

data_processing:
FASTQ files were generated using bcl2fastq v2.20.0.422 from Illumina Inc.
Raw reads were trimmed with Cutadapt (v1.9.1) and aligned to hg38 using Bowtie (v2.2.6) in “--local” mode with parameters “-X 2000 -k 2”
Duplicate reads were identified and removed using MarkDuplicates (Picard Tools) to create filtered BAMs, which were converted to tagAlign format and reads were shifted +4 bp and -5 bp on the + and – strands, respectively.
Peaks were called using MACS2 (v2.1.1) callpeak command with parameters “--shift -75 --extsize 150 --nomodel --keep-dup all --call-summits -p 1.0E-10” and filtered against the ENCODE hg38 blacklist
Irreproducible Discovery Rate (IDR) method was applied, retaining peaks  IDR threshold of 0.05
IDR peak sets were merged across samples to create a consensus peak set. reads falling within the consensus peak set in each sample were counted using featureCounts.
BAM files for sample replicates were merged using Picard MergeSamFiles before create of BigWig files
Counts per million (CPM) normalized tn5 insertion signal tracks were generated using deepTools8 (v3.4.3) bamCoverage command with parameters “--binSize 5 --normalizeUsing CPM --effectiveGenomeSize 2913022398 --ignoreForNormalization chrX” on the position-shifted BAM files
Genome_build: hg38
Supplementary_files_format_and_content: matrix of raw read counts in txt format
Supplementary_files_format_and_content: Normalized tn5 insertion signal tracks in BigWig format
Supplementary_files_format_and_content: peak files in BED format

extract_protocol:
Nuclei extracted and tagmented per the Buenrostro ATAC-seq protocol
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4374986/
Libraries constructed per the Buenrostro ATAC-seq protocol


title: JK202_tis


title: JK163_reg2_tis_1 [scRNA-seq]

data_processing:
Raw sequencing data were demultiplexed using the CellRanger software (10X Genomics; cellranger mkfastq with default parameters; v2.0.0 or v2.1.1)
Alignment, filtering, barcode counting, and UMI counting were done using the CellRanger software (cellranger count with default parameters except --expect-cells set to 1000; v2.1.1). The CellRanger GRCh38-1.2.0 reference was used for alignment.
Additional cell and gene filtering were performed in R on the filtered count matrices output by CellRanger using the scater package (v1.10.0). Outlier cells were identified as those with >3 median absolute deviations (MADs) below the median total UMI counts or total number of genes detected, or with >3 MADs above the median percent of counts from mitochondrial genes (per sample). Genes detected (UMI >0) in at least 10 cells with at least 20 UMIs were retained. Normalization was applied on remaining cells/genes using the scran package (v1.10.1). Putative doublets were identified using the doubletCells frunction from the scran package (k = 30) and cells with outlier doublet scores (>3 MADs above the sample median) were discarded. Gene filtering and normalization were performed again on the final dataset.
Genome_build: GRCh38
Supplementary_files_format_and_content: scRNAseq_all_cells_counts_matrix.mtx is a sparse matrix of raw UMI counts from all cells identified by the CellRanger pipeline. scRNAseq_all_cells_barcodes.tsv and scRNAseq_all_cells_genes.tsv contain associated barcode (column) and gene (row) names. scRNAseq_all_cells_metadata.csv contains associated cell metadata.
Supplementary_files_format_and_content: scRNAseq_filtered_cells_norm_counts_matrix.mtx is a sparse matrix of normalized UMI counts from QC-filtered cells. scRNAseq_filtered_cells_barcodes.tsv and scRNAseq_filtered_cells_genes.tsv contain associated barcode (column) and gene (row) names. scRNAseq_filtered_cells_metadata.csv contains associated cell metadata.

extract_protocol: Single-cell 3’ RNA-seq libraries were generated using the Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10X Genomics) following the manufacturer’s protocol. Briefly, the provided targeted cell recovery table was used to determine the volume of cell suspension added to the Single Cell Master Mix prior to loading onto the Single Cell A chip (2,000 cells for tissue and PDO samples and 1,000 cells for BTIC lines). Following gel beads in emulsion (GEM) generation on the Chromium Controller, the GEM-RT reaction was performed, the GEMs were broken, and cDNA cleanup was performed using Dynabeads MyOne Silane beads. Samples that underwent evident clogs or wetting failures at the GEM generation step were not further processed. cDNA amplification was performed with 12 amplification cycles, and reaction cleanup was then performed using the SPRIselect reagent kit (Beckman Coulter). Total cDNA quantification was performed using the Agilent High Sensitivity DNA Kit. Enzymatic fragmentation, library construction, and additional SPRIselect clean-ups were then performed to generate the final indexed libraries. The number of sample index PCR cycles was determined based on the total cDNA yield and ranged from 10-14 cycles. Library quality was assessed using the Agilent High Sensitivity DNA kit and libraries were quantified using the Qubit dsDNA HS Assay kit (Thermo Fisher Scientific). Libraries were pooled (seven to eight libraries/pool) and sequenced on one lane of an Illumina HiSeq2500 flow cell (San Diego, CA, USA) using v3 or v4 chemistry and paired-end sequencing with single indexing following Illumina protocols and 10X sequencing parameters (26 bp read 1, 98 bp read 2, and 8 bp i7 index).

treatment_protocol: Cryopreserved tissues or PDOs were rapidly thawed in a 37oC water bath. Tissues were washed once in NeuroCult NS-A Basal Medium (human; STEMCELL Technologies), and PDOs were washed in the same media at room temperature for 15 min with rocking. Samples were resuspended in 0.2 mg/mL collagenase (Sigma-Aldrich) plus 0.5 mg/mL DNaseI (Worthington Biochemical Corp) and incubated at 37oC for 30 min with shaking every 10 min. Tissues were dissociated by tituration, incubated for another 10 min at 37oC, and filtered through a 40 μm mesh filter (BD Falcon) with added NeuroCultTM medium (STEMCELL Technologies) to remove larger pieces of debris and undissociated tissue. PDOs were dissociated by tituration and incubated for another 10 min at 37oC. Dissociated cells were then washed twice in Hank’s balanced salt solution (HBSS; Thermo Fisher Scientific) and resuspended in phosphate-buffered saline (PBS; Thermo Fisher Scientific) with 0.04% (w/v) bovine serum albumin (BSA; Thermo Fisher Scientific). Additional HBSS washes were performed in samples with high debris and/or Matrigel content (up to four washes). Single-cell suspensions were filtered through 40 μm FlowMi tip filters (Bel-Art SP Scienceware), and final cell concentrations were determined using the Countess automated cell counter (Thermo Fisher Scientific).


title: Clone EM2 replicate 3 (RNA-seq)


title: JK163_reg1_btic_1 [scRNA-seq]

growth_protocol: Organoid cells that escaped the Matrigel and created neurospheres were collected and propagated in 25cm flasks in neural stem cell media (NeuroCult) supplemented with EGF, FGF-2, and heparin suflate.

value: neurosphere line


title: JK163_reg2_org_2 [scRNA-seq]


title: Clone EM2 replicate 1 (RNA-seq)


title: Clone E replicate 3 (RNA-seq)


title: JK163_reg2_btic_1 [scRNA-seq]


title: JK163_reg2_org_1 [scRNA-seq]


title: JK163_reg1_org_2 [scRNA-seq]


title: Clone E replicate 1 (RNA-seq)


title: JK163_reg1_org_1 [scRNA-seq]


title: Clone EM2 replicate 2 (ATAC-seq)

description:
Tn5 fragmented genomic DNA
EM2_rep2


title: Parental replicate 1 (ATAC-seq)

description:
Tn5 fragmented genomic DNA
Parental_rep1


title: Clone EM1 replicate 2 (ATAC-seq)

description:
Tn5 fragmented genomic DNA
EM1_rep2


title: Clone EM3 replicate 1 (ATAC-seq)

description:
Tn5 fragmented genomic DNA
EM3_rep1


title: Clone E replicate 2 (ATAC-seq)

description:
Tn5 fragmented genomic DNA
E_rep2


title: Clone EM1 replicate 1 (ATAC-seq)

description:
Tn5 fragmented genomic DNA
EM1_rep1


title: Clone EM2 replicate 1 (ATAC-seq)

description:
Tn5 fragmented genomic DNA
EM2_rep1


title: Clone M2 replicate 2 (ATAC-seq)

description:
Tn5 fragmented genomic DNA
M2_rep2


title: Clone M2 replicate 1 (ATAC-seq)

description:
Tn5 fragmented genomic DNA
M2_rep1


title: JK156_reg1_org_3 [scRNA-seq]


title: JK136_reg2_tis


title: Clone M1 replicate 2 (ATAC-seq)

description:
Tn5 fragmented genomic DNA
M1_rep2


title: JK163_reg1_tis_1 [scRNA-seq]


title: JK156_reg2_org_1 [scRNA-seq]


title: Clone M1 replicate 1 (ATAC-seq)

description:
Tn5 fragmented genomic DNA
M1_rep1


title: JK156_reg2_org_3 [scRNA-seq]


title: JK156_reg2_tis_2_br [scRNA-seq]


title: JK156_reg2_tis_1 [scRNA-seq]


title: Clone EM3 replicate 2 (ATAC-seq)

description:
Tn5 fragmented genomic DNA
EM3_rep2


title: H9 TP53 KO NPC rep 1

city: Dallas

first: Sushama

last: Sivakumar

state: Texas

address: 6001 Forest Park Road

department: Pharmacology

institute: UT Southwestern Medical center

description:
H9TP53KO_NPC_rep1
GENES_counts_npc.txt

data_processing:
Raw FASTQ files were analyzed using FastQC (v0.11.2) and FastQ Screen (v0.4.4)
Reads were quality-trimmed using fastq-mcf (ea-utils/1.1.2-806)
The trimmed reads were mapped to the hg19 assembly of the human genome (University of California at Santa Cruz, version from iGenomes) using STAR (v2.5.3a)
The RNA counts generated from FeatureCounts (subread v1.4.6)were TMM normalized, and differential expression analysis was performed using edgeR (v3.20.9)
Genome_build: hg19
Supplementary_files_format_and_content: text tab delimited with raw counts

source_name: hESCs

growth_protocol: hESCs were grown on Matrigel in mTeSR1-cGMP media. In vitro differentiation into NPCs was done using StemDiff Neuron differentiation kit (StemCell Technologies). RNA was isolated from WT ESCs and in vitro differentiated NPCs.

extract_protocol: Tru-Seq library preparation kit (Illumina)

tag: Sex

value: Female

value: TP53 KO NPC


title: H9 TP53 KO C2 NPC rep 1

description:
H9TP53KOC2_NPC_rep1
GENES_counts_npc.txt

value: TP53 KO C2 NPC


title: H9 TP53 KO NPC rep 2

description:
H9TP53KO_NPC_rep2
GENES_counts_npc.txt


title: JK153_reg2_tis_1 [scRNA-seq]


title: JK156_reg1_org_1 [scRNA-seq]


title: JK153_reg2_org_3 [scRNA-seq]


title: JK156_reg1_org_2 [scRNA-seq]


title: H9 WT NPC rep 2

description:
H9WT_NPC_rep2
GENES_counts_npc.txt

value: WT NPC


title: JK156_reg1_tis_1 [scRNA-seq]


title: H9 TP53 KO C1 NPC rep 1

description:
H9TP53KOC1_NPC_rep1
GENES_counts_npc.txt

value: TP53 KO C1 NPC


title: H9 TP53 KO C2 NPC rep 2

description:
H9TP53KOC2_NPC_rep2
GENES_counts_npc.txt


title: JK152_reg2_btic_1 [scRNA-seq]

value: primary


title: JK153_reg1_tis_1 [scRNA-seq]


title: JK153_reg2_org_1 [scRNA-seq]

value: organoid


title: Clone E replicate 1 (ATAC-seq)

description:
Tn5 fragmented genomic DNA
E_rep1


title: JK153_reg2_org_2 [scRNA-seq]


title: H9 WT LC ESC rep 1

description:
LCWT2_ESC_rep1_R1_001
GENES_counts_ESC.txt

value: WT ESC


title: H9 WT LC ESC rep 2

description:
LCWT2_ESC_rep2_R1_001
GENES_counts_ESC.txt


title: JK152_reg2_org_1 [scRNA-seq]


title: JK153_reg1_btic_1 [scRNA-seq]


title: H9 TP53 KO C1 NPC rep 2

description:
H9TP53KOC1_NPC_rep2
GENES_counts_npc.txt


title: JK153_reg1_org_1 [scRNA-seq]


title: H9 TP53 KO ESC rep 2

description:
H9TP53KO_ESC_rep2
GENES_counts_ESC.txt

value: TP53 KO ESC


title: JK152_reg1_btic_1 [scRNA-seq]


title: JK152_reg1_org_2 [scRNA-seq]


title: JK152_reg2_tis_1 [scRNA-seq]


title: JK152_reg2_org_2 [scRNA-seq]


title: H9 TP53 KO C2 ESC rep 2

description:
H9TP53KOC2_ESC_rep2
GENES_counts_ESC.txt

value: TP53 KO C2 ESC


title: H9 WT LC ESC NPC 2

description:
LCWT_NPC_rep2
GENES_counts_npc.txt


title: H9 TP53 KO C2 ESC rep 1

description:
H9TP53KOC2_ESC_rep1
GENES_counts_ESC.txt


title: JK152_reg1_tis_1 [scRNA-seq]


title: H9 TP53 KO ESC rep 1

description:
H9TP53KO_ESC_rep1
GENES_counts_ESC.txt


title: H9 WT LC ESC NPC 1

description:
LCWT_NPC_rep1
GENES_counts_npc.txt


title: JK153_reg1_org_2 [scRNA-seq]


title: H9 WT LC2 ESC rep 2

description:
LCWT_ESC_rep2
GENES_counts_ESC.txt


title: H9 WT LC2 ESC rep 1

description:
LCWT_ESC_rep1
GENES_counts_ESC.txt


title: JK196_reg1_org_3 [scRNA-seq]


title: JK152_reg1_org_1 [scRNA-seq]


title: JK196_reg1_org_2 [scRNA-seq]


title: H9 WT NPC rep 1

description:
H9WT_NPC_rep1
GENES_counts_npc.txt


title: H9 TP53 KO C1 ESC rep 2

description:
H9TP53KOC1_ESC_rep2
GENES_counts_ESC.txt

value: TP53 KO C1 ESC


title: JK196_reg1_tis_2.2_br [scRNA-seq]


title: JK196_reg1_org_1 [scRNA-seq]


title: H9 TP53 KO C1 ESC rep 1

description:
H9TP53KOC1_ESC_rep1
GENES_counts_ESC.txt


title: H9 WT ESC rep 2

description:
H9WT_ESC_rep2
GENES_counts_ESC.txt


title: JK196_reg1_tis_2.1_br [scRNA-seq]


title: H9TP53KOC1rep2

description: RNA-Seq on TP53 KO Teratoma tissue

data_processing:
Raw FASTQ files were analyzed using FastQC (v0.11.2) and FastQ Screen (v0.4.4)
Reads were quality-trimmed using fastq-mcf (ea-utils/1.1.2-806)
The trimmed reads were mapped to the hg19 assembly of the human genome (University of California at Santa Cruz, version from iGenomes) using STAR (v2.5.3a)
The RNA counts generated from FeatureCounts (subread v1.4.6)were TMM normalized, and differential expression analysis was performed using edgeR (v3.20.9)
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text file of raw read counts per sample

source_name: Teratoma grown in mice

growth_protocol: hESCs were subcutaneously injected into immunedeficient mice. Teratomas were isolated and total RNA was purified from tissues.

value: TP53 KO (Clone 1)


title: JK196_reg1_tis_1 [scRNA-seq]


title: H9TP53KOC1rep1

description: RNA-Seq on TP53 KO Teratoma tissue


title: H9WTrep2

description: RNA-Seq on WT Teratoma tissue

value: WT


title: H9WTrep1

description: RNA-Seq on WT Teratoma tissue


title: JK142_reg2_org_2 [scRNA-seq]


title: JK142_reg2_btic_1 [scRNA-seq]


title: JK142_reg2_org_1 [scRNA-seq]


title: JK142_reg2_tis_2.2_br [scRNA-seq]


title: H9 WT ESC rep 1

description:
H9WT_ESC_rep1
GENES_counts_ESC.txt


title: WT NPC unsorted rep 2

description: CRISPR-Cas9 screen for Sox1 expression during differentiation

data_processing:
Library strategy: CRISPR screen
Raw FASTQ files were analyzed using FastQC (v0.11.2) and FastQ_Screen (v0.4.4)
Trimmed FASTQ files were mapped to the reference sgRNA library with mismatch option as 0 using MAGeCK (v0.5.6)
Read counts for each sgRNA were generated and median normalization was performed to adjust for library sizes.  Positively and negatively selected sgRNA and genes were identified with MAGeCK (v0.5.6) using the default parameters
Genome_build: GeCKO v2.0 (A and B) were downloaded from Addgene (https://www.addgene.org/pooled-library/)
Supplementary_files_format_and_content: text tab delimited file with raw sgrna counts per sample.

growth_protocol: Invitro differentiated NPCs (differentiated using StemCell Technologies' StemDiff Neuron differentiation kit by monolayer protocol) were collected and FACS sorted to obtain bottom 1% of Sox1 expressing cells.

extract_protocol:
Genomic DNA was isolated by phenol:Chloroform:isoamyl alcohol and purified by ethanol precipitation
Two rounds of PCR was done with isolated genomic DNA. Barcoded primers were used in PCR reactions to produce CRISPR amplicon library for each sample.
PCR amplicon libraries were sequenced on Illumina Nextseq 500 sequencer.

value: in vitro differentiated NPCs


title: JK142_reg2_tis_2.1_br [scRNA-seq]

value: tissue


title: JK142_reg2_tis_1 [scRNA-seq]


title: WT NPC Sox1 negative rep 2


title: JK142_reg1_btic_1 [scRNA-seq]


title: 145996

type: genomic

city: Doha

first: Georges

last: Nemer

address: Education City

country: Qatar

institute: Hamad Bin Khalifa university

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to IIllumina Infinium EPIC Human Methylation Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Average Beta value

label: Cy3, Cy5

source_name: Blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA extraction

tag: gender

value: Male

tag: disease state

value: Control

value: Blood


title: WT NPC unsorted rep 1

value: Female


title: 142654

tag: tissue


title: WT NPC Sox1 negative rep 1


title: 146501

tag: age


title: 145779


title: PSABLDNA501

value: non-classical progeroid laminopathies


title: 143071


title: 133323


title: UHGABDNA481


title: 146277


title: 141662


title: PSABLDNA199


title: PSABLDNA531


title: SNOS1-GFP rep2

city: Paris

first: Jing

last: An

address: 630 Rue Noetzlin

country: France

institute: Universite Paris Saclay

data_processing:
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar SE $input $output ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads data were mapped using bowtie2 v 2.3.5 with the following setting "bowtie2 --very-sensitive" against the genome of TAIR10.
Filtering step: Mapped reads were filtered with samtools v.1.9 with the command "samtools view -h -b -q 30  "mapping_quality >= 30"
Duplicate filtering: duplicated reads were removed with samtools v.1.9 with the command "samtools fixmate -m  and samtools markdup -r "
Peak calling: peaks of read density were called with macs2 2.2.7.1 with the command "macs2 callpeak --broad  -t sample.bam   -c Input.bam -g 7.8e8 -q 0.05 --extsize 150 --bw 500 -B -n --outdir "
Bigwig generation: read density was scored with s3norm with the default paramaters
Genome_build: TAIR10
Supplementary_files_format_and_content: s3norm normalized bigwig for plots generated with ComputeMatrix plotprofile of Deeptools

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis thaliana ecotype Colombia (Col-0)  was used in this study. Plants were grown in chambers at 20°C on sterile half-strength MS medium and 0.8% agar under long-days (16h of light at 20°C, 8h of darkness at 18°C). Seeds were surface-sterilized by treatment with bayrochlore for 20 min, washed, and imbibed in sterile-water for 2–4 days at 4 °C to obtain homogeneous germination.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to NEB instructions using the « NEBNext Ultra II DNA library kit for Illumina »

tag: genotype

tag: chip antibody

value: Anti-GFP (Abcam, ab290)

tag: molecule subtype

value: GFP IP chromatin


title: UHGABLDNA351

value: classical Hutchinson Gilford Progeria Syndrome (HGPS)


title: 141993


title: 148780


title: HGABLDNA331


title: PSABLDNA316


title: JK142_reg1_org_2 [scRNA-seq]

value: organoid

value: primary


title: WT NPC input rep 2

description: TP53 ChIP in hESCs and hNPCs

data_processing:
Raw FASTQ files were analyzed using FastQC (v0.11.2) and FastQ_Screen (v0.4.4)
Reads were quality-trimmed using fastq-mcf (ea-utils/1.1.2-806)
Trimmed reads were mapped to the hg19 with bowtie2 (v2.2.3)
ChIP-seq peaks were called using MACS2 (v2.0.10) with a q-value threshold of 0.05
bigWig files were generated using HOMER (v4.10)
Genome_build: hg19
Supplementary_files_format_and_content: signal bigWig files per sample

growth_protocol: hESCs and in vitro differentiated NPCs (differentiated using StemCell Technologies' StemDiff Neuron differentiation kit) were harvested and TP53 ChIP was performed. ChIP DNA was then subjected to library preparation

extract_protocol: Libraries were made using KAPA HTP library preparation kit according to manufacturer's instructions.

tag: ip target

value: none (input)


title: PSABLDNA406


title: HGABLDNA352


title: PSABLDNA295


title: 152466


title: JK142_reg1_org_1 [scRNA-seq]


title: Col_27C_SIM4D_rep2

city: Yokohama

first: Alice

last: Lambolez

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

data_processing:
Sequencing quality was first checked using FastQC (version 0.11.7).
Reads were then mapped to the TAIR10 Arabidopsis genome using Bowtie2 (version 2.3.4.3) with the "--no-1mm-upfront" option.
Resulting SAM files were converted to BAM using the samtools (version 1.9) function "view".
Duplicated reads were removed with samtools "rmdup".
Resulting BAM files were sorted and indexed with samtools "sort" and "index".
Read counts per gene were determined using the "multicov" function from bedtools (version 2.26.0) and were used to produce the Coverage_all_17C_VS_27C_CIM_SIM_RNA-seq.bed file.
Genome_build: TAIR10
Supplementary_files_format_and_content: Coverage_all_17C_VS_27C_CIM_SIM_RNA-seq.bed is a tab-delimited BED (~.txt) file containing the read counts for each TAIR10 genes in each sequencing sample.

source_name: Hypocotyl explant

growth_protocol: Plants were grown on nylon mesh over MS medium containing 1% sucrose and 0.6% (w/v) gelzan. Plates were placed vertically and kept in the dark at 22°C to induce hypocotyl elongation. 7-day-old etiolated seedlings were dissected with a razor blade to harvest hypocotyls explants located between ~3 mm above the root/hypocotyl junction and ~5 mm below the hypocotyl/shoot junction.

extract_protocol:
~100 hypocotyls explants harvested and frozen with liquid nitrogen. The samples were then ground using zirconia ceramic beads in a TissueLyser (QIAGEN) mixer mill. RNA was extracted using the RNeasy Plant Mini kit (QIAGEN) following the manufacturer's instructions.
Libraries for sequencing were prepared using the KAPA Stranded mRNA-seq Kit (Kapa Biosystems, Roche) with a mix of FastGene (Nippon Genetics) and NEBNext (New England Biolabs) adapters.

treatment_protocol: Explants were first incubated on CIM, i.e. MS medium supplemented with Gamborg’s B5 vitamin, 20 g.L-1 glucose, 0.5 g.L-1 MES, 7.5 g.L-1 Gellan gum, 0.1 mg.L-1 kinetin and 0.5 mg.L-1 2,4 D, for 4 days in continuous light conditions and at 17°C or 27°C. Explants were then transferred on SIM, i.e. MS medium supplemented with Gamborg’s B5 vitamin, 20 g.L-1 glucose, 0.5 g.L-1 MES, 2.5 g.L-1 Gellan gum, 0.5 mg.L-1 2-iP and 0.15 mg.L-1 IAA, for 4 days in continuous light conditions and at 17°C or 27°C.

tag: ecotype

value: 4 days on CIM then 4 days on SIM

tag: temperature

tag: replicate

value: Hypocotyl explant


title: UHGABLDNA172


title: HGABLDNA378


title: UHGABLDNA480


title: WT input rep1

value: Total Chromatin


title: Col_27C_SIM4D_rep1

tag: treatment


title: WT NPC TP53 IP rep 1

description: TP53 ChIP in hESCs and hNPCs

value: WT


title: PSABLDNA379


title: E1M-GFP rep1


title: JK142_reg1_tis_1 [scRNA-seq]

tag: sample type

tag: tumour type

tag: patient id


title: E1M-GFP rep2


title: Col_17C_SIM4D_rep3


title: JK202_reg1_org_2 [scRNA-seq]

value: recurrent


title: SNOS1-GFP rep1


title: HGABLDNA146


title: Col_27C_SIM4D_rep3


title: WT ESC TP53 IP rep 2

description: TP53 ChIP in hESCs and hNPCs

tag: cell type

value: ESC


title: HGABLDNA306

value: Male


title: JK202_reg1_org_3 [scRNA-seq]


title: Col_17C_SIM4D_rep1


title: WT NPC input rep 1

description: TP53 ChIP in hESCs and hNPCs

value: in vitro differentiated NPCs

tag: Sex


title: WT ESC TP53 IP rep 1

description: TP53 ChIP in hESCs and hNPCs


title: Col_27C_CIM4D_rep3

value: 4 days on CIM


title: WT ESC input rep 2

description: TP53 ChIP in hESCs and hNPCs

value: Female


title: WT ESC input rep 1

description: TP53 ChIP in hESCs and hNPCs


title: JK136_reg2_org_3 [scRNA-seq]


title: 4Cseq-LEVER_KO-Viewpoint-4_2

city: Singapore

first: Chan-Shuo

last: Wu

address: 14 Medical Drive, #12-01

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

data_processing:
Library strategy: 4C-seq
For ChIP-seq analysis, reads were mapped by bowtie2 against human reference genome GRCh38 (Langmead and Salzberg 2012).
Only uniquely mapped reads were used and PCR duplicates were removed with samtools rmdup.
The resulting bam files are converted to bigWig format by bedGraphToBigWig from bedGraph generated by bedtools.
For 4C-seq analysis, the long-range genomic interaction regions generated by the 4C-Seq experiment were analyzed by using the R package r3CSeq v1.30.0 on hg19.
Bam files are converted to read coverage by bedGraphToBigWig. The read coverage was normalized according to sequencing depth.
The resulting bedGraph files are converted to bigWig format.
The genome version of bigWig files was converted to hg38 by CrossMap.
For total RNA-seq analysis, the paired-end RNA-seq reads were trimmed for adaptor sequence by TrimGalore and then mapped by STAR to the human reference genome GRCh38 with reference gene annotation GENCODE 26.
PCR duplicates were removed in the paired-end alignments by samtools rmdup.
Alignments with mapping quality < 20 were removed.
Gene expression levels in FPKM were determined by cuffdiff in the Cufflinks package.
For fraction RNA-seq analysis, the paired-end RNA-seq reads were trimmed for adaptor sequence by TrimGalore and then mapped by STAR to the human reference genome GRCh38 with reference gene annotation.
The read count on each EZH2 peak region was generated by featureCount. The read count was normalized according to the sequencing depth.
For RIP-seq analysis, reads from the RIP data set and its control data set were mapped respectively by STAR against human reference genome GRCh38 with gene annotation.
Only uniquely mapped reads were used and PCR duplicates were removed with samtools rmdup.
Bam files was converted to bedGraph to represent read coverage by bedtools. The read coverage was normalized according to the size of transcriptome mapping.
The resulting bedGraph files are converted to bigWig format.
For NANOPOPRE-seq total polyA+ RNA, the reads were mapped to hg38 by Minimap2 with -ax splice -uf -k14.
The bam files were converted to bed12 by bamToBed and were converted to bigBed file by bedToBigBed. Only uniquely mapped reads were retained.
For NANOPORE-seq nuclear cDNA sequencing, the reads were mapped to hg38 by LAST with lastal -d90 -m50 -D10 and last-split -d2
The maf files were converted to psl file with maf-convert -j1e6 psl. The psl files were subsequently converted to bam file with psl2sam.pl and cigar_tweaker scripts within the SAMtools package.
The read alignments were then converted into bedGraph by BEDTools and into bigWig format by bedGraphToBigWig.
Genome_build: hg38
Supplementary_files_format_and_content: RNAseq.genes.fpkm.txt: Tab-delimited text file includes FPKM values.
Supplementary_files_format_and_content: *.ReadCount.txt: Tab-delimited text files include read counts.
Supplementary_files_format_and_content: *bw: bigWig format
Supplementary_files_format_and_content: *.bigBed: bigBed format

source_name: K562 leukemia cell line

growth_protocol: K562 cells and its derivatives were cultured with RPMI supplemented with 10% fetal bovine serum. The cells were passage every 3 to 4 days.

extract_protocol:
1) RIP-seq: Cells were fixed with 1% formaldehyde. RNA was sonicated to around 3000 and protein-RNA complexes were pulled down by antibodies. 2) RNA-seq: Fractionated RNA was harvested by Trizol followed by DNaseI treatment. 3) NANOPRE-seq: Fractionated RNA was harvested by Trizol followed by DNaseI treatment. Superscript IV was used for nuclear cDNA preparation. 4) ChIP-seq: Cells were fixed with 1% formaldehyde and insoluble chromatin fraction was isolated. Chromatin was sonicated to 100 to 500 base pair and protein-DNA complexes were pulled down by antibodies. 5) 4C-seq: Cells were fixed with 2% formaldehyde. gDNA was digested first with DpnII and ligated. The ligated chromatin was digested again with NlaIII, MseI or MluCI and ligated.
1) ChIP-seq: Libraries were prepared using ThruPLEX DNA-seq kit (R400428) according to manufacturer's instruction. Constructed libraries were PAGE purified and only libraries with 250 to 500bp were used for sequencing. 2) RIP-seq and RNA-seq: Libraries were prepared using Scriptseq V2 RNA-seq Library preparation kit (SSV21124) according to manufacturer's instruction.  Constructed libraries were PAGE purified and only libraries with 250 to 500bp were used for sequencing. 3) NANOPORE-seq:  Library for nuclear cDNA was constructed with 1D cDNA library kit (SQK-LSK108) according to manufacturer's instruction. RNA library for total polyA+ RNA was constructed with direct-RNA sequencing kit (SQK-RNA001) according to manufacturer's instruction. 4) 4C-seq: 4C library was constructed with customized primers with Illumina adaptor and barcodes and KAPA HiFi HotStart ReadyMix (KK2602).

treatment_protocol: LEVER knock out was achieved using CRISPR-Cas9 gene editing method. LEVER knock down was achieved using inducible CRISPR-dCas9 strategy.

tag: cell line

value: Leukemia cell line

tag: genotype/variation

value: LEVER KO Cas9

tag: passage


title: Col_17C_CIM4D_rep2

tag: tissue


title: JK202_reg1_org_1 [scRNA-seq]


title: Col_22C_0h_rep3


title: Col_22C_0h_rep1


title: Col_27C_CIM4D_rep2


title: JK202_reg1_tis_1 [scRNA-seq]

value: tissue


title: JK136_reg2_tis_2_br [scRNA-seq]


title: 4Cseq-LEVER_KO-Viewpoint-2_2


title: 4Cseq-ntgRNA-Viewpoint-4_2

value: Wild type / ntgRNA Cas9


title: Heart Chrysin_2

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

institute: University of Toyama

data_processing: Filtering characteristics of fold-change and false discovery rate (FDR) were used to identify the DEGs.

organism: Rattus norvegicus

source_name: Heart

extract_protocol:
Tissue-derived total RNA was prepared according to the manufacturer’s protocol of ISOGEN plus (TAKARA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Male Sprague Dawley rats (SLC, Japan), 130–150 g, were dosed subcutaneously with 20 mg/kg SU-5416 and exposed to 3 weeks of hypoxia (10% oxygen) following 2 weeks of normoxia. Rats were then administered vehicle or chrysin (100 mg/kg/day) for 3 weeks under normoxic conditions (SU_HX group, Chrysin group, respectively). Control rats were maintained in normoxic conditions for 8 weeks (CTRL group).

tag: strain

value: Sprague Dawley

value: Heart

tag: age & sex

value: 5 week-old, Male

value: SU_HX_Chrysin treatment (Chrysin), hypoxic conditions


title: JK136_reg2_tis_1 [scRNA-seq]

value: primary


title: Heart SU_HX_3

value: Sugen treatment (SU_HX), hypoxic conditions


title: JK136_reg2_org_4_br [scRNA-seq]

value: organoid


title: Col_17C_CIM4D_rep3

value: Hypocotyl explant


title: Col_27C_CIM4D_rep1


title: Col_17C_CIM4D_rep1


title: JK136_reg2_org_2 [scRNA-seq]


title: 4Cseq-LEVER_KO-Viewpoint-3_2


title: WT NPC TP53 IP rep 2

description: TP53 ChIP in hESCs and hNPCs

tag: genotype

value: WT


title: Heart Chrysin_3


title: JK136_reg2_org_1 [scRNA-seq]


title: JK136_reg1_org_2 [scRNA-seq]


title: ChIPseq-LEVER_KD-H3K27Me3

description: ChIP-seq H3K27Me3 Ab: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb (9733BC, Cell Signalinf Technology, lot:10/2016)

data_processing:
For ChIP-seq analysis, reads were mapped by bowtie2 against human reference genome GRCh38 (Langmead and Salzberg 2012).
Only uniquely mapped reads were used and PCR duplicates were removed with samtools rmdup.
The resulting bam files are converted to bigWig format by bedGraphToBigWig from bedGraph generated by bedtools.
For 4C-seq analysis, the long-range genomic interaction regions generated by the 4C-Seq experiment were analyzed by using the R package r3CSeq v1.30.0 on hg19.
Bam files are converted to read coverage by bedGraphToBigWig. The read coverage was normalized according to sequencing depth.
The resulting bedGraph files are converted to bigWig format.
The genome version of bigWig files was converted to hg38 by CrossMap.
For total RNA-seq analysis, the paired-end RNA-seq reads were trimmed for adaptor sequence by TrimGalore and then mapped by STAR to the human reference genome GRCh38 with reference gene annotation GENCODE 26.
PCR duplicates were removed in the paired-end alignments by samtools rmdup.
Alignments with mapping quality < 20 were removed.
Gene expression levels in FPKM were determined by cuffdiff in the Cufflinks package.
For fraction RNA-seq analysis, the paired-end RNA-seq reads were trimmed for adaptor sequence by TrimGalore and then mapped by STAR to the human reference genome GRCh38 with reference gene annotation.
The read count on each EZH2 peak region was generated by featureCount. The read count was normalized according to the sequencing depth.
For RIP-seq analysis, reads from the RIP data set and its control data set were mapped respectively by STAR against human reference genome GRCh38 with gene annotation.
Only uniquely mapped reads were used and PCR duplicates were removed with samtools rmdup.
Bam files was converted to bedGraph to represent read coverage by bedtools. The read coverage was normalized according to the size of transcriptome mapping.
The resulting bedGraph files are converted to bigWig format.
For NANOPOPRE-seq total polyA+ RNA, the reads were mapped to hg38 by Minimap2 with -ax splice -uf -k14.
The bam files were converted to bed12 by bamToBed and were converted to bigBed file by bedToBigBed. Only uniquely mapped reads were retained.
For NANOPORE-seq nuclear cDNA sequencing, the reads were mapped to hg38 by LAST with lastal -d90 -m50 -D10 and last-split -d2
The maf files were converted to psl file with maf-convert -j1e6 psl. The psl files were subsequently converted to bam file with psl2sam.pl and cigar_tweaker scripts within the SAMtools package.
The read alignments were then converted into bedGraph by BEDTools and into bigWig format by bedGraphToBigWig.
Genome_build: hg38
Supplementary_files_format_and_content: RNAseq.genes.fpkm.txt: Tab-delimited text file includes FPKM values.
Supplementary_files_format_and_content: *.ReadCount.txt: Tab-delimited text files include read counts.
Supplementary_files_format_and_content: *bw: bigWig format
Supplementary_files_format_and_content: *.bigBed: bigBed format

value: LEVER KD dCas9

tag: antibody

value: H3K27Me3 Ab:Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb (9733BC, Cell Signaling Technology, lot:10/2016)


title: Col_22C_0h_rep2

tag: ecotype


title: Heart CTRL_3

value: Control (CTRL), normoxic conditions


title: Heart Chrysin_4


title: Heart SU_HX_4


title: Heart CTRL_1


title: JK136_reg1_org_3 [scRNA-seq]


title: Heart SU_HX_1


title: 4Cseq-ntgRNA-Viewpoint-2_2


title: RNAseq Nuclear PolyA+

description: RNA-seq Nuclear PolyA+ fraction

value: Wild type


title: 4Cseq-ntgRNA-Viewpoint-3_2

value: Leukemia cell line


title: Heart SU_HX_2


title: RNAseq Nuclear

description: RNA-seq Nuclear fraction


title: ChIPseq-LEVER_KD-Input

description: ChIP-seq Input


title: RNAseq Cytoplasmic

description: RNA-seq cytoplasmic fraction


title: ChIPseq-LEVER_KD-H3K27Me2

description: ChIP-seq H3K27Me2 Ab: Di-Methyl-Histone H3 (Lys27) (D18C8) XP® Rabbit mAb (#9728 Cell Signalinf Technology, lot:)

value: H3K27Me2 Ab:Di-Methyl-Histone H3 (Lys27) (D18C8) XP Rabbit mAb (#9728 Cell Signaling Technology)


title: JK134_reg2_org_2 [scRNA-seq]


title: Heart Chrysin_1


title: Monoecious WT PolII ChIP-seq  rep1

description:
PolII IP chromatin
Bioreplicate 1

data_processing:
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar SE $input $output ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads data were mapped using bowtie2 v 2.3.5 with the following setting "bowtie2 --very-sensitive" against the genome of Melon_v4.0_PacBio.
Filtering step: Mapped reads were filtered with samtools v.1.9 with the command "samtools view -h -b -q 30  "mapping_quality >= 30"
Duplicate filtering: duplicated reads were removed with samtools v.1.9 with the command "samtools fixmate -m  and samtools markdup -r "
Peak calling: peaks of read density were called with macs2 2.2.7.1 with the command "macs2 callpeak --broad  -t sample.bam   -c Input.bam -g 7.8e8 -q 0.05 --extsize 150 --bw 500 -B -n --outdir "
Bigwig generation: read density was scored with s3norm with the default paramaters
Genome_build: Melon_v4.0_PacBio
Supplementary_files_format_and_content: bigwig file, containing Chr, start position, end position.
Supplementary_files_format_and_content: sharp Peak file from macs2

organism: Cucumis melo

source_name: Leaf

growth_protocol: Germinated seeds were transfer to 10L pots and place in a glasshouse under long day conditions (16h/8h), a temperature of 27 °C during the day and 21 °C during the night, and a relative humidity of 60%.

extract_protocol:
1g of fresh leaves was crosslinked in 1% (v/v) formaldehyde for 15min. Crosslinking was then stopped by adding glycine in a final solution of 0.25M solution for 5min. Samples were homogenized, and nuclei was isolated and lysed. Cross‐linked chromatin was sonicated using a Covaris S220 (Peak Power: 175, cycles/burst: 200. Duty Factory: 20) for 9 min. Protein-DNA complexes were immunoprecipitated with rabbit anti-H3K27me3 (Millipore, ref. 07-449)  antibodies overnight at 4 °C with gentle shaking and later incubated for 2h at 4 °C. Posteriorly, for H3K27me3 IP, chromatin-antibody complexes were incubated for 50 μL of Dyna- beads Protein A (Invitrogen, Ref. 100-02D). Beads were washed for 2 × 5 min in ChIP Wash Buﬀer 1 (0.1% SDS, 1% Triton X-100, 20mM Tris-HCl pH 8, 2 mM EDTA pH 8, 150 mM NaCl), 2 × 5 min in ChIP Wash Buﬀer 2 (0.1% SDS, 1% Triton X-100, 20 mM Tris-HCl pH 8, 2 mM EDTA pH 8, 500 mM NaCl), 2 × 5 min in ChIP Wash Buﬀer 3 (0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 10 mM Tris-HCl pH 8,1 mM EDTA pH 8) and twice in TE (10 mM Tris-HCl pH 8, 1 mM EDTA pH 8).  ChIPed DNA was eluted by two 15-min incubations at 65 °C with 250 μL Elution Buﬀer (1% SDS, 0.1 M NaHCO3). Chromatin was reverse‐cross‐linked by adding 20 μl of NaCl 5M and incubated overnight at 65°C. Reverse cross‐linked DNA was then treated with RNase and proteinase K digestion, and extracted with phenol−chloroform. DNA was ethanol precipitated in the presence of 20 μg of glycogen and incubated overnight at -20°C. DNA pellet was then resuspended in 20 μL of nuclease- free water (Ambion) in a DNA low-bind tube. 10 ng of IP or input DNA was used for ChIP-Seq library construction using NEB-Next Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturer’s recommendations.
NEBNext Ultra II FS DNA Library Prep Kit for Illumina (E5745S)

tag: cultivar

value: Charantais type:Cucumis melo L. subsp. melo var cantalupensis

tag: genotypes

value: CharMONO inbreed line

tag: chip antibody

value: anti-PolII(Millipore, ref. 07-449)


title: ChIPseq-LEVER_KD-H3K27Ac

description: ChIP-seq H3K27Ac Ab: abcam (ab4729 lot: GR232896-1)


title: Heart CTRL_2

value: Sprague Dawley

value: Heart

tag: treatment


title: ChIPseq-ntgRNA-H3K27Me2

value: Wild type / ntgRNA dCas9


title: Cmlhp1ab input

description:
Bioreplicate 1
Total Chromatin

data_processing:
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar SE $input $output ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads data were mapped using bowtie2 v 2.3.5 with the following setting "bowtie2 --very-sensitive" against the genome of Melon_v4.0_PacBio.
Filtering step: Mapped reads were filtered with samtools v.1.9 with the command "samtools view -h -b -q 30  "mapping_quality >= 30"
Duplicate filtering: duplicated reads were removed with samtools v.1.9 with the command "samtools fixmate -m  and samtools markdup -r "
Peak calling: peaks of read density were called with macs2 2.2.7.1 with the command "macs2 callpeak --broad  -t sample.bam   -c Input.bam -g 7.8e8 -q 0.05 --extsize 150 --bw 500 -B -n --outdir "
Bigwig generation: read density was scored with s3norm with the default paramaters
Genome_build: Melon_v4.0_PacBio
Supplementary_files_format_and_content: bigwig file, containing Chr, start position, end position.
Supplementary_files_format_and_content: broadPeak file from macs2

value: CharMONO cmlhp1ab double mutant carrying EMS mutations for Cmlhp1a (G1970A, genomic position from ATG ) and cmlhp1b (C1930T genomic position from ATG )


title: JK134_reg2_org_1 [scRNA-seq]

tag: sample type

tag: tumour type

value: primary


title: RNAseq Nuclear PolyA-

description: RNA-seq Nuclear PolyA- fraction

tag: cell type


title: Cmlhp1ab H3K27me3 ChIP-seq rep2

description:
Bioreplicate 2
H3K27me3 IP chromatin

value: anti-H3K27me3 (Millipore, ref. 07-449)


title: JK134_reg2_org_3 [scRNA-seq]

value: organoid

tag: patient id


title: Monoecious WT Input

description:
Bioreplicate 1
Total Chromatin


title: Cmlhp1abRNA-seq rep3

description: Bioreplicate 3

data_processing:
Trimming:Adapters were trimmed using  trimmomatic v0.38, Parameters: ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30
mapping: Reads were mapped against Melonomics PacBIO V4 genome using STAR with the parameter: sjdbOverhang=75, outFilterType=BySJout and outFilterIntronMotifs=RemoveNoncanonical
Raw read counts were then extracted using featureCounts based on the gene annotations in Melon_PacBio_v4_liftover_Chr.gtf
Differentially expressed genes were identified using R 3.5.1 (www.R-project.org) and the package DESeq2 (adj. p value < 0.05).
Genome_build: MELONOMICS V4.0 Cucumis melo L. (DHL92)

extract_protocol:
Total RNA were extracted from 1g of fresh leaves using the Nucleospin RNA plus kit (Macherey–Nagel), according to the manufacturer’s instructions.  For RNA-seq analysis, libraries were synthetized using NEBNext UltraII Directional RNA library Preparation Kit (NEB) according to the manufacturer’s instructions.
RNA-seq libraries were prepared using 2 μg of total RNA with the NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs), according to manufacturer’s recommendations. The quality of the libraries was assessed with Agilent 2100 Bioanalyzer (Agilent).


title: ChIPseq-ntgRNA-H3K27Me3

tag: cell line


title: Cmlhp1abRNA-seq rep2

description: Bioreplicate 2


title: JK134_reg2_tis_1 [scRNA-seq]

value: tissue


title: Monoecious WT RNA-seq  rep3

description: Bioreplicate 3


title: JK126_reg2_org_3 [scRNA-seq]


title: ChIPseq-ntgRNA-H3K27Ac

tag: genotype/variation


title: Monoecious WT RNA-seq  rep1

description: Bioreplicate 1


title: JK126_reg2_org_1 [scRNA-seq]


title: JK134_reg1_org_3 [scRNA-seq]


title: Monoecious WT H3K27me3 ChIP-seq  rep1

description:
Bioreplicate 1
H3K27me3 IP chromatin


title: JK134_reg1_org_2 [scRNA-seq]


title: 4Cseq-LEVER_KO-Viewpoint-1

value: LEVER KO Cas9

tag: passage


title: U2OS.-HHV6A.+TSA.B

description: small RNAseq

data_processing:
Reads that passed the chastity filter on the NextSeq 500 were subject to de-multiplexing and trimming of TriLink adapter residuals using Illumina’s bcl2fastq v2 software (v2.19.1). To refine the output, read quality was checked with FastQC software (v0.11.5) and reads shorter 10 bases or longer 25 bases or containing “N” as a base call, were discarded.
STAR_2.5.3a was used to map all reads against a combined index prepared for the human genome (Ensembl 90) and the HHV6A genome (genbank accession X83413). The following parameters were used: --alignIntronMax 1 --outFilterMismatchNmax 1 --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 10 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 16.
Reads were counted using Gedi 1.0.3.
Genome_build: hg38, X83413

source_name: Human Osteosarcoma cellls carrying no HHV-6A

extract_protocol:
Cells were washed once with PBS and total cellular RNA was extracted using Qiagen RNeasy mini kit.
RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina) using both, Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad). For sequencing, samples were diluted and pooled into NGS libraries in equimolar amounts and were sequenced using NextSeq 500.

tag: time post induction

tag: treated with

value: TSA (80 ng/ml)


title: U2OS.-HHV6A.+TSA.A

description: small RNAseq

value: Human Osteosarcoma cellls carrying no HHV-6A


title: JK126_reg2_tis_1 [scRNA-seq]

source_name: glioblastoma


title: Cmlhp1abRNA-seq rep1

description: Bioreplicate 1


title: Monoecious WT H3K27me3 ChIP-seq rep2

description:
Bioreplicate 2
H3K27me3 IP chromatin


title: JK134_reg1_tis_1 [scRNA-seq]


title: ChIPseq-ntgRNA-Input

description: ChIP-seq Input


title: 4Cseq-ntgRNA-Viewpoint-3_1

value: Wild type / ntgRNA Cas9


title: Col_17C_SIM4D_rep2

value: 4 days on CIM then 4 days on SIM

tag: temperature

tag: replicate

tag: tissue

value: Hypocotyl explant


title: Cmlhp1ab H3K27me3 ChIP-seqrep1

description:
Bioreplicate 1
H3K27me3 IP chromatin

value: Charantais type:Cucumis melo L. subsp. melo var cantalupensis


title: JK126_reg1_org_13mix [scRNA-seq]


title: Monoecious WT RNA-seq  rep2

description: Bioreplicate 2

value: CharMONO inbreed line


title: U2OS.-HHV6A.-TSA.B

description: small RNAseq

value: DMSO (solvent control)


title: JK126_reg2_org_2 [scRNA-seq]


title: 4Cseq-LEVER_KO-Viewpoint-4_1

value: Leukemia cell line


title: U2OS.+HHV6A.-TSA.B

description: small RNAseq

source_name: Human Osteosarcoma cellls Carrying latent HHV-6A


title: 4Cseq-LEVER_KO-Viewpoint-3_1


title: 4Cseq-LEVER_KO-Viewpoint-2_1


title: U2OS.-HHV6A.-TSA.A

description: small RNAseq


title: JK126_reg1_org_2 [scRNA-seq]


title: RIPseq-IgG-rep2

description: RIP-seq IgG Ab: Cell Signaling Mouse IgG

value: Wild type

tag: antibody

value: IgG Ab:Cell Signaling Mouse IgG


title: U2OS.+HHV6A.+TSA.B

description: small RNAseq

value: Human Osteosarcoma cellls Carrying latent HHV-6A


title: U2OS.+HHV6A.-TSA.A

description: small RNAseq


title: RIPseq-IgG-rep1


title: JK126_reg1_tis_1.2 [scRNA-seq]

value: primary


title: U2OS.+HHV6A.+TSA.A

description: small RNAseq


title: JK126_reg1_tis_1.1 [scRNA-seq]


title: 4Cseq-ntgRNA-Viewpoint-2_1


title: HeLa.-sncRNAU14.+AHT.B

description: small RNAseq

source_name: Human cervical carcinoma cells carrying mock lentivirus

value: Doxycycline (1 ug/ml)


title: patient_tumor_HBCx172_H3K4me3

first: Céline

last: Vallot

address: 26 Rue D'Ulm

institute: Institut Curie

data_processing:
Library strategy: Bulk CUT&Tag
CUT&TAG: Read #1 and Read #2 were aligned to hg38 Human genome reference using bowtie2 with options ‘-k 1 -N 1 –end-to-end’
CUT&TAG: After sorting by genomic coordinates, duplicates were removed using Picard tools MarkDuplicates.
CUT&TAG: Coverage BigWigs files were created from sorted deduplicated files using Deeptools bamCoverage function with options ‘--normalizeUsing CPM --binSize 50 --smoothLength 500 --extendReads 150 --ignoreForNormalization chrX’.
CUT&TAG: Reads were counted on 10kbp-region around TSS for both H3K27me3 and H3K4me3 (52138 TSS). The matrice was normalized with log2(RPKM). Each TSS with a normalized signal greater than the 85th percentile of the distribution of all TSS respectively in both H3K4me3 and H3K27me3 were considered bivalent’.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file of the normalized signal at TSS for each H3K27me3-H3K4me3 couple, indicating if the TSS is considered bivalent (‘Significant’ column).   Coverage files (.bw) for each histone mark.

source_name: Patient Triple-negative breast tumor

growth_protocol: Patient samples used in this study (n=9) originated from patient treated at Institut Curie with residual triple-negative breast cancers post-neoadjuvant chemotherapy, who gave informed consent for the profiling.

extract_protocol: CUT&Tag on frozen tumor samples. CUT&Tag was performed as in Kaya-Okur et al. with minor modifications on 50,000 to 100,000 nuclei with 1:50 antibody (Cell Signaling Antibodies : Anti-H3K27me3, Ref: 9733- C36B11, Anti-H3K4me3, Ref: 9751- C42D8) (Kaya-Okur et al., Bartosovic et al.,). All washes were performed in a volume of 500µL and all centrifugations were done using a swinging bucket centrifuge at 1300g, 4min, at 4°C for nuclei preparation and  600g, 8min, 4°C for subsequent steps. Nuclei were extracted and permeabilized from 10-20mg frozen tumor tissues by incubating samples 10min on ice in 6mL ice-cold NE1 buffer (20mM HEPES pH7.2, KCl 10mM, spermidine 0.5mM, glycerol 20%, BSA 1%, NP-40 1%, digitonin 0.01%, proteases inhibitor 1x) after mechanical dissociation. Following antibody incubation and tagmentation, samples were incubated for 1h at 55°C with max speed agitation with 3uL SDS10% and 2,5uL 20mg/mL proteinase K. After DNA extraction (Qiagen, Ref: 139046 MaXtract High density), PCR amplification (with 17 cycles, 20s at 63°C combined annealing/extension step) of the sequencing libraries was performed and profiles were checked on the Agilent TapeStation using High-sensitivity D1000 reagents. CUT&Tag libraries were sequenced on a NovaSeq 6000 (Illumina) in PE50 mode.

value: Patient Triple-negative breast tumor

value: Post-NAC

tag: experiment

value: H3K4me3 bulk Cut&Tag

value: TRUE


title: patient_tumor_HBCx172_H3K27me3

value: H3K27me3 bulk Cut&Tag


title: 4Cseq-ntgRNA-Viewpoint-4_1

value: Wild type / ntgRNA Cas9


title: patient_tumor_HBCx95_H3K4me3


title: 4Cseq-ntgRNA-Viewpoint-1


title: RIPseq-EZH2-rep2

description: RIP-seq EZH2 Ab: Active Motif (#39875, lot: 06313005)


title: HeLa.-sncRNAU14.-AHT.A

description: small RNAseq

value: Human cervical carcinoma cells carrying mock lentivirus


title: HeLa.+sncRNAU14.+AHT.B

description: small RNAseq

source_name: Human cervical carcinoma cells carrying lentiviral backbone with sncRNA-U14


title: JK125_reg2_org_4_r1 [scRNA-seq]

value: organoid


title: Heart CTRL_4

tag: strain

value: Sprague Dawley

value: Heart

tag: age & sex

value: 5 week-old, Male

value: Control (CTRL), normoxic conditions


title: patient_tumor_HBCx39_H3K4me3

tag: treatment


title: Sed_Plasma_sEV2

city: Xi 'an

first: Hang

last: Zhao

address: 127 Changle west road, Xi 'an  China

country: China

institute: Air force military medical university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: rawcounts

source_name: plasma small extracellular vesicle

extract_protocol:
total miRNA was extracted from sEVs from different samples by using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 90 min twice per day, lasts for 4 weeks

value: plasma

tag: exercise protocal

value: 90 min twice per day, lasts for 4 weeks

tag: molecule type

value: microRNA


title: patient_tumor_HBCx39_H3K27me3


title: HeLa.+sncRNAU14.-AHT.B

description: small RNAseq

tag: cell type

value: Human cervical carcinoma cells carrying lentiviral backbone with sncRNA-U14

value: DMSO (solvent control)


title: Exe_BAT sEV3

source_name: brown adipose tissue small extracellular vesicle

value: brown adipose tissue


title: RNAseq

description: RIP-seq Input

value: Leukemia cell line

value: Wild type


title: JK125_reg2_org_1 [scRNA-seq]

data_processing:
Raw sequencing data were demultiplexed using the CellRanger software (10X Genomics; cellranger mkfastq with default parameters; v2.0.0 or v2.1.1)
Alignment, filtering, barcode counting, and UMI counting were done using the CellRanger software (cellranger count with default parameters except --expect-cells set to 1000; v2.1.1). The CellRanger GRCh38-1.2.0 reference was used for alignment.
Additional cell and gene filtering were performed in R on the filtered count matrices output by CellRanger using the scater package (v1.10.0). Outlier cells were identified as those with >3 median absolute deviations (MADs) below the median total UMI counts or total number of genes detected, or with >3 MADs above the median percent of counts from mitochondrial genes (per sample). Genes detected (UMI >0) in at least 10 cells with at least 20 UMIs were retained. Normalization was applied on remaining cells/genes using the scran package (v1.10.1). Putative doublets were identified using the doubletCells frunction from the scran package (k = 30) and cells with outlier doublet scores (>3 MADs above the sample median) were discarded. Gene filtering and normalization were performed again on the final dataset.
Genome_build: GRCh38
Supplementary_files_format_and_content: scRNAseq_all_cells_counts_matrix.mtx is a sparse matrix of raw UMI counts from all cells identified by the CellRanger pipeline. scRNAseq_all_cells_barcodes.tsv and scRNAseq_all_cells_genes.tsv contain associated barcode (column) and gene (row) names. scRNAseq_all_cells_metadata.csv contains associated cell metadata.
Supplementary_files_format_and_content: scRNAseq_filtered_cells_norm_counts_matrix.mtx is a sparse matrix of normalized UMI counts from QC-filtered cells. scRNAseq_filtered_cells_barcodes.tsv and scRNAseq_filtered_cells_genes.tsv contain associated barcode (column) and gene (row) names. scRNAseq_filtered_cells_metadata.csv contains associated cell metadata.

tag: sample type

tag: tumour type

value: primary

tag: patient id


title: JK125_reg2_tis_2_r1 [scRNA-seq]

value: tissue


title: JK125_reg2_btic_1 [scRNA-seq]

value: neurosphere line


title: HeLa.-sncRNAU14.+AHT.A

description: small RNAseq

value: Human cervical carcinoma cells carrying mock lentivirus

value: Doxycycline (1 ug/ml)


title: Exe_BAT sEV1


title: JK125_reg2_org_2 [scRNA-seq]

value: organoid


title: HeLa.-sncRNAU14.-AHT.B

description: small RNAseq


title: patient_tumor_HBCx167_H3K27me3

value: Patient Triple-negative breast tumor

value: Post-NAC

value: H3K27me3 bulk Cut&Tag

value: FALSE