title: ATRXKO_EZH2_Rep2

data_processing:
Alignment (CUT&RUN): Bowtie2
Alignment (ChIP-Seq): Bowtie2
Alignment (RNA-Seq): STAR
CUT&RUN bigwig files were made from .bam files using "deepTools bamCoverage --extendReads --binSize 5", an ENCODE blacklist file for biased regions (Amemiya et al. Nature 2019), and a spike-in normalization factor determined by alignment of reads to the Drosophila genome.
ChIP-Seq bigwig files were made from .bam files using "deepTools bamCoverage --ignoreDuplicates --extendReads --binSize 5", an ENCODE blacklist file for biased regions (Amemiya et al. Nature 2019), and RPM normalization.
RNA expected counts were generated with RSEM.
Assembly: mm10
Supplementary files format and content: bigwig files compatible with UCSC genome browser and IGV, TPM output in .counts tab-delimited for RNA-Seq alignment
Library strategy: CUT&RUN

value: ATRX knockout


title: Persister 1 day

status: Public on Sep 01 2022

type: SRA

city: Memphis

first: Douglas

middle: R

last: Green

state: United States

address: 262 Danny Thomas Pl

department: Immunology

country: USA

institute: St Jude Children's Research Hospital

library_source: transcriptomic

data_processing:
Cell Ranger (10X Genomics) (version 6.0.1) was used to process the raw sequencing data and align the reads to the GRCh38 reference genome with default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: HDF5. Filtered feature-barcode matrices of Cell Ranger output.

molecule: polyA RNA

organism: Homo sapiens

source_name: PC9 cell line

growth_protocol: Cells were maintained in complete DMEM media (10% fetal bovine serum (FBS), 2 mM L-glutamine and 100 units/ml penicillin-streptomycin)

extract_protocol:
Chromium Next GEM Chip G Single Cell Kit
Chromium Next GEM Single Cell 3ʹ Library Kit v3.1

treatment_protocol: Persisters were generated by treatement with ABT737 and S63845

tag: cell type

value: PC9 cell line

tag: genotype

value: Wild type


title: PHD-FV5_EZH2_Rep1

city: Philadelphia

first: Anna

last: Bieluszewska

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

growth_protocol: Mouse embryonic stem cells were grown in DMEM medium with 15% FBS, 25mM HEPES, 1x GlutaMAX, 1x non-essential amino acids, 100 U/mL penicillin-steptomycin, LIF, 3µM GSK inhibitor, 1µM MEK1/2 inhibitor at 37 ˚C.

extract_protocol:
CUT&RUN was performed on cells as previously described (Skene and Henikoff, eLife 2017).
ChIP was performed on cells as previously described (Trizzino et al., Cell Rep 2018).
Total RNA was collected using Trizol (Invitrogen) and digested with Turbo Dnase (Ambion). rRNA was selectively depleted using FastSelect (Qiagen).
rRNA-depleted RNA was converted to cDNA using the Ultra II Directional RNA kit for Illumina (NEB #E7760).
DNA samples were end-repaired using End-Repair Mix (Enzymatics), A-tailed using Klenow exonuclease minus (Enzymatics), purified with MinElute columns (Qiagen), and ligated to Illumina adapters (NEB E7600) with T4 DNA ligase (Enzymatics).  Size selection for fragments >150 bp was performed with AMPure XP (Beckman Coulter).  Libraries were PCR amplified with dual index barcode primers for Illumina sequencing (NEB E7600) using Q5 DNA polymerase (NEB M0491) and purified with MinElute.

value: ATRX Flag-V5-Tag Knock-in-PHDmut

tag: antibody


title: WT_Input_Rep1

data_processing:
Alignment (CUT&RUN): Bowtie2
Alignment (ChIP-Seq): Bowtie2
Alignment (RNA-Seq): STAR
CUT&RUN bigwig files were made from .bam files using "deepTools bamCoverage --extendReads --binSize 5", an ENCODE blacklist file for biased regions (Amemiya et al. Nature 2019), and a spike-in normalization factor determined by alignment of reads to the Drosophila genome.
ChIP-Seq bigwig files were made from .bam files using "deepTools bamCoverage --ignoreDuplicates --extendReads --binSize 5", an ENCODE blacklist file for biased regions (Amemiya et al. Nature 2019), and RPM normalization.
RNA expected counts were generated with RSEM.
Assembly: mm10
Supplementary files format and content: bigwig files compatible with UCSC genome browser and IGV, TPM output in .counts tab-delimited for RNA-Seq alignment

value: Wildtype


title: K1input

city: Aurora

first: Joaquin

middle: M

last: Espinosa

state: CO

department: Pharmacology, Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the HiSeq 4000 RTA software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
FASTQC (v0.11.5) was used to assess sequence data quality.
Low quality bases (Q <10) were trimmed from the 3' end of reads and short reads (<30 nt after trimming) and adaptor sequences were removed using the fastqc-mcf(v1.04) tool from EAutils.
FastQ Screen (v0.11.0) was used to check for common sequencing contaminants
Alignment to the Human reference genome (GRCh37/hg19) was carried out using Bowtie2 (v2.2.9, --sensitive –-end-to-end)  with the UCSC hg19 GTF annotation file provided in the iGenomes UCSC hg19 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Aligned reads were then filtered to remove low quality mapped reads (MAPQ < 10) using SAMtools (v1.3.1)
Reads were coordinate sorted and duplicates were marked using Picard (v1.129)
Quality assessment of final mapped reads was performed using RSeQC (v2.6.4)
BigWig files for visualization of p53 occupancy were generated with deepTools [8] (version 2.2.2, settings --binSize=1 –extendReads FRAGMENT_LENGTH --minMappingQuality 10 –normalizeUsingRPKM). Read density was displayed at 1 bp resolution as reads per million of mapped reads per 1 kb (RPM/kb).
Genome_build: GRCh37/hg19; Bowtie2 index and GTF from iGenomes UCSC hg19 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Supplementary_files_format_and_content: BigWig - coverage visualization

growth_protocol: TPC1 and K1 cells were cultivated in RPMI (TPC1) or DMEM (K1) media (Gibco, Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Peak Serum) and 1% antibiotic-antimycotic mixture (Gibco). Cells were plated a day before the treatment and maintained in a humidified atmosphere with 5% of CO2 at 37°C.

extract_protocol:
Sub-confluent cultures of TPC1 and K1 cells were treated for 24 hours with indicated compounds. After the treatment period, cultivation media was replaced with crosslinking solution (1% formaldehyde in PBS) and plates were incubated for 15 minutes at room temperature. Next, formaldehyde was quenched with glycine (0.125 mM final) for 5 minutes and cells were washed twice with ice-cold PBS. Crosslinked cells were lysed in RIPA buffer (150 mM NaCl, 50 mM Tris pH 8.5 mM EDTA, 1% IGEPAL 630 (NP-40 substituent), 0.5% sodium deoxycholate, 0.1% SDS and protease/phosphatase inhibitors) and sonicated to generate 200-300 bp fragments of DNA (Qsonica Q800R, 70% amplitude, 30 sec on/30 sec off cycle, 20 cycles for TPC1 lysates and 25 cycles for K1 lysates). Next, samples were centrifugated at 20 000 g for 20 min at °C, protein concentration in collected supernatants was measured using a BCA Protein Assay Kit and all samples were diluted to final protein concentration of 1 mg/ml. Lysates were pre-cleared with 15 l of Dynabeads M-280 (sheep anti-mouse IgG, Thermo Fisher Scientific) and immunoprecipitated overnight with 5 l/sample of anti-p53 antibody (DO-1, EMD Millipore) and 30 l of Dynabeads at 4C. In total, 4 (TPC1) or 5 (K1) lysate aliquots per sample were used in immunoprecipitation reactions. Next day beads were washed (5 minutes each washing step) twice with RIPA, four times with IP wash buffer (500 mM LiCl, 100 mM Tris pH 8.5, 1% IGEPAL, 1% sodium deoxycholate), again twice with RIPA and twice briefly with TE (10 mM Tris pH 8, 1 mM EDTA). Washed beads were resuspended in 100 l of TE and 200 l of elution buffer (70 mM Tris pH 8, 1 mM EDTA and 1.5% SDS) and incubated at 65C for 10 minutes. After adding NaCl to final concentration of 200 mM, eluted immunocomplexes were incubated at 65C for 5 hours to reverse formaldehyde crosslinks. Remaining protein was digested by proteinase K (20 g/sample, 45C for 30 minutes). DNA was recovered by one phenol/chloroform and one chloroform extraction followed by ethanol precipitation and resuspension in 50 l of TE. Input DNA was extracted from reverse cross-linked lysates using the same extraction protocol as for sample DNA.
NEBNext Ultra II DNA sequencing library preparation kit

treatment_protocol: Cells were treated treated with vehicle (0.2% DMSO), 10 microM Nutlin-3a, 25 microM GSK2830371, and drug combinations for 24 hours.

tag: cell line

value: papillary thyroid carcinoma


title: WT_H3K27me3_Rep2


title: Sample_p53_ChiPseq_TPC1 - DMSO - rep2

tag: chip antibody

tag: treatment

value: DMSO


title: K1584R-FV5_EZH2_Rep1

value: ATRX Flag-V5-Tag Knock-in-K1584R


title: K1584R-FV5_EZH2_Rep2


title: Sample_p53_ChiPseq_TPC1 - GSK - rep1


title: PC9 A/S treated, BAX/BAK/BOK knockout 3

data_processing:
The reads were trimmed with Trim Galore (version 0.5.0) with default parameters.
Then reads were aligned to the reference mouse hg38 assembly plus ERCC spike-in sequences using STAR (version 2.7.5a).
The resulting alignments, recorded in BAM file, were sorted, indexed, and marked for duplicates with Picard MarkDuplicates function (version 2.19.0).
Transcript quantification was calculated using RSEM.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include read count values for each sample

molecule: total RNA

extract_protocol:
RNeasy Mini Kit, QIAGEN
TruSeq total Stranded RNA kits (Illumina)

treatment_protocol: Where indicated siRNA pretreatment was performed for 2d, followed by specific drug treatments. A/S stands for ABT737 and S63845.

value: ABT737 and S6

value: BAX/BAK/BOK knockout


title: ATRXKD_EZH2_Rep1

value: ATRX knockdown


title: PHD-FV5_EZH2_Rep2


title: PC9 A/S treated, BAX/BAK/BOK knockout 2


title: Sample_p53_ChiPseq_K1 - NutlinGSK - rep1


title: Persister 1 week


title: ATRXKO_EZH2_Rep1


title: ESC-HA_WT_8_GSK_rep2-RNA

city: Jerusalem

first: Lea

last: Cohen

address: Edmond J. Safra Campus

country: Israel

institute: HUJI

data_processing:
ChIP FASTQ files were aligned to the mm9 genome using Bowtie2
ChIP BAM files were sorted and duplicates were removed  using SAMtools
ChIP BAM files were converted to Bedgragh files were made using BEDTools
RNA FASTQ files were aligned to the mm9 genome using STAR  (version 2.7.1)
Genome_build: mm9

source_name: Embriyonic stem cells

growth_protocol: Cells were cultured on gelatin-coated tissue culture plates in ESC media

extract_protocol:
Cells were flash frozen in liquid nitrogen, RNA was prepared using RNeasy (Qiagen) according to the manufacturer's instructions.
Library preparation was done using QuantSeq 3′-mRNA-Seq Library Prep Kit (Lexogen) or KAPA mRNA-seq kit (Roche). Libraries were subjected to single-end sequencing using Illumina NextSeq500.

treatment_protocol: 1uM Dox for 4, 8, 24 or 72 (renewed every 24 ) hours pre- extraction of DNA/RNA

value: ES

tag: genotype/variation

value: WT

value: Dox amd GSK for 8 hours


title: WT_EZH2_Rep1


title: ESC-HA_WT_4_GSK_rep2-RNA

value: Dox and GSK for 4 hours


title: Persister 3 day


title: Parental


title: ESC-HA_WT_8_GSK_rep1-RNA

value: Dox and GSK for 8 hours


title: PC9 BAX/BAK/BOK knockout 4


title: ATRXKD_EZH2_Rep2


title: WT_H3K27me3_Rep1


title: PC9 BAX/BAK/BOK knockout 3


title: ESC-HA_WT_4_GSK_rep1-RNA

value: Dox amd GSK for 4 hours


title: WT_EZH2_Rep2


title: PC9 A/S treated, BAX/BAK/BOK knockout 1


title: ESC-HA_WT_24_GSK_rep1-RNA

value: Dox amd GSK for 24 hours


title: ESC-HA_WT_72_GSK_rep1-RNA

value: Dox and GSK for 72 hours


title: PC9 BAX/BAK/BOK knockout 2

value: PC9 cell line


title: PC9 BAX/BAK/BOK knockout 1


title: ESC-HA_WT_72_GSK_rep2-RNA

value: Dox amd GSK for 72 hours


title: PC9 A/S treated, BAX/BAK/BOK knockout 4


title: ESC-HA_WT_24_GSK_rep2-RNA

value: Dox and GSK for 24 hours


title: PC9 A/S treated, siBAX/BAK 4

tag: sirna

value: siBAX/BAK


title: PC9 A/S treated, siBAX/BAK 3


title: PC9 A/S treated, siBAX/BAK 2


title: ESC-HA_WT_8_GSK_rep2-H3K27Me3

extract_protocol:
Chromatin was digested using MNase. Barcoded adapters that contain a T7 promoter were ligated to the DNA ends of the fragmented nucleosomes, and samples were pooled and splitted according to the different antibodies.
We used T7 promoter to amplify the ChIP DNA in an in vitro transcription reaction. A second barcode was added during the library construction - as is described in van Galen et al. (2016).

value: [alpha]-H3K27me3 (Millipore, 07-449)


title: ESC-HA_WT_4_GSK_rep2-H3K27Me3


title: PC9 A/S treated, siBAX/BAK 1


title: ESC-HA_WT_24_GSK_rep2-H3K27Me3


title: WT_ATRX_Rep1

value: Wildtype

value: ATRX


title: PC9 siBAX/BAK 2

value: DMSO


title: PC9 siBAX/BAK 3


title: ESC-HA_WT_8_GSK_rep1-H3K27Me3


title: ESC-HA_WT_72_GSK_rep2-H3K27Me3


title: PC9 siBAX/BAK 1


title: PC9 A/S treated, siATF4 3

value: ABT737 and S6


title: ESC-HA_WT_24_GSK_rep1-H3K27Me3

value: ES


title: PC9 A/S treated, siATF4 2


title: PC9 siATF4 3


title: ESC-HA_WT_72_GSK_rep1-H3K27Me3

value: WT


title: ESC-HA_WT_8_GSK_rep2-H3K27ac

value: [alpha]H3K27ac (a gift from Hitoshi Kimura, Osaka University)


title: PC9 A/S treated, siATF4 1


title: PC9 siATF4 2


title: PC9 siATF4 1


title: PC9 A/S treated, siRNA control 3

value: Non-targeting siRNA


title: ESC-HA_WT_24_GSK_rep2-H3K27ac


title: PC9 siBAX/BAK 4


title: PC9 A/S treated, siRNA control 2


title: PC9 A/S treated, siRNA control 1


title: ESC-HA_WT_4_GSK_rep1-H3K27ac

value: Dox and GSK for 4 hours


title: PC9 siRNA control 3


title: ESC-HA_WT_8_GSK_rep1-H3K27ac

value: Dox and GSK for 8 hours


title: ESC-HA_WT_72_GSK_rep1-H3K27ac


title: ESC-HA_WT_24_GSK_rep1-H3K27ac


title: PC9 siRNA control 2


title: ESC-HA_WT_4_GSK_rep1-H3K27Me3


title: ESC-HA_WT_8_GSK-H3


title: HT29 A/S treated 1

source_name: HT29 cell line

value: HT29 cell line


title: ESC-HA_WT_4_GSK-H3


title: PC9 siRNA control 1


title: ESC-HA_WT_72_GSK-H3

value: Dox and GSK for 72 hours


title: HT29 A/S treated 2


title: HT29 Vemurafenib treated 2

value: Vemurafenib


title: ESC-HA_WT_4_GSK_rep2-ChIP

value: [alpha]-HA (ab9110)


title: HT29 Vemurafenib treated 1


title: HT29 Vemurafenib treated 3


title: ESC-HA_WT_8_GSK_rep2-ChIP

value: Dox amd GSK for 8 hours


title: HT29 A/S treated 3


title: ESC-HA_WT_4_GSK_rep1-ChIP

value: Dox amd GSK for 4 hours


title: ESC-HA_WT_72_GSK_rep2-H3K27ac


title: ESC-HA_WT_8_GSK_rep1-ChIP


title: ESC-HA_WT_24_GSK_rep2-ChIP

value: Dox and GSK for 24 hours


title: HT29 Irinotecan treated 2

value: Irinotecan


title: HT29 Irinotecan treated 1


title: HT29 3


title: ESC-HA_K27L_8-H3

value: Dox for 8 hours


title: ESC-HA_WT_72_GSK_rep2-ChIP

value: Dox amd GSK for 72 hours


title: ESC-HA_WT_72_GSK_rep1-ChIP


title: HT29 Irinotecan treated 3


title: HT29 2

value: DMSO


title: PC9 A/S treated 3

value: PC9 cell line

value: ABT737 and S6


title: ESC-HA_K27L_4-H3

value: ES

value: Dox for 4 hours


title: HT29 1


title: ESC-HA_K27L_72-H3

value: Dox for 72 hours


title: PC9 A/S treated 2


title: ESC-HA_K27M_4-H3


title: ESC-HA_K27M_8-H3


title: PC9 Paclitaxel treated 3

value: Paclitaxel


title: ESC-HA_WT_4_GSK_rep2-H3K27ac

value: [alpha]H3K27ac (a gift from Hitoshi Kimura, Osaka University)

value: WT

value: Dox and GSK for 4 hours


title: ESC-HA_WT_4-H3


title: ESC-HA_WT_24_GSK_rep1-ChIP

value: [alpha]-HA (ab9110)

value: Dox amd GSK for 24 hours


title: PC9 Erlotinib treated 3

value: Erlotinib


title: PC9 Paclitaxel treated 1


title: ESC-HA_WT_8-H3


title: ESC-HA_WT_72-H3


title: PC9 Paclitaxel treated 2


title: PC9 Erlotinib treated 1


title: OPC-HA_K27M_24_rep2-RNA

source_name: oligodendrocyte progenitor cells

value: ES-derived oligodendrocyte progenitor cells

value: Dox for 24 hours


title: OPC-HA_WT_24_rep2-RNA


title: PC9 3


title: OPC-HA_K27M_72_rep1-RNA


title: PC9 1


title: PC9 2


title: PC9 A/S treated 1


title: EGR1 CHIP-seq CD34 HSPC-3

city: Chicago

first: Angela

last: Stoddart

state: IL

address: 900 E. 57th Street, Lab 5220A

department: Pathology

institute: University of Chicago

data_processing:
Illumina's bcl2fastq was used for basecalling
For RNA seq analysis, reads were aligned to hg19 with Tophat, mapping quality <30 were removed. Generalized linear model in EdgeR2 was used to derive pvalue, correcting for batch effects and multiple testing, restricting the analysis ot genes with counter per million >2 in 3 or more samples.
For ChIP seq analysis, sequencing reads were aligned to the human hg19 genome using BWA and low quality reads were removed using the SAMtools q30 filter. Peaks were called using MACS2 with a q value threshold of 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: For RNA seq analysis, tab-delimited text files include cpm (counts per million) values for each sample. For ChIP seq analysis, tab-delimited text files include EGR1 peaks with fold enrichment over input DNA.

source_name: CD34+ Hematopoietic and Stem Progenitor Cell

growth_protocol: CD34+ HSPC were isolated from cord blood and expanded in 50 ng/mL each of IL- 3, IL-6, TPO, SCF and FLT3 ligand.

extract_protocol:
RNA was isolated from CD34+ HSPCs with Trizol. ChIP samples were generated from isolated HSPC nuceli using the EGR1 specific antibody 588 from Santa Cruz (sc-110)
RNA libraries were constructed using Illumina's TruSeq Stranded mRNA kit. DNA libraries for ChIP seq were constructed using Tecan's Ovation DNA library preparation kit.

treatment_protocol: HSPCs were transduced with a shRNA specific for EGR1 or Ren (control). Cells were sorted for GFP (shRNA+) 4 days later.

tag: shRNA

tag: days post shrna infection

value: anti-EGR1 588 (Santa Cruz sc-110)


title: EGR1 CHIP-seq CD34 HSPC-2

value: CD34+ Hematopoietic and Stem Progenitor Cell


title: ESC-HA_K27L_8_rep2-H3K27ac

value: Dox for 8 hours


title: Input DNA CD34 HSPC


title: OPC-HA_WT_72_rep1-RNA


title: ESC-HA_K27L_8_rep1-H3K27ac


title: ESC-HA_K27M_72-H3


title: ESC-HA_K27M_8_rep2-H3K27ac


title: RNA-CD34 HSPC REN KD2

value: Ren

value: 4 days


title: ESC-HA_K27M_8_rep1-H3K27ac

value: ES


title: ESC-HA_WT_8_rep2-H3K27ac


title: RNA-CD34 HSPC EGR1 KD1


title: RNA-CD34 HSPC  EGR1 KD2


title: RNA-CD34 HSPC REN KD1


title: ESC-HA_WT_8_rep1-H3K27ac


title: ESC-HA_K27M_4_rep2-H3K27ac

value: Dox for 4 hours


title: ESC-HA_K27L_4_rep1-H3K27ac


title: ESC-HA_K27M_4_rep1-H3K27ac


title: PC9 Erlotinib treated 2

value: PC9 cell line


title: Patient3

city: Erzurum

first: Selçuk

last: Özdemir

address: Atatürk University Faculty of Veterinary Medicine

country: Turkey

institute: Atatürk University

data_processing:
Library strategy: circRNA-Seq
Raw data (raw reads) of FASTQ format were firstly processed through in-house scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. An upgraded computational pipeline (CIRCexplorer2) is applied to detect circRNAs and identify alternative (back-)splicing in back-spliced circular RNAs (circRNAs).
The expression of circRNAs is usually represented by the fragments that are mapped to the back-spliced exon–exon junction sites. In addition to the raw fragment numbers, normalized RNA-seq fragments that are mapped to a specific back-spliced exon–exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM (Fragments mapped to back-spliced junction Per Million mapped fragments), circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. (For DESeq2 with biological replicates) Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed.
A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology (GO) annotates genes to biological processes, molecular functions, and cellular components in a directed acyclic graph structure, and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotates genes to pathways. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large- scale molecular datasets generated by genome sequencing and other high- throughput experimental technologies (http://www.genome.jp/kegg/). We used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways.
circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs, microRNA target site in exons of circRNA loci were identified using miRanda (animal species) or psRobot (plant species). Software could be used to construct the circRNA-miRNA-gene networks.
Genome_build: UMD3.1
Supplementary_files_format_and_content: CircRNA_TPM.xlsx
Supplementary_files_format_and_content: CircRNA_up_and_down_regulation.xlsx

source_name: Serum/Exosome

extract_protocol:
Firstly, exosomes were extracted and then total RNA was isolated with Trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: diagnosis

value: Hepatic alveolar echinococcosis (HAE)

tag: tissue

value: Serum exosomes


title: Patient2


title: ESC-HA_WT_4_rep1-H3K27ac

value: [alpha]H3K27ac (a gift from Hitoshi Kimura, Osaka University)

value: WT


title: ESC-HA_K27L_4_rep2-H3K27ac


title: Patient1


title: Control3

value: Healthy


title: ESC-HA_WT_4_rep2-H3K27ac


title: ESC-HA_K27L_24_rep2-H3K27ac


title: ESC-HA_K27L_24_rep1-H3K27ac


title: ESC-HA_K27M_24_rep2-H3K27ac


title: HC2_100

city: Beijing

first: Xiangjun

last: Liu

address: No.8 Xishiku Street

country: China

institute: Peking University First Hospital

data_processing:
RNA sequencing data produced by Illumina HiSeq 4000 was subjected to quality control (QC) that determine if a resequencing step is needed.
After filtering raw reads via SOAPnuke,clean reads were mapped to the human hg38 reference genome via HISAT.
Clean reads were aligned to the reference gene sequence using Bowtie2 and gene expression levels were calculated by RSEM,which was normalized as FPKM（fragments per kilobase million）.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for 12 samples

source_name: Blood

growth_protocol: PBMCs were cultured in RPMI 1640 medium with 10% fetal bovine serum , containing 100 U/mL penicillin and 0.1 mg/mL streptomycin

extract_protocol:
200ng total RNA samples were extracted from PBMCs obtained from Healthy donors or leukemic CTCL patients using EZNA total RNA kit II (Omega Bio-tek)
RNA libraries were prepared for sequencing using standard Illumina and BGISEQ protocols

treatment_protocol: PBMCs from HC or CTCL patients were subjected with recombinant SEB or PBS

value: peripheral blood mononuclear cells

tag: disease state

value: Healthy Donor

value: Blood

tag: tumor stage

value: recombinant SEB 100 μg/mL


title: HC2_500

value: recombinant SEB 500 μg/mL


title: ESC-HA_WT_24_rep2-H3K27ac

value: Dox for 24 hours


title: Control1


title: ESC-HA_K27M_72_rep2-H3K27ac

value: Dox for 72 hours


title: ESC-HA_K27L_72_rep1-H3K27ac


title: ESC-HA_K27M_72_rep1-H3K27ac


title: HC1_0

value: PBS


title: HC2_0


title: ESC-HA_WT_24_rep1-H3K27ac


title: HC1_100


title: ESC-HA_WT_72_rep2-H3K27ac


title: ESC-HA_K27L_72_rep2-H3K27ac


title: HC1_500


title: CTCL2_500

value: CTCL

value: tumor


title: CTCL2_0


title: Control2


title: CTCL2_100


title: CTCL1_500


title: CTCL1_100


title: ESC-HA_K27L_8_rep2-H3K27Me3

value: ES

value: [alpha]-H3K27me3 (Millipore, 07-449)

value: Dox for 8 hours


title: ESC-HA_K27L_8_rep1-H3K27Me3


title: ESC-HA_WT_72_rep1-H3K27ac


title: ESC-HA_K27M_24_rep1-H3K27ac


title: CTCL1_0


title: ESC-HA_K27M_8_rep2-H3K27Me3


title: ESC-HA_K27M_8_rep1-H3K27Me3


title: ESC-HA_WT_8_rep2-H3K27Me3


title: ESC-HA_WT_8_rep1-H3K27Me3


title: ESC-HA_K27M_4_rep2-H3K27Me3

value: Dox for 4 hours


title: ESC-HA_WT_4_rep2-H3K27Me3


title: ESC-HA_WT_4_rep1-H3K27Me3


title: HAP1_ATAC-seq_WT_shControl_Testosterone_r6

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description: ATAC-seq for wild type HAP1 cell line with control shRNA, treated with Testosterone, replicate 6

data_processing:
Sequenced reads were trimmed for adaptor sequences with Skewer
Reads were mapped to hg19 whole genome using bowtie2 v2.2.4 with the –very-sensitive parameter
Duplicate reads were marked and removed with picard tools version 1.118
Peaks for ATAC-seq samples were called with MACS2 version 2.1.1.20160309 using the “–nomodel” and “–extsize 147” parameters
ATAC-seq read coverage at every reference genome position using BEDTools coverage and divided by the total number of reads, converted into bedgraph files and subsequently to bigwig format using bedGraphToBigWig.
Genome_build: hg19
Supplementary_files_format_and_content: Narrow peak files have MACS2 peak calls, BigWig files have read counts per million mapped reads

source_name: cell line

growth_protocol: HAP1 WT and knock-out cells were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM, Thermo Fisher Scientific, 21980-032) supplemented with 10% heat inactivated Fetal Bovine Serum (FBS, Thermo Fisher Scientific, 10500) and 1% Pen Strep (100 units/ml Penicillin, 100 µg/ml Streptomycin, Thermo Fisher Scientific, 15140-122). A549 cells were cultured in F-12K Nut Mix (Thermo Fisher Scientific, 21127-022) supplemented with 10% FBS and 1% Pen Strep.

extract_protocol: 50000 cells were resuspended in 25 µl transposase reaction mix (0.05% digitonin, 1x TD buffer, 0.08% TDE1 (Nextera DNA Library Preparation Kit, Illumina, FC-121-1031)) and incubated for 30 min, 37°C, 300 rpm. Then DNA was purified using MinElute kit (Qiagen, 28004) and eluted in 11 µl elution buffer. 1 µl was used to determine cycle number for PCR using a qPCR approach. The remaining 10 µl were complemented with 1x NEBnext High-Fidelity PCR master mix (New England BioLabs, M0541), 1.25 µM index primer 1 and 1.25 µM index primer containing a barcode. PCR was performed: 5 min 72°C, 30 sec 98°C, X cycles of 10 sec 98°C + 30 sec 63°C + 1 min 72°C, 1 min 72°C and then cleaned-up using Agencourt AMPure XP beads (Beckman Coulter, A63880).

tag: library

value: ATAC-seq

tag: replicate

tag: knockout

tag: knockdown

value: Control

value: Testosterone


title: HAP1_ATAC-seq_WT_shControl_Testosterone_r5

description: ATAC-seq for wild type HAP1 cell line with control shRNA, treated with Testosterone, replicate 5

value: WT


title: HAP1_ATAC-seq_WT_shControl_GSK126_r5

description: ATAC-seq for wild type HAP1 cell line with control shRNA, treated with GSK126, replicate 5


title: HAP1_ATAC-seq_WT_shControl_GSK126_r6

description: ATAC-seq for wild type HAP1 cell line with control shRNA, treated with GSK126, replicate 6


title: ESC-HA_K27L_24_rep2-H3K27Me3

tag: cell type


title: ESC-HA_K27M_24_rep2-H3K27Me3


title: HAP1_ATAC-seq_WT_shCHAF1A_Testosterone_r5

description: ATAC-seq for wild type HAP1 cell line with shRNA against CHAF1A, treated with Testosterone, replicate 5


title: HAP1_ATAC-seq_WT_shCHAF1A_GSK126_r5

description: ATAC-seq for wild type HAP1 cell line with shRNA against CHAF1A, treated with GSK126, replicate 5


title: HAP1_ATAC-seq_WT_shCHAF1A_GSK126_r6

description: ATAC-seq for wild type HAP1 cell line with shRNA against CHAF1A, treated with GSK126, replicate 6


title: HAP1_ATAC-seq_WT_dCHAF1A-Control_r5

description: ATAC-seq for wild type HAP1 cell line with control for CHAF1A degradation, replicate 5

tag: degradation


title: HAP1_ATAC-seq_WT_shControl_DMSO_r6

description: ATAC-seq for wild type HAP1 cell line with control shRNA, treated with DMSO, replicate 6

tag: cell line

value: DMSO


title: ESC-HA_K27L_24_rep1-H3K27Me3

tag: chip antibody


title: HAP1_ATAC-seq_WT_shControl_DMSO_r5

description: ATAC-seq for wild type HAP1 cell line with control shRNA, treated with DMSO, replicate 5


title: HAP1_ATAC-seq_WT_dCHAF1A-24h_r6

description: ATAC-seq for wild type HAP1 cell line with degradation of CHAF1A for 24 hours, replicate 6

value: dTAG 24h


title: ESC-HA_WT_24_rep1-H3K27Me3

tag: treatment


title: ESC-HA_WT_24_rep2-H3K27Me3

tag: genotype/variation


title: HAP1_ATAC-seq_WT_dCHAF1A-24h_r5

description: ATAC-seq for wild type HAP1 cell line with degradation of CHAF1A for 24 hours, replicate 5


title: HAP1_ATAC-seq_WT_dCHAF1A-12h_r6

description: ATAC-seq for wild type HAP1 cell line with degradation of CHAF1A for 12 hours, replicate 6

value: dTAG 12h


title: ESC-HA_K27L_4_rep2-H3K27Me3


title: HAP1_ATAC-seq_WT_shCHAF1A_Testosterone_r6

description: ATAC-seq for wild type HAP1 cell line with shRNA against CHAF1A, treated with Testosterone, replicate 6


title: ESC-HA_K27L_4_rep1-H3K27Me3


title: ESC-HA_K27M_4_rep1-H3K27Me3


title: ESC-HA_K27L_72_rep2-H3K27Me3


title: HAP1_ATAC-seq_WT_dCHAF1A-12h_r5

description: ATAC-seq for wild type HAP1 cell line with degradation of CHAF1A for 12 hours, replicate 5


title: ESC-HA_K27L_72_rep1-H3K27Me3


title: HAP1_ATAC-seq_WT_shCHAF1A_DMSO_r6

description: ATAC-seq for wild type HAP1 cell line with shRNA against CHAF1A, treated with DMSO, replicate 6


title: HAP1_ATAC-seq_WT_shCHAF1A_DMSO_r5

description: ATAC-seq for wild type HAP1 cell line with shRNA against CHAF1A, treated with DMSO, replicate 5


title: HAP1_ATAC-seq_WT_dCHAF1A-Control_r6

description: ATAC-seq for wild type HAP1 cell line with control for CHAF1A degradation, replicate 6


title: ESC-HA_K27M_72_rep2-H3K27Me3


title: ESC-HA_K27M_24_rep1-H3K27Me3


title: ESC-HA_WT_72_rep2-H3K27Me3


title: ESC-HA_K27M_72_rep1-H3K27Me3


title: ESC-HA_K27L_8_rep1-ChIP

value: [alpha]-HA (ab9110)


title: HAP1_ATAC-seq_WT_HIRA_Hairpin3_R1

description: ATAC-seq for wild type HAP1 cell line with shRNA against HIRA hairpin 3, replicate 1

value: HIRA


title: HAP1_ATAC-seq_WT_HIRA_Hairpin3_R2

description: ATAC-seq for wild type HAP1 cell line with shRNA against HIRA hairpin 3, replicate 2


title: HAP1_ATAC-seq_WT_HIRA_Hairpin1_R2

description: ATAC-seq for wild type HAP1 cell line with shRNA against HIRA hairpin 1, replicate 2


title: HAP1_ATAC-seq_WT_Control_R2

description: ATAC-seq for wild type HAP1 cell line, replicate 2


title: HAP1_ATAC-seq_WT_HIRA_Hairpin1_R1

description: ATAC-seq for wild type HAP1 cell line with shRNA against HIRA hairpin 1, replicate 1


title: HAP1_ATAC-seq_WT_Control_R1

description: ATAC-seq for wild type HAP1 cell line, replicate 1


title: HAP1_ATAC-seq_WT_CHAF1B_Hairpin4_R2

description: ATAC-seq for wild type HAP1 cell line with shRNA against CHAF1B hairpin 4, replicate 2


title: ESC-HA_K27L_4_rep2-ChIP


title: ESC-HA_K27M_8_rep1-ChIP


title: ESC-HA_WT_8_rep2-ChIP


title: ESC-HA_K27L_4_rep1-ChIP


title: HAP1_ATAC-seq_WT_CHAF1B_Hairpin3_R2

description: ATAC-seq for wild type HAP1 cell line with shRNA against CHAF1B hairpin 3, replicate 2


title: HAP1_ATAC-seq_WT_HIRA_Hairpin2_R2

description: ATAC-seq for wild type HAP1 cell line with shRNA against HIRA hairpin 2, replicate 2


title: ESC-HA_K27M_4_rep2-ChIP


title: HAP1_ATAC-seq_WT_CHAF1B_Hairpin3_R1

description: ATAC-seq for wild type HAP1 cell line with shRNA against CHAF1B hairpin 3, replicate 1


title: HAP1_ATAC-seq_WT_CHAF1B_Hairpin2_R1

description: ATAC-seq for wild type HAP1 cell line with shRNA against CHAF1B hairpin 2, replicate 1


title: HAP1_ATAC-seq_WT_CHAF1B_Hairpin2_R2

description: ATAC-seq for wild type HAP1 cell line with shRNA against CHAF1B hairpin 2, replicate 2


title: ESC-HA_K27L_8_rep2-ChIP


title: ESC-HA_WT_4_rep2-ChIP


title: ESC-HA_K27M_8_rep2-ChIP


title: ESC-HA_WT_4_rep1-ChIP


title: ESC-HA_WT_72_rep1-H3K27Me3

value: Dox for 72 hours


title: HAP1_ATAC-seq_WT_HIRA_Hairpin2_R1

description: ATAC-seq for wild type HAP1 cell line with shRNA against HIRA hairpin 2, replicate 1


title: ESC-HA_K27M_4_rep1-ChIP


title: ESC-HA_K27L_24_rep2-ChIP

value: Dox for 24 hours


title: HAP1_ATAC-seq_WT_CHAF1A_Hairpin3_R2

description: ATAC-seq for wild type HAP1 cell line with shRNA against CHAF1A hairpin 3, replicate 2


title: ESC-HA_K27M_24_rep2-ChIP


title: HAP1_ATAC-seq_WT_CHAF1A_Hairpin3_R1

description: ATAC-seq for wild type HAP1 cell line with shRNA against CHAF1A hairpin 3, replicate 1


title: HAP1_ATAC-seq_WT_CHAF1A_Hairpin2_R2

description: ATAC-seq for wild type HAP1 cell line with shRNA against CHAF1A hairpin 2, replicate 2


title: HAP1_ATAC-seq_WT_CHAF1B_Hairpin4_R1

description: ATAC-seq for wild type HAP1 cell line with shRNA against CHAF1B hairpin 4, replicate 1


title: HAP1_ATAC-seq_WT_CHAF1A_Hairpin2_R1

description: ATAC-seq for wild type HAP1 cell line with shRNA against CHAF1A hairpin 2, replicate 1


title: HAP1_ATAC-seq_WT_CHAF1B_Hairpin1_R1

description: ATAC-seq for wild type HAP1 cell line with shRNA against CHAF1B hairpin 1, replicate 1


title: ESC-HA_WT_24_rep2-ChIP


title: HAP1_ATAC-seq_WT_CHAF1A_Hairpin1_R1

description: ATAC-seq for wild type HAP1 cell line with shRNA against CHAF1A hairpin 1, replicate 1


title: ESC-HA_WT_24_rep1-ChIP


title: ESC-HA_K27L_72_rep2-ChIP


title: ESC-HA_K27M_24_rep1-ChIP


title: HAP1_ATAC-seq_ARID1A_shControl_Testosterone_r6

description: ATAC-seq for HAP1 cell line with ARID1A knockout and control shRNA, treated with Testosterone, replicate 6


title: ESC-HA_K27L_72_rep1-ChIP


title: HAP1_ATAC-seq_WT_CHAF1B_Hairpin1_R2

description: ATAC-seq for wild type HAP1 cell line with shRNA against CHAF1B hairpin 1, replicate 2


title: HAP1_ATAC-seq_ARID1A_shControl_Testosterone_r5

description: ATAC-seq for HAP1 cell line with ARID1A knockout and control shRNA, treated with Testosterone, replicate 5


title: ESC-HA_K27M_72_rep1-ChIP


title: HAP1_ATAC-seq_ARID1A_shControl_GSK126_r6

description: ATAC-seq for HAP1 cell line with ARID1A knockout and control shRNA, treated with GSK126, replicate 6


title: ESC-HA_WT_72_rep2-ChIP


title: ESC-HA_K27L_24_rep1-ChIP


title: HAP1_ATAC-seq_ARID1A_shControl_GSK126_r5

description: ATAC-seq for HAP1 cell line with ARID1A knockout and control shRNA, treated with GSK126, replicate 5


title: ESC-HA_K27M_72_rep2-ChIP


title: HAP1_ATAC-seq_ARID1A_shControl_DMSO_r6

description: ATAC-seq for HAP1 cell line with ARID1A knockout and control shRNA, treated with DMSO, replicate 6


title: ESC-HA_WT_72_rep1-ChIP


title: HAP1_ATAC-seq_ARID1A_shCHAF1A_Testosterone_r6

description: ATAC-seq for HAP1 cell line with ARID1A knockout and shRNA against CHAF1A, treated with Testosterone, replicate 6


title: ESC-HA_K27L_8_rep2-RNA


title: ESC-HA_K27L_8_rep1-RNA


title: HAP1_ATAC-seq_ARID1A_shControl_DMSO_r5

description: ATAC-seq for HAP1 cell line with ARID1A knockout and control shRNA, treated with DMSO, replicate 5


title: HAP1_ATAC-seq_WT_CHAF1A_Hairpin1_R2

description: ATAC-seq for wild type HAP1 cell line with shRNA against CHAF1A hairpin 1, replicate 2


title: ESC-HA_K27M_8_rep2-RNA


title: ESC-HA_K27M_8_rep1-RNA


title: HAP1_ATAC-seq_ARID1A_shCHAF1A_DMSO_r6

description: ATAC-seq for HAP1 cell line with ARID1A knockout and shRNA against CHAF1A, treated with DMSO, replicate 6


title: HAP1_ATAC-seq_ARID1A_shCHAF1A_Testosterone_r5

description: ATAC-seq for HAP1 cell line with ARID1A knockout and shRNA against CHAF1A, treated with Testosterone, replicate 5


title: HAP1_ATAC-seq_ARID1A_shCHAF1A_GSK126_r6

description: ATAC-seq for HAP1 cell line with ARID1A knockout and shRNA against CHAF1A, treated with GSK126, replicate 6


title: HAP1_ATAC-seq_ARID1A_shCHAF1A_DMSO_r5

description: ATAC-seq for HAP1 cell line with ARID1A knockout and shRNA against CHAF1A, treated with DMSO, replicate 5


title: HAP1_ATAC-seq_ARID1A_shCHAF1A_GSK126_r5

description: ATAC-seq for HAP1 cell line with ARID1A knockout and shRNA against CHAF1A, treated with GSK126, replicate 5


title: ESC-HA_WT_8_rep1-RNA


title: HAP1_ATAC-seq_ARID1A_dCHAF1A-Control_r6

description: ATAC-seq for HAP1 cell line with ARID1A knockout and degradation of CHAF1A for Control, replicate 6


title: HAP1_ATAC-seq_ARID1A_dCHAF1A-Control_r5

description: ATAC-seq for HAP1 cell line with ARID1A knockout and degradation of CHAF1A for Control, replicate 5


title: ESC-HA_K27L_4_rep1-RNA


title: ESC-HA_WT_8_rep2-RNA


title: ESC-HA_K27M_4_rep2-RNA


title: HAP1_ATAC-seq_ARID1A_dCHAF1A-24h_r5

description: ATAC-seq for HAP1 cell line with ARID1A knockout and degradation of CHAF1A for 24 hours, replicate 5


title: ESC-HA_WT_4_rep2-RNA


title: ESC-HA_K27M_4_rep1-RNA


title: HAP1_ATAC-seq_ARID1A_dCHAF1A-24h_r6

description: ATAC-seq for HAP1 cell line with ARID1A knockout and degradation of CHAF1A for 24 hours, replicate 6


title: ESC-HA_K27L_24_rep2-RNA


title: ESC-HA_K27L_4_rep2-RNA


title: ESC-HA_WT_4_rep1-RNA


title: HAP1_ATAC-seq_ARID1A_dCHAF1A-12h_r5

description: ATAC-seq for HAP1 cell line with ARID1A knockout and degradation of CHAF1A for 12 hours, replicate 5


title: HAP1_ATAC-seq_ARID1A_dCHAF1A-12h_r6

description: ATAC-seq for HAP1 cell line with ARID1A knockout and degradation of CHAF1A for 12 hours, replicate 6


title: HAP1_ATAC-seq_ARID1A_HIRA_Hairpin3_R2

description: ATAC-seq for HAP1 cell line with ARID1A knockout and shRNA against HIRA hairpin 3, replicate 2


title: ESC-HA_K27L_24_rep1-RNA


title: ESC-HA_K27M_24_rep1-RNA


title: ESC-HA_WT_24_rep2-RNA


title: HAP1_ATAC-seq_ARID1A_HIRA_Hairpin1_R2

description: ATAC-seq for HAP1 cell line with ARID1A knockout and shRNA against HIRA hairpin 1, replicate 2


title: HAP1_ATAC-seq_ARID1A_HIRA_Hairpin2_R2

description: ATAC-seq for HAP1 cell line with ARID1A knockout and shRNA against HIRA hairpin 2, replicate 2


title: ESC-HA_K27M_24_rep2-RNA


title: HAP1_ATAC-seq_ARID1A_HIRA_Hairpin3_R1

description: ATAC-seq for HAP1 cell line with ARID1A knockout and shRNA against HIRA hairpin 3, replicate 1


title: HAP1_ATAC-seq_ARID1A_HIRA_Hairpin2_R1

description: ATAC-seq for HAP1 cell line with ARID1A knockout and shRNA against HIRA hairpin 2, replicate 1


title: HAP1_ATAC-seq_ARID1A_Control_R2

description: ATAC-seq for HAP1 cell line with ARID1A knockout and control shRNA hairpin, replicate 2


title: HAP1_ATAC-seq_ARID1A_Control_R1

description: ATAC-seq for HAP1 cell line with ARID1A knockout and control shRNA hairpin, replicate 1


title: ESC-HA_K27L_72_rep2-RNA


title: ESC-HA_WT_24_rep1-RNA


title: HAP1_ATAC-seq_ARID1A_CHAF1B_Hairpin4_R2

description: ATAC-seq for HAP1 cell line with ARID1A knockout and shRNA against CHAF1B hairpin 4, replicate 2


title: HAP1_ATAC-seq_ARID1A_HIRA_Hairpin1_R1

description: ATAC-seq for HAP1 cell line with ARID1A knockout and shRNA against HIRA hairpin 1, replicate 1


title: HAP1_ATAC-seq_ARID1A_CHAF1B_Hairpin4_R1

description: ATAC-seq for HAP1 cell line with ARID1A knockout and shRNA against CHAF1B hairpin 4, replicate 1


title: ESC-HA_K27L_72_rep1-RNA


title: ESC-HA_WT_72_rep2-RNA


title: ESC-HA_K27M_72_rep1-RNA


title: HAP1_ATAC-seq_ARID1A_CHAF1B_Hairpin3_R2

description: ATAC-seq for HAP1 cell line with ARID1A knockout and shRNA against CHAF1B hairpin 3, replicate 2


title: ESC-HA_K27M_72_rep2-RNA


title: RA-HA_K27M_72_rep1-ChIP

source_name: RA-treated embriyonic stem cells

value: ES-derived neural progenitor cells


title: HAP1_ATAC-seq_ARID1A_CHAF1B_Hairpin2_R2

description: ATAC-seq for HAP1 cell line with ARID1A knockout and shRNA against CHAF1B hairpin 2, replicate 2


title: RA-HA_K27L_24_rep2-ChIP


title: ESC-HA_WT_72_rep1-RNA


title: HAP1_ATAC-seq_ARID1A_CHAF1B_Hairpin2_R1

description: ATAC-seq for HAP1 cell line with ARID1A knockout and shRNA against CHAF1B hairpin 2, replicate 1


title: HAP1_ATAC-seq_ARID1A_CHAF1B_Hairpin3_R1

description: ATAC-seq for HAP1 cell line with ARID1A knockout and shRNA against CHAF1B hairpin 3, replicate 1


title: HAP1_ATAC-seq_ARID1A_CHAF1B_Hairpin1_R2

description: ATAC-seq for HAP1 cell line with ARID1A knockout and shRNA against CHAF1B hairpin 1, replicate 2


title: HAP1_ATAC-seq_ARID1A_CHAF1A_Hairpin2_R2

description: ATAC-seq for HAP1 cell line with ARID1A knockout and shRNA against CHAF1A hairpin 2, replicate 2


title: RA-HA_WT_24_rep2-ChIP


title: HAP1_ATAC-seq_ARID1A_CHAF1A_Hairpin3_R2

description: ATAC-seq for HAP1 cell line with ARID1A knockout and shRNA against CHAF1A hairpin 3, replicate 2


title: RA-HA_WT_72_rep1-ChIP


title: RA-HA_WT_72_rep1-RNA


title: RA-HA_K27M_24_rep2-ChIP


title: RA-HA_K27M_72_rep1-RNA


title: HAP1_ATAC-seq_ARID1A_CHAF1A_Hairpin2_R1

description: ATAC-seq for HAP1 cell line with ARID1A knockout and shRNA against CHAF1A hairpin 2, replicate 1


title: RA-HA_K27L_72_rep1-RNA


title: NPC_ATRXKO_RNA-Seq_Rep2

data_processing:
library strategy: CUT&RUN
Alignment (CUT&RUN): Bowtie2
Alignment (RNA-Seq): STAR
RNA expected counts were generated with RSEM.
Bigwig files were made from .bam files using "deepTools bamCoverage --extendReads --binSize 5", an ENCODE blacklist file for biased regions (Amemiya et al. Nature 2019), and RPM normalization.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files compatible with UCSC genome browser and IGV, TPM output in .counts tab-delimited for RNA-Seq alignment

growth_protocol: Mouse embryonic stem cells were grown in DMEM medium with 15% FBS, 25mM HEPES, 1x GlutaMAX, 1x non-essential amino acids, 100 U/mL penicillin-steptomycin, LIF, 3µM GSK inhibitor, 1µM MEK1/2 inhibitor at 37 ˚C. Human induced pluripotent stem cell lines were grown on Geltrex (ThermoFisher A1413302) coated plates in Essential 8 media (Gibco A1517001).

extract_protocol:
CUT&RUN was performed on cells as previously described (Skene and Henikoff, eLife 2017).
Total RNA was collected using Trizol (Invitrogen) and digested with Turbo Dnase (Ambion). rRNA was selectively depleted using FastSelect (Qiagen).
rRNA-depleted RNA was converted to cDNA using the Ultra II Directional RNA kit for Illumina (NEB #E7760).
DNA samples were end-repaired using End-Repair Mix (Enzymatics), A-tailed using Klenow exonuclease minus (Enzymatics), purified with MinElute columns (Qiagen), and ligated to Illumina adapters (NEB E7600) with T4 DNA ligase (Enzymatics).  Size selection for fragments >150 bp was performed with AMPure XP (Beckman Coulter).  Libraries were PCR amplified with dual index barcode primers for Illumina sequencing (NEB E7600) using Q5 DNA polymerase (NEB M0491) and purified with MinElute.

tag: genotype

value: ATRX knockout NPC Differentiated


title: RA-HA_K27L_72_rep1-ChIP


title: NPC_ATRXKO_RNA-Seq_Rep1


title: NPC_ATRXKO_RNA-Seq_Rep3


title: HAP1_RNA-seq_WT_shCHAF1A_Testosterone_r5

description: RNA-seq for wild type HAP1 cell line with shRNA against CHAF1A, treated with Testosterone, replicate 5

data_processing:
Reads were trimmed with Trimmomatic, aligned to the GRCh37/hg19 human genome assembly using Bowtie1 and quantified transcript isoforms from Ensembl version 75 using BitSeq with default parameters. Read counts per gene are the maximum counts per isoform.
Genome_build: hg19
Supplementary_files_format_and_content: CSV file contains read counts for each sample for each gene

extract_protocol: RNA was isolated with RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol

value: RNA-seq


title: HAP1_RNA-seq_WT_shCHAF1A_GSK126_r6

description: RNA-seq for wild type HAP1 cell line with shRNA against CHAF1A, treated with GSK126, replicate 6


title: NPC_PHD-FV5_RNA-Seq_Rep3

value: ATRX Flag-V5-Tag Knock-in-PHDmut NPC Differentiated


title: HAP1_ATAC-seq_ARID1A_CHAF1A_Hairpin1_R1

description: ATAC-seq for HAP1 cell line with ARID1A knockout and shRNA against CHAF1A hairpin 1, replicate 1


title: HAP1_ATAC-seq_ARID1A_CHAF1B_Hairpin1_R1

description: ATAC-seq for HAP1 cell line with ARID1A knockout and shRNA against CHAF1B hairpin 1, replicate 1


title: NPC_PHD-FV5_RNA-Seq_Rep2


title: HAP1_RNA-seq_WT_shCHAF1A_GSK126_r5

description: RNA-seq for wild type HAP1 cell line with shRNA against CHAF1A, treated with GSK126, replicate 5


title: HAP1_RNA-seq_WT_shCHAF1A_DMSO_r6

description: RNA-seq for wild type HAP1 cell line with shRNA against CHAF1A, treated with DMSO, replicate 6


title: HAP1_RNA-seq_WT_dCHAF1A_24h_r6

description: RNA-seq for wild type HAP1 cell line with degradation of CHAF1A for 24 hours, replicate 6


title: NPC_K1584R-FV5_RNA-Seq_Rep3

value: ATRX Flag-V5-Tag Knock-in-K1584R NPC Differentiated


title: NPC_PHD-FV5_RNA-Seq_Rep1


title: HAP1_RNA-seq_WT_shCHAF1A_DMSO_r5

description: RNA-seq for wild type HAP1 cell line with shRNA against CHAF1A, treated with DMSO, replicate 5


title: NPC_K1584R-FV5_RNA-Seq_Rep2


title: HAP1_ATAC-seq_ARID1A_CHAF1A_Hairpin3_R1

description: ATAC-seq for HAP1 cell line with ARID1A knockout and shRNA against CHAF1A hairpin 3, replicate 1


title: NPC_K1584R-FV5_RNA-Seq_Rep1


title: HAP1_RNA-seq_WT_dCHAF1A_24h_r5

description: RNA-seq for wild type HAP1 cell line with degradation of CHAF1A for 24 hours, replicate 5


title: HAP1_RNA-seq_WT_shCHAF1A_Testosterone_r6

description: RNA-seq for wild type HAP1 cell line with shRNA against CHAF1A, treated with Testosterone, replicate 6


title: HAP1_RNA-seq_WT_Control_r6

description: RNA-seq for wild type HAP1 cell line with control for CHAF1A degradation, replicate 6


title: ESC_ATRXKO_RNA-Seq_Rep3

value: ATRX knockout


title: HAP1_RNA-seq_WT_dCHAF1A_12h_r6

description: RNA-seq for wild type HAP1 cell line with degradation of CHAF1A for 12 hours, replicate 6


title: HAP1_RNA-seq_WT_dCHAF1A_12h_r5

description: RNA-seq for wild type HAP1 cell line with degradation of CHAF1A for 12 hours, replicate 5


title: ESC_PHD-FV5_RNA-Seq_Rep3

value: ATRX Flag-V5-Tag Knock-in-PHDmut


title: ESC_ATRXKO_RNA-Seq_Rep1


title: HAP1_ATAC-seq_ARID1A_CHAF1A_Hairpin1_R2

description: ATAC-seq for HAP1 cell line with ARID1A knockout and shRNA against CHAF1A hairpin 1, replicate 2

value: ATAC-seq


title: ESC_ATRXKO_RNA-Seq_Rep2


title: HAP1_RNA-seq_WT_Control_r5

description: RNA-seq for wild type HAP1 cell line with control for CHAF1A degradation, replicate 5

value: Control


title: ESC_PHD-FV5_RNA-Seq_Rep2


title: HAP1_RNA-seq_WT_Control_GSK126_r6

description: RNA-seq for wild type HAP1 cell line trated with GSK126, replicate 6

value: WT


title: HAP1_RNA-seq_WT_Control_Testosterone_r6

description: RNA-seq for wild type HAP1 cell line trated with Testosterone, replicate 6

value: Testosterone


title: HAP1_RNA-seq_WT_Control_Testosterone_r5

description: RNA-seq for wild type HAP1 cell line trated with Testosterone, replicate 5


title: ESC_K1584R-FV5_RNA-Seq_Rep3

value: ATRX Flag-V5-Tag Knock-in-K1584R


title: ESC_PHD-FV5_RNA-Seq_Rep1


title: ESC_K1584R-FV5_RNA-Seq_Rep2


title: E14_ATRXKD_IgG

data_processing:
library strategy: CUT&RUN
library strategy: CUT&RUN
Alignment (CUT&RUN): Bowtie2
Alignment (RNA-Seq): STAR
RNA expected counts were generated with RSEM.
Bigwig files were made from .bam files using "deepTools bamCoverage --extendReads --binSize 5", an ENCODE blacklist file for biased regions (Amemiya et al. Nature 2019), and RPM normalization.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files compatible with UCSC genome browser and IGV, TPM output in .counts tab-delimited for RNA-Seq alignment

value: ATRX knockdown

tag: antibody

value: IgG


title: ESC_K1584R-FV5_RNA-Seq_Rep1


title: HAP1_RNA-seq_WT_Control_DMSO_r6

description: RNA-seq for wild type HAP1 cell line trated with DMSO, replicate 6

value: DMSO


title: E14_WT_IgG

value: Wildtype


title: HAP1_RNA-seq_ARID1A_shCHAF1A_Testosterone_r6

description: RNA-seq for HAP1 cell line with ARID1A knockout and shRNA against CHAF1A, treated with Testosterone, replicate 6


title: NPY.5_964_male

city: Birmingham

first: Melissa

last: Harris

state: AL

address: 1300 University Blvd, CH464

department: Biology

institute: University of Alabama at Birmingham

data_processing:
Basecalling was performed using Illumina’s bcl2fastq software
Read quality of fastq files was assessed using FastQC (v0.11.8) and trimming was performed using Trimmomatic (v0.36).
Reads were aligned to the Ensembl mouse mm10 reference genome with the STAR (v2.5.2) aligner software using default parameters and count tables were generated using the STAR genecounts feature and full Ensembl GTF annotation file.
Differential gene expression analysis performed using DESeq2 (v1.30.1) package in R using default settings.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts after alignment using STAR -genecounts feature

source_name: whole skin

growth_protocol: Mice were reared in standard conditions and euthanized at 22 weeks for tissue harvest.

extract_protocol:
Skin was was placed in TRIzol reagent (Thermo Fisher Scientific, Cat# 15-596-018) and homogenized using a bead homogenizer (MP Biomedicals). Total RNA from skin was purified using the RNAEasy MiniKit (Qiagen) after phenol/chloroform separation.
RNA with a RNA Integrity Number (RIN) of ≥7.0 was used for sequencing library preparation.  RNA passing quality control was converted to a sequencing ready library using the NEBNext Ultra II Directional RNA library kit as per the manufacturer’s instructions (polyA mRNA workflow; NEB, Ipswich, MA). The cDNA libraries were quantitated using qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit for Illumina library quantitation (Kapa Biosystems, Woburn, MA) prior to cluster generation.  Cluster generation was performed according to the manufacturers recommendations for onboard clustering (Illumina, San Diego, CA).  We generated between 30-35 million paired end 75bp sequencing reads per sample for transcript level abundance.

value: whole skin

value: B6;129S4-Npytm2Rpa/J homozygous mutant

tag: age

tag: gender

value: male


title: HAP1_RNA-seq_ARID1A_shCHAF1A_Testosterone_r5

description: RNA-seq for HAP1 cell line with ARID1A knockout and shRNA against CHAF1A, treated with Testosterone, replicate 5

value: RNA-seq


title: HAP1_RNA-seq_WT_Control_DMSO_r5

description: RNA-seq for wild type HAP1 cell line trated with DMSO, replicate 5


title: NPY.4_963_female

tag: tissue

value: female


title: HAP1_RNA-seq_ARID1A_shCHAF1A_GSK126_r6

description: RNA-seq for HAP1 cell line with ARID1A knockout and shRNA against CHAF1A, treated with GSK126, replicate 6


title: NPY.3_962_female


title: HAP1_RNA-seq_ARID1A_shCHAF1A_GSK126_r5

description: RNA-seq for HAP1 cell line with ARID1A knockout and shRNA against CHAF1A, treated with GSK126, replicate 5


title: NPY.2_959_male


title: HAP1_RNA-seq_ARID1A_shCHAF1A_DMSO_r6

description: RNA-seq for HAP1 cell line with ARID1A knockout and shRNA against CHAF1A, treated with DMSO, replicate 6


title: NPY.1_958_female


title: WT.5_966_male

value: B6;129S4-Npytm2Rpa/J wildtype sibling


title: HAP1_RNA-seq_ARID1A_dCHAF1A_24h_r5

description: RNA-seq for HAP1 cell line with ARID1A knockout and degradation of CHAF1A for 24 hours, replicate 5

value: dTAG 24h


title: WT.4_965_male


title: HAP1_RNA-seq_WT_Control_GSK126_r5

description: RNA-seq for wild type HAP1 cell line trated with GSK126, replicate 5


title: WT.3_961_female


title: HAP1_RNA-seq_ARID1A_dCHAF1A_12h_r6

description: RNA-seq for HAP1 cell line with ARID1A knockout and degradation of CHAF1A for 12 hours, replicate 6

value: dTAG 12h


title: HAP1_RNA-seq_ARID1A_dCHAF1A_12h_r5

description: RNA-seq for HAP1 cell line with ARID1A knockout and degradation of CHAF1A for 12 hours, replicate 5


title: WT.2_960_male


title: HAP1_RNA-seq_ARID1A_Control_r6

description: RNA-seq for HAP1 cell line with ARID1A knockout and Control, replicate 6


title: Control_6

city: Vestec

first: Šárka

last: Benešová

address: Prumyslova 595

department: Institute of Biotechnology

country: Czech Republic

institute: Czech Academy of Science

data_processing:
Raw reads of all samples were trimmed with cutadapt tool (version 1.18) according to the respective library preparation manual and bases with phred 33 quality lower than 20 were trimmed.
Reads longer than 20 bp and shorter than 90 bp were kept.
Reads of all samples were aligned to rRNA and Univec database (obtained from sortmerna github repository) using bowtie aligner  (version 1.2.2) with one mismatch allowed and only reads which did not align were kept.
Filtered reads were aligned with STAR (version 2.7.0c) to mouse genome GRm38 with parameters --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 \   --outFilterMismatchNmax 1 --alignEndsType Local.   --outFilterMatchNminOverLread 0 --alignIntronMax 1 --alignEndsType EndToEnd.
Only uniquely mapping reads were counted using Rsubread package version 2.0.1.
Genome_build: Mouse genome GRCm38.p6.
Supplementary_files_format_and_content: tab delimited text files include raw count values generated with featureCounts function (package - Rsubread_2.0.1)

source_name: spiral ganglia from E14.5 embryos

growth_protocol: The mice were housed in 12-hour light/dark cycles and were fed ad libitum. To generate Neurod1Cre;Isl1loxP/loxP, we cross-bred floxed Isl11 (Isl1loxP/loxP; Isl1tm2Sev/J, # 028501, Jackson Laboratory)22 and Neurod1Cre transgenic mice (Tg(Neurod1-cre)1Able/J, # 028364, Jackson Laboratory), which were generated by pronuclear injection of the Neurod1-cre BAC construct that carries Cre-sequence downstream of the translational initiation codon ATG of the Neurod1 gene 21. Heterozygous animals, Neurod1Cre;Isl1+/loxP were viable, born in appropriate Mendelian ratios, and were phenotypically indistinguishable from control (Cre negative) littermate mice (Isl1loxP/loxP and Isl1+/loxP). The mouse line Neurod1Cre was also bred with Cre-reporter tdTomato line (Ai14, B6.Cg-Gt(ROSA)26Sortm14(CAG-tdTomato)Hze, # 7914 Jackson Laboratory). PCR performed genotyping on tail DNA. We used both males and females for experiments. Lines are a mixed C57BL/6/sv129 background. Phenotyping and data analysis was performed blind to the genotype of the mice.

extract_protocol:
Spiral ganglia were micro-dissected in Dulbecco's PBS on ice from E14.5 embryos of either sex from four litters; spiral ganglia from both inner ears of the individual embryo per sample. Spiral ganglia were incubated in 300 µl of lysis solution (0.05% trypsin, 0.53mM EDTA Dulbecco's PBS) in 37 ⁰C, shaking at 900 RPM for 5 min. The lysis was stopped by adding 600 µl of FACS buffer (Dulbecco's PBS, 10mM EGTA, and 2% FBS). After spinning down the samples at 800 G, 4 ⁰C for 10 min, the supernatant was removed, and cell pellets were resuspended in 500 µl of ice-cold FACS buffer. Immediately before sorting, cells were passed through a 50 µm cell sieve (CellTricsTM, Sysmex Amercica Inc.) into a sterile 5 ml polystyrene round-bottom falcon to remove clusters of cells and kept on ice. TdTomato+ neurons were sorted using a flow cytometer (BD FACSAriaTM Fusion), through a 100 µm nozzle in 20 psi, operated with BD FACSDiva™ Software. 100 sorted cells were collected into individual wells of 96-well plate containing 5 µl of lysis buffer of NEB Next single-cell low input RNA library prep kit for Illumina (#E6420 New England Biolabs). Plates were frozen immediately on dry ice and stored at −80 °C. The total time from euthanasia to cell collection was ∼3 hrs.
RNAseq-libraries were prepared from 6 samples per each genotype, Neurod1Cre; Rosa26tdTOM (control) and Neurod1Cre;Isl1loxP/loxP;Rosa26tdTOM (mutant), and each sample contained 100 tdTomato+ neurons. Following the manufacturer's instructions, the NEB Next single-cell low input RNA library prep kit for Illumina was used for cDNA synthesis, amplification, and library generation at the Gene Core Facility (Institute of Biotechnology CAS, Czechia). Fragment Analyzer assessed the quality of cDNA libraries. The libraries were sequenced on an Illumina NextSeq 500 next-generation sequencer. NextSeq 500/550 High Output kit 75 cycles (# 200024906, Illumina) were processed at the Genomics and Bioinformatics Core Facility (Institute of Molecular Genetics CAS, Czechia).

value: control

tag: technical replicate


title: WT.1_953_female


title: HAP1_RNA-seq_ARID1A_Control_Testosterone_r6

description: RNA-seq for HAP1 cell line with ARID1A knockouttrated with Testosterone, replicate 6


title: Control_5


title: Control_4


title: HAP1_RNA-seq_ARID1A_Control_Testosterone_r5

description: RNA-seq for HAP1 cell line with ARID1A knockouttrated with Testosterone, replicate 5


title: Control_2


title: HAP1_RNA-seq_ARID1A_Control_GSK126_r6

description: RNA-seq for HAP1 cell line with ARID1A knockouttrated with GSK126, replicate 6

value: Control


title: Control_3


title: HAP1_RNA-seq_ARID1A_Control_DMSO_r5

description: RNA-seq for HAP1 cell line with ARID1A knockouttrated with DMSO, replicate 5


title: HAP1_RNA-seq_ARID1A_Control_DMSO_r6

description: RNA-seq for HAP1 cell line with ARID1A knockouttrated with DMSO, replicate 6


title: HAP1_RNA-seq_ARID1A_shCHAF1A_DMSO_r5

description: RNA-seq for HAP1 cell line with ARID1A knockout and shRNA against CHAF1A, treated with DMSO, replicate 5


title: HAP1_RNA-seq_ARID1A_Control_GSK126_r5

description: RNA-seq for HAP1 cell line with ARID1A knockouttrated with GSK126, replicate 5


title: HCC tissues, immunotherapy, A12

city: Changsha

first: Hong

last: Shen

state: Hunan

address: Xiangya Road

department: Department of Oncology

institute: Xiangya Hospital

data_processing:
The original image data obtained by Illumina Hiseq sequencing was converted into sequence data via Base Calling, namely FASTQ format, to obtain the most original sequencing data file.
The quality score of Read is expressed as different characters, where the corresponding ASCII value of each character is subtracted by 33 to obtain the corresponding sequencing quality value. In general, the base mass is from 0 to 40, that is, the corresponding ASCII code is from the "! (0+33) to "I" (40+33). If the sequencing error rate is denoted by E (%) and the base quality value of the Illunima sequencing platform is denoted by Q, the following relationship exists: Q = − 10log10(E).
The transcriptome sequencing project was completed on Illumina sequencing platform. Illumina PE library (~300bp) was constructed for sequencing, and the quality of the obtained sequencing data was controlled, and then the transcriptome data were analyzed by bioinformatics methods.
We used Trimmomatic software to Clean raw data. Trimmomatic software is a bioinformatics software developed for the Illumina sequencing platform to process raw sequencing data. After removing low-quality reads, Clean was required A new round of quality control was conducted to obtain the data information of clean reads
Assembly: mm10
Supplementary files format and content: Excel file represents counts for all samples.

source_name: HCC tissues

extract_protocol:
Add 1ml TRIZOL to 50-100mg tissue, stand on ice (or -20℃) for 5min, evenly crush the tissue, and stand on ice for 5-10min; Add 200 μL chloroform, shake up and down fully for 15s and mix well, then stand at room temperature for 10min; Centrifuge at 12000rpm for 15min at 4℃; After centrifugation, absorb the supernatant (about 400-500 μL) to the new Ep tube, add the same volume of isopropyl alcohol, gently shake up and down to mix, and place on ice for 10min. At 12000rpm, centrifuge at 4 ° C for 10min, carefully absorb and discard the supernatant, add 1ml75%ethanol (prepared with DEPC water and chilled in advance), shake gently and do not blow away, centrifuge at 12000rpm at 4 ° C for 5min; After drying, add 20-50 μL DEPC water to dissolve RNA; Store at -80℃.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: HCC tissues

tag: Sex

tag: ethnicity

value: Asian

value: anti-PD-1 immunotherapy


title: HCC tissues, immunotherapy, A11


title: ISL1CKO_6


title: Control_1


title: HAP1_RNA-seq_ARID1A_dCHAF1A_24h_r6

description: RNA-seq for HAP1 cell line with ARID1A knockout and degradation of CHAF1A for 24 hours, replicate 6

tag: library

tag: replicate


title: ISL1CKO_4


title: ISL1CKO_5


title: HCC tissues, immunotherapy, A5


title: ISL1CKO_2


title: HAP1_RNA-seq_ARID1A_Control_r5

description: RNA-seq for HAP1 cell line with ARID1A knockout and Control, replicate 5

tag: knockout

tag: knockdown


title: HCC tissues, immunotherapy, A9


title: HCC tissues, immunotherapy, A6


title: HCC tissues, immunotherapy, A4


title: IL-4Rα-/- 3

first: Patrick

last: Haider

address: Waehringer Guertel 18-20

institute: Medical University of Vienna

data_processing:
fastq generation incl. demultiplexing and adapter trimming, bcl2fastq v2.19.1.403
alignment and extraction of counts/gene, STAR aligner v2.6.1a_08-27, command: STAR --runThreadN 16 --genomeDir GRCm38_RSEM_index --readFilesCommand zcat --readFilesIn $FASTQ --outSAMattributes NH HI NM MD AS nM jM jI XS --outSAMtype BAM SortedByCoordinate --outSAMattrRGline ID:"$sample" SM:"$sample" CN:MUW_CF PG:STAR --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic
count normalization and transformation, DESeq2 v1.22.2
Genome_build: GRCm38 with Gencode vM23
Supplementary_files_format_and_content: plain text, raw counts per gene, one file per sample

source_name: IL-4Rα-/-_spleen monocytes

extract_protocol:
RNA was isolated from spleen monocytes using Maxwell® RSC simplyRNA Tissue Kit (Promega, AS1340)
Sequencing libraries were be prepared using the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext UltraTM II Directional RNA Library Prep Kit for Illumina according to manufacturer's protocols (New England Biolabs). Libraries were QC-checked on a Bioanalyzer 2100 (Agilent) using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay (Invitrogen).

tag: strain

value: spleen

tag: cell type

value: monocytes


title: IL-4Rα-/- 2


title: ISL1CKO_1


title: HCC tissues, immunotherapy, A2


title: IL-4Rα+/+ 3

source_name: IL-4Rα+/+_spleen monocytes


title: IL-4Rα-/- 1


title: IL-4Rα+/+ 1


title: IL-4Rα+/+ 2


title: ISL1CKO_3


title: Healthy indivudual_1

city: Bhopal

first: Himanshu

last: Kumar

state: MADHYA PRADESH

address: Indore bypass road

department: Biological Sciences

country: India

institute: IISER Bhopal

data_processing:
FastQC
Trimmomatic
HISAT2
Cufflinks
DESeq2
Assembly: hg 38
Supplementary files format and content: CSV file containing transcript counts in TPM

source_name: PBMCs isolated from Healthy individuals

growth_protocol: Not applicable

extract_protocol:
Whole RNA was isolated using RNeasy Mini Kit (QIAGEN; Cat No./ID: 74104).
TruSeq RNA Library Prep Kit v2 was used as per the manufacture’s instruction

treatment_protocol: PBMCs were isolated using Histopaque-1077 from whole blood.

tag: subject status

value: Healthy individual

value: PBMCs

tag: molecule type

value: rRNA-depleted RNA


title: mouse_rna_kcl_10h_1

city: Heidelberg

first: Dr. Kyung-Min

last: Noh

address: Meyerhofstrasse 1

department: Genome Biology

country: Germany

institute: EMBL Heidelberg

description: Embryonic cortices were dissected out at E15 and the tissues from all the embryos were dissociated and cultured for 7 days before stimulation treatments followed by RNA-seq

data_processing:
ATAC-seq samples: Trimmomatic, bowtie2, MACS2 and DiffBind. RNA-seq samples: TopHat2 and DESeq2 (see manuscript Methods for details on models, versions and parameter
Genome_build: mm10
Supplementary_files_format_and_content: processed diffbind consensus peaks, and counts per peak

source_name: KCl 10h

growth_protocol: mouse primary cortical neurons. Animal housing in the Laboratory Animal Resources at the EMBL (operated as international animal welfare rules according to the Feration for Laboratory Animal Science Associations guidelines and recommendations) was performed under the supervision from institutional veterinarians under the rules of the European Molecular Biology Laboratory, following the guidelines of the European Commission, revised directive 2010/63/EU and AVMA Guidelines 2007.  Mouse colonies were maintained in specific pathogen-free conditions with 12-12h light-dark cycle.

extract_protocol:
RNA-seq: RNA was extracted with Rneasy kit (QIAGEN) and mRNA was enriched with oligo-dT capture kit (NEB)
RNA-seq: Libraries were prepared with NEBNext Ultra II kit
RNA-seq: Libraries were pooled in equimolar ratios and sequenced on a NextSeq 500 (Illumina), single-end 75 bp read length, with an average number of reads of 20 million per library.

treatment_protocol: mouse primary cortical neurons. During the work, all efforts were made to minimize animal suffering.  Pregnant females were sacrificed by cervical dislocation and embryos were euthanised by decapitation. Cortical tissue was dissected out, dissociated with accutase for 10 minutes and plated at a density of 1x10^6 cells per well in a 6-well plate format. Cells were cultured in neurobasal medium with B27 supplement

tag: background strain

value: CD-1 strain prenatal cortical neurons

value: prenatal cortical neurons

value: 7 days in vitro

tag: treatment

value: 2h treatment with 100 μM AP-5 and 1μ M TTX followed by 10h treatment with 55 mM KCl


title: mouse_rna_kcl_10h_2


title: Healthy indivudual_6


title: Healthy indivudual_5


title: Healthy indivudual_3


title: Healthy indivudual_4


title: Tuberculosis patient_6

source_name: PBMCs isolated from naïve active tuberculosis patients

value: Tuberculosis patient


title: Tuberculosis patient_5


title: mouse_rna_kcl_6h_1

source_name: KCl 6h

value: 2h treatment with 100 μM AP-5 and 1μ M TTX followed by 6h treatment with 55 mM KCl


title: mouse_rna_kcl_6h_2


title: mouse_rna_kcl_1h_2

source_name: KCl 1h

value: 2h treatment with 100 μM AP-5 and 1μ M TTX followed by 1h treatment with 55 mM KCl


title: Tuberculosis patient_2


title: Tuberculosis patient_1


title: Tuberculosis patient_4


title: Tuberculosis patient_3


title: mouse_rna_bdnf_6h_2

source_name: BDNF 6h

value: 2h treatment with 100 μM AP-5 and 1μ M TTX followed by 6h treatment with 10 ng/ml BDNF


title: mouse_rna_kcl_1h_1


title: BT241-shGFP

city: Hamilton

first: Sheila

last: Singh

state: ON

address: 1280 Main Street West

department: Biochemistry and Biomedical Sciences

country: Canada

institute: McMaster University

data_processing:
FASTQ files were first filtered using a bespoke Perl script to remove reads shorter than 36bp.
Reads were mapped to the human reference genome (GRCh38/hg38) and Gencode transcript models (v25) using the STAR short-read aligner (v2.4.2a)
Read counts were exported by STAR, and merged with the Ensembl gene annotations in R.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text read counts

source_name: BT241 cell line

growth_protocol: Brain tumor initiating cells (BTICs) originating from Glioblastoma (GBM) primary samples were processed and maintained in Neurocult media (STEMcell Technolgies) as brain tumor initiating cells (BTICs). BTICs were grown as tumorspheres that were maintained at 37°C with a humidified atmosphere of 5% CO2

extract_protocol:
Total RNA was extracted using the Norgen Total RNA isolation kit (Cat #48400) and quantified using a NanoDrop Spectrophotometer ND-1000
Library prep was performed using the NEBNext Ultra Directional RNA Library Prep Kit along with the NEBNext Poly(A) mRNA Magnetic Isolation Module. Libraries were subject to further BioAnalyzer QC and quantified by qPCR.

treatment_protocol: Cells were transduced with a lentiviral vector expressing either shRNA directed against CD70, or a control shGFP vector, at an MOI of 1. Cells were grown for two days post-transduction, followed by selection with puromycin (1ug/mL) for three days.  Finally, cells were cultured for a further 48 hours in NeuroCult Complete media prior to RNA extraction.

tag: cell line

value: BT241 cell line

value: shGFP

tag: tumour type

value: glioblastoma


title: mouse_rna_bdnf_10h_2

source_name: BDNF 10h

tag: age

value: 2h treatment with 100 μM AP-5 and 1μ M TTX followed by 10h treatment with 10 ng/ml BDNF


title: mouse_rna_bdnf_1h_2

source_name: BDNF 1h

tag: tissue

value: 2h treatment with 100 μM AP-5 and 1μ M TTX followed by 1h treatment with 10 ng/ml BDNF


title: mouse_rna_bdnf_10h_1


title: BT241-shA2


title: mouse_rna_bdnf_1h_1


title: Healthy indivudual_2


title: GBM4-shA2

source_name: GBM4 cell line

value: GBM4 cell line


title: mouse_rna_bdnf_6h_1


title: mouse_rna_control_10h_2

source_name: Control 10h

value: 12h treatment with 100 μM AP-5 and 1μ M TTX


title: GBM4-shGFP


title: mouse_rna_control_10h_1


title: GBM8-shGFP

source_name: GBM8 cell line

value: GBM8 cell line


title: Male WNV M2

city: St Louis

first: Sarah

last: Rosen

state: MO

address: 320 S. Euclid Ave.

department: Infectious Diseases

institute: Washington University School of Medicine

library_source: transcriptomic single cell

data_processing:
Generation of fastq files via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Alignment to mm10 genome build via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Assembly: mm10
Supplementary files format and content: barcodes.tsv, genes.tsv, matrix.mtx

source_name: Cortex and hippocampus

extract_protocol: 10x Genomcis Chromium single cell preparation

tag: genotype

value: Male

value: Cortex and hippocampus


title: mouse_rna_control_6h_1

source_name: Control 6h

value: CD-1 strain prenatal cortical neurons

value: prenatal cortical neurons

value: 8h treatment with 100 μM AP-5 and 1μ M TTX


title: mouse_rna_control_1h_1

source_name: Control 1h

value: 7 days in vitro

value: 3h treatment with 100 μM AP-5 and 1μ M TTX


title: EGR1 CHIP-seq CD34 HSPC-1

source_name: CD34+ Hematopoietic and Stem Progenitor Cell

tag: shRNA

tag: days post shrna infection

tag: chip antibody

value: anti-EGR1 588 (Santa Cruz sc-110)


title: mouse_rna_control_1h_2


title: mouse_rna_control_6h_2


title: Female Mock F1

tag: Sex

value: Female

value: MOCK (.5% FBS in HBBS)


title: GBM8-shA2


title: mouse_atac_kcl_10h_2

description: Embryonic cortices were dissected out at E15 and the tissues from all the embryos were dissociated and cultured for 7 days before stimulation treatments followed by ATAC-seq

extract_protocol:
ATAC-seq: neurons were lysed to get intact nuclei and tagmented with Tn5 enzyme from Nextera kit from Illumina
ATAC-seq: Libraries were prepared with Nextera DNA Library Prep kit (Illumina)
ATAC-seq: Libraries were pooled in equimolar ratios and sequenced on a NextSeq 500 (Illumina), paired-end 75 bp read length, with an average number of reads of 50 million per library.

value: 2h treatment with 100 μM AP-5 and 1μ M TTX followed by 10h treatment with 55 mM KCl


title: Female WNV F2


title: Male Mock M1


title: mouse_atac_kcl_10h_1


title: Wild-Type 32 Wks Replicate 2, Intact (no castration or DHT)

city: New York

first: Dana

last: Pe'er

state: NY

address: 417 E 68th St

institute: Memorial Sloan Kettering Cancer Center

description: Analysis of GEMM

data_processing:
SEQC alignment
EmptyDrops for empty droplet detection
DoubletDetection for doublet detection
sctransform for normalization
scanpy for downstream analysis
Assembly: mm38, hg38
Supplementary files format and content: counts matrices (.csv)
Supplementary files format and content: adata objects (.h5ad)
Supplementary files format and content: obs cell annotations (.csv)

source_name: GEMM

growth_protocol: The construction and genotyping of all GEMMs has been previously described (Ku et. al 2017, Science). 7 PtR (7 mice, PbCre:Rosa26mT/mGPtenfl/flRb1fl/fl), and 13 PtRP (13 mice, PbCre: Rosa26mT/mGPtenfl/flRb1fl/flTp53fl/fl) mice analyzed were on a mixed C57BL/6:129Sv: FVB/NJ background. Organoids were cultured under standard conditions (Karthaus et al 2014. Cell).

extract_protocol:
Fresh benign and malignant GEMM and human biopsy tissue was mechanically cut using a scalpel into small pieces (~1–5 mm3). The tissue was then processed and dissociated in 5–10 mg/ml collagenase type II (Gibco) solution in adDMEM/F12+/+/+ with 10 μM Y–27632 37 dihydrochloride for 30 minutes to 2 hours on a 37oC shaking platform. This was followed by a 1 minute 0.5 M EDTA wash at room temperature, and subsequent digestion with TrypLE (Life technologies) with 10 μM Y–27632 dihydrochloride for 5–10 minutes at 37oC on a shaking platform until a single cell suspension was obtained. For human samples, if more than 10% of doublets were present (visual inspection) or there was evidence for <80% viability (hemocytometer, using 0.2% Trypan Blue), then cells were FACS–sorted for singlets and viability using a DAPI. For GEMM tissue, all cells were subsequently FACS–sorted for singlets and viability using DAPI. Organoids were isolated from basement membrane extract digested to single-cell suspension by incubating with TrypLE (Life technologies) supplemented with Y-27632 (10 μM) for 10 min at 37 °C with shaking, followed by a 2-min incubation with EDTA (1 mM), Y-27632 (10 μM) in PBS0 and a second digestion with TrypLE (Life technologies) supplemented with Y-27632 for 5 min at 37 °C with shaking. Cells were filtered and resuspended in PBS0, Y-27632 (10 μM) and BSA (0.04%) before processing further for single-cell sequencing. Cells were checked for viability using 0.2% (w/v) Trypan Blue staining (Countess II) and all sequencing experiments were performed on samples with a minimum of 80% viable cells.
Single-cell encapsulation and scRNA-seq library prep of FACS-sorted cell suspensions was performed on the Chromium instrument (10x Genomics) following the user manual (Reagent Kit 3’ v2 for organoids and GEMM or v3 for HMP samples). Each sample loaded onto the cartridge contained approximately 5,000 - 10,000 cells at a final dilution of ~500 - 1000 cells/µl. Transcriptomes of encapsulated cells were barcoded during reverse transcription and the resulting cDNA was purified with DynaBeads, followed by amplification per the user manual. Next, PCR-amplified product was fragmented, A-tailed, purified with 1.2X SPRI beads, ligated to sequencing adapters and indexed by PCR. Indexed DNA libraries were double-size purified (0.6–0.8X) with SPRI beads and sequenced on an Illumina HiSeq (R1 – 26 cycles, i7 – 8 cycles, R2 – 70 cycles or higher) to a depth of >50 million reads per sample (>13,000 reads/cell).

treatment_protocol: Six PtRP mice were castrated at 8 weeks of age for either a total of 4 weeks (3 mice, ‘Cas’), or 2 weeks followed by 2 weeks of dihydrotestosterone (DHT, ‘Cas/Reg’) addback (3 mice). DHT pellet was implanted subcutaneously. Organoids were transduced using cre expressing lentivirus followed by culturing under standard conditions.

tag: sample type

value: Wild-Type 32 Weeks


title: Wild-Type 32 Wks Replicate 3, Intact (no castration or DHT)

description: Analysis of GEMM


title: Wild-Type 8 Wks Replicate 1, Intact (no castration or DHT)

description: Analysis of GEMM

value: Wild-Type 8 Weeks


title: Wild-Type 32 Wks Replicate 1, Intact (no castration or DHT)

description: Analysis of GEMM


title: Wild-Type 24 Wks Replicate 2, Intact (no castration or DHT)

description: Analysis of GEMM

value: Wild-Type 24 Weeks


title: Wild-Type 12 Wks Replicate 2, Intact (no castration or DHT)

description: Analysis of GEMM

value: Wild-Type 12 Weeks


title: Wild-Type 24 Wks Replicate 1, Intact (no castration or DHT)

description: Analysis of GEMM


title: mouse_atac_kcl_6h_2

value: 2h treatment with 100 μM AP-5 and 1μ M TTX followed by 6h treatment with 55 mM KCl


title: mouse_atac_kcl_1h_2

value: 2h treatment with 100 μM AP-5 and 1μ M TTX followed by 1h treatment with 55 mM KCl


title: mouse_atac_kcl_6h_1


title: Wild-Type 12 Wks Replicate 1, Intact (no castration or DHT)

description: Analysis of GEMM


title: mouse_atac_bdnf_10h_2

value: 2h treatment with 100 μM AP-5 and 1μ M TTX followed by 10h treatment with 10 ng/ml BDNF


title: mouse_atac_bdnf_6h_1

value: 2h treatment with 100 μM AP-5 and 1μ M TTX followed by 6h treatment with 10 ng/ml BDNF


title: mouse_atac_bdnf_10h_1

value: CD-1 strain prenatal cortical neurons


title: mouse_atac_bdnf_1h_2

value: prenatal cortical neurons

value: 2h treatment with 100 μM AP-5 and 1μ M TTX followed by 1h treatment with 10 ng/ml BDNF


title: mouse_atac_bdnf_1h_1

value: 7 days in vitro


title: mouse_atac_control_10h_2

value: 12h treatment with 100 μM AP-5 and 1μ M TTX


title: mouse_atac_control_6h_1

value: 8h treatment with 100 μM AP-5 and 1μ M TTX


title: mouse_atac_control_10h_1


title: PbCre_Pten/Rb/P53 9 Wks Replicate 1, Intact (no castration or DHT)

description: Analysis of GEMM

value: PbCre_Pten/Rb/P53 9 Weeks


title: PbCre_Pten/Rb/P53 12 Wks Replicate 4, Intact (no castration or DHT)'

description: Analysis of GEMM

value: PbCre_Pten/Rb/P53 12 Weeks


title: mouse_atac_control_6h_2


title: PbCre_Pten/Rb/P53 16 Wks Replicate 1, Intact (no castration or DHT)

description: Analysis of GEMM

value: PbCre_Pten/Rb/P53 16 Weeks


title: Wild-Type 24 Wks Replicate 3, Intact (no castration or DHT)

description: Analysis of GEMM


title: PbCre_Pten/Rb/P53 8 Wks Replicate 1, Intact (no castration or DHT)

description: Analysis of GEMM

value: PbCre_Pten/Rb/P53 8 Weeks


title: mouse_atac_kcl_1h_1


title: PbCre_Pten/Rb/P53 12 Wks Replicate 3, Intact (no castration or DHT)

description: Analysis of GEMM


title: PbCre_Pten/Rb/P53 12 Wks Replicate 2, Intact (no castration or DHT)

description: Analysis of GEMM


title: mouse_atac_control_1h_2

value: 3h treatment with 100 μM AP-5 and 1μ M TTX


title: mouse_atac_bdnf_6h_2


title: PbCre_Pten/Rb/P53 12 Wks Replicate 1, Intact (no castration or DHT)

description: Analysis of GEMM


title: mouse_atac_control_1h_1


title: PbCre_Pten/Rb/P53 12 Wks Replicate 3, surgical castration at 8 wks of age, followed by DHT pellet at 10 wks of age.

description: Analysis of GEMM


title: PbCre_Pten/Rb/P53 12 Wks Replicate 1, surgical castration at 8 wks of age, followed by DHT pellet at 10 wks of age.

description: Analysis of GEMM


title: PbCre_Pten/Rb/P53 12 Wks Replicate 12 surgical castration at 8 wks of age, followed by DHT pellet at 10 wks of age.

description: Analysis of GEMM


title: PbCre_Pten/Rb/P53 12 Wks Replicate 3, surgical castration at 8 wks of age

description: Analysis of GEMM


title: PbCre_Pten/Rb 47 Wks Replicate 2, Intact (no castration or DHT)

description: Analysis of GEMM

value: PbCre_Pten/Rb 47 Weeks


title: PbCre_Pten/Rb/P53 12 Wks Replicate 1, surgical castration at 8 wks of age

description: Analysis of GEMM


title: Biozzi ECS 3 [MBE3]

first: Smadar

last: Goldfarb

state: Israel

address: Hadassah Hospital

department: Department of Neurology

institute: Hadassah – Hebrew University Medical Center

description:
Following electroconvulsive seizures
M_ect_2

data_processing:
Libraries were sequenced using Illumina NextSeq 500 according to the manufacturer's protocol to generate 82-bp single-end reads. Sequenced reads were trimmed for adaptor and low-quality sequences were filtered. Raw sequencing reads were aligned to the GRCm38 reference genome using Tophat2 (Kim et al., 2013) and Fragment per kilobase per million fragments mapped (FPKM) values were calculated using Cuffquant and normalized using Cuffnorm in Cufflinks (Trapnell et al., 2010)
Genome_build: GRCm38
Supplementary_files_format_and_content: FPKM

source_name: Biozzi ECS_spinal cord

extract_protocol:
Spinal cord tissue was extracted and dissociated to single cell suspension using the Neural Tissue Dissociation Kit (Milteny). Myelin was removed using Percoll (GE Healthcare) followed by cell isolation using CD11b microbeads (Milteny) and MS columns (Milteny) according to manufacturer instructions. RNA was isolated using RNeasy Plus Mini Kit (Qiagen).
Total RNA samples were enriched for mRNAs by pull-down of poly(A)+ RNA using PolyA Kit (Truseq). RNA-seq libraries were prepared from 100ng RNA using the SENSE Kit (lexogen).

treatment_protocol: Naïve Biozzi ABH mice received three ECS or sham treatments on consecutive days and sacrificed the next day.

value: Biozzi ABH mice

value: 3 month old

value: electroconvulsive seizures (ECS)

value: Spinal cord


title: Biozzi ECS 1 [MBE1]

description:
Following electroconvulsive seizures
M_ect_0


title: Biozzi Con 2 [MBC2]

description:
Naïve
M_control_1

source_name: Biozzi Con_spinal cord

value: control


title: Biozzi Con 1 [MBC1]

description:
Naïve
M_control_0


title: PbCre_Pten/Rb 30 Wks Replicate 2, Intact (no castration or DHT)

description: Analysis of GEMM

value: PbCre_Pten/Rb 30 Weeks


title: PbCre_Pten/Rb 24 Wks Replicate 1, Intact (no castration or DHT)

description: Analysis of GEMM

value: PbCre_Pten/Rb 24 Weeks


title: XPRO-0496-T

first: Prabhjot

middle: Singh

last: Mundi

address: 1130 St. Nicholas Avenue

department: Medicine; Systems Biology

institute: COLUMBIA UNIVERSITY HEALTH SCIENCES

data_processing:
Alignment with STARv2.5.3 to GRCh38
Gene-level raw counts summarization with STARv2.5.3 quant-mode.
Assembly: GRCh38.v90
Supplementary files format and content: Tab delimited text output of raw counts from STAR alignment and gene count quantification.
Supplementary files format and content: RNAseq: Raw Counts (aligned to GRCh38v90 with STAR)

source_name: MSKCC Wilms Tumor Patient Tumor

extract_protocol:
Ribo-Zero for rRNA depletion kits were used, Illumina
RNA Sequencing was performed on an Illumina NextSeq 500

value: Wilms Tumor


title: PbCre_Pten/Rb 47 Wks Replicate 1, Intact (no castration or DHT)

description: Analysis of GEMM


title: PbCre_Pten/Rb 30 Wks Replicate 1, Intact (no castration or DHT)

description: Analysis of GEMM


title: XPRO-0608-T


title: XPRO-0528-T


title: XPRO-0484-T


title: Biozzi ECS 2 [MBE2]

description:
Following electroconvulsive seizures
M_ect_1


title: XPRO-0467-T


title: XPRO-0466-T


title: XPRO-0363-T


title: XPRO-0305-T


title: Prostate organoid at 4 wks following cre mediated RB1 and TP53 deletion with dihydrotestosterone  exposure

description: Re-analysis of GSM5677677

source_name: Prostate organoid cell line

value: Prostate organoid at 4 weeks following cre mediated RB1 and TP53 deletion and cultured under standard organoid conditions with dihydrotestosterone (DHT) exposure


title: Prostate organoid at 8 wks following cre mediated RB1 and TP53 deletion with dihydrotestosterone  exposure

description: Re-analysis of GSM5677678

value: Prostate organoid at 8 weeks following cre mediated RB1 and TP53 deletion and cultured under standard organoid conditions with dihydrotestosterone (DHT) exposure


title: Prostate organoid at 2 wks following cre mediated RB1 and TP53 deletion with dihydrotestosterone  exposure

description: Re-analysis of GSM5677676

value: Prostate organoid at 2 weeks following cre mediated RB1 and TP53 deletion and cultured under standard organoid conditions with dihydrotestosterone (DHT) exposure


title: XPRO-0581-T2


title: XPRO-0120-T


title: Wild-type prostate organoid isolated from TP53 loxP/loxP and RB1 loxP/loxP mice with dihydrotestosterone exposure

description: Re-analysis of GSM5677675

value: Wild-type prostate organoid isolated from TP53 loxP/loxP and RB1 loxP/loxP mice and cultured under standard organoid conditions with dihydrotestosterone (DHT) exposure


title: XPRO-0105-T


title: XPRO-0581-T


title: XPRO-0010-T2


title: PbCre_Pten/Rb 24 Wks Replicate 3, Intact (no castration or DHT)

description: Analysis of GEMM


title: Post, 23, no, negative, 30-100

city: Boston

first: Beth

last: Overmoyer

state: MA

address: 450 Brookline Avenue

department: Susan F. Smith Center for Women’s Cancers

institute: Dana-Farber Cancer Institute

data_processing:
STAR 2.6.1d alignment to hg38
quantification with salmon 0.14.2
Assembly: hg38/ensembl v94 transcriptome reference
Supplementary files format and content: counts.raw.csv - csv file with raw counts for all samples
Supplementary files format and content: counts.tpm.csv - csv file with tpm counts for all samples

source_name: tumor biopsy

extract_protocol: Illumina Stranded total RNA preparation kit

value: tumor biopsy

tag: time point

value: post

tag: study id

tag: response

value: No

tag: er

value: Negative

tag: tumor percentage


title: Pre, 23, no, negative, 30-100

value: pre


title: Prostate organoid at 4 wks following cre mediated RB1 and TP53 deletion with enzalutamide  exposure

description: Re-analysis of GSM5677679

value: Prostate organoid at 4 weeks following cre mediated RB1 and TP53 deletion and cultured under standard organoid conditions with enzalutamide (ENZ) exposure


title: Post, 21, no, positive, 30-100

value: Positive


title: PbCre_Pten/Rb 24 Wks Replicate 2, Intact (no castration or DHT)

description: Analysis of GEMM


title: Prostate organoid at 8 wks following cre mediated RB1 and TP53 deletion with enzalutamide  exposure

description: Re-analysis of GSM5677680

value: Prostate organoid at 8 weeks following cre mediated RB1 and TP53 deletion and cultured under standard organoid conditions with enzalutamide (ENZ) exposure


title: Post, 22, no positive, 30-100


title: Pre, 22, no, positive, 30-100


title: XPRO-0043-T

source_name: MSKCC Malignant Rhabdoid Tumor Patient Tumor

value: Malignant Rhabdoid Tumor


title: Biozzi Con 3 [MBC3]

description:
Naïve
M_control_2

tag: strain

value: Biozzi ABH mice

value: 3 month old

value: control

value: Spinal cord

tag: cell type


title: Pre, 21, no, positive, 30-100


title: Pre, 18, no, positive, 30-100


title: Post, 20, no, negative, <1


title: Pre, 19, no, negative, 30-100


title: Post, 19, no, negative, 1-29


title: Pre, 16, yes, positive, 30-100

value: Yes


title: Pre, 14, no, negative, 30-100


title: Pre, 15, no, negative, 30-100


title: Post, 18, no, positive, 1-29


title: Post, 15, no, negative, 1-29


title: Post, 13, yes, negative, 1-29


title: Post, 14, no, negative, 1-29


title: Pre, 13, yes, negative, 1-29


title: Pre, 20, no, negative, 1-29


title: Pre, 10, yes, negative, 30-100


title: Post, 11, no, negative, 1-29


title: Pre, 12, yes, negative, 1-29


title: Pre, 7, yes, negative, 30-100


title: Pre, 8, no, positive, 30-100


title: Post, 9, no, negative, 1-29


title: Pre, 17, yes, negative, 30-100


title: PbCre_Pten/Rb/P53 12 Wks Replicate 2, surgical castration at 8 wks of age

description: Analysis of GEMM

value: PbCre_Pten/Rb/P53 12 Weeks


title: Pre, 5, yes, positive, 1-29


title: Post, 4 yes, positive, 30-100


title: Pre, 4, yes, positive, 30-100


title: Post, 3, no, positive, 1-29


title: Post, 16, yes, positive, 30-100


title: Pre, 9, no, negative, 30-100


title: Post, 12, yes, negative, <1


title: Pre, 3, no, positive, 1-29


title: Post, 17, yes, negative, 1-29


title: Post,1 ,yes, positive, 30-100


title: Pre, 2, no, positive, 30-100


title: Post, 8, no, positive, 1-29


title: Post, 5, yes, positive, 1-29


title: TTC549 cells, DS-3201b, rep3

city: Tokyo

first: Haruka

last: Shinohara

address: 5-1-1 Tsukiji, Chuo-ku

country: Japan

institute: National Cancer Center Research Institute

data_processing:
CLC Genomics Workbench v10.1.1
Reads were mapped on hg19 human reference genome and quantified using CLC Genomics Workbench v10.1.1.
Assembly: hg19

growth_protocol: A204.1 and TTC549 cells were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated FBS and 1% penicillin/streptomycin and maintained at 37 °C with 5% CO2.

extract_protocol:
Total RNA samples were extracted using TRIzol.
500 ng total RNA was ribosomal RNA-depleted using NEBNext rRNA Depletion Kit and converted to Illumina sequencing library using NEBNext Ultra Directional RNA Library Prep Kit.

treatment_protocol: A204.1 or TTC549 cells. A204.1 or TTC549 cells were treated with DS-3201b (100 nM) or EPZ-6438 (100 nM) for 14 days.

tag: cell line

value: malignant rhabdoid tumor

tag: treatment


title: Pre, 11, no, negative, 30-100


title: Post, 7, yes, negative, 1-29


title: Post, 10, yes, negative, 1-29


title: A204.1 cells, EPZ-6438, rep2


title: Post, 2, no, positive, 1-29


title: TTC549 cells, DS-3201b, rep1


title: A204.1 cells, DS-3201b, rep3


title: Pre, 1, yes, positive, 30-100


title: A204.1 cells, EPZ-6438, rep3


title: TTC549 cells, Control, rep3

value: Control


title: TTC549 cells, Control, rep2


title: A204.1 cells, EPZ-6438, rep1


title: A204.1 cells, DS-3201b, rep2


title: A204.1 cells, Control, rep3


title: TTC549 cells, Control, rep1


title: A204.1 cells, Control, rep2


title: A204.1 cells, Control, rep1


title: TTC549 cells, DS-3201b, rep2


title: s42

city: Prague

first: Jiri

last: Baloun

address: Na Slupi 450/4

department: Department of experimental rheumatology

institute: Institute of Rheumatology

data_processing:
Count-based miRNA expression data were generated by the Chimira (Vitsios et al, Bioinformatics, 2015) tool from FASTQ files.
All sequences were adapter trimmed and mapped against miRBase v22 allowing up to two mismatches per sequence.
Raw reads were analysed by DESeq2 method
Genome_build: miRBase v22
Supplementary_files_format_and_content: tab-delimited text file containing miRNAs mapped in ech sample and its read count

source_name: Human serum

extract_protocol:
Circulating miRNAs were isolated from the serum using the NucleoSpin miRNA Plasma, Mini kit for circulating miRNA (Macherey-Nagel) according to the manufacturer`s protocol. Libraries for sequencing were prepared from 10.5 µL of isolated miRNAs using a NEXTflex Small RNA-Seq Kit v3 (Bioo Scientific) according to the manufacturer`s protocol.
small RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human serum

tag: before/after ovariectomy

value: after

tag: ID

tag: menopause

value: yes

tag: estrogen treatment


title: s36

tag: tissue


title: s30


title: s15


title: s07


title: s24


title: s04


title: A204.1 cells, DS-3201b, rep1


title: s09


title: s18


title: s35

value: no


title: s12


title: s08


title: s41


title: s25


title: s38


title: s40


title: s23


title: s14


title: s03


title: s11


title: s17


title: s29


title: s46


title: s05


title: s48


title: s02


title: s47

value: before


title: s20


title: s28


title: s27


title: s22


title: s33


title: s34


title: s32


title: s45


title: s43


title: s39


title: s44


title: s19


title: s31


title: s37


title: s21


title: R11

city: Glasgow

first: Katherine

last: West

address: University of Glasgow

department: College of Medical, Veterinary and Life Sciences

country: United Kingdom

institute: University of Glasgow

description:
EPZ6438
Chip sample

data_processing:
RNA-seq reads were aligned with HiSat2
Transcripts were assembled with Stringtie
DESeq2 was used to compare all drug treated samples with control samples, for each cell line
ChIP-seq reads were aligned with Bowtie2
ChIP-seq peaks were called with MACS2 using the broad peak setting, FDR 0.05.
Bigwig files were generated using bamcoverage
Genome_build: Hg38
Supplementary_files_format_and_content: RNA-seq processed data files are the normalised counts output from DESeq2, comparing the three drugs with the control.
Supplementary_files_format_and_content: ChIP-seq processed datafiles are the bigwig and MACS peak files.

source_name: glioblastoma stem cell line

growth_protocol: Cells were grown on Matrigel coated plates in AdDMEM F12 medium supplemented with 20ng/ml EGF, 10ng/ml bFGF,1% B27, 0.5% N2, 4ng/μl Heparin, and  L-Glutamine (Fael Al-Mayhani et al., 2009, Gomez-Roman et al., 2017)

extract_protocol:
RNA was purified using Qiagen Rneasy kit with DNase I treatment. Chromatin was formaldehyde crosslinked, purified, sonicated and subject to ChIP using antibodies to H3K27me3 or H3K4me3.
RNAseq library prep and sequencing was performed by BGI genomics. ChIP-seq library prep and sequencing was performed by Novagen.
paired end RNA-seq and paired end ChIP-seq.

treatment_protocol: Cells were incubated with 2 μM of GSK343, UNC1999, EPZ6438 or DMSO for 5 days

tag: antibody


title: R7

description:
untreated
Chip sample

value: untreated


title: R9

description:
untreated
Chip sample

value: input


title: R8

description:
untreated
Chip sample


title: R6

description:
EPZ6438
Chip sample


title: s01


title: R5

description:
EPZ6438
Chip sample


title: R3

description:
untreated
Chip sample


title: R2

description:
untreated
Chip sample


title: G7S-UNC-3

description:
UNC1999 Rep3
RNASeq

value: UNC1999 Rep3


title: G7S-UNC-2

description:
UNC1999 Rep2
RNASeq

value: UNC1999 Rep2


title: G7S-UNC-1

description:
UNC1999 Rep1
RNASeq

value: UNC1999 Rep1


title: G7S-GSK-3

description:
GSK343 Rep3
RNASeq

value: GSK343 Rep3


title: G7S-EPZ-3

description:
EPZ6438 Rep3
RNASeq

value: EPZ6438 Rep3


title: G7S-EPZ-2

description:
EPZ6438 Rep2
RNASeq

value: EPZ6438 Rep2


title: G7S-EPZ-1

description:
EPZ6438 Rep1
RNASeq

value: EPZ6438 Rep1


title: R12

description:
EPZ6438
Chip sample


title: R10

description:
EPZ6438
Chip sample


title: G7S-CONTROL-3

description:
Control Rep3
RNASeq

value: Control Rep3


title: G7S-GSK-1

description:
GSK343 Rep1
RNASeq

value: GSK343 Rep1


title: E2S-UNC-2

description:
UNC1999 Rep2
RNASeq


title: G7S-CONTROL-2

description:
Control Rep2
RNASeq

value: Control Rep2


title: E2S-GSK-2

description:
GSK343 Rep2
RNASeq

value: GSK343 Rep2


title: E2S-GSK-1

description:
GSK343 Rep1
RNASeq


title: E2S-EPZ-2

description:
EPZ6438 Rep2
RNASeq


title: E2S-EPZ-3

description:
EPZ6438 Rep3
RNASeq


title: G7S-GSK-2

description:
GSK343 Rep2
RNASeq


title: E2S-CONTROL-2

description:
Control Rep2
RNASeq


title: E2S-UNC-3

description:
UNC1999 Rep3
RNASeq


title: E2S-CONTROL-3

description:
Control Rep3
RNASeq


title: R1

description:
untreated
Chip sample


title: E2S-CONTROL-1

description:
Control Rep1
RNASeq

value: Control Rep1


title: E2S-EPZ-1

description:
EPZ6438 Rep1
RNASeq


title: 2102EP_Quisinostat

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Moorenstr. 5

department: Dep. of Urology

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

data_processing:
Mapping was done against the Homo sapiens (hg38) (May 25, 2017) genome sequence.
For each sample peak values, average peak values were mapped against genome position. Shrunken logarithmic fold changes were calculated for treated sample in comparison to DMSO solvent control.
Genome_build: hg38
Supplementary_files_format_and_content: ATAC-Seq_HDACi_in_urological_malignancies.xlsx

source_name: non-seminoma germ cell tumor, embryonal carcinoma

growth_protocol: 2102EP cells were cultivated in DMEM medium (10% FCS, 1% Penicillin / Streptomycin); VM-CUB-1, Caki-1 and DU-145 were cultivated in RMPI medium (10% FCS, 1% Penicillin / Streptomycin).

extract_protocol:
Cells were harvested and shock frozen, extraction was performed by Active Motif (1. Prepare nuclei. To prepare nuclei, we spun 50,000 cells at 500g for 5 min, which was followed by a wash using 50 μL of cold 1× PBS and centrifugation at 500g for 5 min. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min using a refrigerated centrifuge. To avoid losing cells during the nuclei prep, we used a fixed-angle centrifuge and carefully pipetted away from the pellet after centrifugations. 2. Transpose and purify. Immediately following the nuclei prep, the pellet was resuspended in the transposase reaction mix (25 μL 2× TD buffer, 2.5 μL transposase (Illumina) and 22.5 μL nuclease-free water). The transposition reaction was carried out for 30 min at 37 °C. Directly following transposition the sample was purified using a Qiagen MinElute kit).
Following purification, we amplified library fragments using 1× NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers 1 and 2 (Supplementary Table 1), using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min. To reduce GC and size bias in our PCR, we monitored the PCR reaction using qPCR in order to stop amplification before saturation. To do this, we amplified the full libraries for five cycles, after which we took an aliquot of the PCR reaction and added 10 μl of the PCR cocktail with Sybr Green at a final concentration of 0.6×. We ran this reaction for 20 cycles to determine the additional number of cycles needed for the remaining 45-μL reaction. The libraries were purified using a Qiagen PCR cleanup kit yielding a final library concentration of ∼30 nM in 20 μL. Libraries were amplified for a total of 10–12 cycles.
During the ATAC-seq protocol, we chose to avoid a size-selection step to maximize the library complexity. The sequenced insert size is a distribution between 40 bp and 1 kb with a mean of ∼120 bp. From the bioanalyzer and gels we observed fragments >2 kb, which would make Qubit and other mass-based quantitation methods hard to interpret. For this reason we quantified our libraries using qPCR-based methods.

treatment_protocol: Cells were treated with corresponding EC50 values of LAK31, MZ-1, Romidepsin or Quisinostat for 16 h.

value: Quisinostat


title: 2102EP_Romidepsin

value: Romidepsin


title: 2102EP_MZ-1


title: DU-145_DMSO

source_name: prostate cancer

value: solvent control (DMSO)


title: E2S-GSK-3

description:
GSK343 Rep3
RNASeq


title: DU-145_LAK31


title: Caki-1_LAK31

source_name: renal cell carcinoma


title: G7S-CONTROL-1

description:
Control Rep1
RNASeq


title: Caki-1_DMSO


title: VM-CUB-1_DMSO

source_name: urothelial carcinoma


title: 2102EP_DMSO