title: ovarian cells_S116

source_name: ovarian cells_S116


title: STS26T-p75 RNA-seq

status: Public on Jun 28 2021

type: SRA

city: Cambridge

first: Ayush

middle: T

last: Raman

state: MA

address: 75 Ames St

department: Epigenomics Program

country: USA

institute: Broad Institute of MIT and Harvard

description: PRC2 WT

library_source: transcriptomic

data_processing:
The quality of raw reads was assessed using FastQC (Andrews, 2010). The average per base quality score across all the files were greater than 32 and had passed all the major tests.
The raw reads were aligned to the Homo sapiens genome (hg19) using STAR v2.4.2a (Dobin et al., 2013). The mappability of unique reads on average was ~82%. The raw counts were computed using quantMode function in STAR.
The obtained read counts are analogous to the expression level of each gene across all the samples. The differential expression analysis was done using DESeq2 (Love et al., 2014a). Genes with raw mean reads greater than 10 were used for normalization and differential gene expression analysis using DESeq2 package in R. Wald test defined in the DESeq function of the package was used for differential expression analysis and shrunken log fold-changes (i.e., obtaining reliable variance estimates by pooling information across all the genes) were used for further analysis. Principal Component Analysis (PCA), hierarchical clustering plots (hclust) and XY plots between replicates of same genotypes were used to examine for nominal amounts of non-technical variation and other latent factors. PCA, hclust and bar plots were generated using ggplot2 (Wickham). All the heatmaps of differentially expressed genes were generated using pheatmap package (Kolde, 2012) in R environment.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files; raw counts file output from STAR and Diff Expressed Genes using DESeq2

molecule: total RNA

organism: Homo sapiens

source_name: MPNST cells

growth_protocol: MPNST cells were grown in DMEM with 10% FBS. NSC, MPNST4970, MPNST181 were grown in Schwann cell medium and transferred to 10% DMEM 24 hrs before harvesting for RNA.

extract_protocol:
RNA was isolated from cultured cells using TRIzol (Cat# 10296010 Invitrogen) and purified using the RNeasy Mini Kit (Cat# 74106 Qiagen, Valencia, CA, USA) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Tumor cell line

tag: cell type

value: MPNST cells

tag: genotype

value: PRC2 WT


title: Dry-Col0-Rep1

city: Stanford

first: Yanniv

last: Dorone

address: 371 Jane Stanford Way

institute: Stanford University

data_processing:
Reads were mapped with HISAT2 to the Arabidopsis thaliana TAIR10 reference genome using the Galaxy (Version 2.1.0+galaxy5) web platform.
The resulting BAM files were then analyzed on R using the DESeq2 and TxDB.Athaliana.BioMart.plantsmart28 (Bioconductor) packages. Genes with padj<0.05 were considered differentially expressed.
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel

organism: Arabidopsis thaliana

source_name: Dry seeds

growth_protocol: For imbibed and salt: dry seeds were sown onto separate agar plates of MS medium conditions with either 0 or 220mM NaCl and cold-stratified for 5 days at 4˚C in the dark. All plates were subsequently transferred to and held in a growth cabinet (Percival) for 4 hours under light (130 μmol.m−2.s−1) and 22˚C.

extract_protocol:
DNA-free total RNA was extracted from seeds and siliques as described in Meng & Feldman (2010). The extraction buffer utilized 0.5% β-mercaptoethanol.
Library preparation (250-300 bp insert cDNA library) was conduced by Novogene Corporation Inc.

treatment_protocol: RNA-seq analysis was carried out on six conditions: 1) dry floe1-1 seeds; 2) dry Col-0 seeds; 3) imbibed floe1-1 seeds; 4) imbibed Col-0 seeds; 5) floe1-1 seeds imbibed with 220 mM NaCl; and 6) Col-0 seeds imbibed with 220 mM NaCl.

tag: treatment

value: No


title: ovarian cells_S111

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

country: China

institute: Beijing Institute of Radiation Medicine

data_processing:
Checked the quality control of reads data by FastQC
The reads data mapped and quantified as TPM using Salmon
Genome_build: mm10
Supplementary_files_format_and_content: Plain txt file for illumina RNA-seq data, each file contain 5 column, the first column represents gene name, the second column represents the total length of genes, the third column represents the effective legnth of genes, the fourth column represents the TPM of genes and the fifth column represents the number of reads.

molecule: polyA RNA

organism: Mus musculus

source_name: ovarian cells_S111

growth_protocol: Mice were housed under SPF environmental conditions with free access to water and food, 20–22°C ,50–70% humidity, and a 12/12-hour light and dark cycle in the Animal Core Facility of Nanjing Medical University. Animal care and experimental procedures were conducted according to the guidelines of the Animal Research Committee of Nanjing Medical University.

extract_protocol:
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM ethylenediaminetetracetic acid (EDTA), and 0.01% DNase I and incubated at 37℃ for 10 min with gentle agitation. To stop the digestion, 500 µl HBSS (plus 10% FBS) was added and the cell suspensions were centrifuged at 400g for 5min at 4℃. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS and transferred under the microscope.The collected oocyte were washed twice with 1xPBS and then immediately placed in lysis buffer( Combine 0.2% (vol/vol) Triton X-100 and 2 U µl–1 RNase inhibitor).The lysis solution also contains free dNTPs and tailed oligo-dT oligonucleotides (30-nt poly-dT stretch and a 25-nt universal 5′ anchor sequence) that are prepared of the Reverse Trianscription reaction on polyadenylated RNA sequences.
We used tagmentation to quickly and efficiently construct sequencing libraries from the amplified cDNA. The fragments in the tagmented DNA library have an average size that ranges from 200 to 300 bp and then purified for Illimina. The quantity of the libraries was assessed and defined by qPCR, respectively. All samples were sequenced using HiSeq XTen (Illumina) with paired-end 125-bp sequencing.

treatment_protocol: Newborn female pups from the same litter were collected immediately after delivery and ovaries (n=5) were harvested by carefully removing oviducts and ovarian bursa in calcium- and magnesium-free Hanks balanced salt solution (HBSS).

tag: strain

value: ovary

tag: age


title: ovarian cells_S119

source_name: ovarian cells_S119


title: shCtrl-rep3

city: Guangzhou

first: Yi

last: Niu

address: No.2, Zhishan Garden, No.132, East Outer Ring Road

institute: Sun Yat-sen University

description: Gene changes in ALDOA-KD cells.xlsx

data_processing:
Shalem, O., Sanjana, N.E., Hartenian, E., Shi, X., Scott, D.A., Mikkelson, T., Heckl, D., Ebert, B.L., Root, D.E., Doench, J.G., et al. (2014). Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 343, 84-87.
Paired-end sequencing was performed with Illumina HiSeq 3000 at RiboBio Co., Ltd. TopHat2 and HTSeq are used for RNAseq data analysis
Genome_build: genome-wide CRISPR/Cas9 KO sgRNA library; hg38
Supplementary_files_format_and_content: Matrix table with  gene foldchange for every gene

growth_protocol: The HCC cells are cultured in 20% O2 and 1% O2 to mimic normoxia and hypoxia

extract_protocol:
genome-wide CRISPR/Cas9 knockout library HepG2 cells are collected,and genome DNA was harvested and sgRNAs were amplified with PCR.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA library preparation is performed by using NEBNext UltraDirectional RNA Library Prep Kit for Illumina (E7420L).

treatment_protocol: genome-wide CRISPR/Cas9 knockout library HepG2 cells are cultured in normoxia and hypoxia. shCtrl and shALDOA HepG2 cells are cultured in hypoxia

value: HCC cells

tag: cell line


title: day10_Jc1infected3

type: RNA

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the Illumina beadarray Assay System Manual

data_processing: For each probe, replicated mesurements (beads) were averaged after removing outliers by Genome Studio software v.3 (Illumina). Data were were then normalized using qubic spline algorithm implemented in GenePattern Illumina normalizer module (www.broadinstitute.org/genepattern) after setting a floor value of 1.

label: biotin

growth_protocol: Huh7.5.1 cells were cultured in DMEM with 1% DMSO for 10 days.

extract_protocol: RNA was isolated using RNeasy kit (Qiagen) according to manufacturer’s protocol.

treatment_protocol: DMSO-differentiated Huh7.5.1 cells were infected with HCV Jc1 clone.

tag: time post infection

value: Day 10 post infection

tag: infection

value: HCV Jc1 infection


title: STS26T-p74 RNA-seq

description: PRC2 WT


title: day10_Jc1infected1

scan_protocol: Refer to the Illumina beadarray Assay System Manual


title: ovarian cells_S110

source_name: ovarian cells_S110


title: shCtrl-rep2

description: Gene changes in ALDOA-KD cells.xlsx


title: day10_mock3

label_protocol: Refer to the Illumina beadarray Assay System Manual

value: Mock infection (control)


title: day10_Jc1infected2


title: NSC-p4 RNA-seq

description: PRC2 WT

source_name: Normal Schwann cells

value: Normal control cells

value: Normal Schwann cells


title: day10_mock2


title: NSC-p2 RNA-seq

description: PRC2 WT


title: shCtrl-rep1

description: Gene changes in ALDOA-KD cells.xlsx


title: Pre-treatment [200742440049_D]

city: Doha

first: Darawan

last: Rinchai

state: Qatar

address: Al Gharrafa St

department: Research

country: Qatar

institute: Sidra Medicine

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with preprocessCore in R

source_name: PBMCs

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Qiazole reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: disease

value: metastatic renal cell carcinoma (mRCC)

tag: time point

value: Pre-treatment


title: ST88_p133 RNA-seq

description: PRC2 mutant

value: PRC2 mutant


title: ovarian cells_S112

source_name: ovarian cells_S112


title: ovarian cells_S108

source_name: ovarian cells_S108


title: ovarian cells_S107

source_name: ovarian cells_S107


title: Crispr-cas9 library screening-hypoxia

description:
Genome-wide CRISPR/Cas9 library sgRNA
Loss-of-function and RNA sequencing.xlsx

library_source: genomic

data_processing:
Library strategy: CRISPR screen
Shalem, O., Sanjana, N.E., Hartenian, E., Shi, X., Scott, D.A., Mikkelson, T., Heckl, D., Ebert, B.L., Root, D.E., Doench, J.G., et al. (2014). Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 343, 84-87.
Paired-end sequencing was performed with Illumina HiSeq 3000 at RiboBio Co., Ltd. TopHat2 and HTSeq are used for RNAseq data analysis
Genome_build: genome-wide CRISPR/Cas9 KO sgRNA library; hg38
Supplementary_files_format_and_content: Matrix table with  gene foldchange for every gene

molecule: genomic DNA


title: day10_mock1


title: day7_Jc1infected3

value: Day 7 post infection


title: ST88_p124 RNA-seq

description: PRC2 mutant


title: Crispr-cas9 library screening-normoxia


title: S462-p69 RNA-seq

description: PRC2 mutant


title: FL-LSKCD021+_3

city: Hangzhou

first: Wei

last: Shan

state: Zhejiang

address: Bone Marrow Transplantation Center, The First Afﬁliated Hospital, School of Medicine, Zhejiang University, No.79 Qingchun Road, Hangzhou, Zhejiang, PR China.

institute: Zhejiang University

data_processing:
Library sequencing was performed on an Illumina HiSeq X Ten platform (Illumina) to generate 150-bp paired-end reads.
The paired-end reads were processed and aligned to the reference genome (GRCm38) using HISAT2 (v.2.0.5).
Mapped reads for each sample were assembled into transcriptome data using StringTie (v.1.3.3) with a reference-based approach. The normalized expression value was represented by fragments per kilobase of transcript per million mapped reads (FPKMs).
Cuffdiff (v1.3.0) was used to calculate the differential expression genes for each sample. Only comparisons with q-values < 0.05 and absolute log2 (fold change) values ≥1 were considered as significantly differentially expressed genes.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: C57BL/6 mouse Fetal liver derived  LSKCD201+ cells

growth_protocol: 3D inducment derived hematopoietic like colonies were seeded on OP9 stromal and 0.1% gelatin

extract_protocol:
Total RNA was extracted from sorted cell samples using TRIzol Reagent (Life Technologies) following the manufacturer’s instructions.
cDNA libraries were constructed using the VAHTS mRNA-seq v2 Library Prep Kit for Illumina (Vazyme) according to the manufacturer’s protocol

treatment_protocol: using FACS to sort total cells from 3D+OP9 and3D+0.1%gelatin. In the 3D+OP9 hematopoietic differentiation system, we sorted D5-LSKCD201+ and D5-LSKCD201- cells, at the same time, we used  PE-anti-mouse-SSEA-1 to  sort mESC and sorted bone marrow derived  D5-LSKCD201+ and fetal liver derived  D5-LSKCD201+

tag: strain background

value: Fetal liver derived  LSKCD201+ cells


title: STS26T-p73 RNA-seq

description: PRC2 WT


title: ovarian cells_S106

source_name: ovarian cells_S106


title: day7_Jc1infected2


title: ovarian cells_S105

source_name: ovarian cells_S105


title: day7_Jc1infected1


title: FL-LSKCD021+_2


title: ovarian cells_S109

source_name: ovarian cells_S109


title: FL-LSKCD021+_1


title: ST88_p130 RNA-seq

description: PRC2 mutant


title: day7_mock3


title: MPNST724-p96 RNA-seq

description: PRC2 WT


title: BM-LSKCD021+_3

source_name: C57BL/6 mouse bone marrow derived  LSKCD201+ cells

value: bone marrow derived  LSKCD201+ cells


title: S462-p61 RNA-seq

description: PRC2 mutant

value: Tumor cell line


title: ovarian cells_S103

source_name: ovarian cells_S103


title: day7_mock2


title: ovarian cells_S102

source_name: ovarian cells_S102


title: BM-LSKCD021+_2


title: ovarian cells_S101

source_name: ovarian cells_S101


title: MPNST724-p74 RNA-seq

description: PRC2 WT

source_name: MPNST cells

value: MPNST cells


title: BM-LSKCD021+_1


title: ovarian cells_S100

source_name: ovarian cells_S100


title: MPNST724-p101 RNA-seq

description: PRC2 WT

value: PRC2 WT


title: D5-LSKCD021-_3

source_name: mouse pluripotent stem cells derived  LSKCD201- cells


title: S462-p64 RNA-seq

description: PRC2 mutant


title: day7_mock1


title: day3_Jc1infected2

value: Day 3 post infection


title: ovarian cells_S104

source_name: ovarian cells_S104

value: ovary


title: day3_Jc1infected3


title: Mut1819

city: Nashville

first: Volker

middle: Hans

last: Haase

state: TN

department: Medicine

institute: Vanderbilt University Medical Center

data_processing:
Data analysis was performed using a combination of programs including Bowtie2, Tophat2, Htseq, Cufflink.
Alignments were parsed using Tophat program and differential expressions were determined through DESeq2/DEGseq.
GO and KEGG enrichment were implemented by the Goseq R parckage and KOBAS.
Genome_build: mm10
Supplementary_files_format_and_content: counts

source_name: renal cortex

extract_protocol:
RNA isolation performed with Qiagen Rneasy Kit plus DNAse step
performed by Novogene

tag: mouse line

value: Six2-Tfam knockout mouse

value: postnatal day 7 mouse


title: SNF02_2p27 RNA-seq

description: PRC2 WT


title: SNF02_2p26 RNA-seq

description: PRC2 WT


title: ovarian cells_S099

source_name: ovarian cells_S099


title: Mut1454


title: D5-LSKCD021-_1

value: pluripotent stem cells derived  LSKCD201- cells


title: day3_mock3

value: Mock infection (control)


title: ovarian cells_S096

source_name: ovarian cells_S096


title: MPNST181p25 RNA-seq

description: PRC2 WT


title: day3_mock1


title: SNF02_2p25 RNA-seq

description: PRC2 WT


title: D5-LSKCD021+_3

source_name: mouse pluripotent stem cells derived  LSKCD201+ cells


title: D5-LSKCD021+_2

value: pluripotent stem cells derived  LSKCD201+ cells


title: MPNST181p24 RNA-seq

description: PRC2 WT


title: Mut1393


title: D5-LSKCD021+_1


title: MPNST181p22 RNA-seq

description: PRC2 WT


title: D5-LSKCD021-_2


title: day3_Jc1infected1

value: HCV Jc1 infection


title: Con1823

value: Cre-


title: Con1822


title: ovarian cells_S094

source_name: ovarian cells_S094


title: MPNST4970p30 RNA-seq

description: PRC2 WT


title: ovarian cells_S093

source_name: ovarian cells_S093


title: ovarian cells_S097

source_name: ovarian cells_S097


title: mESC-2

source_name: mouse embryonic stem cell

value: embryonic stem cell


title: ovarian cells_S098

source_name: ovarian cells_S098


title: Con1452


title: MPNST4970p28 RNA-seq

description: PRC2 WT


title: Mut1453


title: MPNST4970p29 RNA-seq

description: PRC2 WT


title: mESC-1


title: ovarian cells_S092

source_name: ovarian cells_S092


title: ovarian cells_S091

source_name: ovarian cells_S091


title: MPNST3813E_P27 RNA-seq

description: PRC2 mutant

value: PRC2 mutant


title: ovarian cells_S090

source_name: ovarian cells_S090


title: Hepatic Fibrosis PZH6

city: Shanghai

first: Jinhang

last: Zhu

address: Huashan Road 1954

institute: Shanghai Jiao Tong University

description: Small RNA

data_processing:
Trimming low quality reads, adapters and quality control using Cutadapt and FastQC software
Mapping trimmed reads to mouse reference genome using BWA software.
Classification of small RNA and miRNA annotation was obtained using Rfam and miRbase databases.
Normalized miRNA expression counts using DESeq2 R package.
Genome_build: Mus_musculus.GRCm38
Supplementary_files_format_and_content: Table-delimited text files include raw count of 1929 miRNAs across 12 samples

source_name: hepatic fibrosis mice model

growth_protocol: The mice of Control group received intraperitoneal injection of CCl4 solvent two time once a week and the double distilled by intragastric administration water one time once a day, while the mice of PZH group underwent intraperitoneal injection of CCl4 solvent two time once a week and the PZH prepared reagent by intragastric administration one time every day.

extract_protocol:
Small RNA was extracted from each liver tissue sample using Trizol reagent (Invitrogen, CA, USA).
The small RNA library was constructed  by manufacturer’s recommended protocol of TruseqTM Small RNA sample prep Kit.

treatment_protocol: We construct two groups hepatic fibrosis mice model using CCl4, one group using PZH treatment and another group replacing PZH with  the double distilled water.

value: Liver

value: hepatic fibrosis


title: Patient2_Erlotinib

hyb_protocol: Refer to the NanoString nCounter Assay System Manual

data_processing: For each probe, transcript count data were log2 transformed and scaled by geometric mean of the normalization genes by NanoString normalizer module of GenePattern toolkit (www.broadinstitute.org/genepattern) after setting a floor value of 1.1.

growth_protocol: Huh7.5.1 cells, HepG2 cells, and clinical liver tissue slices were cultured in DMEM with 1% DMSO for 2 to 10 days.

treatment_protocol: DMSO-differentiated Huh7.5.1 cells, HepG2-NTCP cells, Huh7.5.1-NTCP cells or clinical liver tissue slices were exposed to mock, HCV, HBV, or EtOH, and treated with interferon, direct-acting anti-HCVs, erlotinib, pioglitazone, or metformin or co-culture with hepatic stellate cell line, LX2. Cells/tissues were harvested for RNA isolation and gene expression profiling by NanoString assay.

tag: sample type

value: Tissue

tag: exposure with etiological agent

value: HBV

tag: duration with etiological agent

tag: intervention

value: Erlotinib (5 microM)

tag: duration of intervention

value: 2 days

value: liver


title: Con1391


title: Hepatic Fibrosis PZH5

description: Small RNA

tag: tissue

tag: cell type


title: MPNST3813E_P21 RNA-seq

description: PRC2 mutant

source_name: MPNST cells

value: Tumor cell line

value: MPNST cells

tag: genotype


title: mESC-3


title: ovarian cells_S088

source_name: ovarian cells_S088

tag: strain

value: ovary


title: ovarian cells_S095

source_name: ovarian cells_S095

tag: age


title: Hepatic Fibrosis PZH4

description: Small RNA


title: Hepatic Fibrosis PZH3

description: Small RNA


title: ovarian cells_S087

source_name: ovarian cells_S087


title: MPNST007p15 RNA-seq

description: PRC2 WT

value: PRC2 WT


title: MPNST3813E_P25 RNA-seq

description: PRC2 mutant


title: MPNST007p17 RNA-seq

description: PRC2 WT


title: Patient1_Erlotinib

scan_protocol: Refer to the NanoString nCounter Assay System Manual

tag: cell line


title: ovarian cells_S086

source_name: ovarian cells_S086


title: MPNST007p14 RNA-seq

description: PRC2 WT


title: Patient1_DMSO

label_protocol: Refer to the NanoString nCounter Assay System Manual

value: DMSO


title: T265-p59 RNA-seq

description: PRC2 mutant


title: Hepatic Fibrosis PZH2

description: Small RNA


title: Hepatic Fibrosis Control6

description: Small RNA


title: Metformin_3

value: Cell (Huh7.5.1dif)

value: HCV Jc1 infection (TCID50/mL=10^6/mL)

value: 10 days

value: Metformin (3 microM)

value: 3 days


title: T265-2 RNA-seq

description: PRC2 mutant

value: PRC2 mutant


title: Hepatic Fibrosis PZH1

description: Small RNA

value: Liver

value: hepatic fibrosis


title: Metformin_1


title: ovarian cells_S089

source_name: ovarian cells_S089


title: ovarian cells_S085

source_name: ovarian cells_S085


title: Patient2_DMSO

value: Tissue

value: HBV


title: ovarian cells_S084

source_name: ovarian cells_S084


title: Hepatic Fibrosis Control5

description: Small RNA


title: Metformin_2


title: Pioglitazone_3

value: Pioglitazon (1 microM)


title: ovarian cells_S083

source_name: ovarian cells_S083


title: T265-1 RNA-seq

description: PRC2 mutant


title: SNF96-2p26 RNA-seq

description: PRC2 mutant


title: ovarian cells_S082

source_name: ovarian cells_S082


title: Pioglitazone_2


title: ovarian cells_S081

source_name: ovarian cells_S081


title: SNF96-2p25 RNA-seq

description: PRC2 mutant


title: Hepatic Fibrosis Control4

description: Small RNA


title: Hepatic Fibrosis Control3

description: Small RNA


title: ovarian cells_S080

source_name: ovarian cells_S080


title: ovarian cells_S079

source_name: ovarian cells_S079


title: Pioglitazone_1


title: Hepatic Fibrosis Control2

description: Small RNA


title: Control_to_Pioglitazone_3


title: Control_to_Pioglitazone_2


title: ovarian cells_S078

source_name: ovarian cells_S078


title: Control_to_Pioglitazone_1


title: SNF96-2p22 RNA-seq

description: PRC2 mutant


title: MPNST642-2p5 RNA-seq

description: PRC2 mutant


title: ovarian cells_S077

source_name: ovarian cells_S077


title: ovarian cells_S076

source_name: ovarian cells_S076


title: MPNST642-2p4 RNA-seq

description: PRC2 mutant


title: ovarian cells_S075

source_name: ovarian cells_S075


title: Erlotinib_1

value: Erlotinib (0.1 microM)


title: Erlotinib_2


title: siRNAAR454.2

city: Oxford

first: Carlo

last: Rinaldi

address: South Parks Road

department: Department of Paediatrics

country: United Kingdom

institute: University of Oxford

description:
Counts.txt
TPM.txt

data_processing:
Illumina Casava software for basecalling.
Sequence reads adapter and quality trimmed with Trim galore! QC performed with FastQC and MultiQC.
Quantification done with Salmon using --seqBias --gcBias and --validateMapping flags
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: tab deliimted text file  for raw counts and TPMs

source_name: Human myoblasts

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina was used with 1.5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Immortalised cells

tag: passages

tag: treatment

value: siRNA targeting AR-2


title: ovarian cells_S074

source_name: ovarian cells_S074

value: ovary


title: siRNAAR454.1

description:
Counts.txt
TPM.txt


title: HDV_2

value: Cell (Huh7.5.1dif-NTCP)

value: HDV


title: Erlotinib_3

value: Cell (Huh7.5.1dif)


title: MPNST642-2p6 RNA-seq

description: PRC2 mutant

source_name: MPNST cells

value: Tumor cell line

value: MPNST cells


title: ovarian cells_S073

source_name: ovarian cells_S073


title: NTC2.3

description:
Counts.txt
TPM.txt

value: siRNA mock sequence


title: Hepatic Fibrosis Control1

description: Small RNA

source_name: hepatic fibrosis mice model


title: ovarian cells_S072

source_name: ovarian cells_S072


title: HCV_1

value: 10 days


title: siRNAAR454.3

description:
Counts.txt
TPM.txt


title: NTC2.2

description:
Counts.txt
TPM.txt


title: Control_to_HDV_2


title: ovarian cells_S071

source_name: ovarian cells_S071


title: ovarian cells_S070

source_name: ovarian cells_S070


title: Control_to_HDV_1


title: NTC2.1

description:
Counts.txt
TPM.txt


title: HBV_3

value: Cell (HepG2-NTCP)

value: HBV (genotype D)


title: AR458.3

description:
Counts.txt
TPM.txt

value: AR45 overexpression


title: ovarian cells_S069

source_name: ovarian cells_S069


title: AR458.2

description:
Counts.txt
TPM.txt


title: HBV_2


title: L428 non-SP#1

city: Tokyo

first: Makoto

last: Nakashima

address: Building 2, West-side of 3rd floor, 1-4-6 Shirokanedai, Minatoku

country: Japan

institute: University of Tokyo

hyb_protocol: Labeled cRNA samples were hybridized to 44K Whole Human Genome Oligonuclotide Microarrays (Agilent Technologies) at 65 ℃ for 17 h.

scan_protocol: The microarrays were scanned with a Scanner C (Agilent Technologies).

data_processing: Signal intensities were evaluated by Feature Extraction 10.7

source_name: KMH2 non-SP

label_protocol: The RNA was Cy3-labeled using a Low Input Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: RPMI with 10%FBS

extract_protocol: Total RNA isolation in sorted SP or MP cells of HL cell lines were extracted with Trizol (Invitrogen) according to the manufacturer's protocol. Treatment with DNaseⅠ(TakaraBio) was conducted to eliminate genomic DNA contamination.

value: HL-derived cell line

tag: cell population

value: non-SP


title: L428 non-SP#2


title: L428 non-SP#3


title: ovarian cells_S068

source_name: ovarian cells_S068


title: AR458.1

description:
Counts.txt
TPM.txt


title: HBV_1


title: L428 SP#3

source_name: KMH2 SP

value: SP


title: L428 SP#1


title: L428 SP#2


title: Control_to_HBV_3

value: Mock infection


title: ovarian cells_S067

source_name: ovarian cells_S067


title: ovarian cells_S066

source_name: ovarian cells_S066


title: EV6.2

description:
Counts.txt
TPM.txt

value: Immortalised cells

value: Empty transfection


title: Control_to_HBV_2


title: KMH2 non-SP#3


title: EV6.1

description:
Counts.txt
TPM.txt


title: P-W-3

city: Chengdu

first: Liming

last: Chang

state: Sichuan

address: No.9 Section 4,Renmin Nan Road,Chengdu, Sichuan, P.R. China

institute: Chengdu Institute of Biology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence;The total clean reads from all libraries were assembled using Trinity as a reference transcriptome.
Genome_build: de novo
Supplementary_files_format_and_content: fasta file includes the sequences of all unigenes across samples

organism: Microhyla fissipes

source_name: whole tadpole

extract_protocol:
Total RNA of each sample was extracted and purified using Trizol (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions. After purified with poly-T oligo-attached magnetic beads, the mRNAs were fragmented.
First-strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H−). Second-strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. The remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of the 3′ ends of the DNA fragments, NEBNext Adaptors with a hairpin loop structure were ligated to prepare for hybridization. To preferentially select cDNA fragments of 150–200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then, 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then, PCR was performed with a Phusion High-Fidelity DNA polymerase, universal PCR primers and Index (X) primer. Finally, PCR products were purified (AMPure XP system), and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina HiSeq 2500 platform by NovoGene (Beijing), and paired-end reads were generated.

value: whole tadpole

tag: developmental stage

value: stage 29

tag: collection sites

value: farmlands (E103.459885, N30.744614, 701 m) in Shifang City, Sichuan Province, China

value: White background with 1μmol/L corticosterone exposure


title: KMH2 non-SP#2


title: KMH2 SP#3


title: ovarian cells_S065

source_name: ovarian cells_S065

value: ovary


title: Control_to_HBV_1


title: P-W-1


title: KMH2 SP#1


title: KMH2 SP#2


title: P-b-3

value: Black background with 1μmol/L corticosterone exposure


title: ovarian cells_S064

source_name: ovarian cells_S064


title: KMH2 non-SP#1


title: ovarian cells_S063

source_name: ovarian cells_S063


title: Control_E12.5OFT_scRNAseq

city: Columbus

first: Vidu

last: Garg

state: OH

address: 700 Children's Drive WB4239

department: Cardiovascular Research

institute: Research Institute at Nationwide Children's Hospital

data_processing:
Illumina .bcl files were demultiplexed and converted into per-sample FASTQ files using the 10x Genomics cellranger `mkfastq` command. The FASTQ files were then used to create a gene-count matrix using the cellranger command `count` using the mm10 genome version index from 10X genomics (https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz) modified to include Neomycin resistance sequence using ‘reform’ (https://gencore.bio.nyu.edu/reform/; accessed 09/15/2020). The expression of Neomycin resistance gene (NeoR) was used to identify Notch1 heterozygote cells. The count output file was then imported into the Seurat (v 3.0) package in R. (45) Cells with at least 1 read mapping to NeoR gene were removed and the rest of the cells were used for further analysis. These NeoR negative cells were filtered for number of expressed genes and percentage of mitochondrial gene expression, normalized, subject to principal component analysis using the highest variable genes, and scaled as described earlier. (46) Following this, dimensional reduction was performed using the RunUMAP and RunTSNE functions of Seurat using the first 20 principal components, and cells were clustered using the Louvain algorithm using a resolution factor of 0.5. The clustered cells were renamed using markers described in literature into vascular smooth muscle cells (VSMC), mesenchymal cells (Mes), Endothelial cells (EC), Myocardial cells (Myo), Epicardial (epi), Blood, and Ectodermal cells. Blood and ectodermal cells were removed for further analysis and dimensional reduction and clustering were repeated for the mesodermal cells.
Using these clusters, we examined cell-type specific expression of genes. Cell type-specific expression was examined by comparing a gene in an individual cluster against all other cells in the dataset using the ‘FindAllMarkers’ function in R. As changes in the number of cells expressing a gene as well as the changes in the average expression per cell can contribute to differential expression, we used a threshold for both of these attributes. For differential expression between a cluster and rest of the cells, log fold change threshold was set to 0.5 (logfc.threshold = 0.5) and minimal percentage of cells positive for a gene’s expression within a cluster set to 25% (min.pct =0.25) and Wald test was used to evaluate statistical significance. The genes that showed a significant differential expression between a cluster vs. rest of the cells (adj.P-value <= 0.05) were deemed to have tissue/cell type-specific expression patterns. Genes which were found to have a cell-type specific expression in blood or ectodermal clusters were removed from further analysis for comparison to congenital heart gene candidates. Heatmaps created using the pheatmap function in R was used to visualize the tissue-specific expression of various genes.
Genome_build: mm10 genome version index from 10X genomics (https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz) modified to include Neomycin resistance sequence using ‘reform’ (https://gencore.bio.nyu.edu/reform/; accessed 09/15/2020)
Supplementary_files_format_and_content: xlsx, tissue specifc expression analysis output from Seurat of differentially expressed genes identified in RNAseq data

source_name: Outlfow tract

extract_protocol:
E12.5 cardiac OFTs (both Notch1+/- and wildtype) were microdissected from five mouse embryos and pooled for single-cell RNA sequencing. To prepare single cells suspensions, pooled OFT tissues were incubated with 1 mg/ml Collagenase II (Worthington Biochemical Corporation# LS004176) for 15 mins at 37°C with occasional stirring at every 5 minutes for complete dissociation. The digestion reaction was quenched immediately with 1 ml. DMEM supplemented with 10% FBS and pelleted down at 1000 rpm for 5 mins at 4°C. Pelleted cells were washed with cold PBS and resuspended in 0.04% BSA in PBS at concentration 9.74 X 105 cells/ml with 83% viability (8.03 X 105 live cells/ml).
A single-cell droplet library of the pooled Notch1+/-  / wildtype OFTs samples was generated using the 10xGenomics Chromium controller from this suspension according to the manufacturer’s instructions. The quality and integrity of the cDNA library was quantitated using the High Sensitivity D5000 and D1000 ScreenTape (Agilent# 5067-5592 and 5067-5584) on the Agilent-2200 TapeStation.
The library was sequenced (150bp paired-end) using the Illumina HiSeq 4000 platform at the Steve and Cindy Rasmussen Institute for Genomic Medicine at Nationwide Children’s Hospital. A total of 337,081,925 paired end reads and a total of 2,116 cells were detected for the pooled sample. Thus, on average, the transcriptome of each cell was evaluated using 159,301 reads.

value: Notch1+/- and wildtype pooled

value: Embryonic cardiac outflow tract


title: P-b-1


title: ovarian cells_S061

source_name: ovarian cells_S061


title: ovarian cells_S062

source_name: ovarian cells_S062


title: SI_Tissue_KO_1

city: Gainesville

first: Liang

last: Zhou

state: FL

address: 2015 SW 16th Ave

department: IDI

institute: University of Florida

data_processing:
FastQC was used to ensure high per-base sequence quality of reads.
Sequenced reads were mapped with STAR (Dobin, A. et al., 2013) to the Mus musculus genome (GRCm38/mm10 assembly) and filtered for uniquely mapped reads. Quantitated mRNA expression levels, FPKM aligned reads, were calculated based on exon regions using RSEM (Li, B. D. & Dewey, C. N., 2011) . Significantly changed genes (max FPKM ≥ 1, fold change >1.5, q-value ≤ 0.05) were identified by DESeq2 (Michael Love et al., 2014) analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes count values for each sample

source_name: Small Intestine Tissue

extract_protocol:
For RNA-Seq analyses of gdT17 cells, 2×10^3 sorted gdT17 cells from the spleen, small intestine, or large intestine of control or Tfamfl/flRorc-cre littermate mice were used. RNA was isolated by RNAeasy Micro Kit. For RNA-Seq analyses of small intestinal tissues, control or Tfamfl/flRorc-cre littermate mice were used. RNA was isolated by RNAeasy Mini Kit (Qiagen).
For RNA-Seq analyses of gdT17 cells, cDNA generation was performed with SMART-Seq® HT Kit (Takara). Sequencing libraries were generated with Nextera® XT DNA Library Preparation Kit (Illumina). For RNA-Seq analyses of small intestinal tissues, libraries were generated with NEBNext Ultra II RNA library Prep Kit (NEB).

value: Small Intestine

value: whole tissue

value: Tfamfl/flRorc-cre


title: SI_Tissue_KO_2


title: ovarian cells_S060

source_name: ovarian cells_S060


title: C-W-3

value: White background and no corticosterone exposure


title: LX2_20percent_2

value: Cell (Huh7.5.1dif)

value: HCV Jc1 infection (TCID50/mL=10^6/mL)

value: 10 days

value: Co-culture with LX2 cells (20%)


title: C-W-2


title: C-W-1


title: LX2_20percent_1


title: EV6.3

description:
Counts.txt
TPM.txt

source_name: Human myoblasts

value: Immortalised cells

value: Empty transfection


title: Control_to_LX2_20percent_2

value: Mock infection


title: SI_Tissue_Ctr_2

value: Tfam+/+Rorc-cre


title: Control_to_LX2_20percent_3


title: P-b-2

value: whole tadpole

value: stage 29

value: farmlands (E103.459885, N30.744614, 701 m) in Shifang City, Sichuan Province, China


title: ovarian cells_S059

source_name: ovarian cells_S059

value: ovary


title: ovarian cells_S058

source_name: ovarian cells_S058


title: LX2_20percent_3


title: SI_Tissue_Ctr_1


title: SI_Tissue_KO_3


title: ovarian cells_S057

source_name: ovarian cells_S057


title: LX2_10percent_3

value: Co-culture with LX2 cells (10%)


title: C-b-2

value: Black background and no corticosterone exposure


title: Control_to_LX2_20percent_1


title: LX2_10percent_2


title: LI_KO_3

source_name: Large Intestine gdT17

value: Large Intestine


title: ovarian cells_S056

source_name: ovarian cells_S056


title: LX2_10percent_1


title: C-b-1


title: C-b-3


title: ovarian cells_S055

source_name: ovarian cells_S055


title: Control_to_LX2_10percent_3


title: SI_Tissue_Ctr_3

value: Small Intestine

value: whole tissue


title: LI_KO_1

value: Tfamfl/flRorc-cre


title: ovarian cells_S054

source_name: ovarian cells_S054


title: ovarian cells_S052

source_name: ovarian cells_S052


title: ovarian cells_S053

source_name: ovarian cells_S053


title: PR2181_15_a

city: Saitama

first: Hideki

last: Nakasone

address: 1-847, Amanuma-cho, Omiya-ku

department: Hematology

institute: Jichi Medical University Saitama Medical Center

description: #16 late

data_processing:
Novaseq Control Software v1.6.0 or v1.7.0
Real Time Analysis (RTA) v3.4.4
bcl2fastq2 v2.20
DRAGEN Bio-IT Platform v3.6.3
Genome_build: CRCh38.primary_assembly.genome.fa.gz (GENCODE 35, accessed on Aug-25, 2020)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: sorted CTL in peripheral blood

extract_protocol:
SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara Bio, Inc.)  with modified lysis protocol
SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara Bio, Inc.)  with modified thermal cylces, and standarad Illumina kit

tag: phase of allo-hct

value: late

tag: donor cmv status

value: negative

tag: cmv reactivation pattern

value: no

tag: cells of cmv-ctls


title: PR2181_11_a

description: #7 late

value: One


title: PR2181_14_a

description: #13 late


title: LI_Ctr_3


title: Control_to_LX2_10percent_2

tag: sample type

value: Cell (Huh7.5.1dif)

tag: exposure with etiological agent

tag: duration with etiological agent

value: 10 days

tag: intervention


title: Control_to_LX2_10percent_1

value: Mock infection

tag: duration of intervention


title: LI_Ctr_1

tag: tissue

tag: cell type

tag: strain

tag: genotype

value: Tfam+/+Rorc-cre


title: PR2181_10_a

description: #21 late

value: positive


title: LX2_5percent_3

value: HCV Jc1 infection (TCID50/mL=10^6/mL)

value: Co-culture with LX2 cells (5%)

tag: cell line


title: SI_KO_3

source_name: Small Intestine gdT17


title: LI_Ctr_2


title: ovarian cells_S051

source_name: ovarian cells_S051

value: ovary

tag: age


title: LX2_5percent_2


title: LX2_5percent_1


title: PR2181_09_a

description: #20 late


title: SI_KO_2


title: ovarian cells_S049

source_name: ovarian cells_S049


title: Control_to_LX2_5percent_3


title: PR2181_12_a

description: #12 late


title: PR2181_08_a

description: #19 late

value: Repeat


title: ovarian cells_S050

source_name: ovarian cells_S050


title: ovarian cells_S048

source_name: ovarian cells_S048


title: PR2181_07_a

description: #18 late


title: SI_KO_1


title: ovarian cells_S047

source_name: ovarian cells_S047


title: Control_to_LX2_5percent_2


title: SI_Ctr_3


title: Control_to_LX2_5percent_1


title: PR2181_06_a

description: #17 late


title: ovarian cells_S046

source_name: ovarian cells_S046


title: PR2181_05_a

description: #21 early

value: early


title: SI_Ctr_1

value: Small Intestine


title: SI_Ctr_2


title: ovarian cells_S045

source_name: ovarian cells_S045


title: LX2_0percent_3

value: Co-culture with LX2 cells (0%)


title: Sp_KO_3

source_name: Spleen gdT17

value: Spleen

value: Tfamfl/flRorc-cre


title: PR2181_04_a

description: #20 early


title: PR2181_03_a

description: #19 early


title: Sp_KO_2


title: ovarian cells_S044

source_name: ovarian cells_S044


title: LX2_0percent_1


title: Sp_KO_1


title: Control_to_LX2_0percent_3


title: ovarian cells_S043

source_name: ovarian cells_S043


title: ovarian cells_S042

source_name: ovarian cells_S042


title: PR2181_01_a

description: #17 early


title: Sp_Ctr_3


title: PR2181_02_a

description: #18 early


title: PR1413_07_a

description: #11 late

value: late

value: negative


title: LI_KO_2

source_name: Large Intestine gdT17

value: Large Intestine


title: Control_to_LX2_0percent_1

value: Cell (Huh7.5.1dif)


title: ovarian cells_S041

source_name: ovarian cells_S041


title: ovarian cells_S040

source_name: ovarian cells_S040


title: Sp_Ctr_2


title: Sp_Ctr_1


title: ovarian cells_S039

source_name: ovarian cells_S039


title: PR1413_05_a

description: #8 late

source_name: sorted CTL in peripheral blood

value: no


title: LX2_0percent_2

value: 10 days


title: ovarian cells_S038

source_name: ovarian cells_S038


title: DAA_2

value: DAA (daclatasvir 1 nM and sofosbuvir 1 microM)

value: 3 days


title: DAA_3

value: HCV Jc1 infection (TCID50/mL=10^6/mL)


title: DAA_1


title: PR1413_04_a

description: #4 late

value: positive


title: PR1413_03_a

description: #9 late

value: one


title: ovarian cells_S037

source_name: ovarian cells_S037

value: ovary


title: PR1413_02_a

description: #3 late


title: ovarian cells_S036

source_name: ovarian cells_S036


title: Control_to_LX2_0percent_2

value: Mock infection


title: Control_to_DAA_3


title: PR1413_01_a

description: #2 late


title: Control_to_DAA_2


title: PR1364_16_a

description: #16 early

value: early


title: PR1413_06_a

description: #15 late

value: Repeat


title: ovarian cells_S034

source_name: ovarian cells_S034


title: Control_to_DAA_1


title: Interferon_3

value: Interferon-alpha2a (10 IU/mL)


title: PR1364_14_a

description: #14 early


title: ovarian cells_S032

source_name: ovarian cells_S032


title: Interferon_1


title: ovarian cells_S031

source_name: ovarian cells_S031


title: PR1364_13_a

description: #13 early


title: Control_to_Interferon_3


title: ovarian cells_S035

source_name: ovarian cells_S035


title: PANC-1 cells, GEM2

city: Minato-ku

first: Ryoga

last: Hamura

state: Tokyo

address: Nisi-shinbashi, 3-25-8

department: Research Center of Medical Sciences

institute: Jikei University School of Medicine

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: PANC-1 cell, treated with gemcitabine 24 hr

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

value: human pancreatic cancer

tag: treatment

value: gemcitabine


title: ovarian cells_S030

source_name: ovarian cells_S030


title: Interferon_2


title: Control_to_Interferon_2


title: PR1364_12_a

description: #12 early

value: negative

value: One


title: ovarian cells_S033

source_name: ovarian cells_S033


title: Control_to_Interferon_1

value: Cell (Huh7.5.1dif)


title: PR1364_11_a

description: #11 early


title: PR1364_15_a

description: #15 early


title: PANC-1 cells, Ctl1

source_name: PANC-1 cell, control

value: control


title: PANC-1 cells, Ctl2


title: PANC-1 cells, GEM1


title: PR1364_10_a

description: #10 early


title: HCVflag_3

value: HCV Jc1E2flag infection

value: 7 days


title: PANC-1 cells, GEM3


title: PANC-1 cells, Ctl3


title: ovarian cells_S027

source_name: ovarian cells_S027


title: HCVflag_2


title: HCVflag_1


title: PR1364_07_a

description: #7 early


title: PR1364_08_a

description: #8 early

value: no


title: ovarian cells_S029

source_name: ovarian cells_S029


title: ovarian cells_S023

source_name: ovarian cells_S023


title: PR1364_06_a

description: #6 early


title: ovarian cells_S026

source_name: ovarian cells_S026


title: ovarian cells_S028

source_name: ovarian cells_S028


title: siClGALT1-2, 2-7

city: Taipei

first: Min-Chuan

last: Huang

address: No. 1, Sec. 1, Ren-Ai RD, Taipei, Taiwan, R.O.C.

department: Graduate Institute of Anatomy and Cell Biology

country: Taiwan

institute: National Taiwan University

description: Gene expression after 72 hours transfection, collected on 2018/2/7

hyb_protocol: Agilent Gene Expression Hybridization Kits was used for hybridization according to the manufacturer’s instruction. Briefly, 16 ul of dye labeled cDNA in water was fragmented at 98°C for 3 mins in a reaction volume of 40 ul containing 4 ul Agilent 10x blocking agenr and 20 ul of Agilent 2xGExHybridization Buffer HI-RPM and hybridized to Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarray (G4851B) at 65°C and rotated at 10 rpm for 17 hours. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (US9230696) using one color scan setting for 8x60k array slides (Scan Area 61x21.6mm, Scan resolution 2um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid:072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: SAS cells siClGALT1-2, 2-7

label_protocol: cDNA prepared from 10μg of total RNA were labeled with aa-dUTP using Invitrogen SuperScriptTM Plus Indirect cDNA Labeling System according to the manufacturer's protocol, followed by aa-cDNA column purification (QIAGEN, Valencia, CA).  Alexa/CyDye was incorporated to aa-cDNA followed by column purification with Alexa/CyDye-cDNA cRNA purification (Qiagen).

growth_protocol: In 10% FBS/DMEM

extract_protocol: RNA was prepared using the Genejet RNA Purification kit (Thermo Scientific) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: SAS

tag: sirna


title: ovarian cells_S024

data_processing:
Checked the quality control of reads data by FastQC
The reads data mapped and quantified as TPM using Salmon
Genome_build: mm10
Supplementary_files_format_and_content: Plain txt file for illumina RNA-seq data, each file contain 5 column, the first column represents gene name, the second column represents the total length of genes, the third column represents the effective legnth of genes, the fourth column represents the TPM of genes and the fifth column represents the number of reads.

source_name: ovarian cells_S024


title: siClGALT1-2, 2-8

description: Gene expression after 72 hours transfection, collected on 2018/2/8

source_name: SAS cells siClGALT1-2, 2-8


title: PR1364_05_a

description: #5 early

source_name: sorted CTL in peripheral blood

tag: phase of allo-hct

value: positive


title: Control_to_HCVflag_1


title: siControl, 2-8

source_name: SAS cells siControl, 2-8

value: siControl


title: siClGALT1-1, 2-7

source_name: SAS cells siClGALT1-1, 2-7


title: siControl, 2-7

source_name: SAS cells siControl, 2-7


title: PR1364_04_a

description: #4 early

tag: donor cmv status


title: PR1364_09_a

description: #9 early

tag: cmv reactivation pattern


title: ovarian cells_S022

source_name: ovarian cells_S022

value: ovary


title: Control_to_HCVflag_2

value: Mock infection


title: HCV10^6ml_1

value: HCV Jc1 infection (TCID50/mL=10^6/mL)

value: 10 days


title: ovarian cells_S025

source_name: ovarian cells_S025


title: Control_to_HCVflag_3


title: PR1364_03_a

description: #3 early

value: early

tag: cells of cmv-ctls


title: ovarian cells_S021

source_name: ovarian cells_S021


title: ovarian cells_S020

source_name: ovarian cells_S020


title: siControl, 2-6

description: Gene expression after 72 hours transfection, collected on 2018/2/6

source_name: SAS cells siControl, 2-6


title: PC3_-R, rep2

city: Hsinchu

first: Sheng-Chieh

last: Hsu

address: No. 101, Section 2, Kuang-Fu Road

department: Institute of Biotechnology

institute: National Tsing Hua University

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) Software.

source_name: PC3 cultured in arginine-free medium for 48 h

label_protocol: standard Affymetrix protocol

growth_protocol: All cells were maintained in RPMI 1640 supplemented with 100 U/ml penicillin/streptomycin and 10% FBS before experiments.

extract_protocol: RNA was extracted with RNAspin Mini RNA Isolation Kit (GE Healthcare, 25-0500-72).

treatment_protocol: On the day of arginine deprivation experiments, culture medium was aspirated, and cells were rinsed with PBS once. Cells were culture in arginine-free RPMI supplied with 10% dialyzed FBS, 100 U/ml penicillin/streptomycin and 10 mM HEPES for indicated durations. For the control group, 200 mg/L L-arginine was added.

value: arginine-free medium for 48 h


title: ovarian cells_S019

source_name: ovarian cells_S019


title: Control_to_HCV10^6ml_2

tag: sample type


title: Control_to_HCV10^6ml_1

tag: exposure with etiological agent


title: siClGALT1-2, 2-6

source_name: SAS cells siClGALT1-2, 2-6


title: HCV10^6ml_3

tag: duration with etiological agent


title: ovarian cells_S018

source_name: ovarian cells_S018


title: ovarian cells_S017

source_name: ovarian cells_S017


title: HCV10^5/ml_3

value: HCV Jc1 infection (TCID50/mL=10^5/mL)

tag: intervention


title: M2-PGE2-rep2

first: Miao

last: Xu

address: 37#,Guoxue alley, Wuhou district

department: Clinical Nutrition

institute: West China hospital of Sichuan university

data_processing:
Illumina novaseq6000 sequencer and software used for sequencing and basecalling.
Sequenced reads were trimmed for adaptor sequence,reads containing ploy-N and low quality reads from raw data, then mapped to reference genome of hg38 using HISTA2. The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach.featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.  Differential expression analysis of two groups were performed using DESeq2.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected.
Genome_build: GRCh38(hg38)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: in vitro induced cells

growth_protocol: THP-1 derived macrophage were routinely generated by incubating THP-1(at 2*10e6/well) with PMA (in growth medium) for 48h.Then remove PMA and repace with growth medium without PMA and rest for 24h, collect cells for M0.

extract_protocol:
After treatment, cells were collected and flash frozen liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For M1 activation, add LPS(100ng/ml) and IFNγ(25ng/ml) to M0 cells.For M2 activation, add IL-4(20ng/ml)and IL-13(20ng/ml)to M0 cells. For PGE2 or MEHP treatment, add PGE2(2μM/ml)or MEHP(200μM）to growth medium with LPS+IFNγ(for M1) or IL-4+IL-13(for M2)during activation.

value: THP-1 derived macrophage

value: Maintained in growth medium with extra lipid mixture (0.25%)and treated with IL-4 20ng/ml+IL-13 20ng/ml

tag: phenotype

value: Alternatively activated(M2)


title: HCV10^5/ml_2

value: Cell (Huh7.5.1dif)

tag: duration of intervention


title: M2-PGE2-rep1

tag: cell type


title: PC3_+R, rep1

source_name: PC3 cultured in control medium for 48 h

value: control medium for 48 h


title: CWR22Rv1, -R+DMKG

source_name: CWR22Rv1 cultured in arginine-free medium with 5 mM DMKG for 48 h


title: PC3_+R, rep2


title: ovarian cells_S015

first: Wenjie

last: Shu

institute: Beijing Institute of Radiation Medicine

source_name: ovarian cells_S015

extract_protocol:
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM ethylenediaminetetracetic acid (EDTA), and 0.01% DNase I and incubated at 37℃ for 10 min with gentle agitation. To stop the digestion, 500 µl HBSS (plus 10% FBS) was added and the cell suspensions were centrifuged at 400g for 5min at 4℃. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS and transferred under the microscope.The collected oocyte were washed twice with 1xPBS and then immediately placed in lysis buffer( Combine 0.2% (vol/vol) Triton X-100 and 2 U µl–1 RNase inhibitor).The lysis solution also contains free dNTPs and tailed oligo-dT oligonucleotides (30-nt poly-dT stretch and a 25-nt universal 5′ anchor sequence) that are prepared of the Reverse Trianscription reaction on polyadenylated RNA sequences.
We used tagmentation to quickly and efficiently construct sequencing libraries from the amplified cDNA. The fragments in the tagmented DNA library have an average size that ranges from 200 to 300 bp and then purified for Illimina. The quantity of the libraries was assessed and defined by qPCR, respectively. All samples were sequenced using HiSeq XTen (Illumina) with paired-end 125-bp sequencing.

tag: strain

tag: tissue


title: ovarian cells_S016

source_name: ovarian cells_S016


title: HCV10^5/ml_1

tag: cell line


title: PC3_-R, rep1


title: M2-MEHP-rep3

value: Maintained in growth medium with extra lipid mixture (0.25%) and treated with LPS 100ng/ml+IFNγ 25ng/ml


title: PR1364_01_a

description: #1 early

source_name: sorted CTL in peripheral blood

value: no


title: CWR22Rv1, -R48h

source_name: CWR22Rv1 cultured in arginine-free medium for 48 h


title: HCV10^4/ml_3

value: HCV Jc1 infection (TCID50/mL=10^4/mL)


title: CWR22Rv1, +R

source_name: CWR22Rv1 cultured in control medium for 48 h


title: siClGALT1-1, 2-6

source_name: SAS cells siClGALT1-1, 2-6

value: SAS


title: [RNA-seq] B. anthracis 34F2 ΔxrrC #3

city: Sapporo

first: Yoshikazu

last: Furuta

state: Hokkaido

address: North 20 West 10, Kita-ku

department: International Institute for Zoonosis Control

institute: Hokkaido University

data_processing:
[ChIP-seq] Sequence reads were applied for adapter trimming and quality filtering using Trim Galore! version 0.6.4_dev with the option "-a GATCGGAAGAGCACACGT", followed by mapping to the genome sequence of B. anthracis Ames ancestor strain (RefSeq assembly accession no. GCF_000008445.1 with manual modification for sequence difference in xrrC) using BWA-mem 0.7.17. The mapping data was applied for R package csaw 1.22.1 with 158 bp of fragment length and 50 bp of window width.
[Cappable-seq] For the analysis of sequence reads, adapter sequence was removed using cutadapt 2.1 with the option "-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", followed by mapping to the genome sequence of B. anthracis Ames ancestor (RefSeq assembly accession no. GCF_000008445.1 with manual modification for sequence difference in xrrC) using Bowtie2 2.3.5 with the option "-L 16". Coverage of the first base of mapped reads was calculated for each position with considering strands.
[3´-RACE] Reads were mapped to B. anthracis Ames ancestor (RefSeq assembly accession no. GCF_000008445.1 with manual modification for sequence difference in xrrC) using BWA-backtrack 0.7.17.
[RNA-seq] Reads were trimmed using Trim Galore! 0.6.4_dev with the option "-a AGATCGGAAGAGA", mapped to B. anthracis Ames ancestor (RefSeq assembly accession no. GCF_000008445.1 with manual modification for sequence difference in xrrC) using BWA-mem 0.7.17, and tag counted with htseq-count.

organism: Bacillus anthracis

source_name: B. anthracis 34F2 ΔxrrC

growth_protocol: A colony of the strain grew on BHI plate at 37°C for overnight was inoculated into NBY medium supplemented with 8% NaHCO3, followed by shaking at 37°C under 15% CO2 for 3 h. 100-fold diluted in NBY medium supplemented with NaHCO3 and cultured at 37°C under 15% CO2 for 3 h.

extract_protocol:
[ChIP-seq] Cells were pelleted and treated with 1% formaldehyde for for crosslinking. 250 mM glycine was added for quenching. After pelleting and resuspension in lysis buffer with cOmplete Mini Protease Inhibitor Cocktail, the samples were sonicated using Covaris S2. Supernatants were combined with Anti-FLAG M2 affinity gel for enrichment, followed by wash and protease K treatment at 65°C. [Cappable-seq] RNA was extracted using TRIzol after incubating the pellet with 2% SDS. After removing DNA with DNA-free DNA removal kit, RNA samples followed the protocol described before (Ettwiller et al, BMC Genomics 17:199, 2016) [3´-RACE] RNA was extracted using TRIzol after incubating the pellet with 2% SDS. DNA was removed with DNA-free DNA removal kit. [RNA-seq] RNA was extracted using TRIzol after incubating the pellet with 2% SDS. DNA was removed with DNA-free DNA removal kit. rRNA was depleted by the protocol described before (Culviner et al, mBio, 2020), followed by fragmentation with the treatment with a divalent cation and heat.
[ChIP-seq] Library was constructed with NEBNext Ultra II DNA Library Prep Kit for Illumina. [Cappable-seq, 3´-RACE, and RNA-seq] Library was constructed with NEBNext Multiplex Small RNA Library Prep Set for Illumina.

tag: genotype

value: B. anthracis 34F2 {delta}xrrC


title: ovarian cells_S014

city: Beijing

address: Taiping Road 27

source_name: ovarian cells_S014

value: ovary

tag: age


title: M2-MEHP-rep2

tag: treatment


title: [RNA-seq] B. anthracis 34F2 ΔxrrC #2


title: [RNA-seq] B. anthracis 34F2 ΔxrrC #1


title: CWR22Rv1, -R24h

source_name: CWR22Rv1 cultured in arginine-free medium for 24 h

value: arginine-free medium for 24 h


title: CWR22Rv1, -R


title: M2-MEHP-rep1


title: HCV10^4/ml_1

first: Yujin

last: Hoshida

institute: University of Texas Southwestern Medical Center

extract_protocol: RNA was isolated using RNeasy kit (Qiagen) according to manufacturer’s protocol.


title: ovarian cells_S012

source_name: ovarian cells_S012


title: HCV10^3/ml_3

value: HCV Jc1 infection (TCID50/mL=10^3/mL)


title: M2-CT-rep3

value: Maintained in growth medium with extra lipid mixture (0.25%)


title: ovarian cells_S011

source_name: ovarian cells_S011


title: M2-CT-rep1


title: ovarian cells_S010

source_name: ovarian cells_S010


title: HCV10^3/ml_2

value: 10 days


title: M2-CT-rep2


title: [RNA-seq] B. anthracis 34F2 ΔxrrB #2

source_name: B. anthracis 34F2 ΔxrrB

value: B. anthracis 34F2 {delta}xrrB


title: CWR22Rv1, -R0h

source_name: CWR22Rv1 cultured in control medium for 24 h

value: control medium for 24 h


title: M1-PGE2-rep3

source_name: in vitro induced cells

value: THP-1 derived macrophage

value: Maintained in normal growth medium and treated with IL-4 20ng/ml+IL-13 20ng/ml

value: Classically activated (M1)


title: [RNA-seq] B. anthracis 34F2 ΔxrrA #3

source_name: B. anthracis 34F2 ΔxrrA

value: B. anthracis 34F2 {delta}xrrA


title: ovarian cells_S013

source_name: ovarian cells_S013


title: [RNA-seq] B. anthracis 34F2 ΔxrrB #1


title: ovarian cells_S009

source_name: ovarian cells_S009


title: M1-PGE2-rep2


title: M1-PGE2-rep1


title: HCV10^3/ml_1

value: Cell (Huh7.5.1dif)


title: HCV10^4/ml_2


title: [RNA-seq] B. anthracis 34F2 ΔxrrA #2


title: Control_to_HCV10^3-5/ml_3

value: Mock infection


title: [RNA-seq] B. anthracis 34F2 ΔxrrB #3


title: Control_to_HCV10^3-5/ml_1


title: Control_to_HCV10^3-5/ml_2


title: ovarian cells_S006

source_name: ovarian cells_S006


title: M1-MEHP-rep3

value: Maintained in normal growth medium and treated with LPS 100ng/ml+IFNγ 25ng/ml


title: HT22-OGD-6h-rep2

city: Luzhou city

first: Qiancheng

last: Mu

state: Sichuan Province

address: Taiping Street, 25

department: Department of Neurosurgery

institute: the Affiliated Hospital of Southwest Medical University

data_processing:
Illumina Casava software used for basecalling.
In order to ensure the quality of information analysis, raw reads must be filtered to obtain clean reads, and subsequent analysis is based on clean reads.In addition, we used Hisat to perform sequence alignment analysis using reference sequences.If the reference genome is properly selected and the relevant experiment is free of contamination, the percentage of localization of the sequence produced by the experiment is normally higher than 70%.
In order to make the estimated gene expression levels of different genes and different experiments comparable, and to consider the influence of sequencing depth and gene length on reads count, we used FPKM method, which is the most commonly used method for estimating gene expression levels at present
Genome_build: mm39
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: mouse hippocampal neuron

extract_protocol:
Total RNA was extracted from OGD-treated cells and control cells by using the RNeasy kit (TIANGEN, China).
Libraries were prepared according to VAHTS® Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, NR604-01/02, China).

value: mouse hippocampal neuron

value: Oxygen-glucose deprivation for 6 hours


title: [RNA-seq] B. anthracis 34F2 ΔatxA #3

source_name: B. anthracis 34F2 ΔatxA

value: B. anthracis 34F2 {delta}atxA


title: HT22-OGD-6h-rep1


title: M1-MEHP-rep2


title: HT22-OGD-3h-rep2

value: Oxygen-glucose deprivation for 3 hours


title: ovarian cells_S005

source_name: ovarian cells_S005

value: ovary


title: [RNA-seq] B. anthracis 34F2 ΔatxA #2


title: M1-MEHP-rep1


title: ovarian cells_S003

source_name: ovarian cells_S003


title: [RNA-seq] B. anthracis 34F2 ΔatxA #1


title: ovarian cells_S008

source_name: ovarian cells_S008


title: HT22-OGD-3h-rep1


title: ovarian cells_S007

source_name: ovarian cells_S007


title: M1-CT-rep3

value: maintained in normal growth medium without treatment.


title: M1-CT-rep2


title: ovarian cells_S004

source_name: ovarian cells_S004


title: [RNA-seq] B. anthracis 34F2 WT #2

source_name: B. anthracis 34F2 WT

value: B. anthracis 34F2 WT


title: [RNA-seq] B. anthracis 34F2 WT #3


title: HT22-OGD-control-rep2

value: untreated


title: ovarian cells_S002

source_name: ovarian cells_S002


title: ovarian cells_S001

source_name: ovarian cells_S001


title: M1-CT-rep1


title: HT22-OGD-control-rep1


title: [RNA-seq] B. anthracis 34F2 WT #1


title: PR1364_02_a

description: #2 early

source_name: sorted CTL in peripheral blood

tag: phase of allo-hct

value: early

value: positive

value: no


title: r2c645

status: Public on Jun 27 2021

city: Nice

first: Andreas

last: Schedl

address: Parc Valrose

department: iBV

country: France

institute: University of Nice

data_processing: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis was performed using the DESeq R package (1.18.0). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value < 0.05 found by DESeq were assigned as differentially expressed.

source_name: Male control

extract_protocol:
Adrenal glands were frozen upon extraction. Total RNA was purified using the Rneasy mini kit (Qiagen) according to manufacturer's instructions. The sample’s quality was assessed using a Bioanalyzer 2100 (Agilent technologies) and a RIN cut-off value of 7.0 was applied.
Library preparation and sequencing, as well as differential expression analysis were conducted by Novogene Co. Briefly, library preparation was conducted using a NEBNext Ultra RNA Library Prep kit for Illumina (NEB). After cluster generation, the library preparations were sequenced on an Illumina platform and 150 bp paired-end reads were generated.

value: adrenal gland

value: control

tag: Sex

value: Male

value: 4 weeks

value: mixed genetic background


title: r2c641

source_name: Male Rspo1 GOF

value: Rspo1 GOF


title: r2c560


title: r2c581

source_name: Female Rspo1 GOF

value: Female


title: r2c553


title: r2c646


title: r2c582

source_name: Female control


title: r2c622


title: r2c554


title: r2c551


title: r2c579


title: M2-PGE2-rep3

source_name: in vitro induced cells

value: THP-1 derived macrophage

value: Maintained in growth medium with extra lipid mixture (0.25%)and treated with IL-4 20ng/ml+IL-13 20ng/ml

value: Alternatively activated(M2)


title: r2c556


title: [RNA-seq] B. anthracis 34F2 ΔxrrA #1

source_name: B. anthracis 34F2 ΔxrrA

value: B. anthracis 34F2 {delta}xrrA


title: r2c583


title: r2c584


title: r2c555


title: Bap1KO-WT-RA-rep2

city: Milan

first: Federico

last: Rossi

address: Via Adamello 16

country: Italy

institute: Istituto Europeo Oncologia

data_processing:
For ChIP-seq data, paired-end DNA reads were processed through fastp to trim adapters and to remove low quality nucleotides at read ends (Chen et al., 2018). Quality-filtered DNA reads were aligned to the mouse reference genome mm10, or mm10 and fly reference genome (dm6) for histone ChIP-Rx using Bowtie v1.2.2 retaining only uniquely aligned reads (-m 1) and using the parameters -I 10, -X 1000 (Langmead et al., 2009). Reads mapped to both mm10 and dm6 were discarded. Peaks were identified using MACS2 v2.1.1 in narrow mode with parameters –format BAMPE –keep-dup all -m 3 30 and p-value 1e-10 (Zhang et al., 2008). Peaks were annotated using the R package ChIPpeakAnno v3.15 using for each peak the 5 kbp region around the center of the peak  (Zhu et al., 2010).
For RNA-seq, reads were aligned to the mouse reference genome mm10 using STAR v2.7 without allowing for multimapping. PCR duplicates were removed using samblaster (Faust and Hall, 2014). Mapped reads were assigned to genes using featureCounts (Liao et al., 2014) with unstranded read counting on exons and using the gene name as attribute type in the annotation. Genes were annotated as in Gencode M21 (GRCm38) downloaded from https://www.genecodegenes.org/mouse/. Differentially expressed genes were identified using the R package DESeq2 v1.24 using default parameters (Love et al., 2014). The fold change of lowly expressed genes was corrected using the lfcShrink function of the apeglm R package with the type option set to apeglm v1.6 (Zhu et al., 2019). The adjusted p-value was corrected by the independent hypothesis weighting (IHW) method as implemented in the R package IHW v1.12 (Ignatiadis et al., 2016). Genes were considered differentially expressed when presenting an absolute log2 fold change equal or greater than 1.5 and an adjusted p-value lower than 0.05.
For HiC data, DNA reads were filtered for low-quality bases and adapters using fastp (Chen et al., 2018). Filtered DNA reads were processed through the HiCpro pipeline to obtain contact matrices reporting the chromatin interactions at the genome-wide level (Servant et al., 2015). Using default settings, DNA reads were aligned to the mouse reference genome mm10 using bowtie2 in end-to-end mode, uniquely aligned DNA reads were assigned to the DpnII genomic restriction fragments, valid interactions were identified and used to generate interaction matrices. The HiCpro matrices containing all of the valid pairs were converted in hic format using the hicpro2juicebox function (Robinson et al., 2018), and in cool format using the hic2cool function (https://github.com/4dn-dcic/hic2cool). Contact matrices in cool format where corrected using the ICE algorithm as implemented in the hicCorrectMatrix function (Wolff et al., 2020). Plots of the interactions occurring at single locus or whole-chromosome level were obtained by HiCplotter (Akdemir and Chin, 2015). Hi-C was performed in duplicate with key findings being overserved in each before pooling replicates to make the final high-depth analyses.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bed (MACS2), counts (counts.tsv), differential expression (DESeq2), validpairs (HiCPro).

source_name: Mouse Embryonic Stem Cells

growth_protocol: mESCs (both E14 and TCF background) were grown on 0.1% gelatin-coated dishes in 2i/LIF-containing GMEM medium (Euroclone) supplemented with 20% fetal calf serum (Euroclone), 2 mM glutamine (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Gibco), 0.1 mM non-essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), 50 µM ß-mercaptoethanol phosphate buffered saline (PBS; Gibco), 1000 U/ml leukemia inhibitory factor (LIF; produced in-house), and GSK3β and MEK 1/2 inhibitors (ABCR GmbH) to a final concentration of 3 μM and 1 μM, respectively. For ATRA stimulation of ESCs, cells were washed twice with PBS 24 hours after seeding and media was replaced with ESC media lacking LIF, GSK3β and MEK1/2 inhibitors, and instead supplemented with 1μM ATRA for 24 hours.

extract_protocol:
ChIP-seq: DNA was purified with QIAquick PCR purification kit (Qiagen) according to manufacturer’s instructions.
DNA was purified with QIAquick PCR purification kit (Qiagen) according to manufacturer’s instructions. DNA libraries were prepared with 2–10 ng of DNA using an in-house protocol (Blecher-Gonen et al., 2013) by the IEO genomic facility and sequenced on an Illumina HiSeq 2000.
RNA-seq: RNA-seq was performed following SMART-seq2 protocol (Picelli et al., 2014)  with minor modifications. Briefly, poly-A containing mRNA molecules obtained from 1 μg of total RNA were copied into first-strand cDNA by reverse transcription and template-switching using oligo (dT) primers and an LNA-containing template-switching oligo (TSO). Resulting cDNA was pre-amplified with KAPA HotStart Taq enzyme (Kapa Biosystems) and then purified with Ampure beads (Agencourt AMPure XP- Beckman Coulter). One nanogram of pre-amplified cDNA was tagmented with in-house produced Tn5 transposase and further amplified with KAPA HotStart Taq enzyme. After purification with Ampure beads, the quality of the obtained library was assessed by Bioanalyzer (High Sensitivity DNA kit, Agilent Technologies), prior to sequencing. Each RNA-seq experiment was performed in triplicate.
Hi-C: In situ Hi-C was performed as described (Rao et al., 2014) with slight alterations to the protocol. 5x10^6 ESCs were crosslinked for 10 minutes in 1% formaldehyde before quenching in 125mM Glycine for 5 minutes. Cell pellets were washed twice in PBS before contact generation. Pellet was resuspended in 500uL Hi-C lysis buffer (10mM Tris-HCl pH8.0, 10mM NaCl, 0.2% NP40 and protease inhibitors) and incubated with rotation for 30 minutes at 4°C. Cells were pelleted and washed in 500uL Hi-C lysis buffer. Pellet was resuspended in 100uL 0.5% SDS and incubated for 10 minutes at 62°C. 285uL of H20 and 50uL of 10% Triton X-100 was added to quench the SDS at 37°C for 15 minutes. 50uL of 10xNEB DpnII buffer and 750U of DpnII were added (NEB R0453M) then incubated at 37°C overnight with shaking. Digestion was heat inactivated the next day for 20 minutes at 62°C. Biotin fill in was performed by addition of 52uL fill-in mix (0.288mM dCTP/dTTP/dGTP, 50U DNA Polymerase I, Large Klenow fragment (NEB M0210) and 0.288mM biotin-dATP (Thermo 19524016)). Fill-in reaction was incubated at 37°C for 1 hour with shaking. Ligation was performed by adding 150uL 10x NEB T4 DNA ligase buffer, 125uL 10% Triton X-100, 3uL 50mg/mL BSA and 8000U of T4 DNA ligase and H20 up to 1.5mL. Ligation was performed overnight at 25°C with shaking. Nuclei were pelleted before resuspending in IP buffer (33 mM Tris-HCl pH 8, 100 mM NaCl, 5 mM EDTA, 0.2% NaN3, 0.33% SDS, 1.66% Triton X-100) and sonicating to fragment size between 200-1000bp. 15uL of the sample was de-crosslinked overnight at 65°C with 85ul of decrosslinking buffer (0.1M NaHCO3, 1% SDS) before clean up using QiaQuick PCR clean up kit from Qiagen.
Library prep was performed as described (Mumbach et al., 2016). Streptavidin C-1 beads (Thermo 65001) were washed and resuspended in 2x biotin binding buffer (10mM Tris-HCl pH7.5, 1mM EDTA, 2M NaCl). 10ng of DNA was used for biotin capture, streptavidin C-1 beads were added and incubated for 15 minutes at room temperature with shaking. Beads were washed twice at 55°C for 2 minutes in Tween wash buffer (5mM Tris-HCl pH7.5, 0.5mM EDTA, 1M NaCl, 0.05% Tween). Beads were washed once in 1xTD buffer (20mM Tris-HCl pH7.5, 10mM MgCl2, 20% DMF) before being tagmented with in-house produced Tn5 transposase in TD buffer for 55°C for 10 minutes. TN5 was quenched in 50mM EDTA for 30 minutes at 55°C before washing twice in 50mM EDTA, twice in Tween wash buffer and once in 10mM Tris. PCR amplification was carried out on beads using KAPA HotStart Taq enzyme. After purification of PCR product with Ampure beads, the quality of the obtained library was assessed by Bioanalyzer (High Sensitivity DNA kit, Agilent Technologies), prior to sequencing.

treatment_protocol: To generate stable KO cell lines, 10ug pX458 2.0 plasmid pairs (Addgene) encoding Cas9 and sgRNAs (Table S3) were transfected using Lipofectamine 2000 (Invitrogen), according to manufacturer’s instruction. Sorting of GFP positive cells was carried out 48 hours after transfection and 1000 cells were seeded onto a 15-cm dish. Clones were isolated 10-14 days later and grown further before screening for knockout by Western blot. For rescue clone generation, mESCs were transfected with 10ug pCAG vectors encoding 2xFlag-HA-tagged BAP1 wild-type or BAP1 C91S using Lipofectamine 2000 (ThermoFisher Scientific), according to manufacturer’s instructions. 24 hours post-transfection puromycin selection (1µg/ml) was added for a further 24 hours. Cells were then split to clonal density (~1:40) onto a 15cm plate. Clones were isolated 10-14 days later and grown further before screening for rescue allele expression by Western blot.

value: Mouse embryonic stem cells


title: r2c549


title: WT-EV-HiC

value: WT-EV-HiC


title: Bap1KO-EV-DMSO-rep3


title: Bap1KO-EV-DMSO-rep1


title: Bap1KO-C91S-RA-rep1


title: Bap1KO-WT-RA-rep1


title: Bap1KO-C91S-DMSO-rep2


title: Bap1KO-C91S-DMSO-rep3


title: Bap1KO-EV-RA-rep3


title: Bap1KO-EV-RA-rep2


title: WT-EV-DMSO-rep1

value: WT-EV-DMSO


title: Bap1KO-C91S-RA-rep3


title: WT-EV-RA-rep2

value: WT-EV-RA


title: Bap1KO-WT-DMSO-rep2


title: Bap1KO-WT-DMSO-rep3


title: Bap1KO-C91S-DMSO-rep1


title: Bap1KO-WT-DMSO-rep1


title: Bap1KO-EV-HiC


title: Bap1KO-EV-RA-rep1


title: WT-EV-DMSO-rep2


title: WT-EV-RA-rep1


title: WT-EV-DMSO-rep3


title: Bap1KO-C91S-RA-rep2


title: Bap1KO-EV-DMSO-rep2


title: Bap1KO-EV-S2-210315

description: Input

tag: chip antibody


title: WT-EV-S2-210315

description: Input


title: PclKO-Input-S2

description: Input


title: TcfKO-Input-S2

description: Input


title: Bap1KO-WT-S2-210315

description: Input


title: TcfBap1KO-Input-S2

description: Input


title: Bap1KO-C91S-S2-210315

description: Input


title: WT-EV-SUZ12-rep2


title: WT-EV-RYBP-rep2

value: RYBP

value: WT-EV-RYBP


title: WT-EV-RING1B-rep1


title: WT-EV-RYBP-rep1


title: WT-EV-RA-rep3


title: WT-EV-RING1B-rep2


title: Bap1KO-WT-RA-rep3


title: PclBap1KO-Input-S2

description: Input


title: WT-EV-H3K36me2-rep2


title: WT-EV-H3K27me3-rep2


title: WT-EV-CBX7-rep2


title: WT-EV-H3K36me2-rep1


title: WT-EV-H2AK119Ub1-rep2


title: WT-EV-CBX7-rep1


title: TcfKO-H2AK119Ub1


title: PclKO-H3K27me3


title: TcfBap1KO-H2AK119Ub1


title: PclKO-H2AK119Ub1


title: PclBap1KO-H3K27me3


title: Bap1KO-WT-SUZ12-rep2


title: PclBap1KO-H2AK119Ub1


title: Bap1KO-WT-RYBP-rep2


title: Bap1KO-WT-RING1B-rep2


title: Bap1KO-WT-RING1B-rep1


title: Bap1KO-WT-H3K36me2-rep2


title: Bap1KO-WT-RYBP-rep1


title: Bap1KO-WT-H3K36me2-rep1


title: Bap1KO-WT-CBX7-rep2


title: Bap1KO-WT-H2AK119Ub1-rep2


title: Bap1KO-WT-H3K27me3-rep2


title: Bap1KO-EV-RING1B-rep1


title: Bap1KO-EV-RYBP-rep2


title: Bap1KO-EV-RING1B-rep2


title: TcfKO-H3K27me3


title: Bap1KO-EV-RYBP-rep1


title: TcfBap1KO-H3K27me3


title: Bap1KO-EV-H3K36me2-rep2


title: Bap1KO-EV-H3K27me3-rep2


title: Bap1KO-EV-CBX7-rep2


title: Bap1KO-EV-CBX7-rep1


title: Bap1KO-EV-H3K36me2-rep1


title: Bap1KO-C91S-RYBP-rep2


title: Bap1KO-C91S-RING1B-rep2


title: Bap1KO-C91S-SUZ12-rep2


title: Bap1KO-C91S-RING1B-rep1


title: Bap1KO-C91S-H3K36me2-rep2


title: Bap1KO-C91S-H3K36me2-rep1


title: Bap1KO-WT-CBX7-rep1


title: Bap1KO-C91S-H3K27me3-rep2


title: Bap1KO-EV-SUZ12-rep2


title: Bap1KO-C91S-H2AK119Ub1-rep2


title: Bap1KO-C91S-CBX7-rep2


title: WT-rep1

data_processing:
Alignment; STAR v2.7; --outSAMattributes Standard --outFilterMultimapNmax 1
Feature-counting; featureCounts; -s 0 -t exon -g gene_name
Differential Gene Expression Analysis; DESeq2 v1.24; default parameters
mm10
WT-rep1.rpkm: Gene Expression Analysis (RPKM); WT-rep2.rpkm: Gene Expression Analysis (RPKM); BAP1-KO-clone1-rep1.rpkm: Gene Expression Analysis (RPKM); BAP1-KO-clone2-rep1.rpkm: Gene Expession Analysis (RPKM); BAP1-KO-clone2-rep2.rpkm: Gene Expression Analysis (RPKM); BAP1-KO-clone1-vs-WT_diffexp_log2fc1.5_pval0.05.tsv: Differential Expression Analysis; BAP1-KO-clone1-vs-WT_diffexp_log2fc1.5_pval0.05.tsv: Differential Expression Analysis

source_name: mESC

growth_protocol: mESCs were grown on 0.1% gelatin-coated dishes in 2i/LIF-containing GMEM medium (Euroclone) supplemented with 20% fetal calf serum (Euroclone), 2 mM glutamine (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Gibco), 0.1 mM non-essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), 50 µM ß-mercaptoethanol phosphate buffered saline (PBS; Gibco), 1000 U/ml leukemia inhibitory factor (LIF; produced in-house), and GSK3β and MEK 1/2 inhibitors (ABCR GmbH) to a final concentration of 3 mM and 1 mM, respectively.

extract_protocol:
Total RNA was extracted with the Quick-RNA™ MiniPrep extraction kit (Zymo Research) and retro-transcribed with ImProm-II™ Reverse Transcription System (Promega) according to the manufacturer’s instructions
RNA-seq was performed following SMART-seq2 protocol (Picelli et al., 2014)

treatment_protocol: Indicated cells were treated for 48 hours with 500nM dTAG-13 (TOCRIS), or DMSO as vehicle, in order to degrade dTAG-BAP1. To generate stable KO cell lines, 10ug pX458 2.0 plasmid pairs (Addgene) encoding Cas9 and sgRNAs were transfected using Lipofectamine 2000 (Invitrogen), according to manufacturer’s instruction. Sorting of GFP positive cells was carried out 48 hours after transfection and 1000 cells were seeded onto a 15-cm dish. Clones were isolated 10-14 days later and grown further before screening for knockout by Western blot. For rescue clone generation, mESCs were transfected with 10ug pCAG vectors encoding 2xFlag-HA-tagged BAP1 wild-type or BAP1 C91S using Lipofectamine 2000 (ThermoFisher Scientific), according to manufacturer’s instructions. 24 hours post-transfection puromycin selection (1µg/ml) was added for a further 24 hours. Cells were then split to clonal density (~1:40) onto a 15cm plate. Clones were isolated 10-14 days later and grown further before screening for rescue allele expression by Western blot.


title: BAP1-KO-clone2-rep2


title: WT-rep2


title: BAP1-KO-plus-EV-HiC

data_processing:
Alignment - detection of pairs - filtering of valid pairs; HiCpro v2.11.4
mm10
.allValidPairs; interaction matrices generated by the HiCpro pipeline

extract_protocol:
Genomic DNA extraction for the HiC was performed as described in Rao et al., 2014.
Library preparation was performed as described in Mumbach et al., 2016.


title: BAP1-KO-clone2-FOXK2

data_processing:
Alignment; bowtie v1.2.2; --chunkmbs 1024 -m 1 --best -S --no-unal -q -I 10 -X 1000
Peak calling; MACS2 v2.1.1 narrow mode; –format BAMPE –keep-dup all -m 3 30 pvalue 1e-10
mm10
bed file format; narrow peaks called with MACS2 having a -log10 p-value higher than 10

extract_protocol:
ChIP experiments were performed according to standard protocols as described previously (Ferrari et al., 2014)
DNA libraries were prepared with 2–10 ng of DNA using an in-house protocol (Blecher-Gonen et al., 2013) by the IEO genomic facility


title: BAP1-KO-clone2-rep1


title: Bap1KO-C91S-CBX7-rep1


title: BAP1-KO-clone2-HCFC1


title: BAP1-KO-clone1-rep2


title: BAP1-KO-clone1-rep1


title: WT-plus-EV-HiC

value: WT-plus-EV-HiC


title: WT-FOXK2


title: BAP1-KO-clone1-FOXK2


title: BAP1-KO-clone1-HCFC1


title: WT-HCFC1


title: Eµ-TCL1;CXCR4C1013G bone marrow B cells #2

city: Berlin

first: Matthias

last: Wirth

address: Hindenburgdamm 30

country: Germany

institute: Charité Berlin

data_processing:
RNA-Seq reads were aligned to the reference index with Salmon (Release 0.8.1), salmon's estimate of the number of reads mapping to each transcript that was quantified.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: B cells

extract_protocol:
B cells from spleen and bone marrow of WT, CXCR4C1013G, Eµ-TCL1, and Eµ-TCL1;CXCR4C1013G were isolated with CD19 directed magnetic beads (Miltenyi Biotec, Bergisch Gladbach, Germany). Only RNA samples with an RNA integrity number (RIN) > 7 were used for RNA-sequencing. RIN was determined using Agilent RNA 6000 Nano Kit (# 5067-1513, Agilent, Santa Clara, CA) and the Agilent 2100 Expert software (version B.02.10.SI764). Library preparation and single-end sequencing was subsequently performed by Novogene (UK) (Cambridge, United Kingdom) on a HiSeq2500 (Illumina, San Diego, CA) with a sequencing depth of more than 20 M reads/sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD19-enriched bone marrow B cells

tag: age group

value: 6 week old age-matched


title: BAP1-KO-clone1-PCGF2

tag: sample type


title: Eµ-TCL1;CXCR4C1013G splenic B cells #4

value: CD19-enriched splenic B cells


title: Eµ-TCL1;CXCR4C1013G bone marrow B cells #3


title: BAP1-KO-clone1-JARID2


title: Eµ-TCL1;CXCR4C1013G splenic B cells #2


title: Eµ-TCL1;CXCR4C1013G splenic B cells #5


title: WT-PCGF2


title: Eµ-TCL1;CXCR4C1013G bone marrow B cells #1


title: Eµ-TCL1;CXCR4C1013G splenic B cells #3


title: BAP1-KO-plus-EV-SUZ12


title: BAP1-KO-plus-WT-SUZ12


title: BAP1-KO-plus-C91S-SUZ12


title: WT-plus-EV-SUZ12


title: Eµ-TCL1;CXCR4C1013G splenic B cells #1


title: WT-SUZ12


title: BAP1-KO-clone2-SUZ12


title: WT-JARID2


title: Eµ-TCL1 bone marrow B cells #4


title: Eµ-TCL1;CXCR4C1013G bone marrow B cells #5


title: BAP1-KO-clone1-SUZ12


title: Eµ-TCL1 bone marrow B cells #3


title: Eµ-TCL1;CXCR4C1013G bone marrow B cells #4


title: Eµ-TCL1 bone marrow B cells #2


title: pCAG-BAP1-EV


title: Eµ-TCL1 splenic B cells #3


title: pCAG-BAP1-HA


title: Eµ-TCL1 splenic B cells #1


title: WT-plus-EV-RING1B


title: PCGF3/5/BAP1-KO-RING1B


title: Eµ-TCL1 splenic B cells #5


title: BAP1-KO-plus-C91S-RING1B


title: CXCR4C1013G bone marrow B cells #4


title: Eµ-TCL1 splenic B cells #4


title: CXCR4C1013G bone marrow B cells #3


title: BAP1-KO-plus-WT-RING1B


title: Eµ-TCL1 bone marrow B cells #5


title: Eµ-TCL1 splenic B cells #2


title: CXCR4C1013G bone marrow B cells #5


title: BAP1-KO-plus-EV-RING1B


title: CXCR4C1013G bone marrow B cells #2


title: Eµ-TCL1 bone marrow B cells #1


title: BAP1-KO-clone2-RING1B


title: PCGF3/5-KO-RING1B


title: WT-RING1B


title: CXCR4C1013G splenic B cells #5


title: CXCR4C1013G bone marrow B cells #1


title: CXCR4C1013G splenic B cells #4


title: BAP1-KO-clone1-RING1B


title: CXCR4C1013G splenic B cells #3


title: CXCR4C1013G splenic B cells #2


title: AEBP2/JARID2/BAP1-KO-H3K27me3


title: AEBP2/JARID2-KO-H3K27me3


title: WT bone marrow B cells #4

value: WT


title: AEBP2/JARID2/BAP1-KO-H2AK119ub1


title: AEBP2/JARID2/BAP1-KO-input

description: Low-depth sequenced genomic DNA input for the normalisation of AEBP2/JARID2/BAP1-KO samples

value: Input


title: CXCR4C1013G splenic B cells #1


title: WT bone marrow B cells #5


title: PCGF3/5-KO-H3K27me3


title: AEBP2/JARID2-KO-input

description: Low-depth sequenced genomic DNA input for the normalisation of AEBP2/JARID2-KO samples


title: PCGF3/5/BAP1-KO-H3K27me3


title: WT bone marrow B cells #3


title: PCGF3/5/BAP1-KO-H2AK119ub1


title: WT bone marrow B cells #2


title: WT splenic B cells #3


title: PCGF3/5-KO-H2AK119ub1


title: WT splenic B cells #4


title: WT bone marrow B cells #1


title: WT splenic B cells #5


title: PCGF1/2/4/6/BAP1-KO-H2AK119ub1


title: PCGF3/5-KO-input

description: Low-depth sequenced genomic DNA input for the normalisation of PCGF3/5-KO samples


title: PCGF3/5/BAP1-KO-input

description: Low-depth sequenced genomic DNA input for the normalisation of PCGF3/5/BAP1-KO samples


title: WT splenic B cells #2


title: WT splenic B cells #1


title: PCGF1/2/4/6-BAP1-KO-H3K27me3


title: PCGF1/2/4/6-KO-H3K27me3


title: PCGF1/2/4/6-KO-H2AK119ub1


title: Female XX genotype subject 180 thoracic aorta

city: Lexington

first: Eric

middle: M

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

data_processing:
Illumina Casava (v 1.8) was used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR (v 2.6.1) in Partek Flow (v 8.0)
Counts were normalized to abundance measures with the TMM algorithm in WebMev
Genes annotated as protein-coding that had at least two samples with TMM measures > 1.5 were retained for statisitcal analysis
Statistical analysis was done using LIMMA in WebMev to perform pairwise comparison among groups to generate p-values, q-values, and log 2 fold-changes
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with TMM abundance measures for every gene and every sample annotated to mm10

source_name: thoracic aorta

extract_protocol:
RNA was extracted from the thoracic aorta (defined as the segment extending from the aortic root to the diaphragm) and abdominal aorta (defined as the segment extending from the diaphragm to the iliac bifurcation) using a Maxwell Rapid Sample Concentrator (RSC) simply RNA Tissue kit (REF#AS1340, Promega, Madison, WI).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Female C57BL/6J Ldlr-/- mice at 14-18 wks of age (n = 5 XX genotype, n =5 X0 genotype) were fed a Western (high fat- TD88137, Envigo) diet for 1 wk

tag: genetic deficiency

value: Ldlr-/-

value: female

value: XX

tag: rin


title: AEBP2/JARID2-KO-H2AK119ub1


title: Female XX genotype subject 171 thoracic aorta


title: PCGF1/2/4/6/BAP1-KO-input

description: Low-depth sequenced genomic DNA input for the normalisation of PCGF1/2/4/6/BAP1-KO samples


title: Female XX genotype subject 166 thoracic aorta


title: BAP1-KO-plus-C91S-H3K27me3


title: Female XX genotype subject 163 thoracic aorta


title: BAP1-KO-plus-EV-H3K27me3


title: Female XX genotype subject 173 abdominal aorta

source_name: abdominal aorta


title: Female XX genotype subject 180 abdominal aorta


title: BAP1-KO-plus-C91S-H2AK119ub1


title: Female XX genotype subject 171 abdominal aorta


title: BAP1-KO-plus-WT-H2AK119ub1


title: Female XO genotype subject 175 thoracic aorta

value: XO


title: LAPC4-CR

city: Seattle

first: Michael

middle: Christoph

last: Haffner

state: WA

address: 1100 Fairview Avenue

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

data_processing:
Colorspace alignment: BioScope v1.3 was used to carry out colorspace alignments using the whole transcriptome workflow in Bioscope using default parameters
Expression counts: Gene expression read counts were derived using HTSeq.count and the hg18 refseq gtf file
Normalized gene abundance measure: Gene expression read counts were normalized to library size and gene length to derive FPKM values for each gene and sample using a custom python script
Genome_build: hg18
Supplementary_files_format_and_content: text files with raw counts, and normalized FPKM values as described in Processed data files below

source_name: prostate cancer cell line

growth_protocol: RPMI supplemented with 10% charcoal-stripped FBS and 1XB27

extract_protocol:
Rneasy, Qiagen
SOLID Total RNA-Seq kit, ABI following standard protocols

treatment_protocol: All cell lines were grown in their respective growth medium without any other treatment

value: castration resistant

value: prostate cancer


title: LAPC4

growth_protocol: RPMI supplemented with 10% FBS

value: castration sensitive


title: Female XO genotype subject 172 thoracic aorta


title: BAP1-KO-plus-EV-H2AK119ub1


title: Female XX genotype subject 163 abdominal aorta


title: VCaP-CR

value: VCaP-CR


title: Female XO genotype subject 174 thoracic aorta


title: WT-plus-EV-H2AK119ub1


title: Female XX genotype subject 173 thoracic aorta


title: BAP1-KO-plus-C91S-input

description: Low-depth sequenced genomic DNA input for the normalisation of WT-plus-C91S samples


title: BAP1-KO-plus-WT-H3K27me3


title: Female XO genotype subject 174 abdominal aorta


title: VCaP

growth_protocol: DMEM supplemented with 10% FBS

value: VCaP


title: WT-plus-EV-H3K27me3


title: PCGF1/2/4/6-KO-input

description: Low-depth sequenced genomic DNA input for the normalisation of PCGF1/2/4/6-KO samples


title: Female XO genotype subject 175 abdominal aorta


title: BAP1-KO-plus-WT-input

description: Low-depth sequenced genomic DNA input for the normalisation of BAP1-KO-plus-WT samples


title: Female XX genotype subject 166 abdominal aorta


title: Female XO genotype subject 172 abdominal aorta


title: Female XO genotype subject 164 abdominal aorta


title: BAP1-KO-plus-EV-input

description: Low-depth sequenced genomic DNA input for the normalisation of BAP1-KO-plus-EV samples


title: WT-plus-EV-input

description: Low-depth sequenced genomic DNA input for the normalisation of WT-plus-EV samples

value: WT-plus-EV-input


title: Female XO genotype subject 165 thoracic aorta


title: SNI 3, input

city: Tian Jin

first: Xianhu

address: NO.154,Anshan Road,Heping District

department: Department of Orthopedics

institute: Tianjin Medical University General Hospital

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
clean reads of all libraries were aligned to the reference genome  by Hisat2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified by MACS software.
Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and choosed by home-made scripts.
Differentially Expressed mRNAs was obtained through the expression profile of input sample
Genome_build: rn5
Supplementary_files_format_and_content: Number of raw junction read

organism: Rattus norvegicus

source_name: Sciatic Nerve

extract_protocol:
Total RNA from each sample was isolated using TRIzol reagent (Invitrogen) and then quantified using a NanoDrop ND-1000 instrument. The Arraystar Seq-StarTMpoly(A) mRNA Isolation Kit (Arraystar, MD, USA) was used to extract Poly(A) mRNA. The concentration, purity and integrity of extracted RNA .  Fragment mRNA into 100-nucleotide fragments, and then use agarose electrophoresis to determine the post-fragmentation size distribution. mRNA was divided into two samples: input and IP samples
m6A RNA immunoprecipitation was performed with the GenSeqTM m6A RNA IP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. Both the input sample without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library  Prep Kit (New England Biolabs, Inc., USA). The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina NovaSeq 6000 instrument with 150bp paired-end reads.

value: Wistar

tag: weight

tag: protocol

value: SNI