title: F_P7_hyperoxia_CD45_1_DC28_E11

tag: gender

tag: cell type

tag: cell subtype

value: Mac II

tag: mousename

tag: coverage


title: MDA-MD-231, WT, Thapsigargin, F10 (RNA-seq)

status: Public on Jun 01 2021

type: SRA

city: South San Francisco

first: Thomas

middle: D.

last: Wu

state: CA

address: 1 DNA Way

country: USA

institute: Genentech, Inc.

library_source: transcriptomic

data_processing:
Sequenced reads were aligned to the genome using GSNAP version 2013-10-10 with parameters -M 2 -n 10 -B 2 -I 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap
Alignments were converted to counts using HTSeqGenie version 4.0.1
Genome_build: GRCh38
Supplementary_files_format_and_content: RNA_counts_matrix.txt  (Matrix table with raw gene counts for every gene and every sample).  RNA_counts_genes.txt (gene annotations)

molecule: total RNA

organism: Homo sapiens

source_name: MDA-MD-231 cells, WT, Thapsigargin

growth_protocol: Cells were cultured in RPMI1640 media supplemented with 10% (v/v) fetal bovine serum (FBS, Sigma), 2 mM glutaMAX (Gibco) and 100 U/ml penicillin plus 100 μg/ml streptomycin (Gibco).

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen #74104) performing on-column DNA digestion for 15 min. The concentration of RNA samples was determined using NanoDrop 8000 (Thermo Scientific) and the integrity of RNA was analyzed by Fragment Analyzer (Advanced Analytical Technologies). Approximately 500 ng of total RNA was used as input for library preparation using TruSeq RNA Sample Preparation Kit v2 (Illumina).
The size of the libraries was confirmed using 4200 TapeStation and High Sensitivity D1K screen tape (Agilent Technologies) and their concentration was determined by qPCR based method using Library quantification kit (KAPA). The libraries were multiplexed and then sequenced on Illumina HiSeq2500 (Illumina) to generate 30M of single end 50 base pair reads.

treatment_protocol: There were four experimental conditions: WT and IRE1α KO, treated with Tg (100nM) or vehicle control (DMSO) for 8 hr with three biological replicates (n=3) for each condition.

tag: cell line

tag: genotype

value: WT

tag: treatment

value: Thapsigargin


title: MDA-MD-231, WT, DMSO, F9 (RNA-seq)

source_name: MDA-MD-231 cells, WT, DMSO

value: DMSO


title: F_P7_hyperoxia_CD45_1_DC28_F6

city: Kensington

first: Fabio

last: Zanini

state: NSW

address: High and Botany St

country: Australia

institute: University of New South Wales

data_processing:
Mapping against human genome with VEEV-TC83-GFP added as an additional chromosome (using STAR 2.5.2b)
Counting gene expression using htseq-count 0.10
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts table: raw read counts, not notmalized, rows are gene names, columns are cell names. Metadata file: rows are cell names, columns are metadata.

organism: Mus musculus

source_name: distal lung

extract_protocol:
no extraction
plate-based illumina-compatible Tn5 transposase single cell RNA-Seq

tag: sequencing run

value: F

tag: plate

tag: well

tag: timepoint

value: hyperoxia

value: immune

value: Mac V

tag: number of genes


title: F_P7_hyperoxia_CD45_1_DC28_B6

value: mast cell


title: T11.WGBS.AD

city: Shenzhen,Guangdong Province,China

first: Yayan

last: Feng

state: --- Select a state ---

address: No. 7 pengfei road, dapeng new district, shenzhen

country: China

institute: Chinese Academy of Agricultural Sciences

library_source: genomic

data_processing:
Raw sequencing reads with more than 30% ‘N’s in over 10% of the sequences or smaller than 30 bp were discarded
Clean reads were aligned to the corresponding reference genome using BSMAP (v2.73) with a of maximal four mismatches and gap size up to 2 nucleotides
Methylation level of each cytosine was calculated as the number of reads ascertained methylated to the total number of reads for each covered CpG sites.
To accurately investigate the methylation levels in each sample, we used CpG sites with a minimal 5× sequencing depth per strand.
Genome_build: T1 reference genome: ABIR00000000; T4 reference genome: PRJNA451013; Other reference genomes: PRJNA257433
Supplementary_files_format_and_content: cout, bed format

molecule: genomic DNA

organism: Trichinella zimbabwensis

source_name: T. zimbabwensis

extract_protocol:
DNA was extracted using the phenol chloroform extraction method
Genomic DNA extracted from three life stages of all Trichinella species were selected for libraries construction of WGBS. Briefly, approx. two to five micrograms of gDNA were first fragmented by Covaris to an average size of ~200-300 bp. End-repair, A-tailing and ligation were conducted as the Illumina PE genomic DNA sample prep kit protocol, except that ligation was performed using methylated cytosine PE adapters provided by Illumina previously. Ligation products were purified and bisulfited converted using the EZ DNA Methylation-Gold KitTM (ZYMO) according to the manufacturer’s instructions. The libraries were sequenced using Illumina HiSeq 2,500 platform.

tag: tag

value: Adult


title: WT.Neu_H3K4me1_rep2

city: Stuttgart

first: Haiyang

last: Yun

address: Auerbachstraße 112

country: Germany

institute: Robert Bosch Center for Tumor Diseases

description: ChIP-seq

data_processing:
Single-read reads were trimmed for adaptor sequence and masked for low-quality sequence.
Then they were aligned to mm10 genome using Bowtie version 2.1.0 allowing two mismatch.
Duplicates were removed using PICARD tools.
For H3K4me1 or H3K4me3, enriched regions (peaks) were identified using findPeaks program from Homer, with the setting of “-size 1000 -minDist 1000”.
For H3K27ac ChIP-seq, peaks were called using MACS2 against input sample of each cell type with a P-value cutoff of 1e-9 and with setting “nomodel”.
Genome_build: mm10
Supplementary_files_format_and_content: bed files containing peak coordinates (chr, start, end)
Supplementary_files_format_and_content: Normalised (CPM) bigwig files including genome-wide enrichment features

source_name: Neutrophils

growth_protocol: Hematopoietic bone marrow (BM) cells were collected by flushing femurs and tibias of WT or mutant mice with sterile PBS and were filtered through 70-µm EASYstrainer (Greiner). Red blood cells were then depleted using RBC lysis buffer (5 PRIME). The isolation of lineage negative (Lin-) HSPCs or neutrophils were performed using Lineage Cell depletion kit or Neutrophil Isolation Kit (Miltenyi Biotec).

extract_protocol:
Chromatin immunoprecipitation was performed with iDeal ChIP-seq kit for Histones (Diagenode). Briefly, 1 x 106 Lin- HSPCs or neutrophils were crosslinked with formaldehyde at a final concentration of 1% for 10 minutes and then quenched by addition of Glycine for 5 minutes incubation. Lysis buffers iL1 and iL2 were used to prepare the nuclei pellets. Chromatin was sheared in Shearing buffer iS1 using the Bioruptor Plus (Diagenode) for 20 cycles (each cycle for 30 seconds “ON” and 45 seconds “OFF”) at high power setting. Immunoprecipitation, wash, decrosslinking and elution were carried out as per the manufacturer’s protocol, using 1 µg antibody. 10% of the sheared chromatins were kept aside as input samples.
Immunoprecipitated DNA or input DNA were used library preparation by using TruSeq ChIP Sample Prep Kit (Illumina), following standard procedures from manufacturer. The library DNA was quantified using KAPA Library Quantification Kit (Kapa Biosystems) and library average size was determined by Agilent DNA 1000 Kit (Agilent Technologies).

tag: strain

tag: chip antibody

value: anti-H3K4me1, #ab8895, Abcam


title: MDA-MD-231, IRE1-alpha KO, DMSO, F7 (RNA-seq)

source_name: MDA-MD-231 cells, IRE1-alpha KO, DMSO

value: IRE1-alpha KO


title: WT.HSPC_H3K4me3_rep2

description: ChIP-seq

source_name: Hematopoietic stem and progenitor cells (HSPC)

value: anti-H3K4me3, #c15410003, Diagenode


title: F_P7_hyperoxia_CD45_1_DC28_A19


title: F_P7_hyperoxia_CD45_1_DC28_O21

value: Mac III


title: MDA-MD-231, WT, Thapsigargin, F6 (RNA-seq)


title: T9.RNA-seq.ML

data_processing:
SOAPnuke was used for trimming adapters and filtering on length and quality of the raw sequencing reads, with the following paramaters: -q 0.5 -d -Q 2 --sanger -l 20
Clean reads were mapped to respective reference genome using hisat2 with default settings
The levels of gene expression were quantified using Cufflinks (v2.2.1) with RPKM (reads per kilobase million).
Differentially expressed genes were estimated by Cuffdiff (v2.2.1) with default paramaters
Genes with a threshold false discovery rate (FDR) ≤ 0.05 and the absolute value of log2Ratio ≥ 1 or ≤ -1 were considered significantly differentially expressed
Genome_build: T1 reference genome: ABIR00000000; T4 reference genome: PRJNA451013; Other reference genomes: PRJNA257433
Supplementary_files_format_and_content: rpkm Bed format

molecule: polyA RNA

organism: Trichinella sp. T9

extract_protocol:
Total RNA of T. spiralis (Ad, NBL and ML) was purified using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer’s instructions.
To degrade any possible DNA contamination, the total RNA samples were dissolved in diethylpyrocarbonate (DEPC)-treated water and treated with DNaseI. NanoDrop 2000 (Thermo Scientific CA, USA) was then used to assess the quantity and quality of the total mRNA enriched using oligo (dT) magnetic beads. Paired-end sequencing libraries with insert size of 300 bp were conducted on the HiSeq 2,500 platform following the Illumina’s protocols.

tag: passages

value: Muscle larvae


title: WT.Neu_H3K4me1_rep1

description: ChIP-seq


title: F_P7_hyperoxia_CD45_1_DC28_L22

tag: gender


title: MDA-MD-231, WT, DMSO, F5 (RNA-seq)


title: T9.RNA-seq.AD


title: F_P7_hyperoxia_CD45_1_DC28_N15

tag: cell type


title: DM.HSPC_H3K4me1_rep2

description: ChIP-seq


title: MDA-MD-231, IRE1-alpha KO, Thapsigargin, F4 (RNA-seq)

source_name: MDA-MD-231 cells, IRE1-alpha KO, Thapsigargin


title: WT.HSPC_H3K4me3_rep1

description: ChIP-seq


title: DM.HSPC_H3K4me1_rep1

description: ChIP-seq


title: T9.WGBS.NBL

value: Newborn larvae


title: T9.RNA-seq.NBL


title: T9.WGBS.AD


title: Flt3-ITD.HSPC_H3K4me1_rep2

description: ChIP-seq


title: F_P7_hyperoxia_CD45_1_DC28_C9

tag: cell subtype

value: basophil


title: T3.RNA-seq.NBL

organism: Trichinella britovi

source_name: T. britovi


title: MDA-MD-231, IRE1-alpha KO, Thapsigargin, F12 (GROseq)

data_processing:
Library strategy: GRO-seq
Sequenced reads were aligned to the genome using GSNAP version 2013-10-10 with parameters -M 2 -n 10 -B 2 -I 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap
Alignments were converted to counts using HTSeqGenie version 4.0.1
Genome_build: GRCh38
Supplementary_files_format_and_content: GRO_counts_matrix.txt (Matrix table with raw gene counts for every gene and every sample).  GRO_counts_genes.txt (gene annotations).

extract_protocol:
Cells were pre-treated with 5-ethynyl uridine (EU) for 30 min prior to nuclei fractionation using Sigma kit (#NUC101) followed by Invitrogen Click-iT™ Nascent RNA Capture Kit protocol for nascent transcript extraction (#C10365). RNA was then extracted using the RNeasy kit (Qiagen #74104) performing on-column DNA digestion for 15min and was subsequently reverse transcribed with Superscript VILO IV Master Mix from Invitrogen.
Libraries were prepared following the protocol from NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB #E7770S) and indexes (NEB #E7335S and #E7500S). The size of the libraries was confirmed using 4200 TapeStation and High Sensitivity D1K screen tape (Agilent Technologies) and their concentration was determined by qPCR based method using Library quantification kit (KAPA). The libraries were multiplexed and then sequenced on Illumina HiSeq2500 (Illumina) to generate 30M of single end 50 base pair reads.


title: MDA-MD-231, WT, DMSO, F1 (RNA-seq)


title: MDA-MD-231, WT, Thapsigargin, F2 (RNA-seq)


title: F_P7_hyperoxia_CD45_1_DC28_M8

value: Mac IV

tag: mousename


title: F_P7_hyperoxia_CD45_1_DC28_B18

value: neutrophil

tag: coverage


title: Npm1c.HSPC_H3K4me1_rep1

description: ChIP-seq


title: T3.RNA-seq.ML


title: MDA-MD-231, IRE1-alpha KO, DMSO, F11 (GROseq)

tag: cell line


title: T3.RNA-seq.AD


title: F_P7_hyperoxia_CD45_1_DC28_A9


title: F_P7_hyperoxia_CD45_1_DC28_N20

value: DC II


title: WT.HSPC_H3K4me1_rep2

description: ChIP-seq


title: MDA-MD-231, WT, Thapsigargin, F10 (GROseq)

tag: genotype

value: WT

value: Thapsigargin


title: T3.WGBS.NBL


title: MDA-MD-231, WT, DMSO, F9 (GROseq)

tag: treatment

value: DMSO


title: F_P7_hyperoxia_CD45_1_DC28_E4

tag: sequencing run

value: F

value: hyperoxia

value: immune


title: MDA-MD-231, IRE1-alpha KO, DMSO, F3 (RNA-seq)


title: T9.WGBS.ML


title: F_P7_hyperoxia_CD45_1_DC28_F1

tag: plate


title: Flt3-ITD.HSPC_H3K4me1_rep1

description: ChIP-seq


title: WT.Neu_pCHiC_rep1

description: promoter capture HiC (pCHiC)

data_processing:
Library strategy: promoter capture HiC (pCHiC)
Paired-end sequences were processed using the HiCUP pipeline with default parameters for the following steps: quality control, identification of reads containing HiC junctions, mapping to reference genome mm10, and filtering duplicated HiC di-tags.
HiCUP output bam files containing valid HiC di-tags were further processed by Bioconductor package CHiCAGO, to call significant promoter-based interactions.
CHiCAGO scores represent -log weighted p-values, the higher the more likelihood of interaction formed. CHiCAGO scores were calculated for each pCHiC sample, and significant interactions were called when CHiCAGO scores > 5.
Significant hign-confidence (HC) interactions were defined by CHiCAGO score > 5 at least in both individual replicates of one cell type, and were combined to form a matrix of total unique interactions.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include CHiCAGO scores for total HC interactions across WT and mutant HSPCs, and significant interactions in WT neutrophils.

extract_protocol:
20-25 million cells were crosslinked by 1% formaldehyde for 10 minutes at room temperature and was then quenched by glycine. Cells were lysed with the help of homogenization. Chromatin digestion was achieved overnight using HindIII. Digested DNA ends were biotinylated by filling with biotin-14-dATP (Invitrogen) and underwent in-nucleus ligation using T4 DNA ligase at 16 °C overnight. Crosslink was then reversed by incubation with Proteinase K at 65  ̊C overnight. RNA was removed by adding RNase A and incubating at 37  ̊C for 1 hour. DNA was purified twice with Phenol:Chloroform:Isoamyl Alcohol. Extra Biotin-14-dATP was first removed using T4 DNA polymerase and incubating at 20  ̊C for 4 hours. 40 μg DDNA was sheared using Covaris S2 to achieve a target peak around 400 bp. Sheared DNA was subject to end repair and purification, followed by addition of dATP as A-tail. DNA fragments were size selected to enrich at 200-650 bp by double-sided SPRI beads (Invitrogen). Biotin-labeled fragments were pulled down using Dynabeads MyOne Streptavidin C1 (Invitrogen) and ligated to pre-annealed paired-end (PE) adapter on beads. Eventually, HiC DNA was amplified using PE PCR primers for 7-9 cycles. HiC library was purified twice using 1.8x SPRI beads.
500 ng of HiC library was used for hybridization with biotinylated RNA bait library (Agilent Technologies), which contained 39684 biotinylated RNA probes covering 22047 promoters. Hybridization was performed as per manufacture’s protocol. Dynabeads MyOne Streptavidin T1 beads were utilized to pull down biotin-labeled DNA-RNA hybrids. Final PCR amplification and DNA purification of promoter capture HiC library were performed similarly as for HiC library, with the difference for 4 cycles of PCR. pCHiC were performed in biological duplicates of each cellular states.

value: Wild-type (WT)

value: Bone marrow neutrophis


title: T3.WGBS.ML


title: Npm1c.HSPC_H3K4me1_rep2

description: ChIP-seq

value: anti-H3K4me1, #ab8895, Abcam


title: F_P7_hyperoxia_CD45_1_DC28_D3

tag: well


title: T3.WGBS.AD

value: Adult


title: DM.HSPC_pCHiC_rep1

description: promoter capture HiC (pCHiC)

value: Npm1flox-cA/+;Flt3ITD/+;Mx1-Cre+ (double mutant, DM)

value: Bone marrow lineage negative cells


title: MDA-MD-231, IRE1-alpha KO, Thapsigargin, F8 (GROseq)

value: IRE1-alpha KO


title: MDA-MD-231, WT, Thapsigargin, F6 (GROseq)


title: Diffrentiated_cells_Hydroxyurea_treated_rep1

city: Kunming

first: Ping

last: Zheng

address: Qingsong Road 21

institute: Kunming Institute of Zoology, Chinease Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using tophat v2.1.1 with parameters -p 8 -r 50
Fragments Per Kilobase of exon model per Million mapped fragments were calculated using Cufflinks software (version 2.1.1)
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

source_name: differentiated cells derived from ESCs

extract_protocol:
RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: differentiated cells

value: treated with Hydroxyurea for 4 hours


title: F_P7_hyperoxia_CD45_1_DC28_H22

tag: timepoint

value: Mac III


title: WT.HSPC_pCHiC_rep1

description: promoter capture HiC (pCHiC)


title: WT.HSPC_pCHiC_rep2

description: promoter capture HiC (pCHiC)


title: F_P7_hyperoxia_CD45_1_DC28_H17

tag: number of genes


title: Diffrentiated_cells_Etoposide_treated_rep2

value: treated with Etoposide for 4 hours


title: MDA-MD-231, WT, DMSO, F5 (GROseq)

value: WT


title: WT.HSPC_H3K4me1_rep1

description: ChIP-seq


title: Diffrentiated_cells_Etoposide_treated_rep1


title: mSECs_Input_Rep4

city: Buffalo

first: Satrajit

last: Sinha

state: NY

address: 701 Ellicott Street

department: Department of Biochemistry

institute: State University of New York at Buffalo

data_processing:
Reads were mapped to the Mus musculus genome (mm9 build) using Bowtie (v1.1.1).
BigWig files (bw) were generated using the deepTools suite with the following flags: -p 16 -bs 10 -e 150 --normalizeUsingRPKM
Genome_build: mm9
Supplementary_files_format_and_content: BigWig Files

extract_protocol:
Salivary glands were dissected and subjected to chemical and enzymatic digestion to generate single cell suspensions which where then cross-linked and processed for down stream applications.
For histone ChIP-seq the Chromatin Shearing Optimization Kit-Low SDS (Diagenode) was used with 10 million cells per cell line and 40 cycles sonication in the Bioruptor Plus (Diagenode). After RNase and proteinase K incubation, chromatin shearing was confirmed as a DNA smear between 100-300 bp on a 1.5% agarose gel. Histone ChIP DNA was prepared with the Auto Histone ChIP-seq kit protein G Kit (Diagenode), with 3 μg H3K4me1, 2 μg H3K4me3, 2.4 μg H3K27ac, and 2 μg H3K27me3  of premium polyclonal antibody (Diagenode) per 1 million cells with the SX-8G IP-Star® Compact System (Diagenode). 1% input sample for each cell line was used as a control for background experimental noise.
ChIP-sequencing on ilumina HiSeq2500
Libraries were prepared using ThruPLEX DNA-seq kits from Rubicon Genomics. The samples were then 50 bp single-end sequenced on an Illumina HiSeq 2500.

tag: age

value: 12 week old

value: male

tag: tissue

value: Murine salivary gland

value: Primary Mouse Salivary Gland Epithelial Cells


title: mSECs_Input_Rep3

tag: strain

tag: chip antibody


title: MDA-MD-231, IRE1-alpha KO, Thapsigargin, F4 (GROseq)

value: Thapsigargin


title: F_P7_hyperoxia_CD45_1_DC28_C12

tag: gender

value: F

value: hyperoxia

value: immune

value: Mac V


title: F_P7_hyperoxia_CD45_1_DC28_M13

tag: cell type

value: B cell


title: mSECs_Input_Rep2


title: MDA-MD-231, IRE1-alpha KO, DMSO, F7 (GROseq)

value: DMSO


title: Diffrentiated_cells_control_rep1

value: untreated


title: Diffrentiated_cells_Hydroxyurea_treated_rep2

value: differentiated cells


title: F_P7_hyperoxia_CD45_1_DC28_F11

tag: cell subtype

value: NK cell


title: Diffrentiated_cells_control_rep2


title: F_P7_hyperoxia_CD45_1_DC28_H5

value: neutrophil

tag: mousename


title: mSECs_Input_Rep1


title: F_P7_hyperoxia_CD45_1_DC28_J17

value: Mac III

tag: coverage


title: mESC_Hydroxyurea_treated_rep1

source_name: embryonic stem cells

value: mESCs

value: treated with Hydroxyurea for 4 hours


title: MDA-MD-231, WT, Thapsigargin, F2 (GROseq)

tag: cell line

value: WT


title: MDA-MD-231, WT, DMSO, F1 (GROseq)

tag: genotype


title: F_P7_hyperoxia_CD45_1_DC28_N3

tag: treatment


title: Genome-wide mapping of ASCL2 binding sites in Huh-6

city: Meguro-ku

first: Genta

last: Nagae

state: Tokyo

address: 4-6-1, Komaba

department: Genome Science Division

country: Japan

institute: RCAST, University of Tokyo

data_processing:
Reads are mapped using bowtie-1.2.1.1 and samtools-0.1.16.
Local coverage is calculated by deepTools package (bamCoverage 2.5.4) with a smoothing length of 300 bp (smoothLength = 300).
The coverage of an alignment of reads or fragments (BAM file) is calculated as the number of reads per bin, where bins are short consecutive counting windows of a defined size. A coverage track was generated as a bigwig file. *bamCoverage* offers normalization by scaling factor, Reads Per Kilobase per Million mapped reads (RPKM).
Genome_build: hg19

source_name: Huh-6 cells

growth_protocol: The cells were cultured in Dulbecco’s modified Eagle medium (DMEM) (Life Technologies) supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin.

extract_protocol:
TF-DNA complexes were isolated by anti-ASCL2 or anti-CTNNB1. Briefly, the cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and cross-linked cell lysates underwent ultrasonic fragmentation and incubated with antibodies bound to Dynabeads (Thermo Fisher, #10001D and #10003D) at 4°C overnight. The beads were washed and eluted with elution buffer (0.5% SDS, 25 mM Tris-HCl, 5 mM EDTA). The eluates were treated with 1.5 μg of pronase at 42°C for 2 h, then incubated at 65°C overnight to reverse the cross-links. The immunoprecipitated DNA was purified by QIAquick PCR Purification Kit (QIAGEN, #28106).
Sequencing libraries were generated using the TruSeq ChIP Sample Prep Kit (Illumina), according to the manufacturer’s instructions.

value: hepatoblastoma cells

tag: antibody

value: ASCL2 (MERCK, MAB4418)


title: Genome-wide mapping of ASCL2 binding sites in HepG2

source_name: HepG2 cells


title: mESC_Etoposide_treated_rep2

value: treated with Etoposide for 4 hours


title: mSECs_H3K4Me3_Rep1

value: 12 week old

value: male

value: Murine salivary gland

value: Primary Mouse Salivary Gland Epithelial Cells

value: H3K4Me3 (Diagenode)


title: F_P7_hyperoxia_CD45_1_DC28_C2

tag: sequencing run

value: F

tag: plate

value: hyperoxia

value: immune

value: B cell


title: F_P7_hyperoxia_CD45_1_DC28_F14

tag: well

tag: timepoint


title: Neu IgG rep 2

city: Toronto

first: Marat

last: Mufteev

address: 686 Bay St.

department: Molecular Genetics

country: Canada

institute: University of Toronto

data_processing:
PCR duplicates were removed using unique molecular identifiers.
Quant-seq reads were aligned to the hg38 genome assembly using STAR version 2.6.0c with the default configurations.
Aligned reads were assgined to polyA sites annotated in PolyA_DB 3 catalog only when the 3'-end of a read fell within the 30 nt window around the polyA site.
Gene count is a sum of assigned reads for all poly A sites of a gene.
Genome_build: hg38
Supplementary_files_format_and_content: csv table with TIA1 binding efficiency (log2_TIA1_Input_CELLTYPE), TIA1 over Input enrichment significance (padj_CELLTYPE), TIA1 over IgG enrichment significance (TIA1_IgG_CELLTYPE), mean and standard deviation of read counts (CELLTYPE.mean and CELLTYPE.sd) for each gene and cell type

source_name: Neuron

growth_protocol: H9 hESC were cultured with mTeSR1 culture medium (STEMCELL Technologies) on Becton Dickinson hESC-qualified matrigel. An embryoid body (EB)-based method was used for neuronal induction of NPCs. To generate neurons, NPCs were cultured for 4 weeks in neural differentiation medium

extract_protocol:
Cells were washed twice in ice-cold PBS and lysed in RIP Lysis Buffer complemented with Protease and RNase Inhibitor Cocktails.
Libraries were prepared using the Agilent Bravo automation system (Agilent Technologies, Santa Clara) using previously established protocol. Library preparation was done using the QuantSeq 3′ mRNA-Seq Library Prep Kit for Illumina (Lexogen, 015.24). The RNA was spiked with SIRV Set 3 Iso Mix E0/ERCC controls (Lexogen, 025.03) following manufacturer’s instructions. Each sample was dual indexed during the final library amplification using the Lexogen’s i5 6 nt Dual Indexing Add-on Kit (#047).

value: ES-derived 4wk Neuron

tag: rip antibody

value: IgG IP Magna RIP Kit (Millipore, 17-700) (Magna RIP Kit)


title: MDA-MD-231, IRE1-alpha KO, DMSO, F3 (GROseq)

value: IRE1-alpha KO

value: DMSO


title: mESC_Etoposide_treated_rep1

value: mESCs


title: mSECs_H3K4Me1_Rep1

tag: age

tag: tissue

value: H3K4Me1 (Diagenode)


title: Neu IgG rep 1


title: NPC IgG rep 3

source_name: Neural progenitor cell

value: ES-derived neural progenitor cell


title: mSECs_H3K27Me3_Rep2

tag: strain

tag: chip antibody

value: H3K27Me3 (Diagenode)


title: mESC_control_rep1

tag: cell type

value: untreated


title: mSECs_H3K4Me3_Rep2

value: 12 week old

tag: gender

value: male


title: mSECs_H3K27Me3_Rep1

value: Murine salivary gland

value: Primary Mouse Salivary Gland Epithelial Cells


title: NPC IgG rep 2


title: F_P7_hyperoxia_CD45_1_DC28_J4

value: F

tag: cell subtype

value: Mac IV

tag: mousename

tag: number of genes


title: F_P7_hyperoxia_CD45_1_DC28_H13

value: hyperoxia

value: immune

value: neutrophil

tag: coverage


title: mESC_Hydroxyurea_treated_rep2

tag: treatment

value: treated with Hydroxyurea for 4 hours


title: mSECs_H3K27Ac_Rep2

value: H3K27Ac (Diagenode)


title: NPC IgG rep 1

tag: cell line

value: IgG IP Magna RIP Kit (Millipore, 17-700) (Magna RIP Kit)


title: F_P7_hyperoxia_CD45_1_DC28_G13

tag: sequencing run

value: Mac III


title: Young tissue 4

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina Casava v1.8.2 software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC mouse genome build mm9) using TopHat2 default settings. The aligned BAM files sorted (SAMTools) and then processed using HTSeq-count to obtain the counts per gene
gene count measurements were obtained using HTSeq-count
Genome_build: mm9
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: young_Kidney cortex

growth_protocol: kidney cortex tissues from ~5-month young mice and 30-month aged mice (4 each).

extract_protocol:
RNA was extracted from the kidney cortex of young mice and aged mice using TRIzol (Cat. #, 15596018, Thermo Fisher Scientific)
Total RNA was used for RNA-Seq library preparation by following the KAPA Stranded RNA-Seq Kit with RiboErase (HMR) sample preparation guide (Cat. #, KR1151, KAPA Biosystems)

treatment_protocol: no treatment

tag: Sex

value: 5 months

value: Kidney cortex


title: Young tissue 3


title: F_P7_hyperoxia_CD45_1_DC28_I12

tag: plate

tag: well

value: B cell


title: Young tissue 2


title: AGM_E11.5_r2

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Raw sequencing data was analyzed by first removing adaptor sequences using Trimmomatic (v0.36)
These RNA-seq reads were then aligned to mouse GRCm38/mm10 genome with STAR (v2.5.0a)
Expression count matrix was computed using featureCounts (v1.6.0)
Raw count matrix was processed using the R/Bioconductor package DESeq2 (v1.20.0), which is used to both normalize the full dataset and analyze differential expression between sample groups.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file containing quantified counts

source_name: Embryonic AGM

extract_protocol:
tissue were removed, flash frozen on dry ice, and RNA was harvested using Qiagen Rneasy Micro Kit
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 100-500ng of total RNA underwent polyA selection and the library preparation according to instructions provided by Illumina or Kapa Biosystems.

value: Embryonic AGM

tag: genotype

value: wild type


title: mSECs_H3K4Me1_Rep2

tag: age

value: 12 week old

value: male

value: H3K4Me1 (Diagenode)


title: ESC IgG rep 3

source_name: Embryonic stem cell

value: Embryonic stem cell

tag: rip antibody


title: ESC IgG rep 2


title: F_P7_hyperoxia_CD45_1_DC28_A15

value: F

tag: timepoint


title: AGM_E10.5_r2

tag: strain

tag: tissue


title: Young tissue 1


title: ESC IgG rep 1

tag: cell type


title: mESC_control_rep2

value: mESCs

value: untreated


title: Aged tissue 4

source_name: Aged_Kidney cortex

value: 30 months


title: AGM_E9.5_r2

value: Embryonic caudal half (including PsP)


title: F_P7_hyperoxia_CD45_1_DC28_G4

source_name: distal lung

tag: gender

value: hyperoxia

value: immune

tag: cell subtype

value: Mac IV


title: AGM_E11.5

description: Project_6708. (Sample_3_1_IGO_06708_3)


title: Aged tissue 3


title: Aged tissue 2


title: Neu TIA1 rep3

value: ES-derived 4wk Neuron

value: TIA1 IP Magna RIP Kit (Millipore, 17-700) (Abcam, ab40693)


title: F_P7_hyperoxia_CD45_1_DC28_L3

value: DC II

tag: mousename

tag: number of genes


title: Neu Input rep3


title: mSECs_H3K27Ac_Rep1

value: Murine salivary gland

value: Primary Mouse Salivary Gland Epithelial Cells

tag: chip antibody

value: H3K27Ac (Diagenode)


title: F_P7_hyperoxia_CD45_1_DC28_E16

tag: treatment

value: Mac III

tag: coverage


title: F_P7_hyperoxia_CD45_1_DC28_D21

tag: sequencing run


title: AGM_E9.5

description: Project_6708. (Sample_1_1_IGO_06708_1)

value: wild type


title: Neu TIA1 rep2

tag: cell line


title: Neu Input rep2


title: AGM_E10.5

description: Project_6708. (Sample_2_1_IGO_06708_2)

value: Embryonic AGM


title: F_P7_hyperoxia_CD45_1_DC28_I23

value: F

tag: plate

tag: well

value: IL cell


title: F_P7_hyperoxia_CD45_1_DC28_C16

value: Mac V


title: 3_LPS_Mse_BMDM [RNA-seq]

city: Santa Cruz

first: Sergio

last: Covarrubias

address: Thimann Receiving/Department Carpenter Lab/Biomed 125, 1156 High St., Thimann Labs

department: MCD

institute: UCSC

data_processing:
RNAseq 1: the 100x100bp pairedEnd reads were trimmed by 50bp at the 3prime end to 100x100bp
RNAseq 2: reads mapping (by bowtie2) to mouse repeatMasker elements were discarded
RNAseq 3: reads were mapped to mm10 by STAR (2.5.3a), aided by a gtf file based on Gencode VM9basic with 100bp overlap
RNAseq 4: duplicate read mappings of the same start and end position were discarded using samtools rmdup.
RNAseq 5: bam files were converted to mm10 genomic coverage using bedtools genomeCoverageBed
RNAseq 6: the dup-removed coverage was used to extract coverage of all exonic positions for each gene in UCSC KnownGenes for mm10.
RNAseq 7: the exonic coverage (from paired-end 100x100bp reads) for each gene was divided by 200 to get read counts per gene for input to DESeq2
RNAseq 8: DESeq2 was run using the read counts for UCSC KnownGenes.
RNAseq 9: DESeq2 pairwise comparisons were separately performed for unstimulated (CTL) vs LPS-stimulated (LPS) BMDMs
Genome_build: mm10
Supplementary_files_format_and_content: xlsx file with DESeq2 text file with all pairwise comparisons of CTL vs LPS

source_name: Primary Bone Marrow Derived Macrophages, Day 8

growth_protocol: Harvest bone marrow from mice, lyse all red blood cells and differentiate hematopoietic stem cells for 8 days using MCSF from L929 cell line. Grow cells in DMEM 10% FCS 10%MCSF, Pen/strep

extract_protocol:
Remove all media, pipette in 400ul of TriReagent into cell culture dish. Isolate RNA using Zimogen kit.
Constructed library using NEXTFLEX Rapid directional RNA-Seq kit from Bioo Scientific.

treatment_protocol: Treat cells with 100ng/ml LPS for 6hrs.

value: Primary BMDM

value: 100ng/ml LPS for 6hrs

tag: age (mice)

value: 10 weeks

tag: genotype


title: ES12.5

description: Project_05996_D (Sample_ES_E12_5_2_IGO_05996_D_3)

source_name: Embryonic dosal skin cells

value: Embryonic dosal skin cells

tag: age


title: 2_LPS_Mse_BMDM [RNA-seq]

tag: strain


title: Neu IgG rep1

tag: rip antibody

value: IgG IP Magna RIP Kit (Millipore, 17-700) (Magna RIP Kit)


title: ES10.5

description: Project_05996_D (Sample_ES_E10_5_2_IGO_05996_D_2)

tag: tissue


title: Neu TIA1 rep1

tag: cell type

value: ES-derived 4wk Neuron


title: F_P7_hyperoxia_CD45_1_DC28_P5

tag: gender

tag: timepoint

value: hyperoxia

value: immune

tag: cell subtype

value: neutrophil


title: F_P7_hyperoxia_CD45_1_DC28_K20

value: Mac IV

tag: mousename

tag: number of genes


title: NPC TIA1 rep3

value: ES-derived neural progenitor cell

value: TIA1 IP Magna RIP Kit (Millipore, 17-700) (Abcam, ab40693)


title: NPC Input rep3


title: E14.5

description: Project_5996 (Sample_E14-5)

value: wild type


title: F_P7_hyperoxia_CD45_1_DC28_G14

tag: treatment

value: Mac III

tag: coverage


title: Aged tissue 1

tag: Sex

value: male

value: 30 months

value: Kidney cortex


title: 2_Ctl_Mse_BMDM [RNA-seq]

value: Primary BMDM


title: ES14.5

description: Project_05996_D (Sample_ES_E14_5_2_IGO_05996_D_4)


title: E12.5

description: Project_5996 (Sample_E12-5)


title: NPC TIA1 rep2

tag: cell line


title: NPC Input rep2


title: dura_old_7_scBCR-seq

city: St. Louis

first: Marco

last: Colonna

state: MO

address: 660 S. Euclid Ave.

institute: Washington University in St. Louis

data_processing:
Library strategy: scBCR-seq
Sample demultiplexing and barcode processing was performed using the Cell Ranger Single-Cell 30 Software Suite (10x Genomics). CellRanger-5.0.12 was used to align reads to the reference genome (vdj_GRCm38_alts_ensembl-5.0.0) and assemble BCRs. BCR sequencing data was processed using hte immcantation framework (immcantation.org) (46, 47). Germline V(D)J gene annotation was performed for all 10x Genomics BCR sequences using IgBLAST v1.16.0, with a curated set of Ig reference alleles specific for the C57BL/6 strain of Mus musculus (48). IgBLAST output was parsed using Change-O v0.4.6 (46). Additional quality control required sequences to be productively rearranged and have valid V and J gene annotations, consistent chain annotation (excluding sequences annotated with H chain V gene and L chain J gene), and a junction length that is a multiple of 3. Cells with exactly the same barcode and BCR sequences between different samples were excluded. Furthermore, only cells with exactly one H chain sequence paired with at least one L chain sequence were kept. After processing, there were 52509 cells with paired H and L chains and 19447 of them have paired gene expression data.
Genome_build: mm10
Supplementary_files_format_and_content: Processd BCR clonotypes. Table formatted according to standard changeo format (https://changeo.readthedocs.io/en/stable/standard.html).

source_name: dura

extract_protocol: Library preparation was performed using the 10X Chromium VDJ + 5' Gene expression v.1 platform, up to 17,500 cells were partitioned into nanoliter Gel-bead-in-Emulsions (GEMs) droplets. Each GEM undergoes retro-transcriptase reaction to generate single-cell cDNA and receives a unique 12 nt cell barcode and unique molecular identifier (UMI). GEM cDNA was amplified for 11 cycles before being purified using SPRIselect beads. 10μl of purified cDNA was used to 5 generate the library for RNA sequencing. Libraries were sequenced on a NovaSeq S4 (Illumina, 300 cycle kit) flow cell, targeting 50K read pairs/cell.

value: aged

value: dura


title: ES9.5

description: Project_05996_D (Sample_ES_E9_5_2_IGO_05996_D_1)

value: Embryonic dosal skin cells


title: EAE

city: Madison

first: Zsuzsanna

last: Fabry

state: WI

address: 1111 Highland Ave.

department: Pathology and Laboratory Medicine

institute: University of Wisconsin Madison

data_processing:
Experiment  data were demultiplexed using the Cell Ranger Single Cell Software Suite, mkfastq command  wrapped around Illumina's bcl2fastq. The MiSeq balancing run was quality controlled using  calculations based on UMI-tools (Smith et al, 2017). Samples libraries were balanced for the  number of estimated reads per cell and run on an Illimina NovaSeq system. Cell Ranger software  was then to perform demultiplexing, alignment, filtering, barcode counting, UMI counting, and  gene expression estimation for each sample according to the 10x Genomics documentation  (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-iscell-ranger). The gene expression estimates from each sample were then aggregated using  Cellranger (cellranger aggr) to compare experimental groups with normalized sequencing-depth  and expression data.
Supplementary_files_format_and_content: Genes identified to be differentially expressed from each cluster were separately assessed by gene ontological analyses using R package clusterProfiler 68.  The genes that passed filtering during alignment were used as the background set during over-representation analyses. Significant gene ontological terms were identified using an adjusted P-value < 0.05. Bar plots, gene-concept network plots, and enrichment maps were visualized and generated using clusterProfiler.

source_name: cpLECs

extract_protocol:
The cribriform plate along with the olfactory bulbs and parts of the nasal mucosa were isolated after removal of the skull cap and brain.  The tissue was then mechanically dissociated in RPMI using a syringe plunger and 70 micron mesh filter to generate a single cell suspension for FACS sorting.  Cells were stained with Podoplanin, CD31, CD45, and Ghost dye.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Wild-type C57BL/6J

value: Meningeal lymphatic endothelial cells near the cribriform plate

value: 10 week-old Females

tag: disease state

value: autoimmune encephalomyelitis (EAE)


title: 1_Ctl_Mse_BMDM [RNA-seq]

tag: age (mice)

value: 10 weeks


title: Healthy

value: healthy


title: E9.5

description: Project_5996 (Sample_E9-5)

tag: genotype


title: KF: human keloid other fibroblasts(except CD266+/CD9- fibroblast)

city: GuangZhou

first: Yongfei

last: Hu

state: GUangDong

address: Road LuJing

institute: Dermatology Hospital of Southern Medical University

data_processing:
We used Hisat2 v2.0.52 to build the index of the reference genome and align the paired-end clean reads with the reference genome (Trapnell et al., 2009). Then, StringTie v2.23 was used to count the read numbers mapped to each gene. Fragments Per Kilobase per Million (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg38
Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each Sample and log fold change between two samples.

growth_protocol: This study was approved by the Medical and Ethics Committees ofDermatology Hospital, Southern Medical University, and each patientsigned an informed consent beforeenrolling in this study.Keloid tissues were harvested during plastic surgery from three patients confirmed to have clinical evidence of keloid (SupplementaryTable S1). No patient had received chemotherapy or radiotherapy prior to surgery. Normal scar tissues were obtained from two patients who underwent elective scar resection surgery(SupplementaryTable S1). Excised skin was immersed in physiological saline and then transferred to the lab immediately. The skin tissue was washed twice with PBS. After removal of the adipose tissue under the reticular dermis, the samples were cut into 5 mm diameter pieces and incubated withdispase II (Sigma)for 2 h at 37°C. The epidermis was peeled off and discarded and the dermis wasminced into small pieces and digested at 37°C for 2 hours using Collagenase IV (YEASEN, China). The resulting cell suspension was filtered through a 70μm cell strainer(BD Falcon), and centrifuged at1500 rpm for 10 min. The supernatant was removed and the pellet was washed oncewith PBS at 1500 rpm for 5 min. The pellet was then resuspended in PBS+1% FBS forflow cytometry.

extract_protocol:
We flow sorted keloid fibroblasts that were CD90+ and CD266+/CD9- or CD90+ other cells (other fibroblasts),performed RNA-seq to compare the gene expression of CD266+/CD9- fibroblasts and other fibroblasts.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human dermal other fibroblasts(except CD266+/CD9- fibroblasts)


title: 1_LPS_Mse_BMDM [RNA-seq]

value: 100ng/ml LPS for 6hrs


title: Neu Input rep1

value: ES-derived 4wk Neuron


title: NPC TIA1 rep1

value: ES-derived neural progenitor cell

value: TIA1 IP Magna RIP Kit (Millipore, 17-700) (Abcam, ab40693)


title: dura_old_6_scBCR-seq

tag: age


title: E10.5

description: Project_5996 (Sample_E10-5)

tag: strain

value: wild type


title: sample A

city: Los Angeles

first: Tran

middle: Hue

last: Do

address: 615 Charles E Young Dr

institute: David Geffen School of Medicine

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR
Each read was tagged with a 12bp barcode and 8bp unique molecular identifier (UMI
After alignment, the reads were grouped by the barcodes and deduplicated using the UMIs. The number of UMIs was then counted for each gene in each cell to generate the digital expression matrix (DEM).
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human Skin

extract_protocol:
Patients were excluded from the study if they had been using acne medication, hormonal regulation medication, or hormonal-related implants in the past three months. Skin samples were obtained from 3mm punch biopsies in the back. Briefly, skin was digested enzymatically at 2 hours with 0.4% Dispase II at 37°C with agitation. The epidermis was separated from the dermis. Epidermis was then treated with 0.25% Trypsin and 10U/mL of DNAse I for 30 minutes. Dermis was homogenized and treated with 0.4% Collagenase II and 10U/mL DNase I for 2 hours.
20µm thick frozen section of an acne lesion into 55µm wells containing spatially-barcoded capture oligonucleotides

value: skin


title: dura_old_5_scBCR-seq


title: NPC Input rep1

tag: rip antibody


title: 3_Ctl_Mse_BMDM [RNA-seq]

value: Primary BMDM


title: DUS3L without 5FUrd treatment 3

city: princeton

first: Ang

last: Li

state: NJ

address: Washington Road

department: chemistry

institute: princeton university

data_processing:
NovaSeq Control Software (NVCS) v1.7 was used for the sequencing run and base calling
alignment(STAR), filtering and peak-calling(Paraclu) were performed by using ICOUNT version2.0.0
Genome_build: GRCh38
Supplementary_files_format_and_content: bed peaks file

source_name: Hek

growth_protocol: 60 x 10 cm dish (20 with 5-FUrd treatment and 40 without 5-FUrd treatment as control) Flp-In T-Rex 293 cells expressing 3xFlag-DUS3L were treated with 1 mg/mL tetracycline once the cells reached 60% confluency.

extract_protocol:
Cells were washed twice with cold PBS and then 500 µl lysis buffer (50 mM Tris–HCL pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS and 0.5% sodium deoxycholate) was added to each dish. Lysates were treated with Turbo DNase (AM2239) and a low (1:200) or high (1:50) concentration of RNaseI (AM2295) at 37 °C for 3 mins with rotation after which they were centrifuged at 13000  rpm for 15 min at 4°C. The supernatant was incubated with anti-FLAG beads (200 μl Protein G beads and 15 µg anti-Flag M2 antibody) at 4 °C overnight with rotation, and the immunoprecipitated material was then washed 3 times with high-salt buffer and then once with CutSmart buffer (NEB) washing. The beads were treated with Quick-CIP (NEB) at 37 °C for 30 mins with rotation, washed twice with high-salt buffer, and then incubated with preadenylated and biotin labeled L3 linker by using T4 RNA ligase I (NEB) at 16 °C overnight. After washing 3 times with high-salt buffer, the beads were boiled with 60 μl sample buffer and 3 μl was analyzed by Western blot for biotinylation with the chemiluminescent nucleic acid detection module (Thermo). The rest of the sample was gel purified based on the position of the biotin signal. Immunoprecipitated RNA was recovered using D-tube dialyzer midi (Merck-Millipore) and digested with proteinase K (Roche).
Reverse transcription was performed using oligonucleotides containing randomized barcodes (UMIs) and two inversely oriented adaptor regions separated by a BamHI restriction site. cDNAs were size-purified (70-80nt, 80-100nt and 100-150nt) on TBE-Urea gels and then circularized by CircLigase II (Epicentre). Circularized cDNAs were digested with BamHI and linearized cDNAs were amplified using Solexa primers and submitted for Illumina sequencing.

treatment_protocol: After 12 hr,the medium was changed to fresh medium containing 1 mg/mL tetracycline (Control) or 1 mg/mL tetracycline and 100 μM 5-FUrd (5-FUrd-iCLIP) and cultured for another 12 hr.

value: Hek

tag: agent


title: ESC TIA1 rep3

tag: cell type

value: Embryonic stem cell


title: dura_old_4_scBCR-seq

value: aged

tag: tissue

value: dura


title: HepG2 Knockout_Input_for_RiboSeq

city: Guangzhou

first: Shuibin

last: Lin

state: China

address: Zhongshan 2nd road, Guangzhou

department: Clincial for Translational Medicine

institute: The First Affliliated Hospital, Sun Yat-sen University

data_processing:
Library strategy: Ribo-Seq
For Ribo-Seq data analysis, Adapter sequences were trimmed and low quality sequences (Q30) were discarded using trim_galore. The sequences with length of at least 25nt were further aligned to human rRNA and tRNA index constructed from Ensembl (Release 91) and GtRNAdb databases , respectively. The remaining reads were aligned to the UCSC canonical known gene transcripts of the human reference genome (hg38) using bowtie with a maximum one mismatch allowed.
Supplementary_files_format_and_content: The txt file of Ribo-seq include the FPKM values for every gene.

source_name: Hepatocellular carcinoma HepG2 cells

growth_protocol: Human HepG2 cells were maintained in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco, USA). Cells were grown in a 5% CO2 cell culture incubator at 37℃.

extract_protocol:
RNA was extracted according to TRIzol protocol.
Libraries were prepared according to Illumina's instructions accompanying the TrueSeq Stranded mRNA library preparation kit, TruSeq Ribo Profile (Mammalian) Library Prep Kit and the NEBNext® Small RNA Library Prep Set.

treatment_protocol: METTL5 was knocked out by sgRNA.

value: METTL5 knockout


title: DUS3L without 5FUrd treatment 2


title: HepG2 Vector_RiboSeq

value: Wild type


title: KZ: human keloid CD266+/CD9- fibroblasts

source_name: human keloid CD266+/CD9- fibroblasts

value: human dermal CD266+/CD9- fibroblasts


title: dura_old_3_scBCR-seq


title: ESC Input rep3


title: DUS3L without 5FUrd treatment 1


title: ESC TIA1 rep2


title: HepG2 Vector_Input_for_RiboSeq


title: ESC Input rep2


title: MCF7 shTET2#2

city: Shanghai

first: Yinghui

last: Shen

address: 131 Dongan Road

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were trimmed to remove adaptor sequence and low-quality sequence using trim_galore v0.6.6 with parameters --paired --fastqc
Trimmed reads were mapped to hg19 whole genome using tophat v2.1.1 with default parameters into BAM files
Fragments Per Kilobase of transcript per M (FPKM) were calculated using FPKM_count.py (RSeQC)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of each Sample

source_name: breast cancer cell line

growth_protocol: MCF7 cells were cultured in DMEM high glucose medium with 10% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol:
RNA was harvested using Trizol reagent. 1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA.The cDNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MCF7 scramble, shTET2#1 and shTET2#2 were cultured with 2μg/ml puromycin

value: breast

value: Knocking down TET2 with shRNA#2


title: dura_old_2_scBCR-seq


title: DUS3L with 5FUrd treatment 2


title: HepG2 Knockout_RiboSeq


title: MCF7 shTET2#1

value: Knocking down TET2 with shRNA#1


title: DUS3L with 5FUrd treatment 3


title: dura_young_7_scBCR-seq

value: young


title: dura_old_1_scBCR-seq


title: dura_young_6_scBCR-seq


title: ESC TIA1 rep1


title: KO_Sham_3

city: Paris

first: Aïssata

last: NIASSE

address: 4 rue de la Chine

country: France

institute: INSERM

data_processing:
Quality of raw data has been evaluated with FastQC
Poor quality sequences were trimmed or removed with fastp tool, with default parameters.
Illumina DRAGEN bio-IT Plateform (v3.7.5) was used for mapping on hg38 reference genome and quantification with gencode v32 annotation gtf file.
Library orientation, library composition and coverage along transcripts were checked with Picard tools.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files including expected counts and TPM

growth_protocol: CRISPR/Cas9 mediated STAT5B gene knockout was performed in HEK293 cells.. The STAT5B knockout clones with a biallelic mutation on the endogenous STAT5B gene were then selected by DNA sequencing and confirmed by Western blot analysis. HEK293 and GS knockout clones were maintained in T25 flasks in a 5% CO2/air mixture, humidified at 37°C. The medium for culture maintenance was Dulbecco's modified Eagle's medium (DMEM, Gibco, Grand Island, NY) supplemented with 10% fetal bovine serum (FBS, Biosera)."

extract_protocol:
The control and STAT5B knock out HEK cells were lyzed, and RNA isolation was performed using the Qiagen RNA isolation kit according to manufacturer’s instructions. All experiments were performed in triplicate.
Libraries were prepared from the extracted RNA using the KAPA hyper mRNA ROCHE kit

value: Human embryonic kidney cell line

tag: genotype/variation

value: STAT5b knock-out


title: MCF7 TET2KO2

value: TET2 knock out single clone 2


title: ESC Input rep1


title: DUS3L with 5FUrd treatment 1


title: dura_young_5_scBCR-seq


title: MCF7 scramble

value: transfected with shRNA of scramble


title: P10PP3: Patient PP Replicate 3

city: Houston

first: Malgorzata

last: Borowiak

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Trim galore to remove adapter sequences
SortMeRNA to remove ribosomal sequences
STAR aligner to human transcriptome
Gene Counts calculated using feature counts
DESeq2 used for post-alignment analysis
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts matrix

source_name: hIPS cell derived Pancreatic Progenitor

growth_protocol: Patient and control iPS cells were differentiated towards pancreatic progenitors and collected at differentiation day start, after 3 (definitive endoderm, DE) or 12 (pancreatic progenitors, PPs) days of differentiation. To initiate differentiation, patient and control iPS cells were dissociated into single cells and seeded at 150,000 cell/cm2 in E8 media supplemented with 10 μM Y27632 (StemGent). Differentiation began 2 days following seeding. Day 1: MCDB-131 media with 0.1% bovine serum albumin (BSA) + 10 mM glucose + 100 ng/ml rh ActivinA and 3 μM CHIR99021. Days 2–3: MCDB-131 media + 0.1% BSA + 10 mM glucose + 100 ng/ml rh ActivinA. Days 4–5: MCDB-131 + 0.1% BSA, + 10 mM glucose, + Vitamin C (VitC) + 50 ng/ml KGF (Peprotech). Days 6–9: MCDB-131 + 2% BSA + 5.5 mM glucose + 0.25 mM VitC + 1:200 Insulin-Transferrin-Selenium (ITS; Invitrogen) +50 ng/ml KGF + 2 μM RA + 0.25 μM SANT-1 + 100 ng/ml rh Noggin. Days 10–12: MCDB-131 + 2% BSA + 5.5 mM glucose + 0.25 mM VitC + 1:200 ITS + 0.25 μM SANT-1 + 100 ng/ml rh Noggin + 1 μM PdBU.

extract_protocol:
RNA was extracted using TRIzol (Thermo Fisher Scientific) according to the manufacturer’s protocol. The quality of extracted RNA samples was determined using a 2100 Bioanalyzer and the Agilent RNA 6000 nano kit (Agilent; Santa Clara, CA). The samples with RIN > 9 were used for mRNA library preparation.
Libraries were prepared using TruSeq stranded mRNA Library Prep Kit LT (Illumina, Inc.; San Diego, CA). The concentration of the libraries was determined using Quantitative PCR KAPA Library Quantification Kit for Illumina (Kapa Biosystems), and the sequencing runs were performed on a NextSeq 500 (Illumina).

value: Ketosis-Prone Diabetes

value: human induced pluripotent stem cells

tag: batch


title: dura_young_4_scBCR-seq


title: KO_Sham_2


title: P10PP2: Patient PP Replicate 2


title: MCF7 TET2KO1

value: TET2 knock out single clone 1


title: KO_Sham_1


title: P10PP1: Patient PP Replicate 1


title: dura_young_3_scBCR-seq


title: MCF7 WT

value: TET2 wild type


title: dura_young_2_scBCR-seq


title: P10DEc: Control PP Replicate 3

value: Control


title: Healthy male, EV-RNA M3

city: Taipei

first: Yu-Feng

last: Huang

address: 128 Academia Road, Section 2, Nankang

country: Taiwan

institute: Academia Sinica

description: EV-RNA

data_processing:
Sequencing adapter trimming by cutadapt. Base and read quality checking by PRINseq and NGS QC Toolkit.
Genome mapping by STAR aligner with hg38.
Read counting by featureCounts with GENCODE v29 annotation.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file with raw gene counts for every gene and every sample

source_name: blood plasma

extract_protocol: RNA TOP-PCR + Illumina standard protocols

value: blood

value: WT


title: HEK_Sham_2

value: wild type


title: dura_young_1_scBCR-seq

value: dura


title: HEK_Sham_3


title: HEK_Sham_1


title: Healthy male, EV-RNA M1

description: EV-RNA


title: Healthy male, EV-RNA M2

description: EV-RNA


title: P10DEa: Control PP Replicate 1


title: MDA231_cell_KDM1BKO_2

city: Boston

first: Yujiang

last: Shi

state: MA

address: 221 longwood Ave, EBRC (LMRC) 222A

department: Division of Endocrinology, Diabetes and Hypertension

institute: Brigham and Women's Hospital

description:
RNA-seq KDM1B KO MDA-MB-231 cells in culture rep2
Expression_FPKM_Count_MDA231_cell_WT_KDM1BKO.txt

data_processing:
Raw sequencing data were trimmed using Trim Galore (v0.4.5) to remove low quality bases and adaptor sequences.
The trimmed reads were mapped onto the hg38 genome for human origin and mm9 genome for mouse origin, using STAR (v2.5.4)  with parameter --twopassMode Basic.
Quantification of gene expression was performed using featureCounts in Rsubread package (v1.32.4). RPKM of genes was calculated using ‘rpkm’ function in edgeR package (v3.24.3) and gene annotations were determined through featureCounts built-in hg38/mm9 annotation.
Genome_build: mm9, hg38

source_name: cells in culture

growth_protocol: MDA-MB-231 cells (WT and KDM1B KO) were cultured in DEME supplemented with 10% FBS and 1% penicillin/streptomycin in a 5% CO2 incubator at 37C. For tumor growth, 1x10E5 4T1 cells were injected subcutaneously at the right flank of BalB/cJ; 3 × 10E6 MDA-MB-231 cells were injected subcutaneously at the right flank of athymic BALB/c nude mice.

extract_protocol:
Total RNA was first extract by Trizol, and further purified from genomic DNA by on-column DNaseI digestion and Qiagen RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue type

value: cells

value: KDM1B KO


title: P10DEb: Control PP Replicate 2


title: bm_old_3_scBCR-seq

source_name: bone marrow

value: aged

value: bone marrow


title: TCAM2_rep3_ATAC-seq

city: Philadelphia

first: Matthew

middle: E.

last: Johnson

state: PA

address: 3615 Civic Center Boulevard, Abramson Research Center, Suite 1102G

department: Genetics

institute: Children's Hospital of Philadelphia

description: Testicular seminomatous germ cell tumor cell line Replicate 3

data_processing:
Bases were called using Illumina bcl2fastq2 conversion v2.29
Reads were aligned using bowtie2 implimented in the ENCODE pipeline. Reads alignment by offsetting +4bp for all the reads aligned to the forward strand, and -5bp for all the reads aligned to the reverse strand
Open chromatin regions (OCRs) were called using MACS2 implimented in the ENCODE pipeline with the following parameters -p 0.01 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits. The encode blacklist regions (wgEncodeDacMapabilityConsensusExcludable.bed.gz) were removed from called peaks.
Genome_build: hg19

source_name: TCam-2 (RRID:CVCL_T012)

growth_protocol: NTERA-2 cl.D1 [NT2/D1] Medium: DMEM – one 500 ml bottle, FBS – add contents one 50 ml conical L-Glutamine – add contents of one 5 mL conical (stock 200 mM), Pen/Strep – add contents one 5 mL conical. Growth: Take out the Ntera stock vial from liquid nitrogen and thaw it in 37 degree water bath. Suspend the washed cells in 5 ml growth media. Attention: When thawing the original stock from ATCC, a small flask has to be used to adjust for the smaller cell number. ATCC cells will NOT grow if plated directly into 75 sq. cm. flask. Cells may also grow more slowly when first purchased.  Centrifuge at 1500 rpm for 5 min. Suspend the cells in 15ml growth media and transfer them into a 75 sq. cm. flask.  Cells are grown in 37ºC incubator at 5% CO2.  Split cultures when they reach ~90% confluency (about 2x107 cells per 75 sq. cm. flask). Trypsinize cells and split 1:4 with fresh growth media (about 5x106 cells per 75 sq. cm flask).  Cells typically reach 90% confluency in 2-3 days, at which point they can be harvested or split back.  NCCIT Medium: RPMI, 10% FBS, L-Glutamine, Pen/Strep. Growth: Take out the NCCIT stock vial from liquid nitrogen and thaw it in 37 degree water bath. Suspend the washed cells in 5 ml growth media. Centrifuge at 1500 rpm for 5 min. Suspend the cells in 15ml growth media and transfer them into a 75 sq. cm. flask.  Cells are grown in 37ºC incubator at 5% CO2.  Split cultures when they reach ~90% confluency (about 2x107 cells per 75 sq. cm. flask). Trypsinize cells and split 1:4 to 1:8 with fresh growth media.  2102EP Medium: DMEM, 10% FBS, L-Glutamine, Pen/Strep Growth: Take out the 2102EP stock vial from liquid nitrogen and thaw it in 37 degree water bath. Suspend the washed cells in 5 ml growth media.  Centrifuge at 1500 rpm for 5 min.  Suspend the cells in 15ml growth media and transfer them into a 75 sq. cm. flask.  Cells are grown in 37ºC incubator at 5% CO2.  Split cultures when they reach ~90% confluency (about 2x107 cells per 75 sq. cm. flask). Trypsinize cells and split 1:3 to 1:5 with fresh growth media.  TCAM2 Medium: RPMI, 10% FBS, L-Glutamine, Pen/Strep Growth: Take out the 2102EP stock vial from liquid nitrogen and thaw it in 37 degree water bath. Suspend the washed cells in 5 ml growth media. Centrifuge at 1500 rpm for 5 min. Suspend the cells in 15ml growth media and transfer them into a 75 sq. cm. flask.  Cells are grown in 37ºC incubator at 5% CO2.  Split cultures when they reach ~90% confluency (about 2x107 cells per 75 sq. cm. flask). Trypsinize cells and split 1:3 to 1:5 with fresh growth media.

extract_protocol:
A total of 50,000 cells were centrifuged at 550g for 5 min at 4°C. The cell pellet was washed with cold PBS and resuspended in 50 μL cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40/IGEPAL CA-630) and immediately centrifuged at 550 g for 10 min at 4°C. The tagmented DNA was then purified using the Qiagen MinElute kit and eluted in 10.5 μL Elution Buffer.
Ten microliters of purified tagmented DNA was PCR amplified using the Nextera Indexing Kit for 12 cycles to generate each library. The PCR reaction was subsequently purified using 1.8x AMPure XP beads, and concentrations were measured by Qubit Fluorometer.  Quality of completed libraries was assessed on a Bioanalyzer 2100 high sensitivity DNA Chip.  Libraries were paired-end sequenced at the Center for Spatial and Functional Genomics on the Novaseq 6000 platform (50 bp read length).

tag: testis cancer line

value: derived from Testicular seminomatous germ cell tumor


title: P10ESc: Patient DE Replicate 3

source_name: hIPS cell derived Definitive Endoderm


title: bm_old_2_scBCR-seq


title: TCAM2_rep2_ATAC-seq

description: Testicular seminomatous germ cell tumor cell line Replicate 2


title: MDA231_cell_KDM1BKO_1

description:
RNA-seq KDM1B KO MDA-MB-231 cells in culture rep1
Expression_FPKM_Count_MDA231_cell_WT_KDM1BKO.txt


title: P10ESb: Patient DE Replicate 2


title: bm_old_1_scBCR-seq


title: bm_young_3_scBCR-seq

value: young


title: TCAM2_rep1_ATAC-seq

description: Testicular seminomatous germ cell tumor cell line Replicate 1


title: bm_young_2_scBCR-seq


title: MDA231_cell_WT_1

description:
RNA-seq wild-type MDA-MB-231 cells in culture rep1
Expression_FPKM_Count_MDA231_cell_WT_KDM1BKO.txt


title: MDA231_tumor_KDM1BKO_3

description:
RNA-seq KDM1B KO MDA-MB-231 tumor rep3
Expression_FPKM_Count_MDA231_tumor_WT_KDM1BKO.txt

source_name: tumor in nude mice

value: tumor

tag: mouse

value: athymic BALB/c nude mice


title: NCCIT_rep3_ATAC-seq

description: pluripotent embryonal carcinoma cell line Replicate 3

source_name: ATCC

value: NCCIT

value: derived from anterior mediastinal mixed germ cell tumor


title: C3PP3: Control DE Replicate 3

value: human induced pluripotent stem cells


title: C3PP2: Control DE Replicate 2


title: P10ESa: Patient DE Replicate 1

value: Ketosis-Prone Diabetes


title: blood_old_6_scBCR-seq

source_name: peripheral blood

value: peripheral blood


title: MDA231_tumor_KDM1BKO_1

description:
RNA-seq KDM1B KO MDA-MB-231 tumor rep1
Expression_FPKM_Count_MDA231_tumor_WT_KDM1BKO.txt


title: NCCIT_rep2_ATAC-seq

description: pluripotent embryonal carcinoma cell line Replicate 2


title: MDA231_tumor_KDM1BKO_2

description:
RNA-seq KDM1B KO MDA-MB-231 tumor rep2
Expression_FPKM_Count_MDA231_tumor_WT_KDM1BKO.txt


title: MDA231_tumor_WT_3

description:
RNA-seq wild type MDA-MB-231 tumor rep3
Expression_FPKM_Count_MDA231_tumor_WT_KDM1BKO.txt


title: NCCIT_rep1_ATAC-seq

description: pluripotent embryonal carcinoma cell line Replicate 1


title: C3PP1: Control DE Replicate 1

value: Control


title: 2102EP_rep3_ATAC-seq

description: Human embryonal carcinoma cell line Replicate 3

source_name: 2102EP (RRID:CVCL_C522)

value: derived from testis embryonal carcinoma


title: C3DEc: Patient iPS Replicate 3

source_name: hIPS cell


title: blood_old_7_scBCR-seq


title: blood_old_5_scBCR-seq


title: MDA231_tumor_WT_2

description:
RNA-seq wild type MDA-MB-231 tumor rep2
Expression_FPKM_Count_MDA231_tumor_WT_KDM1BKO.txt

value: WT


title: 2102EP_rep2_ATAC-seq

description: Human embryonal carcinoma cell line Replicate 2


title: C3DEa: Patient iPS Replicate 1


title: 2102EP_rep1_ATAC-seq

description: Human embryonal carcinoma cell line Replicate 1


title: MDA231_cell_WT_2

description:
RNA-seq wild-type MDA-MB-231 cells in culture rep2
Expression_FPKM_Count_MDA231_cell_WT_KDM1BKO.txt


title: bm_young_1_scBCR-seq


title: C3DEb: Patient iPS Replicate 2


title: NT2-D1_rep3_ATAC-seq

description: pluripotent human testicular embryonal carcinoma cell line Replicate 3

value: testis; derived from metastatic site:lung


title: MDA231_tumor_WT_1

description:
RNA-seq wild type MDA-MB-231 tumor rep1
Expression_FPKM_Count_MDA231_tumor_WT_KDM1BKO.txt


title: blood_old_3_scBCR-seq


title: C3ESc: Control iPS Replicate 3


title: C3ESb: Control iPS Replicate 2


title: input_ChIP

data_processing:
Raw sequencing data were trimmed using Trim Galore (v0.4.5) to remove low quality bases and adaptor sequences.
The trimmed reads were mapped onto the hg38 genome using bowtie2 (v2.2.9) with parameter -X 1000.
Peaks were called using R package SPP broad peak calling, parameters using window size 500bp, z=6.
Genome_build: hg38

growth_protocol: MDA-MB-231 cells stably expressing 3XFLAG tagged KDM1B from retrovirus vector pOZ were cultured in DEME supplemented with 10% FBS and 1% penicillin/streptomycin in a 5% CO2 incubator at 37C.

extract_protocol:
Formaldehyde crosslinked chromatin was sonicated and enriched by immunoprecipitation using anti-Flag antibodies
DNA libraries were prepared for sequencing using standard Illumina protocols

value: triple negative breast cancer cell line

value: stably expessing 3xFLAG KDM1B


title: NT2-D1_rep2_ATAC-seq

description: pluripotent human testicular embryonal carcinoma cell line Replicate 2


title: KDM1B_ChIP

tag: chip antibody

value: anti-FLAG M2 antibody (Sigma, F1804)


title: blood_old_2_scBCR-seq

value: aged


title: blood_old_1_scBCR-seq


title: NT2-D1_rep3_CaptureC

data_processing:
Library strategy: CaptureC
Bases were called using Illumina bcl2fastq2 conversion v2.29
Paired-end reads from three replicates from ESCs, HPs, and HNs were pre-processed using the HICUP pipeline (v0.5.9) with the default parameters. Reads were aligned to hg19 using bowtie2. We called call significant promoter interactions using the read count from promoters included in our reference bait.
Significant interactions were called CHiCAGO (v1.1.8) with default parameters except for bin-size set to 2,500. In addition to our analysis per individual DpnII fragment (1frag), we also called interactions by binning four fragments, which improves detection of long-distance interactions. Significant interactions at 4-DpnII fragment resolution were also called using CHiCAGO with artificial baitmap and .rmap files where four DpnII fragments were concatenated. Interactions with a CHiCAGO score > 5 in at least one cell type in either 1-fragment or 4-fragment resolution were considered significant.
Genome_build: hg19
Supplementary_files_format_and_content: ibed

source_name: testis; derived from metastatic site: lung

growth_protocol: NTERA-2 cl.D1 [NT2/D1] Medium: DMEM – one 500 ml bottle, FBS – add contents one 50 ml conical L-Glutamine – add contents of one 5 mL conical (stock 200 mM), Pen/Strep – add contents one 5 mL conical. Growth: Take out the Ntera stock vial from liquid nitrogen and thaw it in 37 degree water bath. Suspend the washed cells in 5 ml growth media. Attention: When thawing the original stock from ATCC, a small flask has to be used to adjust for the smaller cell number. ATCC cells will NOT grow if plated directly into 75 sq. cm. flask. Cells may also grow more slowly when first purchased.  Centrifuge at 1500 rpm for 5 min. Suspend the cells in 15ml growth media and transfer them into a 75 sq. cm. flask.  Cells are grown in 37ºC incubator at 5% CO2.  Split cultures when they reach ~90% confluency (about 2x107 cells per 75 sq. cm. flask). Trypsinize cells and split 1:4 with fresh growth media (about 5x106 cells per 75 sq. cm flask).  Cells typically reach 90% confluency in 2-3 days, at which point they can be harvested or split back.

extract_protocol:
For each library, 107 fixed cells were thawed at 37ºC, followed by centrifugation at RT for 5 mins at 14,000 rpm. The cell pellet was resuspended in 1 mL of dH2O supplemented with 5 μL 200X protease inhibitor cocktail, incubated on ice for 10 mins, then centrifuged. The cell pellet was resuspended to a total volume of 650 μL in dH2O.
samples underwent a pre-digestion incubation with the addition of 0.3% SDS, 1x NEBuffer DpnII, and dH2O for 1hr at 37ºC in a Thermomixer shaking at 1,000rpm. A 1.7% solution of Triton X-100 was added to each tube and shaking was continued for another hour. After the pre-digestion incubation, 10 μL of DpnII (was added only to each sample tube, and continued shaking until the end of the day. An additional 10 µL of DpnII was added to each digestion reaction and digestion continued overnight. The next day, another additional 10 µL of DpnII was added and the incubation continued for another 2-3 hours. 100 μL of each digestion reaction was then removed, pooled into one 1.5 mL tube. The remaining samples were heat inactivated at 65°C for 20 min at 1000 rpm in a Thermomixer, and cooled on ice for 20 additional minutes. Digested samples were ligated with 8 μL of T4 DNA ligase (HC 30U/uL) and 1X ligase buffer at 1,000 rpm overnight at 16°C in a Thermomixer. The next day, an additional 2 µL of T4 DNA ligase was spiked into each sample and incubated for another few hours. The ligated samples were then de-crosslinked overnight at 65°C with Proteinase K along with the pre-digestion and digestion controls. The following morning, both controls and ligated samples were incubated for 30 min at 37°C with RNase A, followed by phenol/chloroform/isoamyl alcohol extraction and ethanol precipitation at -20°C. The 3C libraries were centrifuged at 3000 rpm for 45 min at 4°C 14,000 rpm, to pellet the samples. DNA pellets were resuspended in 70% ethanol and again centrifuged as described above. The 3C library pellets were resuspended in 300 μL dH2O and stored at −20°C. 10 μg of isolated DNA from 3C libraries of each library was sheared in dH2O using a QSonica Q800R to an average fragment size of 350bp.  After shearing, DNA was purified using AMPure XP beads. One microgram of adaptor-ligated library was used as input for the SureSelect XT capture kit using manufacturer protocol and our custom-designed 41K promoter Capture-C probe set.

value: pluripotent human testicular embryonal carcinoma

tag: restriction enzyme

value: DpnII


title: NT2-D1_rep1_ATAC-seq

description: pluripotent human testicular embryonal carcinoma cell line Replicate 1

tag: cell line


title: F_P7_hyperoxia_CD45_1_DC28_N17

city: Kensington

first: Fabio

last: Zanini

address: High and Botany St

institute: University of New South Wales

data_processing:
Mapping against human genome with VEEV-TC83-GFP added as an additional chromosome (using STAR 2.5.2b)
Counting gene expression using htseq-count 0.10
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts table: raw read counts, not notmalized, rows are gene names, columns are cell names. Metadata file: rows are cell names, columns are metadata.

source_name: distal lung

extract_protocol:
no extraction
plate-based illumina-compatible Tn5 transposase single cell RNA-Seq

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: treatment

value: hyperoxia

value: immune

tag: cell subtype

value: Mac IV

tag: mousename

tag: coverage

tag: number of genes


title: blood_old_4_scBCR-seq

tag: strain

tag: age

tag: tissue


title: C3ESa: Control iPS Replicate 1

tag: disease state

tag: cell type

value: human induced pluripotent stem cells

tag: batch


title: NT2-D1_rep2_CaptureC

tag: restriction enzyme


title: HCT116 202KO_rep1

city: St Louis

first: Tiandao

address: 4444 Forest Park Ave

institute: Washington University

description: CRISPR/Cas9 cofirmed KO of AP-2α

data_processing:
Sample processing was done by the University of Nebraska
Sequenced reads were groomed using FASTQ Groomer "Sanger and Illumina 1.8+, then processed with HISAT2, then mapped to GRCh37/hg19 whole genome using cufflinks (no bias correction), then cuffmerge cufflinks files by samples.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Human Feb.2009 (GRCh37/hg19) (hg19)

source_name: colorectal carcinoma (ATCC CCL-247)

growth_protocol: Cell lines were cultured and propagated according ATCC recommendations. HCT16: https://www.atcc.org/products/all/CCL-247.aspx#culturemethod Additionally, all media were supplemented with 10% FBS (LS26140079, Gibco, USA), 1% 100X Pen/Strep antibiotics (10378016, Gibco, USA), and 0.2% Plasmocin (Cat# ant-mpp, InvivoGen, USA). The cells were cultured in a standard humidified incubator at 37° C and 5% CO2 (16). The cells were not tested and authenticated by the authors. Only early passages of cell lines (less than 10) were used for experiments.

extract_protocol:
mRNA from cell lysates were obtained from cell lines using the Rneasy Mini Kit (Qiagen, Valencia, CA, USA). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CRISPR/Cas9-mediated TFAP2A knockout in HCC116 cell line. To minimize off-target effect we used pCas9D10A-GFP plasmid for co-expression mutant CasD10A nickase (Addgene plasmid # 44720 ; http://n2t.net/addgene:44720 ; RRID:Addgene_44720) and two gRNAs cloned as gBlocks into pCR™4-TOPO™ Vector (Thermofisher) (Guide A: ATCAAACTGTAATTAAGAA and Guide B: TTCTACATGCTGCAACAAA) within exon 3 of TFAP2A. Lipofectamine 2000 was used for DNA transfection of HCT 116 CCL-247™ cells accordingly to the manufacturer protocol (molar ratio Cas9D10A/gRNAa/gRNAb was 1/5/5). After 24 hours GFP positive cells were sorted as a single cell per well in 96 well plates. Colonies were screened after 14 days for the presence of genomic alterations (insertion/deletion) using a pair of primers TFAP2A_EX3_F1_ctrl AGC TAG CCT GTT GGC ATT ACC and TFAP2A_EX3_R1_ctrl CCT CTT GAG TTG CAA AGC CC. Disruption of ORF was confirmed by sequencing and Western Blot with AP-2 antibody.

tag: modification

value: clone 202 with CRISPR/Cas9 KO of AP-2a

tag: pasages


title: blood_young_7_scBCR-seq

value: young

value: peripheral blood


title: blood_young_6_scBCR-seq


title: HCT116 202KO_rep2

description: CRISPR/Cas9 cofirmed KO of AP-2α


title: HCT116 202KO_rep3

description: CRISPR/Cas9 cofirmed KO of AP-2α


title: blood_young_4_scBCR-seq


title: NT2-D1_rep1_CaptureC


title: HCT116 49KO_rep3

description: CRISPR/Cas9 cofirmed KO of AP-2α

value: clone 49 with CRISPR/Cas9 KO of AP-2a


title: U2OS CDT1OE doxcycyclinne genomic DNA for U2OS CDT1OE control 1&2

city: Bethesda

first: Christophe

middle: E

last: Redon

state: MD

address: 37 Convent Drive

institute: NIH

description:
Unsynchronized doxycycline-treated U2OS gennomic DNA
U2OS CDT1OE doxcycline genomic

data_processing:
Library strategy: NS-seq
For ChIP-Seq, peaks were called using the  MACS algorithms againt input. Default parameters were used for sample calling.
For nascent strand peak calling the MACS was used. Nascent strand reads were called by comparison to genomic DNA.  Peaks were filtered using the “peak-score” MACS2 metric in R (version 3.5.1) by accepting regions above the inflection-point threshold of “peak-scores” from the raw output.
Single read  75bp (NextSeq for ChipSeq) or Pair End 101, 125 and 150 bp (HiSeq or NovaSeq) for NGS sequencing
Genome_build: hg19
Supplementary_files_format_and_content: Bed file format of replication initiation peaks and ChipSeq

source_name: Osteosarcoma

growth_protocol: Cancer cells were grown in DMEM medium, 10% FBS

extract_protocol:
DNA from cell cultures was isolated, size fractionated and subject to exunuclease digestion as described in Aladjem et al., Science 281, 1005, 1998. and Wang et al., Molecular and Cellular Biology 24:3373-86, 2004. For ChipSeq, DNA molecules were enriched using antibodies against proteins of interest. Re-replicated DNA was isolated by by Brdu-cesium chloride gradient
Enriched ChIPed DNA molecules were sequenced by Illumina NextSeq 75 cycle High Output kit with single ennd of 75bp. For nascent  DNA, re-replicated DNA, paired-end libraries of genomic DNA (gDNA) were prepared using Illumina TruSeq Nano DNA Library Prep kits. Control genomic DNA was fragmented to ~ 400 bp insert size on the Covaris which generates dsDNA fragments with 3' or 5' overhangs. The sheared DNA was blunt-ended and library size selection was done using sample purification beads. A single 'A' nucleotide was added to the 3' ends of the blunt fragments to prevent them from ligating to each other during the adapter ligation reaction. A corresponding single 'T' nucleotide on the 3' end of the adapter provided a complementary overhang for ligating the adapter to the fragment. The indexed adapters were ligated to the ends of the DNA fragments and then PCR-amplified to enrich for fragments that have adapters on both ends. The final purified product was then quantitated by qPCR before cluster generation and sequencing.

treatment_protocol: Cells were treated with MLN4924 or doxyclcline to induce re-replication.

value: Cultured cancer cell line

tag: chip antibody

tag: molecule subtype

value: Genomic DNA


title: blood_young_3_scBCR-seq

data_processing:
Library strategy: scBCR-seq
Sample demultiplexing and barcode processing was performed using the Cell Ranger Single-Cell 30 Software Suite (10x Genomics). CellRanger-5.0.12 was used to align reads to the reference genome (vdj_GRCm38_alts_ensembl-5.0.0) and assemble BCRs. BCR sequencing data was processed using hte immcantation framework (immcantation.org) (46, 47). Germline V(D)J gene annotation was performed for all 10x Genomics BCR sequences using IgBLAST v1.16.0, with a curated set of Ig reference alleles specific for the C57BL/6 strain of Mus musculus (48). IgBLAST output was parsed using Change-O v0.4.6 (46). Additional quality control required sequences to be productively rearranged and have valid V and J gene annotations, consistent chain annotation (excluding sequences annotated with H chain V gene and L chain J gene), and a junction length that is a multiple of 3. Cells with exactly the same barcode and BCR sequences between different samples were excluded. Furthermore, only cells with exactly one H chain sequence paired with at least one L chain sequence were kept. After processing, there were 52509 cells with paired H and L chains and 19447 of them have paired gene expression data.
Genome_build: mm10
Supplementary_files_format_and_content: Processd BCR clonotypes. Table formatted according to standard changeo format (https://changeo.readthedocs.io/en/stable/standard.html).

extract_protocol: Library preparation was performed using the 10X Chromium VDJ + 5' Gene expression v.1 platform, up to 17,500 cells were partitioned into nanoliter Gel-bead-in-Emulsions (GEMs) droplets. Each GEM undergoes retro-transcriptase reaction to generate single-cell cDNA and receives a unique 12 nt cell barcode and unique molecular identifier (UMI). GEM cDNA was amplified for 11 cycles before being purified using SPRIselect beads. 10μl of purified cDNA was used to 5 generate the library for RNA sequencing. Libraries were sequenced on a NovaSeq S4 (Illumina, 300 cycle kit) flow cell, targeting 50K read pairs/cell.


title: U2OS CDT1OE conntrol genomic DNA for U2OS CDT1OE control 1&2

description:
Unsynchronized untreated U2OS gernomic DNA
U2OS CDT1OE control genomic


title: blood_young_2_scBCR-seq


title: blood_young_1_scBCR-seq


title: U2OS CDT1OE doxcycline Replicate 1 (Nascent strands)

description:
Unsynchronized doxycycline-treated U2OS nascent strand DNA
U2OS CDT1OE doxcycline NS-1

value: Nascent DNA


title: U2OS CDT1OE doxcycline Replicate 2 (Nascent strands)

description:
Unsynchronized doxycycline-treated U2OS nascent strand DNA
U2OS CDT1OE doxcycline NS-2


title: HCT116 49KO_rep1

description: CRISPR/Cas9 cofirmed KO of AP-2α


title: HCT116 49KO_rep2

description: CRISPR/Cas9 cofirmed KO of AP-2α


title: HCT116 24KO_rep3

description: CRISPR/Cas9 cofirmed KO of AP-2α

value: clone 24 with CRISPR/Cas9 KO of AP-2a


title: dura_old_7_scRNA-seq

data_processing:
Cell Ranger Software Suite (v3.1.0) from 10X Genomics was used for sample demultiplexing, barcode processing, and single-cell counting. Cell Ranger count was used to align samples to the reference genome GRCm38 (mm10), quantify reads, and filter reads and barcodes. Downstream analysis was performed using the Seurat package.
Genome_build: mm10
Supplementary_files_format_and_content: raw aligned barcode and feature count matrices from cellranger count (.h5)

source_name: dura

value: dura


title: dura_old_6_scRNA-seq

value: aged


title: U2OS CDT1OE control Replicate 2 (Nascent strands)

description:
Unsynchronized untreated U2OS nascent strand DNA
U2OS CDT1OE control NS-2


title: U2OS CDT1OE control Replicate 1 (Nascent strands)

description:
Unsynchronized untreated U2OS nascent strand DNA
U2OS CDT1OE control NS-1


title: HCT116 24KO_rep2

description: CRISPR/Cas9 cofirmed KO of AP-2α


title: HCT116 24KO_rep1

description: CRISPR/Cas9 cofirmed KO of AP-2α


title: H295R_AngII_control_24_rep2

city: NEW YORK

first: RUI

last: FU

address: 101 6th Ave

department: Computational Biology

institute: New York Genome Center

data_processing:
Reads were mapped using Salmon with custom index containing ERCC spike-ins and precursor transcripts. Settings for salmon quant: -l A --allowDovetail --validateMappings
Genome_build: GRCh38
Supplementary_files_format_and_content: Salmon output quant.sf files, tab-delimited text file of read counts and TPM for each sample

source_name: H295R cells

growth_protocol: H295R cells cultured in DMEM/F12 with 1% ITS and 10% CCS; cadeveric human adrenocortical cells were isolated and cultured as previously (PMC4475723)

extract_protocol:
H295R cells were washed and treated with TRIzol and RNA was extracted using ZYMO DirectZol RNA Miniprep kit. rRNA was depleted using ribozero gold; RNA from human adrenocortical cells was polyA-selected. For samples treated with 4-thiouridine, labeled RNA was biotinylated and purified using streptavidin as described previously (Methods Mol Biol. 2013;1064:91-100. doi: 10.1007/978-1-62703-601-6_6).
All RNA was made into cDNA libraries using Kappa HyperPrep kit an sequenced on Nova-seq.

treatment_protocol: 24 hours prior to stimulation of H295R cells wiht 10 nM AngII media was replaced with low sera media (DMEM/F12 with 0.1% CCS, 1% ITS); human adrenocortical cells were treated with 10 nM and 10uM of AngII and ACTH respectively.

tag: cell line

value: control, AngII 24hr


title: dura_old_5_scRNA-seq


title: dura_old_4_scRNA-seq


title: HCT116 WT_rep3

description: unmodified

value: parental cell line


title: H295R_AngII_control_6_rep2

tag: treatment

value: control, AngII 6hr


title: dura_old_3_scRNA-seq


title: HFD ethanol replicate 4

type: RNA

city: Rennes

first: Simon

last: Bucher

address: 2 Avenue du Pr. L. Bernard

institute: INSERM U1241

hyb_protocol: The same amount of Cy3-labeled cRNA (600 ng) was fragmented at 60°C for 30 min in a reaction volume of 25 μL containing 1X Agilent fragmentation buffer and 2X Agilent blocking agent according to the manufacturer's instructions. Following the fragmentation reaction, 25 μL of 2X Agilent hybridization buffer (HI-RPM) was added to the fragmentation mixture. Forty μL of the mixture were hybridized to Agilent SurePrint G3 Mouse GE v2 8x60K for 17 h at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with GE Wash Buffer 1 (Agilent) and 1 min with GE Wash buffer 2 at 37 °C (Agilent).

scan_protocol: Microarray were scanned immediately after washing with the Agilent DNA Microarray C Scanner (G2565) using one color scan setting for 8x60k array slides. The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09_ssSurrogates and Grid: 072363_D_F_20150612).

data_processing: All microarrays (n=10) were qualified (QC from feature extraction) and further analyzed using GeneSpring software (Agilent Technologies). Microarray data were first normalized based on the 75th percentile shift. Then, a filtration by “flag” and “signal intensity” was applied. Were retained only the entities in which at least 100% of the values in any of the two conditions had a “detected flag” (i.e. a positive and significant feature as defined by GeneSpring). For the filtration by signal intensity, were retained the entities in which at least 100% of the values in any one of the two conditions were within the range of interest (i.e. 20–100th percentile).

source_name: Male C57BL6J mice HFD ethanol

label_protocol: Total RNA, in presence of an external spike-in RNA mixture, were amplified and labeled with Cy3 fluorescent dye using Agilent one color low-input QuickAmp labeling kit according to the manufacturer's instructions. Starting from 150 ng total RNA purified from liver sample, amplification yield was 6.9 ± 0.7 μg cRNA and specific activity was 13.7 ± 0.4 pmol Cy3 per μg cRNA.

growth_protocol: Twenty 7-week-old male C57BL/6J +/+ mice, weighing 20 to 23 g, were purchased from Janvier (Le-Genest-St-Isle, France). Mice were accommodated in an animal care facility accredited by the French veterinary authorities (accreditation number: A35 23840). Mice were first fed ad libitum on a standard diet (SD) bringing 3 kcal/g of food (Teklad Global 16% Protein Rodent Diet, ENVIGO, Huntingdon, United Kingdom).

extract_protocol: Total RNA were extracted from around 10-15 mg of mouse liver using the Qiagen RNeasy mini kit (Qiagen, Valencia, CA, USA), according to the manufacturer’s recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: After 1 week of acclimatization, mice were split into 2 groups of 10 animals. The two groups were fed a 60% high fat diet (HFD) bringing 5.5 kcal/g (260HF V19, Safe Diet, Augy, France). After one month of HFD, one group was exposed to ethanol via the drinking water for 3 months whereas the other group was not exposed to ethanol. The HFD was maintained for both groups during this 3-month period. In the group of mice exposed to ethanol, the daily ethanol consumption was 5 g/kg body weight (bw) for the first week and then 10 g/kg bw. At the end of the 4-month experiment, mice were sacrificed by cervical dislocation Five mice per group were randomly chosen for the microarray experiments. All experiments were performed according to national guidelines for the use of animals in biomedical research and approved by the local Ethics Committee (Committee n°07; authorization number: 904-201506221708455 v4).

tag: ethanol

value: yes

tag: organ

value: liver


title: HFD ethanol replicate 3


title: HFD ethanol replicate 5


title: HCT116 WT_rep2

description: unmodified


title: HFD ethanol replicate 2


title: HFD ethanol replicate 1


title: HFD control replicate 4

source_name: Male C57BL6J mice HFD control

value: no


title: HFD control replicate 2


title: HFD control replicate 5


title: H295R_AngII_control_0_rep2

value: control, unstimulated


title: H295R_AngII_control_24_rep1


title: HFD control replicate 3


title: dura_old_2_scRNA-seq

city: St. Louis

first: Marco

address: 660 S. Euclid Ave.

institute: Washington University in St. Louis


title: HFD control replicate 1


title: T4.RNA-seq.AD

city: Shenzhen,Guangdong Province,China

first: Yayan

last: Feng

address: No. 7 pengfei road, dapeng new district, shenzhen

institute: Chinese Academy of Agricultural Sciences

data_processing:
SOAPnuke was used for trimming adapters and filtering on length and quality of the raw sequencing reads, with the following paramaters: -q 0.5 -d -Q 2 --sanger -l 20
Clean reads were mapped to respective reference genome using hisat2 with default settings
The levels of gene expression were quantified using Cufflinks (v2.2.1) with RPKM (reads per kilobase million).
Differentially expressed genes were estimated by Cuffdiff (v2.2.1) with default paramaters
Genes with a threshold false discovery rate (FDR) ≤ 0.05 and the absolute value of log2Ratio ≥ 1 or ≤ -1 were considered significantly differentially expressed
Genome_build: T1 reference genome: ABIR00000000; T4 reference genome: PRJNA451013; Other reference genomes: PRJNA257433
Supplementary_files_format_and_content: rpkm Bed format

organism: Trichinella pseudospiralis

source_name: T. pseudospiralis

extract_protocol:
Total RNA of T. spiralis (Ad, NBL and ML) was purified using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer’s instructions.
To degrade any possible DNA contamination, the total RNA samples were dissolved in diethylpyrocarbonate (DEPC)-treated water and treated with DNaseI. NanoDrop 2000 (Thermo Scientific CA, USA) was then used to assess the quantity and quality of the total mRNA enriched using oligo (dT) magnetic beads. Paired-end sequencing libraries with insert size of 300 bp were conducted on the HiSeq 2,500 platform following the Illumina’s protocols.

tag: passages

value: Adult


title: dura_old_1_scRNA-seq

last: Colonna


title: T4.RNA-seq.ML

value: Muscle larvae


title: H295R_AngII_siBTG2_24_rep2

value: siBTG2, AngII 24hr


title: T4.RNA-seq.NBL

value: Newborn larvae


title: T4.WGBS.NBL

data_processing:
Raw sequencing reads with more than 30% ‘N’s in over 10% of the sequences or smaller than 30 bp were discarded
Clean reads were aligned to the corresponding reference genome using BSMAP (v2.73) with a of maximal four mismatches and gap size up to 2 nucleotides
Methylation level of each cytosine was calculated as the number of reads ascertained methylated to the total number of reads for each covered CpG sites.
To accurately investigate the methylation levels in each sample, we used CpG sites with a minimal 5× sequencing depth per strand.
Genome_build: T1 reference genome: ABIR00000000; T4 reference genome: PRJNA451013; Other reference genomes: PRJNA257433
Supplementary_files_format_and_content: cout, bed format

extract_protocol:
DNA was extracted using the phenol chloroform extraction method
Genomic DNA extracted from three life stages of all Trichinella species were selected for libraries construction of WGBS. Briefly, approx. two to five micrograms of gDNA were first fragmented by Covaris to an average size of ~200-300 bp. End-repair, A-tailing and ligation were conducted as the Illumina PE genomic DNA sample prep kit protocol, except that ligation was performed using methylated cytosine PE adapters provided by Illumina previously. Ligation products were purified and bisulfited converted using the EZ DNA Methylation-Gold KitTM (ZYMO) according to the manufacturer’s instructions. The libraries were sequenced using Illumina HiSeq 2,500 platform.

tag: tag


title: dVHLexo_clone44

city: Vienna

first: Artem

middle: V

last: Artemov

address: Spitalgasse 4

department: Center for Brain Research

country: Austria

institute: Medical University of Vienna

data_processing:
Sequenced bcl files were converted to fastq files with cellranger 3.0.1
Reads were mapped to hg19 reference genome with Bismark software
To estimate the efficacy of C-to-T conversion, lambda phage genome was added to the reference genome. Low DNA methylation levels at cytosines in lambda phage DNA indicate good bisulfite conversion. Additionally, we estimated DNA methylation level at C positions outside the CpG context.
Differential methylation analysis was performed by MethPipe/RADmeth software package
Custom scripts were used to iterate through bisulfite bam files and estimate global DNA methylation, per-chromosome methylation levels. To find out how DNA methylation changed in individual CpG islands, we calculated the total number of methylated and unmethylated CpG's in bisulfite reads at each CpG position within the CpG island. Beta-binomial test was applied to estimate if the DNA methylation of a given CpG island significantly differed between two groups of samples.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-separated table, for each CpG island (identified by chr, start, end columns), the number of methylated and umnethylated CpG's in the bisulfite reads at positions overlapping with the island is provided (two columns for each sample)

source_name: clone44, exogenous wildtype VHL reintroduced

growth_protocol: Caki-1 and HEK293t cell lines were grown in Dulbecco’s modified Eagle medium supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin, and 2 mM L-glutamine.

extract_protocol:
VHL mutant: Human pre-natal tissue was retrieved from clinical routine abortions with oral and written consent from the patient. All procedures regarding the acquisition of human pre-natal tissue for research was approved by the Swedish Ethical Research Authority and the National Board of Health and Welfare. Post-conception age was determined using measurement of crown-rump-length (CRL) and anatomical landmarks. After identifying the adrenal glands, this tissue was retrieved and placed in ice-cold PBS pending dissociation. Tissue was chopped into 1 mm pieces and placed in 500 ul 0.05% Trypsin/0.02% EDTA (Sigma, 59417-C) and incubated at 37°C for 15 min with careful mix every 5 min. Following this, the tissue was triturated slowly and carefully with a P-1000, then P-200 pipette until complete dissociation. 500 ul 10% FBS in PBS was added to cell suspension for trypsin inactivation. Cell suspension was centrifuged at 500 rcf for 5 min at 4°C, followed by two washes with 1000 uL PBS. Cell suspension was pass though the 35 um cell strainer (Falcon, 352235 ) and spin down at 500 rcf for 5 min at 4°C. Cell pellet was resuspended in 100 ul 0.04% BSA in PBS and 400 ul of ice cold methanol was added for methanol fixation of the cells for storage. Cells suspension in cryotubes were placed in Mister Frosty (Thermo Scientific) and at -80°C for controlled cooling. Exogenous VHL: VHL-HA was subcloned to pCDF1-MCS2-EF1-Puro vector (System BioSciences). HEK293t cells were transfected with pCDF-VHL-HA, pVSV-G and pFiv-34N vectors. Viral supernatant was collected after 48 and 60 hrs, filtered through a 40um filter. Virus was precipitated by 12,5% PEG 8000 at +40C overnight followed by centrifugation at 4200g during 40 minutes at+4C. Pellet was resuspended in 300 mkl of OPTI-MEM and stored at -80C. Infections were carried out in 4ml medium using polybrene diluted 1:2,000. 100ul of viral concentrate were used per 60-mm cell plate for 12 hrs. Infected cells were selected by puromycine (2 mkg/ml).
DNA methylation was profiled by whole genome bisulfite sequencing (WGBS). Two micrograms of genomic DNA from every cell line and 4 ng of lambda phage DNA were sonicated to average size 250 bp with Covaris S2. The end repair  and an adenine was added to the 3′ end of the DNA fragments according to NebNext DNA  UltraII  protocol (NEB, USA). Preannealed forked Illumina adaptors containing 5′-methylcytosine instead of cytosine were ligated to both ends of DNA fragments using standard NEB adaptor ligation protocol (NEB, USA). Ligated fragments were treated with the sodium bisulfite and subsequent clean-up was performed with the EZ DNA MethylationTM Kit (ZymoResearch, USA) according to the manufacturer’s instructions. The bisulfite-treated DNA fragments were amplified using PCR and the following reaction: 5 µl of eluted DNA, 1 µl of NEB PE PCR two primers (1.0 and 2.0), and EpiMark® Hot Start Taq DNA Polymerase (NEB, USA). The amplification conditions were as follows: 5 min at 95 °C, 30 s at 98 °C then 15 (10 s at 98 °C, 30 s at 65 °C, 30 s at 72 °C), followed by 5 min at 72 °C. The PCR reaction was purified with AMPure XP beads (Beckman Coulter, USA), and final reduced representation bisulfite library was eluted in 30 µl EB buffer. The concentration of the final library was measured using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA). The library was sequenced on Illumina 2500 platform according to standard Illumina cluster generation and sequencing protocols.

treatment_protocol: CRISPR/CAS9–based editing was performed as described in ref. (Ran et al. 2013). Briefly, Caki1 cells were seeded on a 12-well plate. Cells were transfected with Lipofectamine 3000 with PX459-VHL plasmid  to generate frame shift which led to a stop loss in the C-terminal alpha domain of VHL (Zhigalova et al. 2017). Puromycin was applied after 24 h at a concentration of 2 μg ml−1. Cells were incubated for 72 h, passaged into a 96-well plate at a density of 1 cell per 2 wells on medium without puromycin. For further study, we have chosen three clones for each experiment. The frame shift was confirmed by Sanger sequencing of the corresponding amplicons obtained from PCR with genomic DNA.

tag: genotype

value: exogenous VHL


title: T4.WGBS.ML


title: H295R_AngII_siBTG2_24_rep1


title: dVHLexo_clone30

source_name: clone30, exogenous wildtype VHL reintroduced


title: dura_young_6_scRNA-seq

tag: strain

tag: age

value: young


title: H295R_AngII_control_6_rep1


title: dVHLexo_clone12

source_name: clone12, exogenous wildtype VHL reintroduced


title: dura_young_5_scRNA-seq

tag: tissue


title: T4.WGBS.AD


title: HCT116 WT_rep1

description: unmodified


title: H295R_AngII_siBTG2_6_rep2

value: siBTG2, AngII 6hr


title: dura_young_4_scRNA-seq


title: dVHL_clone30

source_name: VHL inactivated, clone30

value: VHL mutant


title: H295R_AngII_siBTG2_6_rep1


title: dura_young_7_scRNA-seq

value: dura


title: std_MO_4.7h

city: Beijing

first: Shuangping

last: Zheng

state: Beijing

address: Qinghuayuan 1

department: School of medicine

institute: Tsinghua University

description: No

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to zv9 whole genome using SOAPaligner/soap2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from mortazavi et al., nature method, 2008.
Genome_build: zv9
Supplementary_files_format_and_content: Excel files include RPKM values and read counts for each gene in the two samples

organism: Danio rerio

source_name: embryos

growth_protocol: Embryos were cultured in the holfretor water.

extract_protocol:
Zebrafish embryos mRNA were extracted using Qiagen RNA extraction kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Embryos were injected with 5 ng standard or Phf14 morpholinos at 1-cell stage

value: Tuebingen

tag: genotype/variation

value: standard MO injected

tag: developmental stage

value: 4.7 hpf

tag: tissue/cell type

value: whole embryos


title: phf_tMO_4.7h

description: No

value: phf14 MO injected


title: dura_young_3_scRNA-seq