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Sample GSM6919596 Query DataSets for GSM6919596
Status Public on Jan 18, 2023
Title DNase Hi-C on RUES2 differentiated to mesoderm with DNaseI - 4DNEXAIR7YJB
Sample type SRA
Source name biosource_summary: RUES2 differentiated to mesoderm
Organism Homo sapiens
Characteristics cell_line: RUES2
tissue: mesoderm
modifications_summary: None
Sex: female
treatments_summary: None
biosample_type: in vitro differentiated cells
life_stage: embryonic
Treatment protocol description: Protocol for passaging hPSCs and differentiating them to endothelial cells
Extracted molecule genomic DNA
Extraction protocol description: The Official 4DN Standard in situ DNase Hi-C Protocol adapted from Ramani et al. PMID: 27685100 and approved by SC 01-16-2018
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
Description lab: Chuck Murry, UW
award: 1U54DK107979-01
4DN accession: 4DNEXAIR7YJB
pcr_cycles: 10
submitted_by: Kris Alavattam
ligation_time: 960
biotin_removed: No
digestion_time: 7
tagging_method: Biotin dTTP
experiment_type: DNase Hi-C
ligation_volume: 1.1
digestion_enzyme: DNaseI
library_prep_kit: Kapa HiFi ReadyStart Master Mix (Roche, KK2602) with barcode-containing primers
contributing_labs: William Noble, UW
crosslinking_time: 10
biosample_quantity: 2000000 cells
crosslinking_method: 2% Formaldehyde
fragmentation_method: none
ligation_temperature: 16
digestion_temperature: 20
crosslinking_temperature: 20
fragment_size_selection_method: SPRI beads
Data processing workflow_run:
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFI8U2VCWX.bam, 4DNFIQBENVT8.bam, 4DNFIWYHWKRH.bam
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
Submission date Jan 06, 2023
Last update date Jan 18, 2023
Contact name 4DN DCIC
Organization name 4D Nucleome - Data Coordination and Integration Center
Street address 10 Shattuck St
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
Platform ID GPL18573
Series (2)
GSE222307 4DNESX5HHBRP - Replicate experiments of DNase Hi-C on RUES2 differentiated to mesoderm with DNaseI
GSE222551 Dynamic chromatin organization and regulatory interactions in human endothelial cell differentiation
BioSample SAMN32545278
SRA SRX18991173

Supplementary file Size Download File type/resource
GSM6919596_4DNFIXBHYYOM.pairs.gz 2.1 Gb (ftp)(http) PAIRS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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