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GEO accession:
Sample GSM6919591
Query DataSets for GSM6919591
Status
Public on Jan 18, 2023
Title
DNase Hi-C on RUES2 differentiated to endothelial progenitor cell with DNaseI - 4DNEX1G8JPA2
Sample type
SRA
Source name
biosource_summary: RUES2 differentiated to endothelial progenitor cell
Organism
Homo sapiens
Characteristics
cell_line: RUES2
tissue: endothelial progenitor cell
modifications_summary: None
Sex: female
treatments_summary: None
biosample_type: in vitro differentiated cells
biosource_vendor: WiCell.org
url:
https://data.4dnucleome.org/biosamples/4DNBSE8ZFQH4/
life_stage: embryonic
Treatment protocol
description: Protocol for passaging hPSCs and differentiating them to endothelial cells
download:
https://data.4dnucleome.org/protocols/5390905f-7a27-4c82-816f-5a848c1ae21d/@@download/attachment/Alavattam-Mitzelfelt_endothelial-cells_protocol_passaging-differentiation.pdf
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
download:
https://data.4dnucleome.org/protocols/1f97bb2b-180f-4a6d-b4ea-4e96c90eecdc/@@download/attachment/4DN_DNase_Hi-C_protocol_20180108.pdf
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: 4DNEX1G8JPA2
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
url:
https://data.4dnucleome.org/experiments-hi-c/4DNEX1G8JPA2/
Data processing
workflow_run:
https://data.4dnucleome.org/workflow-runs-awsem/a918b580-3715-4a99-b0cb-3036b4292210/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFILK7FOID.bam, 4DNFISKML3UE.bam, 4DNFIE3TTZ7E.bam
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline
Submission date
Jan 06, 2023
Last update date
Jan 18, 2023
Contact name
4DN DCIC
E-mail(s)
support@4dnucleome.org
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)
GSE222302
4DNES6MT2D6K - Replicate experiments of DNase Hi-C on RUES2 differentiated to endothelial progenitor cell with DNaseI
GSE222551
Dynamic chromatin organization and regulatory interactions in human endothelial cell differentiation
Relations
BioSample
SAMN32545276
SRA
SRX18991157
Supplementary file
Size
Download
File type/resource
GSM6919591_4DNFI1CFBP14.pairs.gz
1.8 Gb
(ftp)
(http)
PAIRS
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record
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