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GEO accession:
Sample GSM6919593
Query DataSets for GSM6919593
Status
Public on Jan 18, 2023
Title
DNase Hi-C on RUES2 with DNaseI - 4DNEX561P4FA
Sample type
SRA
Source name
biosource_summary: RUES2
Organism
Homo sapiens
Characteristics
cell_line: RUES2
tissue: stem cell
modifications_summary: None
Sex: female
treatments_summary: None
biosample_type: stem cells
biosource_vendor: WiCell.org
url:
https://data.4dnucleome.org/biosamples/4DNBSLLKDVNY/
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: 4DNEX561P4FA
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/4DNEX561P4FA/
Data processing
workflow_run:
https://data.4dnucleome.org/workflow-runs-awsem/9ab3f706-a3e0-4e51-9a87-7c69478206bb/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFIIUMOSSK.bam, 4DNFISDNQN8Q.bam, 4DNFIL988Y1F.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)
GSE222303
4DNES8R5RDVD - Replicate experiments of DNase Hi-C on RUES2 with DNaseI
GSE222551
Dynamic chromatin organization and regulatory interactions in human endothelial cell differentiation
Relations
BioSample
SAMN32545279
SRA
SRX18991159
Supplementary file
Size
Download
File type/resource
GSM6919593_4DNFIZU6KA1G.pairs.gz
1.3 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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