Sample information curated by ChIP-Atlas

Antigen

Antigen Class
DNase-seq
Antigen
DNase-Seq

Cell type

Cell type Class
Cardiovascular
Cell type
Heart
MeSH Description
The hollow, muscular organ that maintains the circulation of the blood.

Attributes by original data submitter

Sample

MOLECULE
genomic DNA
DISEASE
None
BIOMATERIAL_PROVIDER
Lin Laboratory
BIOMATERIAL_TYPE
Primary Tissue
TISSUE_TYPE
Heart
TISSUE_DEPOT
Washington University, St. Louis
COLLECTION_METHOD
After the donor aorta and inferior mesenteric vein (IMV) were cannulated, the aorta was flushed with 5L of 4degC cooled histidine-tryptophan-ketoglutarate solution (HTK) and the IMV was flushed with 3L of HTK which results in the perfusion of all intra-abdominal organs with preservative solution. The abdominal cavity was cooled topically with ice during perfusion. The relevant tissues were then removed and transported to a local laboratory within 1 hour. There, the tissues were minced with a blade and 1gm of tissue was placed into a cryovial with 1mL of freezing solution (freezing solution 50mL: 25mL DMEM, 10mL Normosol-R, 10mL 25% BSA, 5mL DMSO, 1 tablet protease inhibitor) for 15min on ice. The cyrovial was then placed in a 1inch-thick styrofoam container, and then placed into -80C freezer, resulting in a slow freezing to -80C over an 1hour period.
DONOR_ID
STL001
DONOR_AGE
year 3
DONOR_HEALTH_STATUS
NA
DONOR_SEX
Male
DONOR_ETHNICITY
NA
sample_term_id
UBERON_0000948

Sequenced DNA Library

library_name
DNase.DS20383
library_strategy
DNase-Hypersensitivity
library_source
GENOMIC
library_selection
DNase

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
60591666
Reads aligned (%)
75.2
Duplicates removed (%)
10.9
Number of peaks
53005 (qval < 1E-05)

hg19

Number of total reads
60591666
Reads aligned (%)
74.7
Duplicates removed (%)
11.7
Number of peaks
52661 (qval < 1E-05)

Base call quality data from DBCLS SRA