Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
LMNA

Cell type

Cell type Class
Cardiovascular
Cell type
Myocytes, Cardiac
MeSH Description
Striated muscle cells found in the heart. They are derived from cardiac myoblasts (MYOBLASTS, CARDIAC).

Attributes by original data submitter

Sample

source_name
PCM1 positive cardiac myocyte nuclei
Sex
female
age
59
group
Control
antibody
anti LMNA A/C

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cardiomyocyte nuclei were isolated by FACS using anti PCM1 antibody. The nuclei were crosslinked using 1% formaldehyde for 2 min at room temperature. Crosslinked nuclei were fragmented using Bioruptor Pico (Diagenode) to achieve frgament size of 200-500bp. A portion of nuclear extract was kept aside to serve as input. Immunoprecipitation was carried out using anti LMNA A/C antibody. Immunecomplexes were washed, eluted the DNA and reverse crosslinked at 65 O/N. the DNA was precipitated after phenol chloroform extraction by glycogen. ChIP libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs, Inc.) following the manufacturer's protocol. Sequencing was done on an Illumina HiSeq3000 for sequencing using a Single Read 50 bp run.

Sequencing Platform

instrument_model
Illumina HiSeq 3000

hg19

Number of total reads
59992497
Reads aligned (%)
33.0
Duplicates removed (%)
60.9
Number of peaks
10722 (qval < 1E-05)

hg38

Number of total reads
59992497
Reads aligned (%)
34.7
Duplicates removed (%)
59.4
Number of peaks
11326 (qval < 1E-05)

Base call quality data from DBCLS SRA