|
| Status |
Public on Mar 12, 2019 |
| Title |
DCM4 Input |
| Sample type |
SRA |
| |
|
| Source name |
PCM1 positive cardiac myocyte nuclei
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: Male
age: 49
group: DCM
|
| Treatment protocol |
Not applicable
|
| Growth protocol |
Not applicable
|
| Extracted molecule |
genomic DNA |
| Extraction 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.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Data alignement Bowtie v2.1
Downsizing using Downsampke SAM feature of picard
peak calling using EDD (Enriched domain detector)
Reads were aligned to the hg19 release of the human genome by Bowtie v2.1 and each pair of input and anti-LMNA samples was adjusted so that the same read depth was achieved, using the DownsampleSam feature of Picard software on the larger of the two files. Peaks (lamin-associated domains, LADs) were calculated using EDD (Enriched domain detector) with bin size = 11 kb, gap penalty = 9, FDR = 0.05
Genome_build: HG19
Supplementary_files_format_and_content: Chromosome coordinates of the peaks present in atleast 3 samples
Supplementary_files_format_and_content: Bed coordinates for peaks for all the samples
|
| |
|
| Submission date |
Oct 04, 2018 |
| Last update date |
Mar 12, 2019 |
| Contact name |
AJ Marian |
| E-mail(s) |
Ali.J.Marian@uth.tmc.edu
|
| Phone |
7134476700
|
| Organization name |
The University of Texas Health Science Center Houston
|
| Department |
Institute of Molecular Medicine
|
| Lab |
Cardiovascular Genetics
|
| Street address |
3742 Arnold St
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77005 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE120837 |
Genomic Reorganization of Lamin-Associated Domains in Cardiac Myocytes is Associated with Differential Gene Expression and DNA Methylation in Human Dilated Cardiomyopathy [ChIP-Seq] |
| GSE120838 |
Genomic Reorganization of Lamin-Associated Domains in Cardiac Myocytes is Associated with Differential Gene Expression and DNA Methylation in Human Dilated Cardiomyopathy |
|
| Relations |
| BioSample |
SAMN10176597 |
| SRA |
SRX4797410 |
