|
| Status |
Public on Dec 20, 2021 |
| Title |
LV.Input.ChIP.WT2 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse heart left ventricle
|
| Organism |
Mus musculus |
| Characteristics |
genetic manipulation: Mock
strain: C57BL/6
tissue: left ventricle
chip antibody: none
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Isolated LV, RV or whole ventricles (atria removed) of E13.5 mouse hearts were dissected and tear to smaller pieces by forceps. Tissues were then dual crosslinked by EGS and formaldehyde and followed by sonication and immunoprecipitation with PRDM16 antibody.
For library preparation, ChIP or input DNA were end repaired, ligated with barcoded adaptors, amplified and purified using Kapa HyperPrep PCR-free Kit and Kapa Real Time Amplification Kit. DNA fragments in the range of 200-500 bp were selected using a PippinHT Size Selection System.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Sequencing reads were aligned to the mouse genome (GRCm38, mm10) using bwa (version: 0.7.12-r1039)
ChIP-seq peaks were called using MACS2 (version: 2.1.1.20160309, default parameters). For WT samples, BED files were generated from merging reads from two WT replicates.
Motif analysis was carried out using Homer.
Differential binding analysis was calculated using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited WT and Prdm16cKO narrow peak files generated by MACS2 by combining reads from the same genotype.
Supplementary_files_format_and_content: tab-delimited diffbinding density between LV and RV was generated by DESeq2.
|
| |
|
| Submission date |
Jul 02, 2021 |
| Last update date |
Dec 20, 2021 |
| Contact name |
Ju Chen |
| E-mail(s) |
juchen@health.ucsd.edu
|
| Organization name |
University of California San Diego
|
| Street address |
9500 Gilman Drive 0613
|
| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92122 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE179371 |
PRDM16 Functions as A Compact Myocardium-Enriched Transcription Factor Required to Maintain Compact Myocardial Cardiomyocyte Identity in Left Ventricle (ChIP-seq) |
| GSE179393 |
PRDM16 Is a Compact Myocardium-Enriched Transcription Factor Required to Maintain Compact Myocardial Cardiomyocyte Identity in Left Ventricle |
|
| Relations |
| BioSample |
SAMN20023681 |
| SRA |
SRX11343247 |
