|
| Status |
Public on Aug 30, 2017 |
| Title |
KO_input_DNA |
| Sample type |
SRA |
| |
|
| Source name |
cardiomyocyte
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
chip antibody: none
genotype: G9a flox/flox; alphaMHC-MerCreMer +/-
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed as described elsewhere (Peters AH, et al. (2003) Mol Cell 12(6):1577–1589).
The Libraries were generated using NuGEN Ovation Ultralow System V2 1–96 kit.
ChIP-seq libraries were produced from as little as 1 ng of double-stranded DNA. The workflow consisted of three steps: end repair to generate blunt ends, adaptor ligation with optional multiplexing and PCR amplification to produce the final library.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
ChIP-seq reads were aligned to the mm10 genome assembly using bwa mem v0.7.10-r789 (PMID:19451168)
Reads with mapping quality ≤ 10 and not properly paired were removed with samtools (v1.1)
Differential peak calling was detected using THOR v0.1 (PMID: 27484474). The Input DNA signal was subtracted from each ChIP-seq signal. Differential peaks were filtered by adjusted pValue<= 0.01.
Blacklisted regions identified by the ENCODE project (The ENCODE Project Consortium, 2012) were discarded during differential peaks detection and bigwig profile creation.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.bw: the genomic distribution of ChIP-seq signal subtracted from the input DNA. These profiles were obtained using deeptools2 (PMID: 27079975) and these paramaters: -bs 10 --smoothLength 50 --ratio subtract --normalizeUsingRPKM.
Supplementary_files_format_and_content: *.bed: list of the differential peaks called by THOR after filtering
|
| |
|
| Submission date |
Jan 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Simone Serio |
| E-mail(s) |
simone.serio@humanitasresearch.it
|
| Organization name |
Humanitas Research Hospital
|
| Department |
Cardiovascular Medicine
|
| Street address |
Via Alessandro Manzoni, 56
|
| City |
Rozzano |
| State/province |
Milano |
| ZIP/Postal code |
20089 |
| Country |
Italy |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE93690 |
The genomic distribution of G9a, H3K9me2, H3K27me3 and Mef2c in cardiomyocyte-enriched populations isolated from G9a-KO and Cre mice |
| GSE93754 |
The genomic distribution and gene expression profiling of cardiomyocyte-enriched populations |
|
| Relations |
| BioSample |
SAMN06234899 |
| SRA |
SRX2497460 |
