|
| Status |
Public on May 24, 2016 |
| Title |
H3k4me1 sham rep2 |
| Sample type |
SRA |
| |
|
| Source name |
heart ventricels of wild type mouse at 5-day-post sham surgery
|
| Organism |
Mus musculus |
| Characteristics |
development stage: Postnatal day 6
tissue compartment: ventricles
|
| Treatment protocol |
For ChIP-Seq, P2 LAD-O was performed on Pitx2flag neonates, and 4 days later whole ventricles were collected and subjected to the ChIP-Seq.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Monoclonal anti-Flag BioM2 antibody (Sigma-Aldrich) was used for pulling down Pitx2-Flag.
ChIP libraries were constructed using Kapa Library Preparation Kits for Ion Torrent (Kapa Biosystems)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
Chromatin-immunoprecipitated DNA
|
| Data processing |
Basecalling is performed by Ion Suite version 5.0.4, with BaseCaller script: BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --num-unfiltered 1000 --barcode-filter-postpone 1
Reads are aligned to mouse genome mm9 with Ion Torrent Tmap aligner (v5.0.13): tmap mapall map4
Peak calling were performed by Homer v4.8.1, with findPeaks -style factor for fix-sized transcription factors binding peaks and -style histone for histone marks
Bedgraphs were generated by Homer v4.8.1, with makeUCSCfiles, by default, normalized to 10M reads.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph, The bedGraph format allows display of continuous-valued ChIP-Seq data in track format.
Supplementary_files_format_and_content: bed, genomic interval of ChIP-Seq peaks.
|
| |
|
| Submission date |
May 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Min Zhang |
| E-mail(s) |
minzhang5099@gmail.com
|
| Organization name |
Baylor College of Medicine
|
| Department |
Department of Molecular Physiology
|
| Lab |
James F Martin
|
| Street address |
One Baylor Plaza Room 504E
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL18635 |
| Series (1) |
| GSE70413 |
Pitx2 promotes heart repair by transcriptionally activating the antioxidant response after cardiac injury |
|
| Relations |
| BioSample |
SAMN05163527 |
| SRA |
SRX1792832 |
