|
Status |
Public on May 24, 2016 |
Title |
H3k4me1 5dpr rep1 |
Sample type |
SRA |
|
|
Source name |
heart ventricels of wild type mouse at 5-day-post-resection
|
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 |
SAMN05163528 |
SRA |
SRX1792833 |