|
Status |
Public on Apr 13, 2017 |
Title |
Input DNA |
Sample type |
SRA |
|
|
Source name |
Mouse heart
|
Organism |
Mus musculus |
Characteristics |
Stage: E12.5 tissue: Heart strain: C57BL/6 chip antibody: None
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Chromatin immunoprecipitation of Sap130 was performed with rabbit anti-Sap130 antibody (A302-491A: Bethyl laboratories, 2ug) and iDeal ChIP-seq Kit for Transcription Factors (Diagenode) following the manufacturer’s protocol ChIP-seq libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) following the manufacturer’s protocol.
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 4000 |
|
|
Data processing |
Reads were mapped to the mouse reference genome (GRCm38 from Illumina iGenomes website) using Bowtie1 (Version: 1.1.2) with the commandline options: bowtie -v 2 -t -k 2 -m 1 Peaks were called using MACS2 (Model-based Analysis for ChIP-Seq, version: MACS-2.1.0.20140616) with the command-line options: macs2 callpeak -t sap130File -c ctrlFile -f BOWTIE -g mm -B -q 0.01. (FDR cutoff of 0.01). Genome_build: mm10 Supplementary_files_format_and_content: Chromosome-wise wig files (tar) for each of Sap130 and Input and a BED file with peaks found by comparing Sap130 to Input.
|
|
|
Submission date |
Feb 09, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Cecilia W Lo |
E-mail(s) |
cel36@pitt.edu
|
Organization name |
University of Pittsburgh
|
Department |
Developmental Biology
|
Street address |
530 45th St., 8120 Rangos Research Center
|
City |
Pittsburgh |
State/province |
PA |
ZIP/Postal code |
15201 |
Country |
USA |
|
|
Platform ID |
GPL21103 |
Series (2) |
GSE77746 |
Sap130 ChIP-seq on Mouse E12.5 heart |
GSE77799 |
The complex genetics of hypoplastic left heart syndrome |
|
Relations |
BioSample |
SAMN04482117 |
SRA |
SRX1568883 |