|
| Status |
Public on Apr 13, 2017 |
| Title |
Sap130_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
Mouse heart
|
| Organism |
Mus musculus |
| Characteristics |
Stage: E12.5
tissue: Heart
strain: C57BL/6
chip antibody: Sap130 (A302-491A: Bethyl laboratories)
|
| 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 |
SAMN04482116 |
| SRA |
SRX1568882 |
