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Sample GSM2058467 Query DataSets for GSM2058467
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- 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
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
BioSample SAMN04482117
SRA SRX1568883

Supplementary file Size Download File type/resource
GSM2058467_Input.wiggle.tar.gz 301.6 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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