NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
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-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

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap