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Sample GSM1131317 Query DataSets for GSM1131317
Status Public on Jun 07, 2013
Title COUP-TFII ChIP-seq
Sample type SRA
 
Source name atria
Organism Mus musculus
Characteristics age: E13.5
chip antibody: NR2F2
chip antibody manufacturer: Active Motif
chip antibody catalog #: 61213
strain: C57BL/6
tissue: atria
Extracted molecule genomic DNA
Extraction protocol Flash frozen tissues were sent to Active Motif for chromatin extraction
Libraries were prepared by Active Motif
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1000
 
Data processing Sequence Analysis: The 50-nt sequence reads identified by the Sequencing Service (using Illumina’s Hi-Seq) are mapped to the genome using the BWA algorithm with default settings. Alignment information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, unless stated otherwise, duplicate reads (“PCR duplicates”) are removed.
Determination of Fragment Density: Since the 5 ́-ends of the aligned reads (= “tags”) represent the end of ChIP/IP-fragments, the tags are extended in silico (using Active Motif software) at their 3 ́- ends to a length of 150-250 bp, depending on the average fragment length in the size selected library (normally 150 bp). To identify the density of fragments (extended tags) along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined. This information (“signal map”; histogram of fragment densities) is stored in a Wig file.
Genome_build: mm9
Supplementary_files_format_and_content: wig
 
Submission date Apr 30, 2013
Last update date May 15, 2019
Contact name San-pin Wu
Organization name Baylor College of Medicine
Street address 1 Baylor Plaza
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL15103
Series (2)
GSE46497 Atrial Identity Is Determined by A COUP-TFII Regulatory Network (ChIP-Seq)
GSE46498 Atrial Identity Is Determined by A COUP-TFII Regulatory Network
Relations
BioSample SAMN02087274
SRA SRX272830

Supplementary file Size Download File type/resource
GSM1131317_1_NR2F2_embryo_atrial_i34_uniqnorm_signal.wig.gz 152.6 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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