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Series GSE16940 Query DataSets for GSE16940
Status Public on Jun 04, 2010
Title An effective approach for identification of in vivo protein–DNA binding sites from paired-end ChIP-Seq data
Organism Arabidopsis thaliana
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary ChIP-Seq, which combines chromatin immunoprecipitation (ChIP) with high-throughput massively parallel sequencing, is increasingly being used for identification of protein–DNA interactions in-vivo in the genome. In general, current algorithms for ChIP-seq reads employ artificial estimation of the average length of DNA fragments for peak finding, leading to uncertain prediction of DNA-protein binding sites. Here, we present SIPeS (Site Identification from Paired-end Sequencing), a novel algorithm for precise identification of binding sites from short reads generated from paired-end Solexa ChIP-Seq technology. SIPeS uses a dynamic baseline directly via ‘piling up’ the corresponding fragments defined by the paired reads to efficiently find peaks corresponding to binding sites. The performance of SIPeS is demonstrated by analyzing the ChIP-Seq data of the Arabidopsis basic helix-loop-helix transcription factor ABORTED MICROSPORES (AMS). The robustness of SIPeS was demonstrated in higher sensitivity and spatial resolution in peak finding compared to three existing peak detection algorithms.

Keywords: transcription factors (protein-DNA interactions)
 
Overall design Examination of protein-DNA interactions in buds of Arabidopsis anther cell
 
Contributor(s) Wang C, Xu J, Zhang D, Wilson ZA, Zhang D
Citation(s) 20144209
Submission date Jul 02, 2009
Last update date May 15, 2019
Contact name dabing zhang
E-mail(s) zhangdb@sjtu.edu.cn
Organization name Shanghai Jiao Tong University
Street address Dongchuan RD 800
City Shanghai
ZIP/Postal code 200240
Country China
 
Platforms (1)
GPL9062 Illumina Genome Analyzer (Arabidopsis thaliana)
Samples (1)
GSM424618 AMS_ChIPSeq
Relations
SRA SRP002566
BioProject PRJNA117657

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE16940_RAW.tar 69.1 Mb (http)(custom) TAR (of BED, TXT)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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