GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE60142 Query DataSets for GSE60142
Status Public on May 25, 2016
Title The DNA affinity purification DAP-Seq assay [ChIP-seq]
Organism Arabidopsis thaliana
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary As 5-15% of higher eukaryotes genes are transcription factors (TFs), the lack of transcription factor binding site (TFBS) information for most factors in most organisms limits the study of gene regulation. Here we describe a next-generation sequencing method, DNA affinity purification (DAP-Seq), an in vitro gDNA/TF interaction assay that produces whole-genome TFBS annotation for any factor from any organism. Like ChIP-Seq, DAP-Seq resolves TFBS as discrete peaks at genomic locations which allows for accurate motif prediction direct assignment of functionally relevant target genes, and shows better overlap with ChIP-Seq peaks than indirect motif assignment approaches. We applied DAP-Seq to a set of 50 transcription factors in eight Arabidopsis thaliana and one Zea Mays families to gain novel biological insight into TFBS architectures, functions, evolution and methylation-sensitivity. Overall, DAP-Seq offers a low-cost high-throughput approach to identify TFBS in native sequence context for any organism complete with all DNA chemical modifications.
Overall design Identification of binding sites for 53 transcription factors (52 Arabidopsis thaliana, 1 Zea mays) by direct sequencing of affinity purified genomic DNA fragments. Comparison to ChIP-Seq for ABI5 (AT2G36270).
Contributor(s) O'Malley RC, Huang SC, Song L, Bartlett A, Galli M, Gallavotti A, Nery JR, Ecker JR
Citation(s) 27203113
Submission date Aug 06, 2014
Last update date May 15, 2019
Contact name Joseph R Ecker
Phone 8584534100
Organization name HHMI-Salk-Institute
Department Genomic Analysis Laboratory
Lab Ecker lab
Street address 10010 North Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
Platforms (1)
GPL17639 Illumina HiSeq 2500 (Arabidopsis thaliana)
Samples (6)
GSM1466341 ChIPSeq-ABI5_Ab
GSM1466342 ChIPSeq-IgG_mock
GSM1466343 ChIPSeq-ABI5_Ypet_1
This SubSeries is part of SuperSeries:
GSE60143 In vitro, genomic context identification of transcription factor binding sites
BioProject PRJNA257558
SRA SRP045297

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
GSE60142_ChIPSeq-ABI5_YPet.chr1-5_macs02_peaks.narrowPeak.gz 269.9 Kb (ftp)(http) NARROWPEAK
GSE60142_RAW.tar 100.0 Kb (http)(custom) TAR (of NARROWPEAK)
SRA Run SelectorHelp
Processed data provided as supplementary file
Processed data are available on Series record
Raw data are available in SRA

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