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Series GSE67454 Query DataSets for GSE67454
Status Public on Jun 12, 2015
Title A simple method for generating high-resolution maps of genome wide protein binding
Organisms Drosophila melanogaster; Homo sapiens; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Chromatin immunoprecipitation (ChIP) and its derivatives are the main techniques used to determine transcription factor binding sites. However, conventional ChIP with sequencing (ChIP-seq) has problems with poor resolution and newer techniques require significant experimental alterations and complex bioinformatics. Here we build upon our high-resolution crosslinking ChIP-seq (X-ChIP-seq) method and compare it to existing methodologies. By using micrococcal nuclease, which has both endo- and exo-nuclease activity to fragment the chromatin and thereby generate precise protein-DNA footprints, high-resolution X-ChIP-seq achieves single base pair resolution of transcription factor binding. A significant advantage of this protocol is the minimal alteration to the conventional ChIP-seq workflow and simple bioinformatic processing.
Overall design Using High-resolution X-ChIP-seq we determined the genome-wide binding profile of various DNA binding proteins.
Contributor(s) Skene PJ, Henikoff S
Citation(s) 26079792
Submission date Mar 31, 2015
Last update date Jul 13, 2020
Contact name Jorja Henikoff
Phone 206-667-4850
Organization name Fred Hutchinson Cancer Research Center
Department Basic Sciences
Lab Henikoff
Street address 1100 Fairview AV N, A1-162
City Seattle
State/province WA
ZIP/Postal code 98109-1024
Country USA
Platforms (3)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL17275 Illumina HiSeq 2500 (Drosophila melanogaster)
Samples (5)
GSM1647359 Mm_GFP_IN_(20140617_13)
GSM1647360 Mm_GFP_1.1x_IP_(20150213_13)
GSM1647361 Mm_GFP_1.2x_IP_(20150213_13_2)
BioProject PRJNA279984
SRA SRP056749

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
GSE67454_RAW.tar 3.1 Gb (http)(custom) TAR (of BED, WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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