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| Status |
Public on Aug 24, 2016 |
| Title |
PAtCh-Cap: input strategy for improving analysis of ChIP-exo data sets and beyond |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Recently, a number of advances have been implemented into the core ChIP-seq (chromatin immunoprecipitation coupled with next-generation sequencing) methodology to streamline the process, reduce costs or improve data resolution. Several of these emerging ChIP-based methods perform additional chemical steps on bead-bound immunoprecipitated chromatin, posing a challenge for generating similarly treated input controls required for artifact removal during bioinformatics analyses. Here we present a versatile method for producing technique-specific input controls for ChIP-based methods that utilize additional bead-bound processing steps. This reported method, termed protein attached chromatin capture (PAtCh-Cap), relies on the non-specific capture of chromatin-bound proteins via their carboxylate groups, leaving the DNA accessible for subsequent chemical treatments in parallel with chromatin separately immunoprecipitated for the target protein. Application of this input strategy not only significantly enhanced artifact removal from ChIP-exo data, increasing confidence in peak identification and allowing for de novo motif searching, but also afforded discovery of a novel CTCF binding motif.
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| Overall design |
Designed novel method for generation of a ChIP-exo input control
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| Contributor(s) |
Terooatea TW, Buck-Koehntop BA |
| Citation(s) |
27550178 |
| Submission date |
Mar 24, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Bethany Buck-Koehntop |
| E-mail(s) |
koehntop@chem.utah.edu
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| Organization name |
University of Utah
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| Department |
Chemistry
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| Street address |
315 S 1400 E, rm 2020
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| City |
Salt Lake City |
| State/province |
Utah |
| ZIP/Postal code |
84112 |
| Country |
USA |
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| Platforms (1) |
| GPL9052 |
Illumina Genome Analyzer (Homo sapiens) |
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| Samples (7)
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| This SubSeries is part of SuperSeries: |
| GSE79565 |
Input Strategy for Improving Analysis of ChIP-exo Data and Beyond |
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| Relations |
| BioProject |
PRJNA316190 |
| SRA |
SRP072271 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE79563_CTCFnoinput_summits.bed.gz |
543.0 Kb |
(ftp)(http) |
BED |
| GSE79563_CTCFvsInput_summits.bed.gz |
252.2 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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