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| Status |
Public on Aug 24, 2016 |
| Title |
Input Strategy for Improving Analysis of ChIP-exo Data and Beyond [RNA-Seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Several recently emerging ChIP-seq (chromatin immunoprecipitation followed by sequencing) based methods perform chemical steps on bead-bound immunoprecipitated chromatin, posing a challenge for generating similarly treated input controls required for bioinformatics and data quality analyses. Here we present a versatile method for producing technique-specific input controls for ChIP-based methods that utilize additional bead-bound processing steps. Application of this method allowed for discovery of a novel CTCF binding motif from ChIP-exo data.
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| Overall design |
HeLa cells were transfected with either a scrambled siRNA or one of two CTCF siRNAs (Thermo Fisher Scientific ? Life technologies) using Lipofectamine RNAiMAX (Thermo Fisher Scientific - Life technologies) and incubated for 24 hr.
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| |
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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
|
| Organization name |
University of Utah
|
| Department |
Chemistry
|
| Street address |
315 S 1400 E, rm 2020
|
| 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 (9)
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| This SubSeries is part of SuperSeries: |
| GSE79565 |
Input Strategy for Improving Analysis of ChIP-exo Data and Beyond |
|
| Relations |
| BioProject |
PRJNA316189 |
| SRA |
SRP072272 |
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