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| Status |
Public on Jun 16, 2016 |
| Title |
ChIP-seq analysis of Guanylate Cyclase Soluble Subunit Beta-3 (GUCY1B3 or sGCβ1) binding to chromatin DNA |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
To identify sGCβ1 binding sites to chromatin DNA, we performed ChIP analysis by using anti-sGCβ1 antibody (Sigma G4405). We have successfully identified 4169 intervals. In this study, sGCβ1 was found to bind to many genes' promoter region.
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| Overall design |
We used U-87 MG (ATCC® HTB-14) glioma cells which overexpress sGCβ1 (generated by us) to perform ChIP assay by using anti-sGCβ1 antibody (Sigma G4405) and genome-wide sGCβ1 binding was determined with sequencing. The ChIP DNA was processed into a standard Illumina ChIP-Seq library and sequence. The 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the hg19 genome using the BWA algorithm with default settings. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. Intervals (= Peaks) were determined using the MACS peak finding algorithm.
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| Contributor(s) |
Xiao H, Bian K |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Jun 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
haijie xiao |
| E-mail(s) |
hxiao@gwu.edu
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| Phone |
2029945607
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| Organization name |
george washington University
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| Department |
Biochemistry
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| Lab |
Murad
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| Street address |
2300 eye street
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| City |
washington |
| State/province |
DC |
| ZIP/Postal code |
20037 |
| Country |
USA |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA325837 |
| SRA |
SRP076633 |
