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Series GSE83419 Query DataSets for GSE83419
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
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.
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.
Contributor(s) Xiao H, Bian K
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Submission date Jun 15, 2016
Last update date May 15, 2019
Contact name haijie xiao
Phone 2029945607
Organization name george washington University
Department Biochemistry
Lab Murad
Street address 2300 eye street
City washington
State/province DC
ZIP/Postal code 20037
Country USA
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (2)
GSM2202656 1_002OGWU_U87_GUCY1B3
GSM2202657 2_002OGWU_U87_Input
BioProject PRJNA325837
SRA SRP076633

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Supplementary file Size Download File type/resource
GSE83419_RAW.tar 610.0 Kb (http)(custom) TAR (of XLSX)
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Raw data are available in SRA
Processed data provided as supplementary file

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