|
| Status |
Public on Jun 16, 2016 |
| Title |
1_002OGWU_U87_GUCY1B3 |
| Sample type |
SRA |
| |
|
| Source name |
U-87 MG glioma cancer cells overexpressing sGCβ1, sGCβ1 ChIP
|
| Organism |
Homo sapiens |
| Characteristics |
originating cell line: U-87 MG
tissue derivation: malignant glioma
cell type: glioma cancer cell line overexpressing sGC-beta1
chip antibody: anti-sGC-beta1 (Sigma G4405, lot 021M4843)
|
| Treatment protocol |
None
|
| Growth protocol |
U87 cells were grown in Eagle's Minimum Essential Medium supplemented with 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and chromatins were isolated with anti-sGCβ1 antibody (Sigma G4405).
The ChIP DNA was processed into a standard Illumina ChIP-Seq library.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ChIP-seq sample
|
| Data processing |
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.
The resulting histograms (genomic "signal maps") were stored in bigWig files.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: 002OGWU_GUCY1B3_intervals_pvalues.xlsx: Excel file includes intervals.
|
| |
|
| Submission date |
Jun 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
haijie xiao |
| E-mail(s) |
hxiao@gwu.edu
|
| 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 |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE83419 |
ChIP-seq analysis of Guanylate Cyclase Soluble Subunit Beta-3 (GUCY1B3 or sGCβ1) binding to chromatin DNA |
|
| Relations |
| BioSample |
SAMN05255144 |
| SRA |
SRX1849499 |
