 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 01, 2015 |
| Title |
HeK4me3 ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
GIST48 Cells
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: H3K4me3, Abcam, ab8580
tissue: GIST cell line
cell line: GIST48
|
| Growth protocol |
Cells were grown in log phase using standard tissue culture media.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
GIST48 cells were crosslinked for 15-minutes in 1% parformaldehyde. Cells were lysed and chromatin sheared using bioruptor. Sheared chromatin was incubated with anti-rabbit IgG dynabeads pre-conjugated with antibody, washed, eluted, reverse cross-linked, and purified.
Purified ChIP DNA was blunt-ended, ligated to Solexa adaptors, amplified with 18-cycles of PCR, and sequenced on Solexa Genome Analyzer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
G48_H3K4me3
|
| Data processing |
The sequenced reads from fastq files were mapped to hg18 using Bowtie v1.
Duplicate reads were discarded
Peaks were called against input DNA (sequencing deposited in GSE22441) using MACS 1.4
Genome_build: hg18
|
| |
|
| Submission date |
Dec 31, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Yu Chen |
| E-mail(s) |
cheny1@mskcc.org
|
| Phone |
646-888-3356
|
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Department |
Human Oncology and Pathogenesis Program
|
| Lab |
Chen
|
| Street address |
1275 York Ave, Box 20
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (1) |
| GSE64609 |
ChIP-Seq of Histone H3K4me1 and H3K4me3 in human GIST48 cells |
|
| Relations |
| BioSample |
SAMN03274271 |
| SRA |
SRX825987 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1575430_G48_H3K4me3_peaks.bed.gz |
127.7 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data included within Sample table |
|
|
|
|
 |
