|
| Status |
Public on Feb 24, 2014 |
| Title |
ChIPseq_H3K36me3-shCTRL |
| Sample type |
SRA |
| |
|
| Source name |
U2OS cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: U2OS Cells
genotype/variation: shCTRL
chip antibody: H3K36me3, Abcam ab9050, Lot GR59748-1
|
| Treatment protocol |
For stable cell selection, 2ug/ml of puromycin was used selection and subsequent cell maintenance
|
| Growth protocol |
Cells were maintained in DMEM with 10% FBS, 5% CO2, 37oC.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For RNA seq, total RNA was extracted using QiaGen RNAplus kit. ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20.
Library was contracted by the MD Anderson DNA sequencing Core facility following standard protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed by Illumina CASAVA 1.8.2
ChIP-seq reads were aligned to the hg18 genome using Bowtie version 0.12.7
RNA-seq reads were aligned to the hg18 genome using RUM version 2.0.2
Genome_build: hg18
Supplementary_files_format_and_content: ChIP-seq wig files were generated using MACS; Scores represent the ChIP-seq tag numbers
Supplementary_files_format_and_content: RNA-seq RPKM values were extracted using RUM version 2.02
|
| |
|
| Submission date |
Jun 28, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Yuanxin Xi |
| E-mail(s) |
xiyuanxin@yahoo.com
|
| Phone |
530-220-2067
|
| Organization name |
The University of Texas MD Anderson Cancer Center
|
| Department |
Bioinformatics and Computational Biology
|
| Street address |
1400 Pressler St
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE48423 |
Histone variant H3.3-specific readout of H3K36 trimethylation by ZMYND11 links transcription elongation control to tumour suppression |
|
| Relations |
| BioSample |
SAMN02221992 |
| SRA |
SRX316961 |
