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Status |
Public on Feb 24, 2014 |
Title |
RNAseq_shZMYND11-1 |
Sample type |
SRA |
|
|
Source name |
U2OS cells
|
Organism |
Homo sapiens |
Characteristics |
cell type: U2OS Cells genotype/variation: shZMYND11-#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 |
total RNA |
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.
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
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
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|
|
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 |
SAMN02222001 |
SRA |
SRX316968 |