|
| Status |
Public on Jan 18, 2019 |
| Title |
MDA-MB-436 shEZH2 |
| Sample type |
SRA |
| |
|
| Source name |
human MDA-MB-436 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: shEZH2 treatment
|
| Treatment protocol |
Cells were transduced with GSK343 inhibitor, shEZH2 or no treatment as control.
|
| Growth protocol |
Cells were cultured in DMEM medium with 10% FBS and penicillin/streptomycin in 37°C incubator.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Qiagen RNeasy Plus Mini Kit.
Libraries were prepared by BGI (Hongkong).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
All RNAseq fastq files were aligned to human genome (GRCh38) using STAR with parameter --outFilterMismatchNmax 2.
Gene read numbers were counted using HTSeq-count.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for all samples
|
| |
|
| Submission date |
Mar 27, 2018 |
| Last update date |
Jan 22, 2019 |
| Contact name |
Jieyi Xiong |
| Organization name |
VIB-KULeuven Center for Cancer Biology
|
| Street address |
Herestraat 49, box 912
|
| City |
Leuven |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL23227 |
| Series (1) |
| GSE112378 |
Targeting EZH2 increases the vulnerability of triple-negative breast cancer |
|
| Relations |
| BioSample |
SAMN08800368 |
| SRA |
SRX3852244 |
