|
| Status |
Public on Sep 28, 2017 |
| Title |
shEP400-2 rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Merkel cell carcinoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Merkel cell carcinoma cell line
cell line: MKL-1 line with Dox inducible EP400 shRNA #2
mcpyv: positive
dox treatment: +
|
| Treatment protocol |
Cells were treated with doxycycline for 5 days to induce expression of EP400 shRNA -2 and -3. Cells were treated with doxycycline for 2 days to induce expression of MYCL shRNA
|
| Growth protocol |
MKL-1 cells grow as suspension clumps in RPMI medium supplemented with 10% FBS, Penicillin-Streptomycin, and glutamax
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified from MKL-1 cells using RNeasy plus mini kit (Qiagen).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw reads were mapped or aligned to the reference organism using STAR software.
Genome_build: hg19
Supplementary_files_format_and_content: format: txt and csv files. Content: count-based differential expression
|
| |
|
| Submission date |
Jun 19, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jingwei Cheng |
| E-mail(s) |
jingweic@gmail.com
|
| Phone |
617-632-4797
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
James A. DeCaprio
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE69878 |
MCPyV ST activates Max target genes by recruiting TRRAP/EP400 complex |
| GSE100183 |
MYCL and EP400 are required for Max and MCPyV mediated gene activation |
|
| Relations |
| BioSample |
SAMN07255148 |
| SRA |
SRX2932687 |
