|
| Status |
Public on Apr 20, 2020 |
| Title |
Hs944T-shScr replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Hs944T
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: melanoma cell line
passages: 3
shRNA target: Scr negative control
|
| Treatment protocol |
Hs944T cells were infected with lentivirus expressing G9a-targeting or scrambled shRNAs and 72h later the cells were lysed for RNA isolation
|
| Growth protocol |
Hs944T cells were routinely cultured in DMEM with 1% penicillin/streptomycin/L-glutamine and 9% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from lysates using RNeasy (Qiagen)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Hs944T_deseq_de.csv
|
| Data processing |
Reads were aligned to the reference genome (hg19) by STAR 2.5.2.
Reads were counted by HTSeq-0.6.1 using UCSC annotation, as downloaded from the Illumina iGenomes collection.
Only reads with mapping score of 10 or more were counted.
Differentially expressed genes were detected by DESeq2, using the Wald test.
|
| |
|
| Submission date |
Mar 23, 2020 |
| Last update date |
Apr 20, 2020 |
| Contact name |
David E. Fisher |
| E-mail(s) |
[email protected]
|
| Phone |
617-643-5427
|
| Organization name |
Massachusetts General Hospital
|
| Department |
Dermatology
|
| Street address |
55 Fruit Street
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE147427 |
Gain-of-function genetic alterations of G9a drive oncogenesis II |
| GSE147429 |
Gain-of-function genetic alterations of G9a drive oncogenesis |
|
| Relations |
| BioSample |
SAMN14430906 |
| SRA |
SRX7975129 |
