|
| Status |
Public on Dec 31, 2017 |
| Title |
WDR77 shRNA |
| Sample type |
SRA |
| |
|
| Source name |
WDR77 shRNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: breast cancer cell line MDA-MB-231
infection: WDR77 shRNA
treatment: Infected cells were selected with puromycin (1mg/mL) for 5 days
|
| Treatment protocol |
Cells were infected with either control or WDR77 or PRMT5 shRNA. 4 days post-infection, cells were selected with 1mg/mL puromycin (Sigma) for 5 more days and harvested for RNA extraction
|
| Growth protocol |
The human breast cancer cell line, MDA-MB-231 was obtained from ATCC and cultured in Dulbecco’s modified essential medium (DMEM) containing 10% fetal bovine serum (FBS) and passaged one or two times a week.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNEasy kit (Qiagen) and treated with RNAse free Dnase-I (Qiagen)
RNA-seq libraries were prepared from RNEasy extracted RNA samples from which rRNA was removed using Ribo-ZeroTM and following the TruSeq Stranded Total RNA Sample Prep kit protocol (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
WDR77_scrambled_1_shRNA_exp_norm.txt
|
| Data processing |
After filtering contaminant (aligned) reads, the reads with good quality were aligned to several human reference databases including hg19 genome, RefSeq exons, splicing junctions using BWA alignment algorithm.
The filtered reads that are uniquely aligned to the exon and splicing-junction sites for each transcript were then counted as expression level for a corresponding transcript
and was further subjected to log2 transformation and global median normalization, to compare transcripts levels among distinct samples.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized values for each transcript in each sample
|
| |
|
| Submission date |
Dec 07, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Martin J. Walsh |
| E-mail(s) |
martin.walsh@mssm.edu
|
| Organization name |
Mount Sinai School of Medicine
|
| Department |
Structural and Chemical Biology
|
| Street address |
One Gustave L. Levy Pl.
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (2) |
| GSE75741 |
The role of PRMT5/WDR77 complex in promoting breast cancer oncogenesis [RNA-Seq] |
| GSE75743 |
The role of PRMT5/WDR77 complex in promoting breast cancer oncogenesis |
|
| Relations |
| BioSample |
SAMN04321291 |
| SRA |
SRX1466534 |
