|
| Status |
Public on Aug 23, 2023 |
| Title |
CWR22-Rv1 cells, siMLL1, repeat 1 |
| Sample type |
SRA |
| |
|
| Source name |
CWR22-Rv1 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: CWR22-Rv1 cells
cell type: Prostate cancer cell line
treatment: MLL1 knockdown
|
| Treatment protocol |
transfected with 20nM siRNA of SETD7, MLL for 3 days
|
| Growth protocol |
CWR22-Rv1 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Rneasy Mini Kit (QIAGEN) following manufacturer’s protocol
RNA libraries for RNA-seq were prepared using TruSeq Strnd Total,RNA LT (Illumina) mRNA-Seq Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were aligned to the human reference genome (hg19) using STAR (version 2.7.2) followed by counting with featureCounts (v2.0.1) from GRCh37 Ensembl reference.
Gene level read counts was produced by setting the parameter 'quantMode' as 'GeneCounts' in STAR
Assembly: GRCh37
Supplementary files format and content: tab-deliminated text files include raw gene counts
|
| |
|
| Submission date |
Nov 16, 2022 |
| Last update date |
Aug 23, 2023 |
| Contact name |
Zifeng Wang |
| E-mail(s) |
wzifeng8@gmail.com
|
| Phone |
6174709887
|
| Organization name |
UMASS Boston
|
| Department |
CPCT
|
| Lab |
Changmeng Cai
|
| Street address |
100 Morrissey Blvd, ISC/4610
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02125 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE218093 |
SETD7 functions as a transcription repressor in prostate cancer via methylating FOXA1 [RNA-seq] |
| GSE218094 |
SETD7 functions as a transcription repressor in prostate cancer via methylating FOXA1 |
|
| Relations |
| BioSample |
SAMN31756605 |
| SRA |
SRX18285247 |
