|
| Status |
Public on Feb 05, 2018 |
| Title |
siCtrl_4 |
| Sample type |
SRA |
| |
|
| Source name |
Prostate cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: C4-2b
treatment type: Transient transfection
treatment agent: Negative control siRNA
treatment duration: 72 h
|
| Growth protocol |
Cells were grown at 37 °C and 5% CO2 in RPMI 1640 supplemented with 10% fetal bovine serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the RNeasy Plus Mini Kit according to the manufacturer’s instructions.
Library preparation was carried out using the Illumina® TruSeq Stranded mRNA Library Prep Kit (Life Technologies) according to standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Single-end 50 bp reads generated on Illumina HiSeq were aligned to the human genome version GRCh37.64 using TopHat v2.0.4 (Trapnell et al., 2009). Read counts were obtained using HTSeq-count v0.5.3p9 (Anders et al., 2014), normalised and tested for differential gene expression using the Bioconductor package DESeq v1.10.1 (Anders and Huber, 2010).
Multiple testing corrections were applied using the Benjamini-Hochberg method (Benjamini and Hochberg, 1995). Genes were selected as differentially expressed such that FDR < 0.01.
Genome_build: GRCh37.64
Supplementary_files_format_and_content: HTSeq-count gene counts
|
| |
|
| Submission date |
Feb 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Chandra Chilamakuri |
| E-mail(s) |
datasubmissions@cruk.cam.ac.uk
|
| Organization name |
Cancer Research UK Cambridge Institute
|
| Street address |
Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE94570 |
Identification of MELK-regulated genes in prostate cancer cells using next-generation sequencing |
| GSE101539 |
Cross-Species Approach Identifies MELK as a Potential Therapeutic Target in Prostate Cancer |
|
| Relations |
| BioSample |
SAMN06308311 |
| SRA |
SRX2540566 |
