|
| Status |
Public on Apr 01, 2017 |
| Title |
siGRHL2_RNA-seq_replicate1 |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: LNCaP
transfection: siGRHL2
|
| Treatment protocol |
LNCaP cells were grown in baseline conditions (media supplemented with 10% FBS).
|
| Growth protocol |
LNCaP cells were grown in baseline conditions (media supplemented with 10% FBS).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol, according to the manufacturer's instructions.
Libraries were generated using 10 ng of RNA and NEXTflex Rapid Illumina Directional RNA-Seq Library Prep Kits
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalls performed using Illumina software
Reads were aligned using TopHat v2.0.9 in Galaxy, using default parameters and hg19 as the reference genome.
Raw counts per exon (mapped to hg19_genes_2012-03-09.gtf) were estimated using htseq-count.
Subsequently, DESeq2 (implemented in Bioconductor v2.12, R v3.0.1) was used to identify differentially expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: Text file containing normalized read counts. Read counts were normalized using the DESeq2 rlog transformation algorithm
|
| |
|
| Submission date |
Apr 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Luke Selth |
| E-mail(s) |
luke.selth@flinders.edu.au
|
| Organization name |
Flinders University
|
| Department |
College of Medicine and Public Health
|
| Street address |
Flinders Drive
|
| City |
Bedford Park |
| State/province |
SA |
| ZIP/Postal code |
5042 |
| Country |
Australia |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE80450 |
Grainyhead-like 2 is essential for androgen receptor expression and activity in prostate cancer (RNA-seq) |
| GSE80452 |
Grainyhead-like 2 is essential for androgen receptor expression and activity in prostate cancer |
|
| Relations |
| BioSample |
SAMN04870312 |
| SRA |
SRX1714582 |
