|
| Status |
Public on Feb 05, 2018 |
| Title |
89_LP_41299 |
| Sample type |
SRA |
| |
|
| Source name |
Prostate
|
| Organism |
Mus musculus |
| Characteristics |
genotype: ARR2PB-Cre;Ptenflox/flox
strain: FVB
age in months: 12.1
prostate lobe: LP
tumour stage: high-stage tumour
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Prostates were removed, flash frozen on dry ice or immersed in RNA Later, homogenized by bead beating vortex and RNA was harvested using Allprep DNA/RNA/Protein Mini Kit Qiagen. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using 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: GRCh38
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 |
GPL17021 |
| Series (2) |
| GSE94574 |
A Cross-Species Approach Identifies MELK as a Potential Therapeutic Target in Prostate Cancer |
| GSE101539 |
Cross-Species Approach Identifies MELK as a Potential Therapeutic Target in Prostate Cancer |
|
| Relations |
| BioSample |
SAMN06308337 |
| SRA |
SRX2540669 |
