|
| Status |
Public on Oct 16, 2012 |
| Title |
Transcription Start Site Sequencing of LNCaP Cells |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP
|
| Growth protocol |
Cells were grown at 37ºC with 5% CO2 in T medium with 10% fetal calf serum.
See SAMPLES section.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
DeepCAGE was performed by the service provider GeneWorks (www.geneworks.com.au)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
CAGE |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
5' cap-selected single-stranded cDNA
|
| Data processing |
Nine bases were removed from the 5' end of every read, as these are of the multiplexing barcode. Two bases were removed from the 3' end of every read, as these sometimes belonged to the adapter.
Reads were mapped with bowtie 0.12.7 Only reads mapping uniquely to the genome were kept. Upto 3 mismatches to the reference sequence were allowed.
Genome_build: hg18
Supplementary_files_format_and_content: BigWig. After mapping, only the first base position of each read was used, and the number of bases per 1 million bases mapped was calculated for each genomic position.
|
| |
|
| Submission date |
Jun 13, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Aaron Statham |
| E-mail(s) |
a.statham@garvan.org.au
|
| Organization name |
Garvan Institute of Medical Research
|
| Department |
Cancer Department
|
| Lab |
Epigenetics Research Laboratory
|
| Street address |
384 Victoria St
|
| City |
Darlinghurst |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE38677 |
Mapping of Transcription Start Sites of Normal and Cancerous Prostate Cells |
| GSE38685 |
Normal and Cancerous Prostate Cells |
|
| Relations |
| SRA |
SRX154492 |
| BioSample |
SAMN01048174 |
