|
| Status |
Public on Sep 01, 2015 |
| Title |
LNCaP 18h rep2 |
| Sample type |
SRA |
| |
|
| Source name |
prostate cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP
cell type: prostate cancer
treatment: R1881 1 nM 18 h
|
| Treatment protocol |
Cells were treated with vehicle or R1881 10 nM for 24 h.
|
| Growth protocol |
LNCaP and BicR cells were cultured in RPMI 1640 containing 10% FBS. Before hormone treatment, cells were incubated in Phenol red-free RPMI 1640 containing 2.5% charcoal/dextran treated FBS for three days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using ISOGEN reagent.
First strand cDNA was produced using Superscript III (Invitrogen). We chose AMPure RNAClean XP (Beckman Coulter) for the purification of RNA/DNA hybrids. After biotynation, the cap-trapping process, quality control was performed by measuring concentration (Oligreen). Poly-A tailing/blocking is carried out prior to HeliScope sequencing according to the instructions found in the HeliScope(TM) Low-Volume Sample Loading Protocol (LB-017 Rev. 01). .
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
CAGE |
| Instrument model |
Helicos HeliScope |
| |
|
| Description |
processed data file: LNCaP_R1881.txt
|
| Data processing |
Filter out artificial sequences from SMS file using heliscope filterSMS command. heliscope version is 1.0.389.154.
Convert SMS to FASTA format using heliscope sms2txt command. heliscope version is 1.0.389.154.
Remove sequences that match to rRNA references up to [error] errors. rRNAdust version is 1.00.
Mapped to hg19. Gene expression was measured with the number of reads aligned within a 500 bp distance from the RefSeq transcript 5′ ends, where their genomic coordinates were downloaded from the UCSC Genome Browser database.
The read counts were normalized to tags per million (tpm) based on the total number of aligned reads in the human genome reference. All CAGE tags with one or more overlapping base pair were grouped on the same strand into a single tag cluster (TC).
Genome_build: hg19
Supplementary_files_format_and_content: Excel data file including tpm of each TC for each sample
|
| |
|
| Submission date |
Feb 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Ken-ichi Takayama |
| Organization name |
Tokyo Metropolitan Institute of Gerontology
|
| Street address |
Sakaecho
|
| City |
Itabashi-ku |
| ZIP/Postal code |
173-0015 |
| Country |
Japan |
| |
|
| Platform ID |
GPL14761 |
| Series (2) |
| GSE66034 |
Genome wide analysis of androgen-regulated transcriptional startsites |
| GSE66039 |
Global analysis of androgen-signaling reveals the function of miRNAs for the epigenomic regulation in prostate cancer cells |
|
| Relations |
| BioSample |
SAMN03352372 |
| SRA |
SRX882930 |
