|
| Status |
Public on Apr 04, 2012 |
| Title |
LNCaP_abl_Strophanthidin_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
prostate cancer
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: hormone resistant LNCaP-abl
cardioglycoside treatment: Strophanthidin
|
| Growth protocol |
LNCaP-abl cells were cultured in Phenol red-free RPMI 1640 containing 10% charcoal/dextran treated FBS, plus 2 mM GlutaMax, 10 mM HEPES, 1 mM Sodium Pyruvate, 2.5 mg/ml D-(+)-Glucose.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted from LNCaP-abl cells using TRIzol Reagent (Life Technologies, cat# 15596-026) . The cDNAs were synthesized with biotinylated P7-dT(20) oligos by reverse transcription and captured to solid phase. The second strand cDNAs were made with Adpator-hexamer by extension using DNA polymerase. The second strand cDNAs were PCR amplified with P7 and P5-index-Adaptor primers. The PCR products were size-selected, pooled and subjected to Illumina sequencers, reading target sequences followed by reading index (Genomics. 2011:98;266)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
5 uM Strophanthidin treatment for 24 hours
|
| Data processing |
The tags were mapped to the reference human genome( hg19) with Bowtie by allowing maximum 2 mismatches in the first 28 nt.
Genome Build:
LNCaP_abl_Strophanthidin_rep1.bed: hg19
|
| |
|
| Submission date |
Jan 16, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Hai-Ri Li |
| E-mail(s) |
hairili@ucsd.edu
|
| Phone |
858-534-4926
|
| Organization name |
University of California, San Diego
|
| Department |
Medicine
|
| Lab |
Dr. Francesca Telese
|
| Street address |
9500 Gilman Dr.
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (1) |
| GSE35126 |
Effects of Cardiac Glycosides on RNA Expression in Prostate Cancer LNCaP-abl Cells |
|
| Relations |
| SRA |
SRX116030 |
| BioSample |
SAMN00773619 |
