|
Status |
Public on Apr 04, 2012 |
Title |
LNCaP_abl_Control_rep3 |
Sample type |
SRA |
|
|
Source name |
prostate cancer
|
Organism |
Homo sapiens |
Characteristics |
cell line: hormone resistant LNCaP-abl cardioglycoside treatment: Control
|
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 |
vehicle (DMSO) treatment
|
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_Control_rep3.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 |
SRX116023 |
BioSample |
SAMN00773612 |