|
| Status |
Public on Apr 12, 2021 |
| Title |
LNCaP_shControl_EtOH_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP prostate cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP
genotype: shControl_puro, shControl_neo
treatment: 0.1% Ethanol, 4hours
passage: 50
|
| Treatment protocol |
These 4 LNCaP cell types were plated on 6cm culture dishes in the above culture medium and left for 2 days. They were then hormone deprived by culturing in RPMI 1640 medium (-phenol red) with 10% charcoal-stripped serum and 1% penicillin/streptomycin for 3 additional days, reaching 80% confluency. Then they were treated with either vehicle (0.1% EtOH) or 1nM of the synthetic androgen R1881 for 4 hours beofre collection of RNA.
|
| Growth protocol |
LNCaP cells are maintained on uncoated culture dishes in RPMI 1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin. LNCaP cells were previously engineered with the following shRNAs using lentivirus transduction: shControl (puromycin and neomycin constructs), shMAP3K7 (puromycin), shCHD1 (neomycin). This generated 4 groups: 1. shControl(puro/neo), 2. shMAP3K7(puro)/shControl (neo), 3. shCHD1(neo)/shControl(puro), and 4. shMAP3K7(puro)/shCHD1(neo).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After the above 4 hour treatments, total RNA was collected using the 5Prime Perfect RNA Cell Kit (Fisher Scientific) according to the manufacturer's protocol, including the optional DNAase treatment
After quality control, RNA samples were enriched for mRNA using oligo(dT) beads, fragmented for a 250-300 bp target range, then cDNA synthesis using random hexamer primers, second strand synthesis is performed using dNTPs, RNAas H and DNA polymerase I in Illumina synthesis buffer, Illumina sequencing adapters, then the double-stranded cDNA library is size selected and PCR enriched.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina HiSEQ 2000 High-throughput mode using V3 Chemistry, PE100
Libraries were prepared with the Illumina TruSEQ Stranded Total RNA with Ribo-Zero TM library preparation kit.
Gene expression was quantified using default parameter of RSEM (v1.2.1) with Bowtie2 (v2.1.0) as the read aligning program. Reads were aligned to hg19 RefSeq annotated genes
Differential gene expression was calculated using EBSeq (v1.1.5)
Genome_build: hg19
Supplementary_files_format_and_content: The raw transcript counts (LNCaP_compiled_raw) and RSEM-normalized values (LNCaP_compiled_normalized) below contain compiled data for each cell type delineated by column headers.
|
| |
|
| Submission date |
Mar 10, 2021 |
| Last update date |
Apr 12, 2021 |
| Contact name |
Lauren Jillson |
| E-mail(s) |
lauren.jillson@ucdenver.edu
|
| Organization name |
University of Colorado Anschutz Medical Campus
|
| Department |
Pharmacology
|
| Lab |
Scott Cramer
|
| Street address |
12801 E 17th Avenue, Room L18-6213, Mail stop 8303
|
| City |
Aurora |
| State/province |
Colorado |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE168663 |
RNA-Seq of LNCaP human prostate cancer cells with knockdown of MAP3K7 and/or CHD1 |
| GSE168671 |
MAP3K7 loss drives enhanced androgen signaling and independently confers risk of recurrence in prostate cancer with joint loss of CHD1 |
|
| Relations |
| BioSample |
SAMN18248730 |
| SRA |
SRX10307289 |
