|
| Status |
Public on Jan 20, 2021 |
| Title |
control LNCaP R1881 2 |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: 10 nM R1881 overnight
genotype: control
time course: androgen deprivation 3 days
cell line: LNCaP
disease: prostate cancer
|
| Treatment protocol |
Cells were with 10 nM R1881 or ethanol vehicle for 16 hours
|
| Growth protocol |
LNCaP cell lines were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) (Hyclone; Fisher Scientific) and 1% penicillin-streptomycin (Cellgro; Mediatech, Inc.) For assays under androgen deprivation, cells were cultured in androgen-depleted RPMI: phenol red- and L-glutamine-free RPMI-1640 supplemented with 10% FBS dextran charcoal-stripped of androgens (c-FBS, Hyclone) and 1% L-glutamine (Cellgro Mediatech, Inc.). Cells were cultured on poly-d-lysine-coated plates.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy (Qiagen)
Libraries were prepared with ribodepletion using Illumina TruSeq stranded total RNA with RiboZero Gold library preparation kit. Sequencing was performed using the Illumina HiSeq4000 Sequencing system (Paired-End 50 Cycle Lane).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Sample 3
control LNCaP cells 3 days androgen deprivation with 16 h 10 nM R1881 treatment overnight - experiment two - 12-24-17
|
| Data processing |
Data was analyzed by Rosalind (https://rosalind.onramp.bio/), with a HyperScale architecture developed by OnRamp BioInformatics, Inc. (San Diego, CA).
Reads were trimmed using cutadapt. Quality scores were assessed using FastQC.
Reads were aligned using STAR.
Individual sample reads were quantified using HTseq and normalized via Relative Log Expression (RLE) using DESeq2 R library.
DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction.
Functional enrichment analysis of pathways, gene ontology, domain structure and other ontologies was performed using HOMER.
Genome_build: hg19
|
| |
|
| Submission date |
Nov 10, 2020 |
| Last update date |
Jan 20, 2021 |
| Contact name |
Michael Garabedian |
| E-mail(s) |
michael.garabedian@nyumc.org
|
| Phone |
212 263-7662
|
| Fax |
212 263-8276
|
| URL |
http://microbiology-parasitology.med.nyu.edu/node/122
|
| Organization name |
NYU School of Medicine
|
| Department |
Microbiology
|
| Street address |
550 First Avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE161170 |
Transcriptome profiles of alternative MED19 LNCaP and control LNCaP cells cultured under androgen deprivation with vehicle or R1881 |
| GSE161268 |
Stable overexpression of MED19 in androgen-dependent LNCaP cells promotes growth under conditions of androgen deprivation |
|
| Relations |
| BioSample |
SAMN16770526 |
| SRA |
SRX9474670 |
