|
| Status |
Public on Oct 30, 2018 |
| Title |
LNCaP siCtrl-1 |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP_siCtrl
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP
cell type: human prostate cancer cells
passage: 20
transfected with: Allstar control siRNA
|
| Treatment protocol |
For samples 1-8, cells were transfected with either Allstar control siRNA or XBP1-specific siRNA. After two days, the cells were treated with 30 nM thapsigargin for 3 hours. For samples 9-16, LNCaP cells were treated with either DMSO or 10 μM MKC8866 for 24 h before 3h induction with 30 nM thapsigargin.
|
| Growth protocol |
LNCaP cells were cultured in regular growth medium (RPMI1640 + 10% FCS + 1%P/S + 1% Glutamine)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent.
The TruSeq stranded RNA sample prep kit was used for library generation according to Illumina's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Sample_1-LNC-1.Aligned.sortedByCoord.out.bam
|
| Data processing |
Sequenced reads were mapped to human reference genome (hg38) using STAR (2.5.2a) with default parameters.
Aligned reads were summarized into gene counts using the featureCounts (v1.5.0) command of the Subread package with default parameters in conjunction with the human gencode annotation file (hg38 release 85).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file containing raw read counts for all samples
|
| |
|
| Submission date |
Sep 14, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Lukas Simon |
| Organization name |
Baylor College of Medicine
|
| Department |
THINC
|
| Street address |
1 Baylor Plaza
|
| City |
Houston |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE103864 |
Identification of global XBP1s target gene expression in human prostate cancer cells |
|
| Relations |
| BioSample |
SAMN07647760 |
| SRA |
SRX3187310 |
