|
| Status |
Public on Dec 31, 2019 |
| Title |
ICBP112A485_1_RNASeq |
| Sample type |
SRA |
| |
|
| Source name |
Androgen dependent prostate cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP-FGC
cell type: Androgen dependent prostate cancer cell line
treatment: ICBP112 and A485
|
| Treatment protocol |
LNCaP cells were divided into 4 different drug treatment groups (including control) and were treated with I-CBP112 and/or A-485 for 24 h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol prep with DNase digestion.
NEB prep.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
mRNA
12-17_ICBP112A485_RNASeq
12-17_2x column in Cuff_Isoform_Counts.csv file.
processed data file: Cuff_Isoform_Counts.csv
processed data file: DMSO_vs_2x.deseq.xls
|
| Data processing |
QC with RseQC.
Align with STAR.
Batch Correction with Combat.
Expression Matrix with Cufflinks.
Differential expression with DESeq2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Cuff_Isoform_Counts.csv: Comma-separated text file.
Supplementary_files_format_and_content: *.deseq.xls: Excel files include base mean counts and the fold change relative to DMSO controls.
|
| |
|
| Submission date |
Jan 03, 2019 |
| Last update date |
Dec 31, 2019 |
| Contact name |
Beth Zucconi |
| E-mail(s) |
bethzucconi@gmail.com
|
| Organization name |
Brigham & Women's Hospital
|
| Department |
Medicine
|
| Lab |
P.A. Cole
|
| Street address |
77 Avenue Louis Pasteur, NRB 164
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE124643 |
Combination Targeting of the Bromodomain and Acetyltransferase Active Site of p300/CBP [RNA-seq] |
| GSE124644 |
Combination Targeting of the Bromodomain and Acetyltransferase Active Site of p300/CBP |
|
| Relations |
| BioSample |
SAMN10690557 |
| SRA |
SRX5199681 |
