|
| Status |
Public on Jun 09, 2016 |
| Title |
doxorubicin_3 |
| Sample type |
SRA |
| |
|
| Source name |
HCT116 p21-/- cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
|
| Treatment protocol |
HCT116 p21-/- cells were treated with 10 µM Nutlin-3a, 0.2 µM doxorubicin, or the solvent DMSO for 24 h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNeasy Plus Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The raw reads were mapped and the genes were counted using STAR with default parameters and UCSC hg19 reference genome
Cufflinks was used to generate FPKM values at gene level and transcript level
DESeq2 was used with default settings to calculate differential gene expression
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include mean FPKM values, log2 fold changes and p-values for each Sample
|
| |
|
| Submission date |
Feb 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Martin Fischer |
| E-mail(s) |
Martin.Fischer@leibniz-fli.de
|
| Organization name |
Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
|
| Department |
Computational Biology
|
| Lab |
Steve Hoffmann
|
| Street address |
Beutenbergstraße 11
|
| City |
Jena |
| State/province |
Thuringia |
| ZIP/Postal code |
07745 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE77841 |
mRNA-seq from Nutlin-3a, doxorubicin, and DMSO treated HCT116 p21-/- cells |
|
| Relations |
| SRA |
SRX1571360 |
| BioSample |
SAMN04501491 |
