|
| Status |
Public on Jul 21, 2015 |
| Title |
SW480/pRTR +DOX RNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Colorectal cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
vector: pRTR
treatment: 48 hours doxycyclin
cell line: SW480
|
| Treatment protocol |
SW480 cells were treated with DOX (100 ng/ml) for 48 hours to induce ectopic expression of p53.
|
| Growth protocol |
SW480 cells and their derivatives were cultured in DMEM grwoth medium containig 10% FBS at 37°C and 5%CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the High Pure RNA Isolation Kit, Roche.
RNA libraries were prepared for sequencing using standard Illumina protocols according to standard procedures of GATC, Konstanz.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads of both samples were processed separatley in a three step procedure using the short read alignment program bowtie (version 0.12.7). First, reads were aligned to pre-rRNA sequences (18S,5.8S,28S and spacer regions). Second, unaligned reads were aligned to ENSEMBL (version 60) transcripts. Finally, the remaining unaligned reads were aligned to the human genome assembly hg19.
Bowtie alignments were performed with a seed region of 60nt, allowing up to 3 mismatches in the seed and 10 mismatches in the whole read. Reads, that could be aligned equally well to more than one position were discarded.
Gene expression values were calculated via the RPKM (reads per kilobase of gene per million mapped reads) measure.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM file including rpkm values.
|
| |
|
| Submission date |
Mar 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Sabine Huenten |
| E-mail(s) |
[email protected]
|
| Organization name |
Ludwig-Maximilians-Universitaet Muenchen
|
| Street address |
Thalkirchner Strasse 36
|
| City |
Munich |
| ZIP/Postal code |
80336 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE67109 |
Genome-wide RNA-expression analysis after p53 activation in colorectal cancer cells. |
| GSE67110 |
p53 in colorectal cancer cells |
|
| Relations |
| BioSample |
SAMN03435832 |
| SRA |
SRX961221 |
