|
| Status |
Public on Nov 13, 2014 |
| Title |
RNA-Seq_Caco-2_TET1 |
| Sample type |
SRA |
| |
|
| Source name |
Caco-2_induced
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Caco-2
cell type: colon cancer line
|
| Treatment protocol |
Caco-2 cell line stably expressing ectopic inducible TET1 was treated for 96h with Doxycyclin 1ug/ml to express TET1
|
| Growth protocol |
RPMI + 10% FCS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted using Trizol following the manufacturing protocol
library was performed using TruSeq RNA Sample Prep kit v2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
Reads for RNA-Seq were mapped on hg18 using TOPHAT v2.0.6 with the following parameters :--min-anchor=5 --min-isoform-fraction=0.01 --max-multihits=10 --bowtie1
genome_build: hg18
supplementary_files_format_and_content: wig files were generated using WIGGLES v1.2.0
|
| |
|
| Submission date |
Dec 10, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Francesco Neri |
| E-mail(s) |
francesco.neri@unito.it
|
| Organization name |
University of Torino
|
| Street address |
Via Nizza 52
|
| City |
Torino |
| State/province |
Italy |
| ZIP/Postal code |
10126 |
| Country |
Italy |
| |
|
| Platform ID |
GPL15456 |
| Series (1) |
| GSE53172 |
TET1 is a tumour suppressor that inhibits colon cancer growth by derepressing inhibitors of the WNT pathway |
|
| Relations |
| BioSample |
SAMN02439790 |
| SRA |
SRX389530 |
