|
| Status |
Public on Jul 31, 2017 |
| Title |
DIP2C -/- Cl. E3 |
| Sample type |
SRA |
| |
|
| Source name |
DIP2C -/- Cl. E3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: human colorectal cancer cell line RKO
genotype/variation: DIP2C -/-
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using an RNeasy Plus Mini kit (Qiagen). The RNA integrity and concentration was determined on a Bioanalyzer instrument (Agilent) using an RNA 6000 Nano kit.
For preparation of samples for RNA sequencing, 1 x10e6 cells were plated and grown for 48 h. The cells were then detached by trypsination and 2 106 cells were pelleted for RNA isolation. RNA samples were prepared using the Qiagen RNeasy Mini kit with on-column DNase treatment according to the provided protocol. RNA quality and concentration was determined by analysis on a Bioanalyzer 2100 instrument using the RNA 6000 nano chip (Agilent).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
DIP2C -/- Cl. E3
|
| Data processing |
The reads were aligned to the human genome hg19 assembly (https://genome.ucsc.edu) using Tophat2 software (version 2.0.4)
The normalized counts summary and statistical tests were performed using the Cufflinks tool (version 2.2.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with normalized counts values for each Sample.
|
| |
|
| Submission date |
Apr 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
L. H. |
| Organization name |
Uppsala University
|
| Street address |
Dag Hammarskjölds Väg 20
|
| City |
Uppsala |
| ZIP/Postal code |
751 85 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL17303 |
| Series (1) |
| GSE80746 |
Gene regulation of candidate cancer gene DIP2C |
|
| Relations |
| BioSample |
SAMN04910144 |
| SRA |
SRX1734396 |
