|
| Status |
Public on Nov 23, 2016 |
| Title |
siControl rep3 |
| Sample type |
SRA |
| |
|
| Source name |
siControl rep3
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: colon cancer
cell line: HCT116
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified using the Trizol standard protocol and treated with heat-labile dsDNAse (Thermo scientific)
libraries were produced from 150ng total RNA with Nugen complete RNAseq library system according to the manufacturers protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
SCR3
|
| Data processing |
Basecalling was done by RTA1.18.64
Truseq adapter and polyA were removed
reads were aligned to the human genome by STAR RNAseq read mapper
reads overlapping with annotated genes were counted with HTseq count
variance stabilisation and differential gene expression were done by DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: raw count table from HTseq count and vst tranformed expression values from DEseq2
|
| |
|
| Submission date |
Mar 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Stefan Krebs |
| E-mail(s) |
krebs-st@lmb.uni-muenchen.de
|
| Phone |
0049-89-2180 76715
|
| Organization name |
Ludwig-Maximilian University
|
| Department |
Gene Center
|
| Lab |
Lafuga Genomics
|
| Street address |
Feodor-Lynen-Str. 25
|
| City |
Munich |
| ZIP/Postal code |
81377 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18460 |
| Series (1) |
| GSE79395 |
Knockdown of ADNP in HCT116 colon cancer cells |
|
| Relations |
| BioSample |
SAMN04568490 |
| SRA |
SRX1643434 |
