|
| Status |
Public on Oct 18, 2016 |
| Title |
KPC_shRNA_screen_+Dox_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
KPC cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: KPC
treatment1(constitutive ha-omomyc or empty vector): shRNA library
treatment2 (doxycycline to induce myc expression): Doxycycline
antibody: non
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was chloroform/phenol extracted from KPC cells and shRNA sequences were PCR amplified.
Adapter sequences were introduced during a second PCR amplification. DNA was purified with an agarose gel extraction followed by a final Biorad Experion quantification.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
KPC_shRNA_screen_logFC.txt
|
| Data processing |
For the shRNA screen, reads were mapped with Bowtie v0.12.8 (parameters: --nofw -m 1 -3 34 -v 1) to a custome reference containing the guide sequences of all 148 shRNAs present in the screen.
Reads per reference shRNA were counted and samples were normalized to the sample with the smallest number of reads.
CPM was calculated and shRNA with CPM<100 were removed.
After addition of 1 pseudo-read to every shRNA, the mean of replicates, a log2FC and a z-score were calculated.
hg19
txt file containing shRNA name, log2FC (+Dox/-Dox), z-score
Fastq files were generated using Illumina's CASAVA software.
|
| |
|
| Submission date |
Jan 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Martin Eilers |
| Organization name |
University of Wuerzburg
|
| Department |
Chair for Biochemistry and Molecular Biology
|
| Lab |
Martin Eilers
|
| Street address |
Am Hubland
|
| City |
Wuerzburg |
| ZIP/Postal code |
97074 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE77328 |
OmoMYC blunts promoter invasion by oncogenic MYC to inhibit gene expression characteristic of MYC-dependent tumors |
|
| Relations |
| BioSample |
SAMN04445830 |
| SRA |
SRX1550285 |
