|
| Status |
Public on Feb 09, 2017 |
| Title |
scribKD+Tet Exp3 Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
MDCK-II cells
|
| Organism |
Canis lupus familiaris |
| Characteristics |
cell type: Madin-Darby Canine Kidney Epithelial Cells
phenotype/variation: scribble knock-down (scribKD+Tet)
|
| Treatment protocol |
Where specified, 10 µg/ml tetracycline (Tet) was added at the time of plating. Medium +/- Tet was changed one day after plating
|
| Growth protocol |
MDCK-II scribKD cells were plated at 1,300,000 cells/10 cm plate. The cells were cultured in 10 ml DMEM + 10% tetracycline-free FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
67 hours after plating, RNA was harvested using Trizol reagent
Libraries were prepared from 1 µg RNA using TrueSeq RNA sample preparation V2 kit according to the manufacturers instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
fastq file processed by filering out low quality reads (<Q20) and llow quality bases (<Q20) with sickle. Adaptors were removed with cutadapt 1.0.
RNA-seq data have been aligned to C.familaris genome using TopHat 2.0.6
RPKMs were generated using custom scripts
Genome_build: C.familiaris 3.1
Supplementary_files_format_and_content: RPKMs in tsv format
|
| |
|
| Submission date |
Mar 09, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Charles Bradshaw |
| Organization name |
University of Cambridge
|
| Department |
Gurdon Institute
|
| Street address |
Tennis Court Road
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL20988 |
| Series (1) |
| GSE79042 |
Identifying genes differentially expressed in MDCK cells with scribble knock-down (scribKD) |
|
| Relations |
| BioSample |
SAMN04543139 |
| SRA |
SRX1621045 |
