|
| Status |
Public on Sep 30, 2014 |
| Title |
cultured cells sample 5 (T10-5) |
| Sample type |
SRA |
| |
|
| Source name |
888mel melanoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
biological sample: cells cultured in vitro for 10 days
|
| Treatment protocol |
no treatment
|
| Growth protocol |
subcutaneous tumors or cells grown in vitro with regular media
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA extracted using DNeasy Blood and Tissue kit (Quiagen). Samples were divided into half-samples and shRNAs were PCR amplified using a common reverse primer (5’-CAAGCAGAAGACGGCATACGAGATTTCTTTCCCCTGCACTGTACCC-3’) and unique forward primers, containing different 5 base-pairs index sequences, to distinguish between samples (5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCTINDEXCTTGTGGAAAGGACGAAACACCGG-3’). After a second round of PCR, all PCR products were pooled and purified (QIAquick PCR Purification Kit - QIAGEN) and submitted to next generation sequencing (Illumina HiSeq2000).
TRC-Hs1.0 kinome and related factors
|
| |
|
| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
shRNA library
|
| Data processing |
Count data was normalized with DESeq in R per pool.
Pools (n=4) were merged after normalisation.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix with normalised count data
|
| |
|
| Submission date |
Sep 28, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Oscar Krijgsman |
| E-mail(s) |
o.krijgsman@nki.nl, oscarkrijgsman@gmail.com
|
| Phone |
31205122028
|
| Organization name |
Netherlands Cancer Institute
|
| Department |
Molecular Oncology and Immunology
|
| Lab |
Peeper
|
| Street address |
Plesmanlaan 121
|
| City |
Amsterdam |
| State/province |
Outside the US or Canada |
| ZIP/Postal code |
1066CX |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE61826 |
PARALLEL IN VIVO AND IN VITRO MELANOMA RNAi DROPOUT SCREENS |
|
| Relations |
| BioSample |
SAMN03083529 |
| SRA |
SRX713876 |
