|
| Status |
Public on Oct 16, 2020 |
| Title |
RKO PD-L1-EGFP reporter line with sgRNA library |
| Sample type |
SRA |
| |
|
| Source name |
Colon
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RKO
tumor type: Colon carcinoma
genotype: RKO PD-L1-EGFP reporter line
|
| Treatment protocol |
Cells were infected with the custom-made pooled sgRNA library
|
| Growth protocol |
Cells were cultured in DMEM medium supplemented with 10% fetal bovine serum and antibiotics streptomycin and penicillin at 37 degrees celsius and 5% CO2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extracted genomic DNA using DNA blood kit (Qiagen)
The samples were indexed for NGS sequencing in a successive PCR enrichment followed by purification and capillary electrophoresis (Fragment Analyzer, Agilent)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Library strategy: CRISPR screen
Sequencing reads were first trimmed with cutadapt (ver. 1.12) to remove invariable 5' and 3' ends and then scanned with PatMaN (ver. 1.2) for best matches with sgRNA sequences from the library (up to 5 mismatches were allowed).
Genome_build: hg38
Supplementary_files_format_and_content: Abundance files report transcript expression levels, as reported by salmon. The sgRNA count files are in the tsv format, were each row represents abundance of a single sgRNA. The complete list of sgRNA IDs with respective Ensembl gene IDs, gene symbols and sgRNA sequences is provided in a separate file (sgRNA_sequences.txt.gz)
|
| |
|
| Submission date |
Jan 29, 2020 |
| Last update date |
Oct 16, 2020 |
| Contact name |
Maciej Paszkowski-Rogacz |
| Organization name |
Technische Universität Dresden
|
| Department |
UCC / Medical Faculty and University Hospital Carl Gustav Carus
|
| Lab |
Medical Systems Biology (Prof. Buchholz)
|
| Street address |
Tatzberg 47/49
|
| City |
Dresden |
| ZIP/Postal code |
01307 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE144484 |
MLLT6 maintains PD‐L1 expression and mediates tumor immune resistance |
|
| Relations |
| BioSample |
SAMN13940715 |
| SRA |
SRX7647610 |
