|
| Status |
Public on May 11, 2024 |
| Title |
Control_replicate_6 |
| Sample type |
SRA |
| |
|
| Source name |
A375 cultured cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: A375 MR1
treatment: control
|
| Treatment protocol |
TC5A87 treated replicates underwent 4 consecutive rounds of killing at an E:T of 2:1 afterwhich they were allowed to recover for 24 hrs before harvesting for gDNA extraction. Control replicates were harvested after 96 hours of puromycin selection.
|
| Growth protocol |
A375-MR1-Cas9 cell were grown at 37C in RPMI-1640 supplemented with 10% fetal calf serum, 2mM L-Glutamine, 1 mM Sodium Pyruvate, 1x non-essential amino acids, and 50 ug/mL Kanamycin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA purification from cultured cells using Macharey Nagel NucleoSpin Tissue kit
PCR from gDNA and indexing using Nextera indexes following protocol of Shalem et al (2014) and standard Illumina protocols
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
A375-MR1-Cas9 expressing cells transfected with GecKO v2 library unscreened replicate 6
|
| Data processing |
Library strategy: PCR Amplicon Sequencing
reads trimmed to guide seqence using Trimmomatic version 0.36
Trimmed reads aligned to index prepared fromGecKO v2 guide RNA sequences using Bowtie version 2.2.9
Raw counts analysed using edgeR version 3.24
Genome_build: Not applicable
Supplementary_files_format_and_content: raw counts
|
| |
|
| Submission date |
Oct 29, 2020 |
| Last update date |
May 11, 2024 |
| Contact name |
Gennaro De Libero |
| E-mail(s) |
Gennaro.delibero@unibas.ch
|
| Phone |
+41612652327
|
| Organization name |
University of Basel
|
| Department |
Dept of Biomedicine
|
| Lab |
Experimental Immunology
|
| Street address |
Hebelstrasse 20
|
| City |
Basel |
| ZIP/Postal code |
4031 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE160366 |
Nucleobase adducts bind MR1 and stimulate MR1-restricted T cells |
|
| Relations |
| BioSample |
SAMN16591975 |
| SRA |
SRX9395190 |
