|
| Status |
Public on Oct 06, 2023 |
| Title |
m238_gecko_ifng |
| Sample type |
SRA |
| |
|
| Source name |
M238
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: M238
cell type: Melanoma cell line
treatment: gecko_ifng
|
| Treatment protocol |
Cells were treated with or without recombinant Human IFNg (Peprotech, 800 U/ml) and harvested after 10-14 days for genomic DNA extraction.
|
| Growth protocol |
M238 cells were cultured in RPMI supplemented with 10% FBA, 10 mM HEPES, and antibiotic and antimycotic agents. Cultured cells were grown in a 37C incubator with 5% CO2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the PureLink Genomic DNA mini kit (Invitrogen) following the kit protocol.
Library preparation was performed as described in Joung et al, Nature protocols, 2017; https://0-doi-org.brum.beds.ac.uk/10.1038/nprot.2017.016.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
g_ifng
|
| Data processing |
Sequencing was performed on Illumina NextSeq 500. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software.
MAGeCK software package v0.5.9.4 was used to analyze CRISPR screen data. sgRNA counts were obtained with the "mageck count" command using the FASTQ files with sgRNA sequences from the appropriate library.
Assembly: Not applicable
Supplementary files format and content: Tab delimited files containing sgRNA counts for control and IFNg-treated samples
Supplementary files format and content: A separate file is provided for each sgRNA library used for screening
Library strategy: CRISPR screen
|
| |
|
| Submission date |
Jun 20, 2023 |
| Last update date |
Oct 06, 2023 |
| Contact name |
Ameya Champhekar |
| E-mail(s) |
achamphekar@mednet.ucla.edu
|
| Organization name |
University of California, Los Angeles
|
| Department |
Medicine, HemOnc Division
|
| Street address |
700 Tiverton Ave, 11-272 Factor Bldg
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90095-1678 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE235237 |
ERK signaling plays an essential role in the IFNg-mediated apoptosis of melanoma cells. [CRISPR screen] |
| GSE235238 |
ERK signaling plays an essential role in the IFNg-mediated apoptosis of melanoma cells. |
|
| Relations |
| BioSample |
SAMN35801023 |
| SRA |
SRX20726208 |
