|
| Status |
Public on Feb 20, 2023 |
| Title |
Mini_screen_HCC827_end_DMSO_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Human lung adenocarcinoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Lung
genotype: Parental
cell line: HCC827
treatment: DMSO
duration: 10 doublings
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed with Tris/SDS buffer supplemented with protease inhibitor, and DNA was precipitated with 40% isopropanol
Region contatining sgRNA sequence was amplified with two sequenctial PCR and final product was gel purified--focused CRISPR mini-library was recovered
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
20bp sgRNA sequence was extracted from each read.
Each 20bp sequence was aligned to the mini CRISPR library with Bowtie.
Count table was generated through counting the frequency of each sgRNA.
Supplementary files format and content: tab-delimited counts file
Library strategy: CRISPR screen
|
| |
|
| Submission date |
Nov 21, 2022 |
| Last update date |
Feb 20, 2023 |
| Contact name |
Igor Dolgalev |
| Organization name |
NYU Grossman School of Medicine
|
| Street address |
550 1st Ave
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE218489 |
Genome-wide CRISPR/Cas9 Screens Reveal Shared and Bespoke Mechanisms of Resistance to SHP2 inhibition [CRISPR mini screen] |
| GSE218491 |
Genome-wide CRISPR/Cas9 Screens Reveal Shared and Bespoke Mechanisms of Resistance to SHP2 Inhibition |
|
| Relations |
| BioSample |
SAMN31821695 |
| SRA |
SRX18333350 |
