|
| Status |
Public on Aug 15, 2024 |
| Title |
MOLM13 Idasanutlin 200nM D14 Replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
MOLM13
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MOLM13
treatment: Idasanutlin (200nM)
|
| Treatment protocol |
Samples were treated with Idasanutlin (200nM or 50nM) or DMSO for 14 days.
|
| Growth protocol |
MOLM13 cells constitutively expressing Cas9 were expanded in RPM1 supplemented with 10%FBS, 2% glutamine, and 1% Penicillin-Streptomycin to reach 300 million. Cells were then transduced with virus encoding Yusa CRISPR library and selected with puromycin and maintained in the same medium.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
30 million cells were collected from Idasanutlin-treated flasks on day 14. DNA was extracted using Qiagen DNA extraction kit.
100 micrograms of DNA were used to PCR amplify library using Herculase II enzyme following published protocols and instructions supplied by authors on Addgene (Shalem, et al Science 2014. 343(6166): p. 84-87, Tzelepis et al, Cell Rep, 2016. 17(4): p. 1193-1205)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
LIB191203BD_D14_Ida_200nM_1_L006
LIB191203BD_yusa_counts.txt
|
| Data processing |
Read Trimming: cutadapt -j 2 -n 2 -g ACGAAACACCG -a GTTTAAGAGC (Version 2.3)
Alignment: bowtie2 -p 1 -x yusa_library --norc -U {file}.trimmed.fastq {file}.tmp.sam (Version 2.3.5.1)
Conversion to BAM: samtools view -bS {file}.tmp.sam > {file}.bam (Version 1.9)
Filter to unique matches using bamtools (Version 2.5.1)
Counting reads for each sgRNA using MAGeCK: mageck count --norm-method none (Version: v0.5.8)
Assembly: Custom reference created from CRISPR library
Supplementary files format and content: Read counts per sgRNA for each sample
Library strategy: CRISPR/Cas9 Genome Wide Screen
|
| |
|
| Submission date |
Aug 16, 2023 |
| Last update date |
Aug 15, 2024 |
| Contact name |
Peter Ryabinin |
| E-mail(s) |
[email protected]
|
| Organization name |
Oregon Health and Science University
|
| Street address |
3181 SW Sam Jackson Park Rd
|
| City |
Portland |
| State/province |
OR |
| ZIP/Postal code |
97239 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE240977 |
Genome-wide CRISPR screen of MOLM13 cells after Idasanutlin treatment |
| GSE241674 |
Immune signature and monocytic leukemia cells are resistant to MDM2 inhibition |
|
| Relations |
| BioSample |
SAMN37006719 |
| SRA |
SRX21382483 |
