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Sample GSM7507912 Query DataSets for GSM7507912
Status Public on Jun 30, 2023
Title THP-1-libA T0
Sample type SRA
 
Source name AML cells
Organism Homo sapiens
Characteristics cell type: THP-1 cells
cell line: AML
Treatment protocol For CRISPR-PoolTM SAM Screening, cells were transfected with MS2-P65-HSF-Hygro lentivirus and selected with 500 μg/mL hygromycin B (Invitrogen) for 120 h. Then, the sgRNA-dCas9-VP64-blasticidin lentivirus was added to the infected cells and passaged for 2 days. The cells were treated with 4 μg/mL blasticidin (Sigma-Aldrich) for 5 days, and the uninfected control cells were completely killed. After setting aside as a Day 0 baseline for sequencing, the THP-1 cells were then divided into two groups, one that was free to grow and the other that was given constant low doses of IDA treatment. The screening process lasted 7 days.
Extracted molecule total RNA
Extraction protocol sgRNA assays data analysis was performed as previously described (Julia Joung et al., 2017). In brief, genomic DNA quality was assessed by Uv absorption spectrum, Qubit DNA quantification and Agilent 4150 Tapestation System after extraction from the samples. The genomic DNA library was prepared using the CRISPR2 "Self-balancing library preparation technique" and "Non-bias sgRNA fragment capture technique" developed by Gikegiin. After the completion of PCR library construction, 0.4x and 0.8x AMPure Beads were used to purify product DNA to remove residual primer, template and other sequencing interferences. Agilent 4150 TapeStation High Sensitive D1000 Assay was used to evaluate library quality. The mixed library was sequenced by Illumina HiSeq X and decomposed into each sample data using index sequence. SgRNA reads were obtained from one-way reads and then compared with sgRNA library sequences. Data containing sgRNA are obtained in turn. After illumina sequencing, all the data were visualized using R version 4.0.2 (R development core team).
RNA libraries were prepared for sequencing using standard Illumina protocols
sgRNA sequencing
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Data processing Cells were transfected with MS2-P65-HSF-Hygro lentivirus and selected with 500 μg/mL hygromycin B (Invitrogen) for 120 h. Then, the sgRNA-dCas9-VP64-blasticidin lentivirus was added to the infected cells and passaged for 2 days. The cells were treated with 4 μg/mL blasticidin (Sigma-Aldrich) for 5 days, and the uninfected control cells were completely killed. After setting aside as a Day 0 baseline for sequencing, the THP-1 cells were then divided into two groups, one that was free to grow and the other that was given constant low doses of IDA treatment. The screening process lasted 7 days.
 
Submission date Jun 23, 2023
Last update date Jun 30, 2023
Contact name Chunyan Ji
Organization name Qilu Hospital
Street address Wenhua West Road
City Jinan
ZIP/Postal code 250000
Country China
 
Platform ID GPL11154
Series (1)
GSE235688 Genome wide CRISPR screen in AML chemotherapy resistance.
Relations
BioSample SAMN35881793
SRA SRX20765591

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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