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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 21, 2024 |
| Title |
In vivo CRISPR screens in mouse model of bladder cancer |
| Organisms |
Mus musculus; synthetic construct |
| Experiment type |
Other
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| Summary |
To systematcially explore targets that can regulated tumor's response to immune checkpoint therapy, we performed an in vivo targeted CRISPR knockout screen in a mouse model of bladder cancer. Cas9-expressing MB49 cells were transfected with two sub-libraries to make two cell pools. We first validated full representation of sgRNA composition in cell pools by comparing to that in the plasmid pools. For in vivo screen, we first compared PBS or anti-PD-1 treated tumors to original cell pools to get condition specific change, then compared anti-PD-1 treated tumors to PBS treated tumors to identify genes that may regulate anti-PD-1 response.
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| Overall design |
Examination of sgRNA composition in plasmids, cell pools, tumors treated with PBS or anti-PD-1
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| Contributor(s) |
Liu J |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Jun 22, 2023 |
| Last update date |
Jun 21, 2024 |
| Contact name |
Jielin Liu |
| Organization name |
MD Anderson Cancer Center
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| Department |
Genitourinary Medical Oncology
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| Street address |
7455 Fannin St
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77054 |
| Country |
USA |
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| Platforms (2) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL19424 |
Illumina NextSeq 500 (synthetic construct) |
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| Samples (20)
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| GSM7505954 |
plasmid library B, replicate 2 |
| GSM7505955 |
cell pool A, replicate 1 |
| GSM7505956 |
cell pool A, replicate 2 |
| GSM7505957 |
cell pool B, replicate 1 |
| GSM7505958 |
cell pool B, replicate 2 |
| GSM7505959 |
tumor with cell pool A, PBS treated, replicate 1 |
| GSM7505960 |
tumor with cell pool A, PBS treated, replicate 2 |
| GSM7505961 |
tumor with cell pool A, PD1 treated, replicate 1 |
| GSM7505962 |
tumor with cell pool A, PD1 treated, replicate 2 |
| GSM7505963 |
tumor with cell pool B, PBS treated, replicate 1 |
| GSM7505964 |
tumor with cell pool B, PBS treated, replicate 2 |
| GSM7505965 |
tumor with cell pool B, PBS treated, replicate 3 |
| GSM7505966 |
tumor with cell pool B, PBS treated, replicate 4 |
| GSM7505967 |
tumor with cell pool B, PD1 treated, replicate 1 |
| GSM7505968 |
tumor with cell pool B, PD1 treated, replicate 2 |
| GSM7505969 |
tumor with cell pool B, PD1 treated, replicate 3 |
| GSM7505970 |
tumor with cell pool B, PD1 treated, replicate 4 |
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| Relations |
| BioProject |
PRJNA986512 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE235588_PBS_counts.csv.gz |
152.1 Kb |
(ftp)(http) |
CSV |
| GSE235588_PD1_counts.csv.gz |
150.7 Kb |
(ftp)(http) |
CSV |
| GSE235588_plasmid_and_cell_pool_counts.csv.gz |
298.6 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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