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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 13, 2024 |
| Title |
Targeting the Spindle Assembly Checkpoint Pathway Synergizes with Taxanes to Inhibit Anaplastic Thyroid Cancer |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
We used cancer cell line synthetic lethal functional genomics screen to identify pathways to target in combination with taxane therapy.
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| Overall design |
Pooled kinome-wide shRNA-based dropout screen was used to identify kinases and pathways that are synthetic lethal in combination with docetaxel in C643 ATC cells. C643 cells were transduced with MISSION TRC lentiviral pooled kinome shRNA library obtained from the University of Colorado Functional Genomics Shared Resource. This library consisted of 3075 shRNAs targeting 654 kinases as well as two control libraries aimed at essential human genes and control mouse genes. C643 cells were treated for 14 days with 0.35 nM of docetaxel (Selleckchem, Cat #S1148) or vehicle. After treatment, DNA was extracted, hairpin DNA was amplified, barcoded, and sequenced (Illumina HiSeq 2500). Three biological replicates were performed. Raw sequencing data was analyzed using a bioinformatics pipeline based on the edgeR package in R. Up to six shRNA per gene were used.
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| Contributor(s) |
Pozdeyev N, Haugen B, Sharma V |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Mar 14, 2023 |
| Last update date |
Jun 13, 2024 |
| Contact name |
Nikita Pozdeyev |
| E-mail(s) |
nikita.pozdeyev@cuanschutz.edu
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| Organization name |
University of Colorado
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| Department |
Biomedical Informatics
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| Street address |
1890 N. Revere Court | Mailstop F600
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| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (6)
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| GSM7094422 |
C643 cells, kinome shRNA library, vehicle, replicate 1 |
| GSM7094423 |
C643 cells, kinome shRNA library, vehicle, replicate 2 |
| GSM7094424 |
C643 cells, kinome shRNA library, vehicle, replicate 3 |
| GSM7094425 |
C643 cells, kinome shRNA library, docetaxel, replicate 1 |
| GSM7094426 |
C643 cells, kinome shRNA library, docetaxel, replicate 2 |
| GSM7094427 |
C643 cells, kinome shRNA library, docetaxel, replicate 3 |
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| Relations |
| BioProject |
PRJNA944589 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE227290_C643_Docetaxel_all_shRNAs.csv.gz |
157.5 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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