|
| Status |
Public on Jun 13, 2024 |
| Title |
C643 cells, kinome shRNA library, docetaxel, replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
C643
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: C643
cell type: anaplastic thyroid cancer
transduction: kinome shRNA library transduced
treatment: Docetaxel
|
| Treatment protocol |
C643 cells were treated for 14 days with 0.35 nM of docetaxel (Selleckchem, Cat #S1148) or vehicle (DMSO)
|
| Growth protocol |
C643 anaplastic thyroid cancer cells were maintained in RPMI-1650 media supplemented with 5% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
other |
| Extraction protocol |
hairpin DNA was amplified, barcoded, and sequenced (Illumina HiSeq 2500)
|
| |
|
| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
C643_DOCE3_CAC
|
| Data processing |
Raw sequencing data was analyzed as published previously (Dai Z, Sheridan JM, Gearing LJ, Moore DL, Su S, Wormald S, et al. edgeR: a versatile tool for the analysis of shRNA-seq and CRISPR-Cas9 genetic screens. F1000Research 2014;3:95 doi 10.12688/f1000research.3928.2.) using a bioinformatics pipeline based on the edgeR package in R
Supplementary files format and content: C643_Docetaxel_all_shRNAs.csv; comma separated file containing shRNA sequences, targeted kinases, shRNA sequence counts for each sample and statistical analysis
|
| |
|
| Submission date |
Mar 14, 2023 |
| Last update date |
Jun 13, 2024 |
| Contact name |
Nikita Pozdeyev |
| E-mail(s) |
nikita.pozdeyev@cuanschutz.edu
|
| Organization name |
University of Colorado
|
| Department |
Biomedical Informatics
|
| Street address |
1890 N. Revere Court | Mailstop F600
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE227290 |
Targeting the Spindle Assembly Checkpoint Pathway Synergizes with Taxanes to Inhibit Anaplastic Thyroid Cancer |
|
| Relations |
| BioSample |
SAMN33752448 |
| SRA |
SRX19669544 |
