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| Status |
Public on Dec 31, 2020 |
| Title |
Invariant Differential Expression Analysis Reveals Mechanism of Cancer Resistance to Cell Cycle Inhibitors |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Third-party reanalysis
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| Summary |
Cell cycle inhibitors are commonly used drugs against cancer. However, mechanism of developing resistance to this class of drugs is unknown. Retinoblastoma (RB) is a good model to study this process because it is driven by mutations in the core components of cell cycle, i.e, Rb gene. However, there is limited gene expression dataset in RB and reproducibility in standard differential expression analysis is hampered by patient and environment specific variation. To get a diverse human dataset, we performed xenografts and cultured in two different conditions using NCC cell lines. Two different culture conditions were used to grow NCC cell lines: standard tissue culture plates and graphene sponge.
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| Overall design |
Finally, the human dataset included normal retina, retinoblastoma, xenografts, and RB cell lines (Total n = 23; GSE125903 (self-reanalysis), retina n=3, RB, n=7; NCC Xenograft n=3; NCC tissue culture n=3; NCC graphene sponge n=3; GSE141327 (third party-reanalysis), Weri n = 2, Y79 n = 2).
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| Contributor(s) |
Chatterjee A, Pandey S, Danda R, Ranjith Kumar R, Maheswari S, Khetan V, Rishi P, Ramaprabhu S, Elchuri SV, Sahoo D |
| Citation missing |
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| Submission date |
Aug 21, 2020 |
| Last update date |
Dec 31, 2020 |
| Contact name |
Debashis Sahoo |
| E-mail(s) |
dsahoo@ucsd.edu
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| Phone |
6508624736
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| Organization name |
UCSD
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| Department |
Pediatrics
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| Lab |
Boolean
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| Street address |
9500 Gillman Drive
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| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platforms (2) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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| Samples (19)
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| Relations |
| Reanalysis of |
GSM4200864 |
| Reanalysis of |
GSM4200865 |
| Reanalysis of |
GSM4200866 |
| Reanalysis of |
GSM4200867 |
| BioProject |
PRJNA658590 |
| SRA |
SRP278410 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE156657_meta_All23samples.txt.gz |
1.1 Kb |
(ftp)(http) |
TXT |
| GSE156657_sailaja-2020-cells-expr.txt.gz |
6.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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