|
| Status |
Public on Dec 16, 2019 |
| Title |
Determination of CNVs in SKOV3 cells knocked down in BECN1 or MAP1LC3B |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by genome tiling array
Genome variation profiling by SNP array
|
| Summary |
SKOV3 ovarian cancer cells have high basal autophagy levels and were used as a model cell line to enable knockdown of autophagy genes and study the changes of DNA copy number as a consequence of impaired autophagy.
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| |
|
| Overall design |
Four genomic DNA samples per genotype, including control (shScr), shBECN1, and shLC3B were analyzed after passaging 30 times in normal media. Ploidy was verified and normalized in part by the known single allele of chromosome 7 and homozygous deletion of CDKN2A
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| |
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| Contributor(s) |
Delaney JR |
| Citation(s) |
31923184 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| K99 CA207729 |
Copy Number Alterations in Low Mutation Cancer |
DUKE UNIVERSITY |
Joe R Delaney |
| R00 CA207729 |
Copy Number Alterations in Low Mutation Cancer |
MEDICAL UNIVERSITY OF SOUTH CAROLINA |
Joe R Delaney |
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| |
| Submission date |
Nov 13, 2018 |
| Last update date |
Mar 18, 2020 |
| Contact name |
Joe R Delaney |
| Organization name |
Medical University of South Carolina
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
173 Ashley Avenue
|
| City |
Charleston |
| State/province |
SC |
| ZIP/Postal code |
29425 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL21558 |
[OncoScan_CNV] Affymetrix OncoScan CNV FFPE Assay |
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| Samples (12)
|
| GSM3466471 |
shLC3_1: SKOV3 cells passaged 30x, with shRNA to LC3B. Biological replicate 1 |
| GSM3466472 |
shLC3_2: SKOV3 cells passaged 30x, with shRNA to LC3B. Biological replicate 2 |
| GSM3466473 |
shLC3_3: SKOV3 cells passaged 30x, with shRNA to LC3B. Biological replicate 3 |
| GSM3466474 |
shLC3_4: SKOV3 cells passaged 30x, with shRNA to LC3B. Biological replicate 4 |
| GSM3466475 |
shScr_1: SKOV3 cells passaged 30x, with scrambled shRNA. Biological replicate 1 |
| GSM3466476 |
shScr_2: SKOV3 cells passaged 30x, with scrambled shRNA. Biological replicate 2 |
| GSM3466477 |
shScr_3: SKOV3 cells passaged 30x, with scrambled shRNA. Biological replicate 3 |
| GSM3466478 |
shScr_4: SKOV3 cells passaged 30x, with scrambled shRNA. Biological replicate 4 |
| GSM3466479 |
shBECN1_1: SKOV3 cells passaged 30x, with shRNA to BECN1. Biological replicate 1 |
| GSM3466480 |
shBECN1_2: SKOV3 cells passaged 30x, with shRNA to BECN1. Biological replicate 2 |
| GSM3466481 |
shBECN1_3: SKOV3 cells passaged 30x, with shRNA to BECN1. Biological replicate 3 |
| GSM3466482 |
shBECN1_4: SKOV3 cells passaged 30x, with shRNA to BECN1. Biological replicate 4 |
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| Relations |
| BioProject |
PRJNA505247 |
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