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| Status |
Public on Jun 01, 2012 |
| Title |
Gene expression data ARID1A knockdown OE33 cells versus mock OE33 cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
A nonsense mutation in ARID1A was identified by next generation sequencing in non-dysplastic Barrett's esophagus [BE] tissue and esophageal adenocarcinoma [EAC] tissue of a patient diagnosed with EAC. Immunohistochemistry performed on an independent archival cohort demonstrated ARID1A protein loss in 0% (0/76), 4.9% (2/40), 14.3% (4/28), 16.0% (8/50), and 12.2% (12/98) of normal squamous epithelium, BE, low-, high-grade dysplasia, and EAC tissues, respectively. Enhanced cell growth, proliferation and invasion were observed upon ARID1A knockdown in EAC cells.
ARID1A was knocked down in OE33 cells (Sample MS_1 and MS_3) using on-TARGET smartpool ARID1A siRNA. At the same time, OE33 cells were transfected with a non-targeting siRNA, and these experiments (Samples MS_2 and MS_4) functioned as mock controls. Cells were harvested after 48 hours and total RNA was extracted using the Rneasy kit (Qiagen)
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| Overall design |
Aim Affymetrix Human PrimeView Gene Expression Array : to determine the downstream effectors of ARID1A that are likely to contribute to the oncogenic phenotype caused by ARID1A down-regulation. Two biological replicates of each condition (2x ARID1A knockdown, and 2x Mock) were used for the microarray experiment.
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| Contributor(s) |
Maitra A, Streppel MM |
| Citation(s) |
23318448 |
| Submission date |
May 31, 2012 |
| Last update date |
Aug 23, 2018 |
| Contact name |
Mirte Mayke Streppel |
| Organization name |
Johns Hopkins Hospital
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| Department |
Pathology
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| Lab |
GI pathology, Maitra lab
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| Street address |
1550 Orleans street, CRBII rm341
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| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21231 |
| Country |
USA |
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| Platforms (1) |
| GPL15207 |
[PrimeView] Affymetrix Human Gene Expression Array |
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| Samples (4)
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| GSM940993 |
OE33_ARID1Aknockdown_biologicalreplicate1 |
| GSM940994 |
OE33_Mock_biologicalreplicate1 |
| GSM940995 |
OE33_ARID1Aknockdown_biologicalreplicate2 |
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| Relations |
| BioProject |
PRJNA167792 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE38380_RAW.tar |
8.0 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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