|
| Status |
Public on Jul 03, 2018 |
| Title |
HSC-3 CTNNB1 siRNA replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
HSC-3 OSCC cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HSC-3
treatment: CTNNB1 siRNA
|
| Treatment protocol |
Three separate wells (triplicate) from 6 well plates were seeded by HSC-3 and CAL27 cells (around 5x104/ well). After 12-24 hours (i.e. approximately 50% confluency), the cells were treated with either 0.1% DMSO or 10 µM ICG-001. For CTNNB1, Three separate wells (triplicate) from 6 well plates were seeded by HSC-3 cells (around 5x104/ well). After 48 hours, cells were transfected with 25 nM SMART pool ON-TARGET plus CTNNB1 siRNA (L-003482-00-0005, Dharmacon) by reverse transfection. ON-TARGET plus non-targeting Pool 25nM (D-001810-10-05, Dharmacon) was used for negative control
|
| Growth protocol |
Cells were grown at 37oC under 5% CO2 to 70% confluence in DMEM (Invitrogen) supplemented with 10% fetal bovine serum, penicillin, and streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After 48-64 hours, the cells were trypsinized and harvested for RNA purification using miRNeasy Micro Kit (QIAGEN #217084)
|
| Label |
biotin
|
| Label protocol |
Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).
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| |
|
| Hybridization protocol |
The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.
|
| Scan protocol |
After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.
|
| Description |
Gene expression data from HSC-3 cells treated with siRNA targeting CTNNB1.
|
| Data processing |
Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray hugene20sthsentrezg R package (version 17.0.0).
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| |
|
| Submission date |
Mar 06, 2017 |
| Last update date |
Jun 25, 2019 |
| Contact name |
Boston University Microarray and Sequencing Resource |
| E-mail(s) |
msrdata@bu.edu
|
| Organization name |
Boston University
|
| Department |
Microarray and Sequencing Resource
|
| Street address |
72 East Concord Street, E631
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL17930 |
| Series (1) |
| GSE95704 |
Targeting oncogenic β-catenin/CBP activity for the treatment of head and neck squamous cell carcinoma |
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