|
| Status |
Public on Jun 26, 2015 |
| Title |
MDA-Bone-Un_LASPKD_biological_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
MDA-Bone-Un-LASP1-KD cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-Bone-Un
cell type: Basal-like breast cells
|
| Treatment protocol |
Not applicable
|
| Growth protocol |
MDA-MB-231S and MDA-Bone-Un breast cancer cells (Non-silencing and LASP-1 knock down) were cultured on growth factor reduced Matrigel for 3 days to form stellate clusters.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from MDA-MB-231S and MDA-Bone-Un stellate clusters was quantitated using the QuBit RNA assay and were run on the Agilent Bioanalyzer.
|
| Label |
Biotin-Streptavidin-Phycoerythrin
|
| Label protocol |
Ambion kit was used to synthesize the first and second strand RNA. IVT reactions were done overnight, cRNA productswas purified and quantified. Quantitated cRNA was used : random primer heat denaturation, 2nd cycle cDNA synthesis and cRNA hydrolysis with RNase H; cDNA was purified, fragmented and TdT-labeled with biotinylated nucleotides.
|
| |
|
| Hybridization protocol |
Biotinylated reaction products were added to Hybridization mix and targets (final ~25ng/ul) were hybridized in the hybridization cocktail for a total of 2.5ug of fragmented target. The targets are heat denatured, centrifuged, and hybridized overnight to Human Gene 1.0 ST exon array, stained, washed and scanned.
|
| Scan protocol |
Affymetrix 7G plus scanner using AGCC v. 3.2.4
|
| Description |
Grown on Matrigel
|
| Data processing |
Analyzed on Affymetrix Expression Console v. 1.2 using a RMA normalization algorithm producing log base 2 results that forms the value for comparisons or for calcualting fold change.
|
| |
|
| Submission date |
Aug 11, 2014 |
| Last update date |
Jun 27, 2015 |
| Contact name |
Dayanidhi Raman |
| E-mail(s) |
[email protected]
|
| Phone |
615-936-3333
|
| Organization name |
Vanderbilt Universirty
|
| Department |
Cancer Biology
|
| Lab |
Ann Richmond
|
| Street address |
PRB436, 23rd Ave S @ Pierce
|
| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37212 |
| Country |
USA |
| |
|
| Platform ID |
GPL16686 |
| Series (2) |
| GSE60323 |
Effect of knock down of LASP-1 on basal-like breast cancer cells (MDA-MB-231) |
| GSE60324 |
Effect of knock down of LASP-1 on human breast cancer cells |
|
