|
| Status |
Public on Mar 01, 2013 |
| Title |
mcf10erbb2 miNS-1 |
| Sample type |
RNA |
| |
|
| Source name |
mcf10erbb2 miNS-1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF10A
cell type: RB-proficient
|
| Treatment protocol |
Media was aspirated from 8well chamber-slides and added 250ul of RNA-STAT-60 (Tel-Test, Friendswood, TX, USA) to each well. Immediately the mixture of cells and matrigel was resuspened several times and collected in an eppendorf tube.
|
| Growth protocol |
DMEM/F12 supplemented with 2% horse serum, 10μg/ml insulin 1ng/ml cholera toxin, 100μg/ml hydrocortisone, 100 U/ml penicillin/streptomycin and 2mM L-glutamine
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was perfomed Following steps were followed according to manufacturer’s instructions from RNA-STAT-60 (Tel-Test, Friendswood, TX, USA)
|
| Label |
biotin
|
| Label protocol |
Labeling was performed by the WT-Ovation Pico RNA amplification system (NuGen Technologies, Inc.)
|
| |
|
| Hybridization protocol |
Arrays were hybridized with fragmented and biotin-labeled target (2.5 µg) in 110 µl of hybridization cocktail. Target denaturation was performed a 99C for 2 min. and then 45C for 5 min., followed by hybridization for 18 hrs. Arrays then were washed and stained using Genechip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).
|
| Scan protocol |
Arrays were inserted into the Affymetrix autoloader carousel and scanned using the GeneChip® Scanner 3000
|
| Description |
3-D cell culture 7 days
|
| Data processing |
Raw intensity files from the Affymetrix Human Gene 1.0 ST GeneChip arrays were processed using Affymetrix Expression Console version 1.1. Gene-level expression measurements were computed using the iterPLIER algorithm on the “core” probesets and exported with annotation release 32, dated June 23rd, 2011.
|
| |
|
| Submission date |
Mar 11, 2012 |
| Last update date |
Mar 01, 2013 |
| Contact name |
Adam Ertel |
| Organization name |
Thomas Jefferson University
|
| Department |
Cancer Biology
|
| Lab |
BLSB 1009
|
| Street address |
233 S 10TH ST
|
| City |
PHILADELPHIA |
| State/province |
PA |
| ZIP/Postal code |
19107 |
| Country |
USA |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE36425 |
Expression data MCF10A/ErbB2 RB-proficient and RB-deficient cells cultured in 3-D cell culture |
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