|
| Status |
Public on Sep 18, 2018 |
| Title |
10-cell pool-and-split control replicate 8 |
| Sample type |
RNA |
| |
|
| Source name |
ECM-attached MCF10A-5E cells grown in 3D culture for 10 days
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF10A-5E
culture day: 10
|
| Treatment protocol |
None
|
| Growth protocol |
Cells were grown as a matrigel overlay culture in DMEM/F12 containing 2% matrigel, 2% horse serum, 5 ng/ml EGF, 0.5 µg/ml hydrocortisone, 100 ng/ml cholera toxin, 10 µg/ml insulin, and 1x penicillin-streptomycin for 10 days, with refeeding at days 4 and 8.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
3D cultures were cryoembedded and sectioned. Cells were isolate by laser-capture microdissection, and RNA was isolated by proteinase K digestion of the microdissected cells.
|
| Label |
Alexa Fluor 555
|
| Label protocol |
Direct aminoallyl labeling to Alexa Fluor 555
|
| |
|
| Hybridization protocol |
1 µg of labeled cDNA in 5 µl was mixed with 10 µl GEX hybridization buffer, denatured at 94ºC for 4 min and then added directly to the BeadChip prewarmed to 58ºC. Slides were incubated at 58ºC for 20 hr and washed according to the manufacturer's recommendations.
|
| Scan protocol |
Direct hybridization 1
|
| Description |
83107_H
|
| Data processing |
The data were batch processed using the lumi R package (PMID: 18467348) using a detection threshold of 0.05 and simple scaling normalization (ssn).
|
| |
|
| Submission date |
Sep 17, 2018 |
| Last update date |
Sep 18, 2018 |
| Contact name |
Kevin A. Janes |
| E-mail(s) |
kjanes@virginia.edu
|
| Organization name |
University of Virginia
|
| Department |
Department of Biomedical Engineering
|
| Street address |
Box 800759 Health System
|
| City |
Charlottesville |
| State/province |
VA |
| ZIP/Postal code |
22908 |
| Country |
USA |
| |
|
| Platform ID |
GPL6255 |
| Series (1) |
| GSE120030 |
Stochastic profiling of matrix-attached MCF10A-5E cells in 3D culture |
|
