|
| Status |
Public on Jun 25, 2018 |
| Title |
MCAS with miR-200 cluster 1 and 2 knockdown |
| Sample type |
RNA |
| |
|
| Source name |
Mucinous ovarian cancer cells MCAS with knockdown of miR-200 cluster 1 and 2 (miR-200a, miR-200b, miR-200c, miR-141 and miR-429) grown in Matrigel for 7 days
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Ovarian epithelial tumor cell (mucinous subtype)
genotype: Mucinous invasive
|
| Treatment protocol |
The day for collecion, culture medium were removed and the cysts formed were rinsed with PBS and Trizol solution (Ambion) was added to the culture.
|
| Growth protocol |
Eight-well glass-chambered slides (BD Biosciences) were coated with growth factor-reduced Matrigel matrix without phenol red (BD Biosciences) . Primary cultures of normal OSE and cancer cells were trypsinized and resuspended as single cells in complete medium with 10% FBS and 2% Matrigel. Fifty thousand single cells were seeded into each Matrigel-coated well. Complete medium with 2% Matrigel was replaced every 4 days. 3D structures would be formed after 4 to 7 days after seeding.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions with subsequent purification by chloroform extraction and isopropanol precipitation
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (GeneChip WT Terminal Labling User Manual, 2009-2010, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 3.5 ug of cRNA were hybridized for 48C on GeneChip Gene 1.1 ST Array in GeneAtlas Hybridization Station. GeneChip was washed and stained according to GeneAtlas TM System User’s Guide (P/N 08-0246)
|
| Scan protocol |
GeneChips were scanned using the GeneAtlas Instrument.
|
| Description |
Gene expression data from MCAS with knockdown of miR-200 cluster 1 and 2 (miR-200a, miR-200b, miR-200c, miR-141 and miR-429) grown in Matrigel for 7 days
|
| Data processing |
All gene expression data was normalized and summarized with Robust Multi-array Average method RMA algorithm with with Affymetrix Power Tools package using Affymetrix default analysis settings.
|
| |
|
| Submission date |
May 23, 2017 |
| Last update date |
Jun 25, 2018 |
| Contact name |
pui wah Choi |
| E-mail(s) |
puiwahchoi@gmail.com
|
| Phone |
6173563166
|
| Organization name |
Brigham and Women's Hospital
|
| Department |
OB/GYB
|
| Lab |
GYN oncology, Alex Ng
|
| Street address |
221 longwood Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL11532 |
| Series (1) |
| GSE99217 |
Expression data from ovarian cells growing in three dimensional culture (Matrigel) with altered expression of miR-200s |
|
