|
| Status |
Public on Jul 12, 2008 |
| Title |
A172 glioma cells, mock, 6 hr vs. A172 glioma cells, miR-21, 6 hr |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
A172 glioma cells
|
| Organism |
Homo sapiens |
| Characteristics |
A172 glioma cells, mock, 6 hr
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.
|
| Label |
Biotin is incorporated during the amplification. This binds a streptavidin-conjugated phycoerythrin during the post-hybridization staining process that provides the measurable signal.
|
| Label protocol |
The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin. After amplification samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.
|
| |
|
| Channel 2 |
| Source name |
A172 glioma cells
|
| Organism |
Homo sapiens |
| Characteristics |
A172 glioma cells, miR-21, 6 hr
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.
|
| Label |
Biotin is incorporated during the amplification. This binds a streptavidin-conjugated phycoerythrin during the post-hybridization staining process that provides the measurable signal.
|
| Label protocol |
The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin. After amplification samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.
|
| |
|
| |
| Hybridization protocol |
GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45°C with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.
|
| Scan protocol |
Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.
|
| Description |
MiR-21 promotes glioma invasion by targeting MMP regulators. Galina Gabriely, Tom Wurdinger, Santosh Kesari, Christine C. Esau, Julja Burchard, Peter S. Linsley and Anna M. Krichevsky. Molecular and Cellular Biology (2008).
|
| Data processing |
Data were loaded into the Rosetta Resolver® system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260). Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value. The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).
|
| |
|
| Submission date |
Jun 12, 2008 |
| Last update date |
Jun 18, 2008 |
| Contact name |
Galina Gabriely |
| E-mail(s) |
ggabriely@rics.bwh.harvard.edu
|
| Organization name |
HMS
|
| Street address |
4 blackfan circle
|
| City |
boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL6793 |
| Series (1) |
| GSE11778 |
MiR-21 Promotes Glioma Invasion by Targeting MMP Regulators. |
|
