|
| Status |
Public on Oct 07, 2013 |
| Title |
Calu6 miR-4423 overexpression 1 |
| Sample type |
RNA |
| |
|
| Source name |
Calu6 cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
condition: miR-4423 overexpression
batch: 2
|
| Treatment protocol |
Calu6 cells were transduced with a lentivirus overexpressing an empty vector as a control using polybrene at a concentration of 1ug/ml.
|
| Growth protocol |
Calu6 cells were plated in 24-well plates and culture in RPMI-1640 Medium (ATCC) until they reached 40% confluency.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the miRNeasy mini kit (Qiagen) as per manufacturer’s instructions.
|
| Label |
Biotin
|
| Label protocol |
The total RNA was converted to cDNA and subsequently amplified and biotin-labeled.
|
| |
|
| Hybridization protocol |
cDNA was fragmented end-labeled with a biotinylated dideoxynucleotide using terminal transferase and added to a hybridization cocktail, loaded on a Human Gene1.0 ST GeneChip and hybridized for 16 hours at 45 ºC under rotation (60 rpm). Following hybridization, the array was washed and stained according to the standard Affymetrix protocol.
|
| Scan protocol |
Arrays were scanned using an Affymetrix GeneChip Scanner 3000. These scans were used to generate CEL files for each array.
|
| Data processing |
Transcript-level gene expression estimates were generated via the robust multichip average (RMA) algorithm within each batch using the Entrez Gene CDF v11 (http://brainarray.mbni.med.umich.edu) in R v2.9.2.
|
| |
|
| Submission date |
Jul 11, 2013 |
| Last update date |
Oct 07, 2013 |
| Contact name |
Avrum Spira |
| E-mail(s) |
aspira@bu.edu
|
| Organization name |
Boston University
|
| Department |
Computational Biomedicine
|
| Lab |
Spira/Lenburg Lab
|
| Street address |
72 East Concord Street, E631
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL13243 |
| Series (2) |
| GSE48796 |
Identification of miR-4423 as a Primate-Specific microRNA Highly Expressed in Ciliated Airway Epithelium and Associated with Lung Cancer [Affymetrix] |
| GSE48798 |
Identification of miR-4423 as a Primate-Specific microRNA Highly Expressed in Ciliated Airway Epithelium and Associated with Lung Cancer |
|
