|
| Status |
Public on Aug 27, 2014 |
| Title |
4T1 exos_1 |
| Sample type |
RNA |
| |
|
| Source name |
breast carcinoma cells
|
| Organism |
Mus musculus |
| Characteristics |
cell/tissue type: cancer exosomes
|
| Treatment protocol |
Exosomes were extracted from cancer cells and added to the culture media of non-tumorigenic cells.
|
| Growth protocol |
Cells were grown for RNA as well as for extraction of exosomes for posterior RNA extraction in media with FBS depleted of exosomes.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Exosomes used for RNA extraction were resuspended in 500ul of Trizol and protocol as detailed by manufacturer. Cells were resuspended in 1000ul of Trizol and protocol as detailed by manufacturer.Cells were grown for RNA as well as for extraction of exosomes for posterior RNA extraction in media with FBS depleted of exosomes.
|
| Label |
streptavidin-Alexa647 conjugate
|
| Label protocol |
Biotinylated sense-strand DNA for hybridization to Affymetrix exon arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).
|
| |
|
| Hybridization protocol |
The standard Affymetrix hybridization protocol was used - P-AFFY3
|
| Scan protocol |
Standard Affy scanning protoco - array assay. Quantified using GenePix Pro-6.0.
|
| Description |
Biotinylated sense-strand DNA for hybridization to Affymetrix exon arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).
|
| Data processing |
The raw intensity for each probe is the median feature pixel intensity with the median background subtracted. Setting an offset one ensures that there will be no negative values after log-transforming data. Data was quantile normalized followed by log2 transformation (R computing environment (version 3.0.1)). Signals from probes measuring the same miRNA were averaged.
|
| |
|
| Submission date |
Aug 25, 2014 |
| Last update date |
Aug 27, 2014 |
| Contact name |
RAGHU KALLURI |
| Organization name |
MDACC
|
| Department |
CANCER BIOLOGY
|
| Street address |
1881 East Rd.
|
| City |
Houston |
| ZIP/Postal code |
77054-1901 TX |
| Country |
USA |
| |
|
| Platform ID |
GPL19117 |
| Series (2) |
| GSE60715 |
Cells and exosomes after cell-free culture |
| GSE60716 |
Cell-Independent MicroRNA Biogenesis |
|
