|
| Status |
Public on Jan 15, 2015 |
| Title |
SW620 Post-Selection-2 |
| Sample type |
RNA |
| |
|
| Source name |
SW620 Post-Intrahepatic Sample-2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SW620
transduced with: Lenti-miR library
injected into: liver of immunodeficient mice
time point: after in vivo selection
|
| Treatment protocol |
SW620 cells were cultured in McCoy media and transduced with the Lenti-miR library (System Biosciences). A portion of cells were saved as reference samples. A separate portion was injected into the liver of immunodeficient mice to allow for in vivo selection. The resulting liver nodule was extracted after 3-5 weeks.
|
| Growth protocol |
SW620 cells were routinely cultured in McCoy media supplemented with 10% FBS, glutamine, pyruvate, pen-strep and fungizone.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Genomic DNA was extracted from reference samples and from liver nodule using Qiagen Dneasy Kit and lenti-viral derived miRNA were enriched by vector specific PCR and in vitro transcription according to manufacturer's protocol. RNA was cleaned up using Ambion's Mega Clear kit and sent to Genosensor for profiling.
|
| Label |
Cy5
|
| Label protocol |
Labeling was performed by Genosensor using in-house protocol.
|
| |
|
| Hybridization protocol |
Genoexplorer miRNA arrays (human) were used for hybridization. One miRNA microarray chip were used for each sample. The hybrization was performed at 42 dgrees celcius for 16hrs, then stained by streptavidin-Cy5 dye. After washes, the arrays were dried and scanned.
|
| Scan protocol |
Arrays were scanned using Axon 400B. Raw data with signal intensity were analyzed by GenePix Software.
|
| Description |
miRNA present after intrahepatic selection
Post-2
|
| Data processing |
Raw intensity values for each of the three probes for every miRNA or control were averaged and standard deviation was also calculated. Array background was calculated as the average of signal intensity of all negative controls and buffers, and a signal threshold was determined by array background + 2x background's standard deviation, for each array; only averaged miRNA intensities higher than the signal threshold were considered. Across individual samples, raw data was median normazlized.
|
| |
|
| Submission date |
Mar 28, 2014 |
| Last update date |
Jan 15, 2015 |
| Contact name |
Jia Min Loo |
| Organization name |
The Rockefeller University
|
| Street address |
1230 York Avenue #342
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL18485 |
| Series (2) |
| GSE56318 |
Lenti-miR Library SW620, Pre vs Post Intrahepatic Selection |
| GSE56320 |
Identification of miRNAs that regulate Colorectal Cancer Metastasis |
|
