|
| Status |
Public on Jun 15, 2013 |
| Title |
control-shRNA_2_dup1 |
| Sample type |
other |
| |
|
| Channel 1 |
| Source name |
[sample] Jurkat LUC control-shRNA_2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Jurkat T-ALL cell line
shRNA construct for transduction: pLKO1-LUCIFERASE
genotype/variation: control
sample type: Total miRNA
|
| Treatment protocol |
0.5x10^6 Jurkat cells per replicate were transduced with pLKO1 lentiviral supernatants after addition of polybrene and spinocculated at 2500rpm for 90mins. At 24hrs, cells were spun down and media was replaced with fresh RPMI 10%FBS and cells were incubated at 37°C 5% CO2
|
| Growth protocol |
Jurkat cells were grown at 37°C 5% CO2 in 24 well plate format in RPMI and 10% FBS.
|
| Extracted molecule |
other |
| Extraction protocol |
miRNAs were isolated and purified with the High Pure miRNA isolation kit (Roche).
|
| Label |
Hy3
|
| Label protocol |
Total RNA from sample and reference pool were labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array labeling kit (Exiqon, Denmark)
|
| |
|
| Channel 2 |
| Source name |
[reference] Jurkat T-ALL cell lines_pooled
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Jurkat T-ALL cell line
sample type: Pooled miRNA from all samples
|
| Treatment protocol |
0.5x10^6 Jurkat cells per replicate were transduced with pLKO1 lentiviral supernatants after addition of polybrene and spinocculated at 2500rpm for 90mins. At 24hrs, cells were spun down and media was replaced with fresh RPMI 10%FBS and cells were incubated at 37°C 5% CO2
|
| Growth protocol |
Jurkat cells were grown at 37°C 5% CO2 in 24 well plate format in RPMI and 10% FBS.
|
| Extracted molecule |
other |
| Extraction protocol |
miRNAs were isolated and purified with the High Pure miRNA isolation kit (Roche).
|
| Label |
Hy5
|
| Label protocol |
Total RNA from sample and reference pool were labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array labeling kit (Exiqon, Denmark)
|
| |
|
| |
| Hybridization protocol |
The hybridization was performed according to the miRCURY™ LNA array
|
| Scan protocol |
The scanning protocol was performed according to the manufacturers instructions Exiqon (Denmark)
|
| Description |
Jurkat LUC control-shRNA_2_dup1
miRNA profiling
|
| Data processing |
The quantified signals were normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm (LOcally WEighted Scatterplot Smoothing) regression algorithm
All capture probes with both Hy3 and Hy5 signals lower than 1.5x of the median signal intensity of the given slide are annotated ‘null’. miRPLUS miRNAs not annotated in miRBAse 14.0 and all tRNAs were excluded from the final analysis.
|
| |
|
| Submission date |
May 15, 2013 |
| Last update date |
Jun 15, 2013 |
| Contact name |
Marc R Mansour |
| E-mail(s) |
[email protected]
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Pediatric Oncology
|
| Lab |
Look Lab
|
| Street address |
450 Brookline Avenue
|
| City |
Boston |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL11432 |
| Series (1) |
|
