|
| Status |
Public on Jun 15, 2011 |
| Title |
HCT-116 si PAPD1 replicate 1 canonical assay |
| Sample type |
RNA |
| |
|
| Source name |
HCT-116 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HCT-116
transfection: si PAPD1
|
| Treatment protocol |
Treated with 30 nM Dharmacon SMARTpool siRNAs against enzyme of interest or Cyclophilin B as a negative control
|
| Growth protocol |
HCT-116 cells grown in McCoy's media with 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the miRNeasy RNA isolation kit from Qiagen. 400 ng of RNA was used as input for the nCounter sample prep reaction.
|
| Label |
N/A
|
| Label protocol |
N/A
|
| |
|
| Hybridization protocol |
Hybrdization reactions were performed according to the manufacturer's instructions (NanoString) with 5 µl of the 5-fold diluted sample preparation reaction. All hybridization reactions were incubated at 65°C for a minimum of 18 h.
|
| Scan protocol |
Hybridized probes were purified and counted on the nCounter Prep Station and Digital Analyzer (NanoString) following the manufacturer’s instructions. For each assay, a high-density scan (600 fields of view) was performed.
|
| Description |
Canonical
Replicate 1
|
| Data processing |
The data were normalized for lane-to-lane variation with a dilution series of six spike-in positive controls using the vsn R package
|
| |
|
| Submission date |
Jan 21, 2011 |
| Last update date |
Jun 15, 2011 |
| Contact name |
Muneesh Tewari |
| E-mail(s) |
mtewari@fhcrc.org
|
| Organization name |
Fred Hutchinson Cancer Research Center
|
| Department |
Human Biology
|
| Lab |
Tewari
|
| Street address |
1100 Fairview Ave, N
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL11642 |
| Series (2) |
| GSE26803 |
Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity (KD) |
| GSE26970 |
Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity |
|
