|
| Status |
Public on Feb 27, 2010 |
| Title |
ES cells + control microRNA replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
ES cells + control microRNA
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129/SvEv
cell type: Mouse ES cells, Dicer1-null
|
| Treatment protocol |
Cells were co-transfected (Amaxa nucleofection) with 300pmol of microRNA and 1microgram of pEGFP-1, which served as a control for transfection efficiency. GFP-positive cells were sorted 24 hours after transfection.
|
| Growth protocol |
ES cells grown in feeder-free conditions, in ES-cell medium containing 15% FCS, DMEM/F-12 and 2000U/ml LIF.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Qiagen RNeasy Mini kit with on-column DNaseI digestion in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
control replicate 3
|
| Data processing |
The data were transformed with a variance-stabilising algorithm and normalised using quantile normalisation in lumi in R. The selection of the data aims at removing non-expressed genes or data that are too close to the background to be distinguished. Not removing those genes will add noise to the data. The selection was done using the following criteria:
- Threshold for selection: detection p-value inferior to 0.01 for a measurement to be selected.
- A gene must be present in at least one sample.
|
| |
|
| Submission date |
Jan 26, 2010 |
| Last update date |
Feb 17, 2010 |
| Contact name |
Sophie Alexandra Hanina |
| Organization name |
University of Cambridge
|
| Department |
Gurdon Institute
|
| Street address |
Tennis Court Road
|
| City |
Cambridge |
| State/province |
Cambridgeshire |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL6887 |
| Series (1) |
| GSE20048 |
Genome-wide Identification of Targets & Function of Individual MicroRNAs in Mouse Embryonic Stem Cells |
|
