|
| Status |
Public on Dec 01, 2012 |
| Title |
Control at day 1, 24h after switching to differentiation media, 48h after treatment, C1-2 |
| Sample type |
RNA |
| |
|
| Source name |
myogenic cell line, control RNAi, day 1
|
| Organism |
Mus musculus |
| Characteristics |
cell line: C2C12
cell type: myogenic cells
treatment: control RNAi
time point: day 1 (24 h after switching to differentiation media, 48 h after treatment)
|
| Treatment protocol |
RNAi-treated cells were transfected with an RNAi directed against STAC3 (Invitrogen). Control cells were transfected with a high-GC content control RNAi (Invitrogen).
|
| Growth protocol |
Cells at day 0 were grown in growth media, 20% FBS + DMEM. Cells at day 1 were grown in differentiation media, 2% FBS in DMEM.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using an RNeasy Plus RNA extraction kit (Qiagen).
|
| Label |
biotin
|
| Label protocol |
Samples were processed commercially at Cambridge Bioscience, UK.
|
| |
|
| Hybridization protocol |
Samples were processed commercially at Cambridge Bioscience, UK.
|
| Scan protocol |
Samples were processed commercially at Cambridge Bioscience, UK.
|
| Description |
C1-2
|
| Data processing |
The data were filtered to remove any probes with a detection p-value above 0.01 for all the samples in the set. This removes any probes not detected at all in the set. It was done before transformation via variance stabilization and normalization in order to reduce the noise of the set before normalization. As the normalization algorithm is quantile normalization, it uses the data to fit a distribution on to it and having no expressed probe in the set would have an impact on the quality of the data. Quantile normalization was performed using the program R and the Bioconductor package Lumi (PMID 18467348).
|
| |
|
| Submission date |
Dec 15, 2011 |
| Last update date |
Dec 01, 2012 |
| Contact name |
Neil Bower |
| E-mail(s) |
n.bower@uq.edu.au
|
| Organization name |
University of Queensland
|
| Department |
Institute for Molecular Bioscience
|
| Street address |
Carmody Road
|
| City |
St Lucia |
| State/province |
Qld |
| ZIP/Postal code |
4072 |
| Country |
Australia |
| |
|
| Platform ID |
GPL6887 |
| Series (1) |
| GSE34474 |
STAC3 is required for myotube formation and myogenic differentiation in vertebrate skeletal muscle |
|
