|
| Status |
Public on Apr 06, 2018 |
| Title |
Day 1 of differentiation, biological rep2 [Undiff-Day_2 dataset] |
| Sample type |
RNA |
| |
|
| Source name |
C2C12 cells, Day 1 of differentiation
|
| Organism |
Mus musculus |
| Characteristics |
cell line: myoblast cell line C2C12
time: Day 1 of differentiation
|
| Treatment protocol |
Transient siRNA transfection (10nM final concentration) was carried out using RNAiMax (Life Technologies) according to the manufacturer’s protocol. To induce the differentiation process (initiated 24 hours after the transfection), C2C12 cells were cultured in the differentiation medium containing 2% horse serum (Sigma-Aldrich, #H1270) in DMEM with low glucose, pyruvate (Life Technologies, #31885-023) supplemented with antibiotics (penicillin and streptomycin, Sigma-Aldrich, #P4333).
|
| Growth protocol |
Murine myoblast cell line C2C12 cells were cultured in the growth medium containing 20% FBS (Life Technologies, #10270106) in DMEM with high glucose, pyruvate (Life Technologies, # 41966-029) supplemented with antibiotics (penicillin and streptomycin, Sigma-Aldrich, #P4333) at 37°C in a humidified atmosphere containing 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instruction.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
|
| |
|
| Hybridization protocol |
Following fragmentation, cRNA were hybridized, washed and stained in the Affymetrix Fluidics Station 400 according to the standard Affymetrix protocol.
|
| Scan protocol |
GeneChips were scanned according to the standard Affymetrix protocol.
|
| Description |
Day_1.2 [Undiff-Day_2 dataset]
|
| Data processing |
The data were analyzed using noncoder web interface (http://noncoder.mpi-bn.mpg.de).
The CEL files were analyzed through the updated version of noncoder web interface (Gellert et al., 2013) using the pipeline set up for Gene Array Analyzer (GAA) web interface (Gellert et al., 2012). After the normalization by Robust Multi-array Average (RMA) (Irizarry et al., 2003) and the application of moderate t-statitsics via the limma package (Ritchie et al., 2015), Transcript Cluster IDs that match that do not match to a gene or to multiple genes were discarded. Then, a standard deviation is calculated across samples. For a gene that matches to multiple Transcript Cluster IDs, the Transcript Cluster ID with the highest standard deviation was kept for further analysis. siMyolinc-C2C12-Militello2015.xlsx is linked as a supplementary file on the Series record:
“Day_2” sheet: siMyolinc-knockdown C2C12 cells on day 2 of the differentation were compared to C2C12 cells transfected with siRNA against scramble control (siScr) and differentiated for 2 days.
“Undiff-Day_2” sheet: siMyolinc-knockdown C2C12 cells on day 2 of the differentation were compared to normally cultured C2C12 cells in the growth medium (“Undiff”), one and two days after the differentiation (“Day_1” and “Day_2”, respectively).
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| |
|
| Submission date |
Jun 03, 2015 |
| Last update date |
Apr 07, 2018 |
| Contact name |
Shizuka Uchida |
| E-mail(s) |
heart.lncrna@gmail.com, suc@dcm.aau.dk
|
| Organization name |
Aalborg University
|
| Department |
Department of Clinical Medicine
|
| Lab |
Center for RNA Medicine
|
| Street address |
Frederikskaj 10B, 2. (building C)
|
| City |
Copenhagen SV |
| ZIP/Postal code |
DK-2450 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL6246 |
| Series (2) |
| GSE69451 |
An Evolutionarily-Conserved Long Noncoding RNA Myolinc Regulates muscle differentiation [array_knockdown] |
| GSE69530 |
A novel long non-coding RNA Myolinc regulates myogenesis through TDP-43 and Filip1 |
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