|
| Status |
Public on Aug 28, 2018 |
| Title |
Control_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
C2C12 myotubes_7 days of differentiation_24h post transfection with (negative) control
|
| Organism |
Mus musculus |
| Characteristics |
cell line: C2C12
cell type: immortalized mouse myoblast
transfection: negative control
time of cell differentiation (days): 7
time post transfection (hrs): 24
|
| Treatment protocol |
Transfections were performed at day 6 of differentiation. Cells were transfected with miRNA inhibitors using lipofectamine RNAimax, according to the manufacturers protocol. The final LNA concentration was 50nM.
|
| Growth protocol |
Myoblasts were cultured in 12-well plates at a density of 100.000 cells/cm2 in growth media (DMEM 4,5g/L glucose, with 10% Fetal Bovine Serum, 2% HEPES and 1% Non-essential amino acids). Differentiation was perfromed in differentiation medium (DMEM 4,5g/L glucose, with 2% Horse serum, 2% HEPES and 1% Non-essential amino acids) for 6 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Invitrogen, Breda, the Netherlands) and column-purified using the RNeasy mini kit (Qiagen, Venlo, the Netherlands). RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).
|
| Label |
biotin
|
| Label protocol |
Purified total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).
|
| |
|
| Hybridization protocol |
Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.
|
| Scan protocol |
Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).
|
| Description |
NegA 24h-1_Negative Control A
|
| Data processing |
Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.42.0).
|
| |
|
| Submission date |
Jul 09, 2018 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Guido Hooiveld |
| E-mail(s) |
guido.hooiveld@wur.nl
|
| Organization name |
Wageningen University
|
| Department |
Div. Human Nutrition & Health
|
| Lab |
Nutrition, Metabolism & Genomics Group
|
| Street address |
HELIX, Stippeneng 4
|
| City |
Wageningen |
| ZIP/Postal code |
NL-6708WE |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL11533 |
| Series (1) |
| GSE116786 |
MicroRNA-382 silencing induces a mitonuclear protein imbalance and activates the mitochondrial unfolded protein response in muscle cells |
|
