|
| Status |
Public on Dec 18, 2017 |
| Title |
L6_pinosylvin_60microM_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
L6 myotubes, 60 microM pinosylvin, 24h
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell line: L6
cell type: skeletal muscle myotubes
treatment: 60 microM pinosylvin
time: 24h
|
| Treatment protocol |
Myotubes were treated with 60 micromolar test compounds in DMSO or DMSO (control) for 24 hours.
|
| Growth protocol |
Rat L6 skeletal muscle cells (ATCC) were differentiated into myotubes in alpha-MEM containing 2% horse serum for 6 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the RNeasy Mini kit (Qiagen) following the manufacturer's recommendations. RNA quality was assessed with the Agilent Bioanalyzer 2100.
|
| Label |
Cy3
|
| Label protocol |
200 ng of total RNA was primed using oligo-dT(T7) promoter primers and converted to cDNA with AffinityScript RNase Block (Agilent). Primed cDNA was amplified and labeled using Cy3-labeled dNTPs and T7 RNA Polymerase.
|
| |
|
| Hybridization protocol |
Samples (600 ng of cRNA) were mixed with blocking agent, fragmentation and hybridization buffer, and were hybridized to Agilent SurePrint G3 Rat GE 8 x 60K Microarrays for 17 hours at 65°C.
|
| Scan protocol |
Microarrays were washed and scanned with Agilent Scanner using manufacturer provided protocols (Agilent Scan Control version A.8.5.1).
|
| Description |
Gene expression after 24h in pinosylvin-treated rat L6 myotubes.
Replicate 3
|
| Data processing |
Agilent Feature Extraction software (version 12.0.0.7) was used to extract data from raw microarray image files. The data was processed with limma package of the Bioconductor software. The processing included background correction with normexp method, log2 transformation and normalization with quantile method. Next step was filtering which excluded probes that were less than 10% brighter than the 95% percentile of the negative control probes on at least 3 arrays, yielding 37670 probes representing 25848 genes. To obtain results with unique probe names, the data was condensed and values for within-array replicate probes were replaced by their average.
|
| |
|
| Submission date |
Dec 02, 2016 |
| Last update date |
Dec 18, 2017 |
| Contact name |
Tarja Kokkola |
| Organization name |
University of Eastern Finland
|
| Department |
School of Medicine / Internal Medicine
|
| Street address |
Yliopistonranta 1 C
|
| City |
Kuopio |
| ZIP/Postal code |
70210 |
| Country |
Finland |
| |
|
| Platform ID |
GPL22740 |
| Series (1) |
| GSE90833 |
Plant-derived compounds strigolactone GR24 and pinosylvin modulate gene expression in rat L6 skeletal muscle cells |
|
