Normal C57Bl6/NJ mice were housed individually (12hr:12hr day:night cycle) in a temperature- and humidity-controlled environment and fed standard chow and water ad libitum. Right hind limbs were injured while left hind limbs were used as control. Animals were treated either with PHI or vehicle.
Extracted molecule
total RNA
Extraction protocol
Mouse gastrocnemius samples were collected and flash frozen in liquid nitrogen then stored at -80oC. For RNA isolation, ~100mg samples were used in 1ml Trizol and isolation was done according to the manufacturers protocol (Ambion Cat #15596-068). Purified RNA went through Qiagen RNA clean up kit (Cat #74204) and eluted in 50ul elution buffer.
Label
biotin
Label protocol
RNA samples were amplified, labeled, hybridized to Affymetrix HG-U133 plus 2.0 GeneChip® microarrays, and scanned using standard protocols (Q2 Solutions, Inc., Durham, North Carolina, U.S.A.) to generate raw data files (CEL files).
Hybridization protocol
RNA samples were amplified, labeled, hybridized to Affymetrix HG-U133 plus 2.0 GeneChip® microarrays, and scanned using standard protocols (Q2 Solutions, Inc., Durham, North Carolina, U.S.A.) to generate raw data files (CEL files).
Scan protocol
RNA samples were amplified, labeled, hybridized to Affymetrix HG-U133 plus 2.0 GeneChip® microarrays, and scanned using standard protocols (Q2 Solutions, Inc., Durham, North Carolina, U.S.A.) to generate raw data files (CEL files).
Description
Gene expression data from injured, PHi treated gastrocnemius muscle tissue collected after 9 hrs
Data processing
Raw data files (CEL files) were analyzed using a battery of data quality checks and samples failing these checks were removed from subsequent analyses. Raw data was then pre-processed using the RMA (Robust Multi-chip Average) pipeline in combination with the most current re-annotated probeset definitions.
