high throughpt sequence alignment protocol
Reads were aligned to the NCBIM37 mouse genome using TopHat v1.4.1 allowing only uniquely mapped reads (-g 1) and using pre-defined splice junctions from Ensembl v61.
normalization data transformation protocol
Data was quantitated with SeqMonk with log2 transformed read overlap counts to exons of each transcript corrected per million reads of input.
nucleic acid sequencing protocol
Libraries were run on single end 50bp runs on an Illumina HiSeq 1000
nucleic acid library construction protocol
Sequencing libraries prepared using Illumina TruSeq RNA sample prep kit v2 (Illumina) according to the manufacturer's instructions.
nucleic acid extraction protocol
The muscles were harvested and satellite cells were FACS isolated by positively selecting for CD34 and VCAM1 and negatively selecting for CD45 and CD31 and flash frozen in TRIzol reagent (Life Technologies)
Mice were kept until 6-8 weeks of age
To isolate activated, proliferating satellite cells from regenerating muscle, the right and left gastrocnemius of knockout and control mice (4 mice per genotype) was injected with 50 ul of 10 uM cardiotoxin. 50 micrograms cardiotoxin was administered to each animal.