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Pipeline publication

[…] b'pared from six groups of three independently cultured C2C12 myoblast cells were labeled with biotin using an Illumina TotalPrep RNA Amplification Kit (Ambion). Following fragmentation, labeled RNAs were hybridized to a MouseWG-6 v2.0 Expression BeadChip that contains more than 45,200 transcripts (Illumina, USA). Array data were processed and analyzed using the Illumina BeadStudio v3.1.3, ArrayAssistand and R statistical language v.2.4.1 software. For RNA-Seq analysis, mRNA libraries were constructed using the Illumina TruSeq RNA sample preparation kit following the manufacturer\xe2\x80\x99s instruction. Samples were run on an Illumina HiSeq2000 instrument and raw data were processed and analyzed using TopHat and Cufflinks software. Gene ontology analysis was performed by using ANNOVAR software and MGI Gene Ontology Term Finder (http://www.informatics.jax.org/gotools/MGI_Term_Finder.html)., Chromatin immunoprecipitation (ChIP) analysis was performed as previously described (). Briefly, cells were cross-linked with 1% formaldehyde and then neutralized with 0.125 M glycine (Bio-Rad). Chromatins were prepared by sonication and incubated with anti-Flag-M2 agarose (Sigma-Aldrich). Immunoprecipitated DNA was analyzed by PCR followed by agarose gel electrophoresis. Primer sets to amplify MyoD promoter and Actin are previously described () and primers to amplify Nnat gene are as follows. Nnat; 5\xe2\x80\xb2-TGCTGCTGCAGGTGAGTATGTA-3\xe2\x80\xb2 and 5\xe2\x80\xb2-TTGCGGCAATTGGGATAGGA - 3\xe2\x80\xb2., C2C12 cells were' […]

Pipeline specifications

Software tools TopHat, Cufflinks, ANNOVAR