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Pipeline publication

[…] o both the Watson and Crick bisulfite genome. Fractional CpG methylation was calculated at each CG dinucleotide mapped to the amplicon locus as fmCpG = NCi/(NTi+NCi), where NTi and NCi are the number of reads with a C or T in position i., Total RNA was extracted from cells with Trizol using standard procedures and RNA quality was assessed using a BioAnalyzer (Agilent). RNA was labelled and hybridized to Illumina Human Ref8 microarrays as per manufacturer's instructions and data was extracted using BeadStudio software. All subsequent analysis was performed in the R programming environment utilizing Bioconductor packages and custom procedures. Preprocessing of raw data was performed using the lumi package. Differentially expressed transcripts were identified after empirical Bayesian modelling and analysis using the limma package. Gene ontologies overrepresented within the differentially expressed transcripts were identified after calculating hypergeometric p-values conditionally using the structure of the gene ontology database within the GOstats package., We thank Peter Besmer (Memorial Sloan-Kettering Cancer Center), Lorraine Gudas and Barbara Hempstead (Weill-Cornell Medical College) for their support and critical review of this manuscript. We would like to acknowledge Emily McDonald's technical assistance with amplicon preparation for sequencing., Competing Interests: The authors have declared that no competing interests exist., Funding: This research was supported by grant UL1RR024996 of the Clinical and Translation Science Center at Weill Cornell Medical College (JMS) and by Cornell Belfer Family Hematology-Oncology Division startup funds (JMS). The funders had no role in study design, data collection and analysis, deci […]

Pipeline specifications

Software tools lumi, limma, GOstats