Computational protocol: A Novel Functional Role for MMSET in RNA Processing Based on the Link Between the REIIBP Isoform and Its Interaction with the SMN Complex

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Protocol publication

[…] Total RNA was purified using the Trizol (Life Technology) method. Total RNA from 3 replicates of HeLa cell line transduced with cDNA coding for REIIBP and 3 replicates of the control cell line (HeLa) was extracted. These 6 libraries were pulled down and split between 2 lanes of an Illumina HiSeq by Oxford gene technology. Raw fastq files were aligned using Tophat 2.0.8 (http://tophat.cbcb.umd.edu/) with default parameters, and Cufflinks 2.1.1 (http://cufflinks.cbcb.umd.edu/) was used to estimate transcript abundance and calculate differential expression between REIIBP and control samples. The results were visualized using cummerbund 2.0.0 (http://compbio.mit.edu/cummeRbund/). See also Experimental procedures in . […]

Pipeline specifications

Software tools TopHat, Cufflinks, CummeRbund
Applications RNA-seq analysis, Transcriptome data visualization
Diseases Multiple Myeloma