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Pipeline publication

[…] n with Paired-End Cluster Generation Kit v2 (Illumina), followed by 50 (or 26 bp)*2 cycles of sequencing on sequencer with Sequencing Kit v3 (Illumina). Genome Analyzer Sequencing Control Software (SCS) v2.5, which could perform real-time image analysis and base calling, was used to carry out the image processing and base calling during the chemistry and imaging cycles of a sequencing run. The default parameters within the data analysis software (SCS v2.5) from Illumina were used to filter poor-quality reads. In the default setting, a read would be removed if a chastity of < 0.6 is observed on two or more bases among the first 25 bases., To generate a comprehensive catalog of lincRNAs in muscle cells, we applied an integrated analysis on RNA-seq data generated by Trapnell et al. and our own RNA-seq data from proliferating and differentiating C2C12 cells. The raw sequencing reads were aligned to the mouse reference genome (UCSC mm9) using Tophat (v2.0.4) , during which procedure the UCSC gene annotation file downloaded from Cufflinks website (http://cole-trapnelllab.github.io/cufflinks/igenome_table/index.html) was used (the ‘-G’ option). The transcriptome assembly was then performed using Cufflinks (v2.0.4) , and a total of 46,627 transcripts were obtained. Then sebnif (v1.2.2) was employed to identify the high-confidence novel lincRNAs. In this procedure, the annotated genes, transcript size, expression level and coding potential were all considered. As a result, a total of 2413 novel lincRNAs were identified. After further annotating each of them with features including K4-K36 domain, EST tag and MyoD binding, a stringent set of 158 lincRNAs were obtained., To detect the differentially expressed genes betwe […]

Pipeline specifications

Software tools MUSCLE, TopHat, Cufflinks