Pipeline publication

[…] tal number of sequenced reads and the length of a particular mRNA/ncRNA, respectively. A cut-off value of >1 FPKM was used as a limit for mRNA/ncRNA detection across all samples. Canonical and variant human mRNAs were classified by linking UniProt and Ensembl annotated protein sequence databases., mRNAs and ncRNAs enriched in EV samples, relative to CL, were selected using the following criteria: FC (fold change) >2, p-value < 0.05 and a probability >0.7; where FC values represent RNA enrichment changes according to the formula:, , p-values were calculated using the PERL module COMPARISON based on Poisson distribution, and probability values were obtained using the R package NOIseq., TopHat2 and ChimeraScan (v0.4.5) were used to identify alternative splicing and gene fusion events, according to the protocols, respectively., Gene ontology terms for mRNAs enriched in EVs and KEGG pathway analysis were determined using the DAVID Bioinformatics Resource v 6.7 (http://david.abcc.ncifcrf.gov)., EV-enriched mRNAs and lncRNAs identified in this study (relative to CL) were analysed against gene expression data in matched tumour and normal tissues of colon cancer patients from SRA database (https://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?). Two SRA studies with accession numbers of SRP022054 and SRP029880 used deep sequencing technology to identify gene expression levels in 4 and 23 pairs of normal/tumour tissues, respectively. Raw sequencing data was obtained and re-analysed based on the criteria established previously for identification of over-expressed mRNAs and lncRNAs., Total RNA (CL and EVs) were reverse transcribed into cDNA and synthesised with Revers […]

Pipeline specifications

Software tools NOISeq, TopHat, chimerascan, DAVID
Organisms Homo sapiens
Diseases Gastrointestinal Neoplasms, Digestive System Neoplasms, Intestinal Diseases, Gastrointestinal Neoplasms, Digestive System Neoplasms, Intestinal Diseases