Computational protocol: LIN‐28 balances longevity and germline stem cell number in Caenorhabditis elegans through let‐7/AKT/DAF‐16 axis

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Protocol publication

[…] Total RNA of worms fed with empty vector, and lin‐28 RNAi bacteria from L1 were isolated with TRIzol (Invitrogen) at adult day 4 stage and precipitated with isopropanol. RNA sequencing libraries were constructed following the Illumina RNA‐seq protocol with at least 10 μg total RNA. The quality of RNA sequencing data was assessed with Fastqc. Tophat was used to map the reads to the genome of C. elegans (ce10). Cufflinks was used to assembly the reads, and Cuffdiff (Trapnell et al., ) was used to search for the differentially expressed genes (FDR < 0.1). DAVID was used to find enriched GO terms among differentially expressed genes (Huang et al., ). […]

Pipeline specifications

Software tools FastQC, TopHat, Cufflinks, DAVID
Application RNA-seq analysis
Organisms Caenorhabditis elegans
Diseases Neoplasms