Computational protocol: Stochastic loss and gain of symmetric divisions in the C. elegans epidermis perturbs robustness of stem cell number

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Protocol publication

[…] Larvae were synchronized by bleaching and grown to L3 stage (31 hr posthatching) before total RNA was extracted using TRIzol (Invitrogen, Carlsbad, CA) reagent. RNA quality was determined using the Agilent RNA ScreenType System on a 2100 Bioanalyzer (Agilent, Santa Clara, CA). The library preparation was done using the TruSeq stranded mRNA library preparation kit (Illumina, San Diego, CA). The sequencing data were processed and aligned to C. elegans reference genome using Bowtie2 []. The bam files were used to generate counts using bedtools []. The counts were then normalised using DESeq package in R []. Differences in gene expression were then calculated using the negative binomial test in the DESeq package (FDR = 0.1). RNA-seq data are deposited in the NCBI GEO under accession GSE101645. […]

Pipeline specifications

Software tools Bowtie2, BEDTools, DESeq
Application RNA-seq analysis
Organisms Caenorhabditis elegans