GSM8797616: Granulomas, wild-type, enriched, biol rep 1; Mycobacterium marinum; Danio rerio; RNA-Seq
RNA was extracted using Rneasy Plus Mini Kit (Qiagen). 500 ng of total RNA was used to construct sequencing libraries. RNA samples were reverse transcribed into cDNA and then processed into sequencing libraries using the Illumina Total RNA-seq with Ribo-Zero Plus Microbiome kit with extra custom rRNA depletion probes for Zebrafish and Mycobacterium marinum (Illumina Code: 20072063). For bacterial RNA enrichmnet, Zebrafish mRNA was removed from total RNA using two oligo dT captures (Kapa mRNA HyperPrep Kit from Roche (KK8581)). Then, the remaining RNA in the supernatants were pooled, reverse transcribed into cDNA and processed into sequencing libraries as described above.