16s rRNA sequencing data for Downregulating carnitine palmitoyl transferase 1 strongly affects disease progression in the SOD1 G93A mouse model
Raw sequences files (pair-end) and associated metadata for the paper entitled: "Downregulating carnitine palmitoyl transferase 1 strongly affects disease progression in the SOD1 G93A mouse model" are provided here.
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The purified sequencing libraries were pooled in equimolar concentrations and diluted to 2 nM. The samples were paired‐end sequenced (2x300 bp) on a MiSeq (Illumina, USA) using a MiSeq Reagent kit v3 (Illumina, USA) following the standard guidelines for preparing and loading samples on the MiSeq. >10% PhiX control library was spiked in to overcome low complexity issues often observed with amplicon samples. Forward and reverse reads were trimmed for quality using Trimmomatic v. 0.32 (Bolger et al., 2014) with the settings SLIDINGWINDOW:5:3 and MINLEN: 225 . The trimmed forward and reverse reads were merged using FLASH v. 1.2.7 (Magoč and Salzberg, 2011) with the settings ‐m 10 ‐M 250. The trimmed reads were dereplicated and formatted for use in the UPARSE workflow (Edgar, 2013). The dereplicated reads were clustered, using the usearch v. 7.0.1090 ‐cluster_otus command with default settings. OTU abundances were estimated using the usearch v. 7.0.1090 ‐usearch_global command with ‐id 0.97 ‐maxaccepts 0 ‐maxrejects 0. Taxonomy was assigned using the RDP classifier (Wang et al., 2007) as implemented in the parallel_assign_taxonomy_rdp.py script in QIIME (Caporaso et al., 2010), using –confidence 0.8 and the SILVA database, release 132 (Quast et al., 2013). The results were analysed in R v. 4.0.3 (R Core Team, 2017) through the Rstudio IDE using the ampvis package v.2.6.5 (Albertsen et al., 2015).