One hundred fourteen sample libraries were prepared using the Celero DNA-Seq kit (Tecan Genomics, Redwood City, CA) and sequenced on the Illumina NextSeq platform using 2 × 150 bp 550 High Output Kits. The remainder of the samples were not sequenced because of quality issues.
One hundred eleven samples were prepared as RNA-Seq libraries using the Ovation RNA SoLO kit (Tecan Genomics, Redwood City, CA). Eleven 150-bp paired-end libraries were sequenced on the Illumina MiSeq Platform during the optimization phase while the remaining libraries were sequenced as 150-bp paired-end libraries on the Illumina NextSeq platform.
No rRNA depletion methods were used. According to our own experience and reported studies, the commercially available kits can introduce a significant bias in mRNA proportions [27 (link)]. Therefore, and considering that our samples do not have as much host RNA as other types of samples such as fecal or those coming directly from host tissues, no rRNA depletion kits were used. This implied a lower number of samples per run in order to obtain enough sequence coverage after bioinformatic rRNA removal.
One hundred eleven samples were prepared as RNA-Seq libraries using the Ovation RNA SoLO kit (Tecan Genomics, Redwood City, CA). Eleven 150-bp paired-end libraries were sequenced on the Illumina MiSeq Platform during the optimization phase while the remaining libraries were sequenced as 150-bp paired-end libraries on the Illumina NextSeq platform.
No rRNA depletion methods were used. According to our own experience and reported studies, the commercially available kits can introduce a significant bias in mRNA proportions [27 (link)]. Therefore, and considering that our samples do not have as much host RNA as other types of samples such as fecal or those coming directly from host tissues, no rRNA depletion kits were used. This implied a lower number of samples per run in order to obtain enough sequence coverage after bioinformatic rRNA removal.
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