Similar to DNA, all forms of RNA—including messenger RNA (mRNA), noncoding RNA, ribosomal RNA (rRNA), and transfer RNA (tRNA)—undergo modifications that, while not altering their nucleotide sequence, signific
ARTICLE https://doi.org/10.1038/s41467-022-29438-7 OPEN MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants Morten Kam Dahl Dueholm 1✉, Marta Nierychlo1, Kasper Skytte Andersen 1, Vibeke Rudk...
Sequencing of RNA results in a mixture of coding and non-coding RNA fragments, and the highly abundant ribosomal RNA in the samples are filtered out (Fig. 1.14) in order to use only mRNA transcripts for the analysis [52]. Thus, rRNA and tRNA are removed using the software SortMeRNA [41...
Then, the mRNA was purified including rRNA depletion and mRNA fragmentation, cDNA was synthetized, end repair and adaptor addition were performed and the fragments were enriched by PCR. The libraries were sequenced using Illumina (Novogene Co., Cambridge, UK). Bioinformatic analysis was performed ...
Using 16 S rRNA sequencing and fecal metabolite analysis, we characterized the GM composition and metabolite profiles in non-transgenic (Ntg) and SOD1G93A mutant mice of both strains. Our results revealed strain-specific differences in GM composition and functions, particularly in the abundance of ...
Studies of bacterial microbiota by 16 s rRNA sequencing show extensive variations among populations, and even among individuals exposed to identical inoculas [39, 40]. Likewise, extensive variations exist among strains of the same species, even in the context of microbiota [41]. The variations ...
The percentage of variable sites (VS) and the nucleotide diversity (ND) results are summarized for each PCG, rRNA gene, and concatenated sequences of PCGs and rRNAs in Fig.8. There is likely a positive correlation between the two parameters, as they seem to move together. The highest and...
In brief, adapters were trimmed, and reads of poor quality or aligning to rRNA sequences were filtered using Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The later reads were then aligned to the mouse genome (mm10) using STAR [30]. Read counts for each...
Since the nineties, the use of the whole 16S rRNA gene has been the most accepted approach in microbial taxonomic annotation, which could only be reached through first generation Sanger sequencing. This tech- nology became obsolete with the advent of second-gen- eration sequencers, such as ...
Short‑read RNA‑Seq sample prep and sequencing for HBR_ SIRV RNA Triplicate reactions of the HBR_SIRV RNA (500 ng input) was prepared using the NEBNext rRNA Depletion Kit v2 (New England Biolabs #E7400S) for ribodeple- tion and the NEBNext Ultra II Directional RNA Library ...