Journal: Scientific Reports

Article Title: Empirical assessment of the enrichment-based metagenomic methods in identifying diverse respiratory pathogens

doi: 10.1038/s41598-024-75120-x

Figure Lengend Snippet: Schematic of the mNGS assay workflow. Total nucleic acids (TNAs) were extracted by bead beating and guanidinium isothiocyanate-based lysis. Part of TNAs were used for qPCR panel test, the rest of TNAs were split into two aliquots for subsequent DNA and cDNA Illumina library preparation, the libraries were either analysed directly by Novaseq (sMS) or enriched by probes and further analysed by Illumina or Nanopore-based sequencing (eMS). Separate DNA and cDNA libraries were constructed and sequenced in this study.

Article Snippet: Part of TNAs were used for qPCR panel test, the rest of TNAs were split into two aliquots for subsequent DNA and cDNA Illumina library preparation, the libraries were either analysed directly by Novaseq (sMS) or enriched by probes and further analysed by Illumina or Nanopore-based sequencing (eMS).

Techniques: Lysis, Nanopore Sequencing, Construct

Journal: Scientific Reports

Article Title: Empirical assessment of the enrichment-based metagenomic methods in identifying diverse respiratory pathogens

doi: 10.1038/s41598-024-75120-x

Figure Lengend Snippet: Taxonomic identification provided by sMS and eMS compared to qPCR panel.

Article Snippet: Part of TNAs were used for qPCR panel test, the rest of TNAs were split into two aliquots for subsequent DNA and cDNA Illumina library preparation, the libraries were either analysed directly by Novaseq (sMS) or enriched by probes and further analysed by Illumina or Nanopore-based sequencing (eMS).

Techniques: DNA Sequencing, Sequencing, Virus, Bacteria

Journal: International Journal of Molecular Sciences

Article Title: Fecal miRNA Profiling of Yorkshire Terrier Enteropathy

doi: 10.3390/ijms26073385

Figure Lengend Snippet: miRNA primers and housekeeping genes from miRCURY LNA miRNA Probe catalogue (Qiagen, Hilden, Germany). The primers were assigned random numbers for simplification purposes.

Article Snippet: Small RNAs were converted into barcoded complementary DNA (cDNA) libraries for Illumina single-end sequencing using a 75-cycle protocol on the NextSeq500 platform (Illumina Inc., San Diego, CA, USA), following previously established methodologies [ ].

Techniques: Isolation, Control, cDNA Synthesis

Journal: Horticulture Research

Article Title: Transcriptional dynamics of the developing sweet cherry ( Prunus avium L.) fruit: sequencing, annotation and expression profiling of exocarp-associated genes

doi: 10.1038/hortres.2014.11

Figure Lengend Snippet: Summary of all contigs. Contigs were assembled de novo from Illumina sequenced cDNA fragments generated from sweet cherry ‘Regina’ fruit sampled at different developmental stages. Group 1 and 3 were termed ‘high abundance’ and Group 2 ‘low abundance’ contigs, based on the number of mapped reads per contig; threshold 30 mapped reads per sample or 75 reads total in all 24 samples. Group 3 consists of contigs with BLASTn hits ( e -value <1× −100 ) to bacterial, viral, rRNA or other sources as described in the section on ‘Materials and methods’

Article Snippet: Directional complementary DNA (cDNA) libraries were prepared at the GenXPro GmbH (Frankfurt am Main, Germany).

Techniques: Generated