High-throughput sequencing

Part 1 book "Genomics in aquaculture" includes content: The new era of genome sequencing using highthroughput sequencing technology - Generation of the first version of the Atlantic cod genome; the rainbow trout genome, an important landmark for aquaculture and genome evolution; an improved version of the Atlantic cod genome and advancements in functional genomics - implications for the future of cod farming.... and other contents.

135p muasambanhan04 11-01-2024 7 1   Download

Long non-coding RNAs (lncRNAs) have crucial roles in various biological regulatory processes. However, the study of lncRNAs is limited in woody plants. Catalpa bungei is a valuable ornamental tree with a long cultivation history in China, and a deeper understanding of the floral transition mechanism in C. bungei would be interesting from both economic and scientific perspectives.

16p vihagrid 30-01-2023 7 3   Download

The ability to profile and quantify small non-coding RNAs (sRNAs), specifically microRNAs (miRNAs), using highthroughput sequencing is challenging because of their small size. We developed QsRNA-seq, a method for preparation of sRNA libraries for high-throughput sequencing that overcomes this difficulty by enabling a gelfree separation of fragments shorter than 100 nt that differ only by 20 nt in length.

12p vigalileogalilei 27-02-2022 14 2   Download

The Gram-positive bacterium Enterococcus faecium is a commensal of the human gastrointestinal tract and a frequent cause of bloodstream infections in hospitalized patients. The mechanisms by which E. faecium can survive and grow in blood during an infection have not yet been characterized. Here, we identify genes that contribute to growth of E. faecium in human serum through transcriptome profiling (RNA-seq) and a highthroughput transposon mutant library sequencing approach (Tn-seq).

12p vilarryellison 29-10-2021 9 1   Download

As one of “γδ-high” species, chicken is an excellent model for the study of γδ T cells in nonmammalian animals. However, a comprehensive characterization of the TCRγδ repertoire is still missing in chicken. The objective of this study was to characterize the expressed TCRγ repertoire in chicken thymus using highthroughput sequencing.

13p vitzuyu2711 29-09-2021 9 1   Download

Reconstructed monomers were used to design a satellite-specific fluorescent in situ hybridization (FISH) probe. The data were also analysed within a phylogenetic framework built using the internal transcribed spacer (ITS) sequences of 45S nuclear ribosomal DNA.

14p vitzuyu2711 29-09-2021 20 1   Download

Sequencing-based detection and characterization of viruses in complex samples can suffer from lack of sensitivity due to a variety of factors including, but not limited to, low titer, small genome size, and contribution of host or environmental nucleic acids.

14p visilicon2711 20-08-2021 8 1   Download

Long non-coding RNAs (lncRNAs) play crucial roles in gene regulation at the transcriptional and posttranscriptional levels. LncRNAs are belonging to a large class of transcripts with ≥200 nt in length which do not code for proteins, have been widely investigated in various physiological and pathological contexts by highthroughput sequencing techniques and bioinformatics analysis.

14p vijeeni2711 30-06-2021 13 1   Download

After over a decade of developments in field collection, laboratory methods and advances in highthroughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data.

10p vijeeni2711 30-06-2021 12 1   Download

Many tools exist in the analysis of bacterial RNA sequencing (RNA-seq) transcriptional profiling experiments to identify differentially expressed genes between experimental conditions. Generally, the workflow includes quality control of reads, mapping to a reference, counting transcript abundance, and statistical tests for differentially expressed genes.

4p vioklahoma2711 19-11-2020 12 0   Download

RNA molecules fold into complex three-dimensional shapes, guided by the pattern of hydrogen bonding between nucleotides. This pattern of base pairing, known as RNA secondary structure, is critical to their cellular function.

9p vioklahoma2711 19-11-2020 13 1   Download

Recently, rapid improvements in technology and decrease in sequencing costs have made RNA-Seq a widely used technique to quantify gene expression levels. Various normalization approaches have been proposed, owing to the importance of normalization in the analysis of RNA-Seq data.

9p vioklahoma2711 19-11-2020 5 0   Download

Bioinformatics tools designed to identify lentiviral or retroviral vector insertion sites in the genome of host cells are used to address the safety and long-term efficacy of hematopoietic stem cell gene therapy applications and to study the clonal dynamics of hematopoietic reconstitution.

12p viconnecticut2711 29-10-2020 14 1   Download

The European Community has adopted very restrictive policies regarding the dissemination and use of genetically modified organisms (GMOs). In fact, a maximum threshold of 0.9% of contaminating GMOs is tolerated for a “GMOfree” label.

17p vicolorado2711 22-10-2020 19 1   Download

Next-generation sequencing (NGS) is a high throughput sequencing technology, which has revolutionized both basic and clinical research of the human genetic disorders. This technology is also called massively parallel sequencing (MPS) due to its ability to generate a huge amount of output data in a cost- and time-effective manner. NGS is widely utilized for different sequencing applications such as targeted sequencing (a group of candidate genes), exome sequencing (all coding regions), and whole genome sequencing (the entire human genome).

14p caygaocaolon1 13-11-2019 26 1   Download