scholarly journals An efficient method for extracting next‐generation sequencing quality RNA from liver tissue of recalcitrant animal species

2019 ◽  
Vol 234 (9) ◽  
pp. 14405-14412 ◽  
Author(s):  
Davinder Sharma ◽  
Naresh Golla ◽  
Sudhakar Singh ◽  
Pankaj Kumar Singh ◽  
Dheer Singh ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Efficient Method ◽  
Liver Tissue ◽  
Animal Species ◽  
Next Generation ◽  
Sequencing Quality ◽  
Generation Sequencing

scholarly journals A Fun Introductory Command Line Lesson: Next Generation Sequencing Quality Analysis with Emoji!

CourseSource ◽  
2021 ◽  
Vol 8 ◽  
Author(s):  
Rachael M. St. Jacques ◽  
William M. Maza ◽  
Sabrina D. Robertson ◽  
Andrew Lonsdale ◽  
Caylin S. Murray ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Quality Analysis ◽  
Command Line ◽  
Next Generation ◽  
Sequencing Quality ◽  
Generation Sequencing

scholarly journals Using next-generation sequencing of microRNAs to identify host and/or pathogen nucleic acid signatures in samples from children with biliary atresia – a pilot study

2020 ◽  
Vol 2 (7) ◽  
Author(s):  
Melvyn Smith ◽  
Mark Zuckerman ◽  
Apsara Kandanearatchi ◽  
Richard Thompson ◽  
Mark Davenport
Keyword(s):  
Next Generation Sequencing ◽  
Biliary Atresia ◽  
Liver Tissue ◽  
Expression Patterns ◽  
Biliary Tree ◽  
Cyst Formation ◽  
Next Generation ◽  
Tissue Samples ◽  
Type 3 ◽  
Generation Sequencing

Biliary atresia (BA) is a progressive disease affecting infants resulting in inflammatory obliteration and fibrosis of the extra- and intra-hepatic biliary tree. BA may be grouped into type 1 isolated; type 2 syndromic, where other congenital malformations may be present; type 3 cystic BA, where there is cyst formation within an otherwise obliterated biliary tree; and cytomegalovirus-associated BA. The cause of BA is unclear, with immune dysregulation, inflammation and infection, particularly with cytomegalovirus (CMV), all implicated. In this study a total of 50/67 samples were tested for CMV DNA using quantitative real-time PCR. Ten liver tissue and 8 bile samples from 10 patients representing the range of BA types were also analysed by next-generation sequencing. CMV DNA was found in 8/50 (16 %) patients and a total of 265 differentially expressed microRNAs were identified. No statistically significant differences between the various types of BA were found. However, differences were identified in the expression patterns of 110 microRNAs in bile and liver tissue samples (P<0.05). A small number of bacterial and viral sequences were found, although their relevance to BA remains to be determined. No direct evidence of viral causes of BA were found, although clear evidence of microRNAs associated with hepatocyte and cholangiocyte differentiation together with fibrosis and inflammation were identified. These include miR-30 and the miR-23 cluster (liver and bile duct development) and miR-29, miR-483, miR-181, miR-199 and miR-200 (inflammation and fibrosis).

scholarly journals Combining a COI Mini-Barcode with Next-Generation Sequencing for Animal Origin Ingredients Identification in Processed Meat Product

2020 ◽  
Vol 2020 ◽  
pp. 1-9 ◽  
Author(s):  
Yanyi Pan ◽  
Deyi Qiu ◽  
Jian Chen ◽  
Qiaoyun Yue
Keyword(s):  
Next Generation Sequencing ◽  
Animal Species ◽  
Detection Efficiency ◽  
Meat Product ◽  
Animal Origin ◽  
Processed Meat ◽  
Next Generation ◽  
Universal Primer ◽  
Clone Sequencing ◽  
Generation Sequencing

For revealing animal species in complex or adulterated processed meat product, we presented a method combining a novel cytochrome oxidase I (COI) mini-barcode with next-generation sequencing (NGS), which identifies various animal species (swine, bovine, Caprinae, and some of fish, shrimp, and poultry) accurately and efficiently in processed meat products. We designed a universal primer based on 140 sequences from 51 edible animal species. A mixture of 12 species raw meat samples were identified with the clone sequencing and also with a mini-barcode- (136 bp) combined NGS method, respectively. The mini-barcode of these 12 species was 100% identical to the target species sequence by Sanger sequencing. Compared to the clone sequencing method, the NGS method is superior in accuracy, sensitivity, and detection efficiency. Various edible animal species were identified in the species level both in the mixed samples and the 7 heavily processed food products. Moreover, some unlabeled species and dubious contamination were detected as well.

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