Background: RNA-Seq data is inherently nonuniform for different transcripts because of differences in gene expression. This makes it challenging to decide how much data should be generated from each sample. How much should one spend to recover the less expressed transcripts? The sequencing technology used is another consideration, as there are inevitably always biases against certain sequences. To investigate these effects, we first looked at high-depth libraries from a set of well-annotated organisms to ascertain the impact of sequencing depth on de novo assembly. We then looked at libraries sequenced from the Universal Human Reference RNA (UHRR) to compare the performance of Illumina HiSeq and MGI DNBseq™ technologies.
Results: On the issue of sequencing depth, the amount of exomic sequence assembled plateaued using data sets of approximately 2 to 8 Gbp. However, the amount of genomic sequence assembled did not plateau for many of the analyzed organisms. Most of the unannotated genomic sequences are single-exon transcripts whose biological significance will be questionable for some users. On the issue of sequencing technology, both of the analyzed platforms recovered a similar number of full-length transcripts. The missing "gap" regions in the HiSeq assemblies were often attributed to higher GC contents, but this may be an artefact of library preparation and not of sequencing technology.
Conclusions: Increasing sequencing depth beyond modest data sets of less than 10 Gbp recovers a plethora of single-exon transcripts undocumented in genome annotations. DNBseq™ is a viable alternative to HiSeq for de novo RNA-Seq assembly.
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http://dx.doi.org/10.1186/s12864-019-5965-x | DOI Listing |
Chemistry
December 2024
Universitat Duisburg-Essen, Institute of organic chemistry, Universitätsstraße 7, 45117, Essen, GERMANY.
In recent years, researchers studying fluorogenic samples have steadily shifted from using large, expensive, poorly soluble fluorophores with complex synthetic sequences to smaller, simpler p scaffolds with low molecular weight. This research article presents an in-depth study of the photophysical properties of five bridged single-benzene-based fluorophores (SBBFs) investigated for their solution and solid-state emission (SSSE) properties. The compounds O4, N1O3, N2O2, N3O1, and N4 are derived from a central terephthalonitrile core and vary in the amount of oxygen and nitrogen bridging atoms.
View Article and Find Full Text PDFThe genome-wide chromosome conformation capture method, Hi-C, has greatly advanced our understanding of genome organization. However, its quantitative properties, including sensitivity, bias, and linearity, remain challenging to assess. Measuring these properties is difficult due to the heterogenous and dynamic nature of chromosomal interactions.
View Article and Find Full Text PDFInt J Cardiol Congenit Heart Dis
December 2024
Department of Cardiovascular Sciences and NIHR Leicester Biomedical Research Centre, University of Leicester, College of Medicine Biological Sciences and Psychology, Glenfield Hospital, Groby Road LE39QP, Leicester, UK.
Background: Thoracic aortic dissection (TAD) is an uncommon complication in patients with Tetralogy of Fallot (TOF). Information concerning risk factors for TAD in patients with TOF is very limited.
Methods: We report a case of Stanford type A TAD in a female patient with previously repaired TOF.
Front Microbiol
December 2024
Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, Republic of Korea.
This study investigated age-related changes in the gut microbiota and metabolome of Sapsaree dogs through metagenomic and metabolomic analyses. Using Illumina (short-read) and Nanopore (long-read) sequencing technologies, we identified both common and unique bacterial genera in the dogs across different age groups. In metagenomic analysis, Firmicutes were predominant at the family level.
View Article and Find Full Text PDFMol Neurodegener
December 2024
Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.
Background: The gene C9orf72 harbors a non-coding hexanucleotide repeat expansion known to cause amyotrophic lateral sclerosis and frontotemporal dementia. While previous studies have estimated the length of this repeat expansion in multiple tissues, technological limitations have impeded researchers from exploring additional features, such as methylation levels.
Methods: We aimed to characterize C9orf72 repeat expansions using a targeted, amplification-free long-read sequencing method.
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