The chromosome-centric dataset was created by applying several technologies of transcriptome profiling. The described dataset is available at NCBI repository (BioProject ID PRJNA635536). The dataset referred to the same type of tissue, cell lines, transcriptome sequencing technologies, and was accomplished in a period of 8 years (the first data were obtained in 2013 while the last ones - in 2020). The high-throughput sequencing technologies were employed along with the quantitative PCR (qPCR) approach, for data generation using the gene expression level assessment. qPCR was performed for a limited group of genes, encoded on human chromosome 18, for the Russian part of the Chromosome-Centric Human Proteome Project. The data of high-throughput sequencing are provided as Excel spreadsheets, where the data on FPKM and TMP values were evaluated for the whole transcriptome with both Illumina HiSeq and Oxford Nanopore Technologies MinION sequencing.
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http://dx.doi.org/10.1016/j.dib.2021.107130 | DOI Listing |
Equine Vet J
January 2025
Department of Veterinary Clinical Sciences, University of Copenhagen, Taastrup, Denmark.
Background: MicroRNAs, a class of small noncoding RNAs, serve as post-transcriptional regulators of gene expression and are present in a stable and quantifiable form in biological fluids. MicroRNAs may influence intra-articular responses and the course of disease, but very little is known about their temporal changes in osteoarthritis.
Objectives: To identify miRNAs and characterise the temporal changes in their abundance in SF from horses with experimentally induced osteoarthritis.
Planta
January 2025
ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, Delhi, India.
Small RNA sequencing analysis in two chickpea genotypes, JG 62 (Fusarium wilt-susceptible) and WR 315 (Fusarium wilt-resistant), under Fusarium wilt stress led to identification of 544 miRNAs which included 406 known and 138 novel miRNAs. A total of 115 miRNAs showed differential expression in both the genotypes across different combinations. A miRNA, Car-miR398 targeted copper chaperone for superoxide dismutase (CCS) that, in turn, regulated superoxide dismutase (SOD) activity during chickpea-Foc interaction.
View Article and Find Full Text PDFJ Vet Sci
December 2024
College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Korea.
Importance: This study is essential for comprehending the zoonotic transmission, antimicrobial resistance, and genetic diversity of enteropathogenic (EPEC).
Objective: To improve our understanding of EPEC, this study focused on analyzing and comparing the genomic characteristics of EPEC isolates from humans and companion animals in Korea.
Methods: The whole genome of 26 EPEC isolates from patients with diarrhea and 20 EPEC isolates from companion animals in Korea were sequenced using the Illumina HiSeq X (Illumina, USA) and Oxford Nanopore MinION (Oxford Nanopore Technologies, UK) platforms.
Microbiome
December 2024
Faculty of Medicine, Human Microbiome Research Program, University of Helsinki, Helsinki, Finland.
Background: Amplicon sequencing of kingdom-specific tags such as 16S rRNA gene for bacteria and internal transcribed spacer (ITS) region for fungi are widely used for investigating microbial communities. So far most human studies have focused on bacteria while studies on host-associated fungi in health and disease have only recently started to accumulate. To enable cost-effective parallel analysis of bacterial and fungal communities in human and environmental samples, we developed a method where 16S rRNA gene and ITS1 amplicons were pooled together for a single Illumina MiSeq or HiSeq run and analysed after primer-based segregation.
View Article and Find Full Text PDFPlant Dis
December 2024
Jiangsu Academy of Agricultural Sciences, Institute of Plant Protection, Nanjing, Jiangsu, China;
Faba bean (Vicia faba L.) is the fourth most cultivated temperate legume (Lyu et al., 2021).
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