Project description:China produces more than 77.9% of the world's production of silver carp in 2020 with the production of 3812.9 kiloton.3 The high consumption of silver carp in China is mainly by using its edible muscles for manufacture of surimi-based seafoods or other muscle foods, which may contribute high quality protein resource and other valuable nutrients in human diets. This project is to understanding the muscle composition of slaughtered fish skeletal muscle use the proteomics methods. The proteomics was performed based on the improved DDA experiment with extensive fractionation and prolonged separation of peptides, and protein searching database was informed by the Iso-seq transcriptomics.
Project description:We applied high throughput sequencing technology to identify microRNA genes in bighead carp and silver carp. We identified 167 conserved miRNAs in bighead carp and 166 in silver carp. By two computational stragegies, we obtained 39 novel miRNAs in bighead carp and 54 in silver carp, for which, no homologs were found in other species. Several miRNA* sequences were found in our dataset as well, some particular ones might have gene regulation function. Gain and loss of family members were observed in several miRNA families, which partially reflected the fate of miRNA gene duplicates.
Project description:We applied high throughput sequencing technology to identify microRNA genes in bighead carp and silver carp. We identified 167 conserved miRNAs in bighead carp and 166 in silver carp. By two computational stragegies, we obtained 39 novel miRNAs in bighead carp and 54 in silver carp, for which, no homologs were found in other species. Several miRNA* sequences were found in our dataset as well, some particular ones might have gene regulation function. Gain and loss of family members were observed in several miRNA families, which partially reflected the fate of miRNA gene duplicates. Total RNA of juvenile bighead carp and silver carp were sequenced on one Solexa lane, respectively.
Project description:Long-read sequencing technologies such as Iso-Seq (PacBio Inc.) generate highly accurate sequences of full-length mRNA transcript isoforms. Long-read transcriptomics may be especially useful in the context of lymphocyte functional plasticity as it relates to human health and disease. However, no long-read isoform-aware reference transcriptomes of human circulating lymphocytes seem to be publicly available despite being valuable as benchmarks in a variety of transcriptomic studies. To begin to fill this gap, we purified four lymphocyte subsets (CD4 T, CD8 T, NK, and Pan B cells) from the peripheral blood of a healthy male donor and obtained high-quality RNA (RIN>8) for PacBio Iso-Seq analysis and parallel RNA-Seq analysis.
Project description:Long-read sequencing technologies such as Iso-Seq (PacBio Inc.) generate highly accurate sequences of full-length mRNA transcript isoforms. Long-read transcriptomics may be especially useful in the context of lymphocyte functional plasticity as it relates to human health and disease. However, no long-read isoform-aware reference transcriptomes of human circulating lymphocytes seem to be publicly available despite being valuable as benchmarks in a variety of transcriptomic studies. To begin to fill this gap, we purified four lymphocyte subsets (CD4 T, CD8 T, NK, and Pan B cells) from the peripheral blood of a healthy male donor and obtained high-quality RNA (RIN>8) for PacBio Iso-Seq analysis and parallel RNA-Seq analysis.
2022-09-16 | GSE202327 | GEO
Project description:Silver carp kidney gut microbe