Transcriptome Analysis of Common Carp (Cyprinus carpio) Fed with Animal and Plant Diets
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PROVIDER: PRJNA515924 | ENA |
REPOSITORIES: ENA
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Project description:purpose?To elucidate the relationship of utilization different type of diets in fish method?enzyme activity determination and transcriptome sequencing were performed in common carp fed with single animal diet group (group AD), plant diet group (group PD) and mix diets group (group MD). Group MD as control group results? 916 and 1296 differentially expressed genes were identified between group AD vs MD and PD vs MD. Protein digestion and absorption, bile secretion, hematopoietic cell lineage and intestinal immune network for IgA production pathways were significantly differentially expressed between common carp fed with single type of diet and mix diets. Conclusion?common carp fed with mix diets had stronger immunity than common carp fed with single type of diets.
2019-01-19 | GSE125366 | GEO
Project description:Common carp is one of the main commercial fishes captured and cultured worldwide. Although common carp genome is not finished yet, this study provides a first large scale cloning and characterization of common carp miRNAs and their potential targets. These miRNAs add to the growing database of new miRNA and lay the foundation for further understanding of miRNA function in gene regulation of common carp. We constructed a small RNA library from 17 Cyprinus carpio samples.
2012-07-16 | E-GEOD-35131 | biostudies-arrayexpress
Project description:Ichthyophthirius multifiliis is a ciliated protozoan parasite recognized as one of the most pathogenic diseases of wild and cultured freshwater fish. Fish skin mucus plays a significant role against invading pathogens. However, the protein-based modulation against infection with I. multifiliis, of host fish at this barrier is unknown. The aim of this study was to investigate the modulation of the skin mucus after infection with I. multifiliis using quantitative proteomics to provide insights into the post-transcriptional and post-translational regulation of skin mucus proteins. Thus, we investigated the skin mucus proteome of common carp (Cyprinus carpio) using a shotgun proteomic approach at days 1 and 9 after I. multifiliis exposure.
2018-11-14 | PXD011148 | Pride
Project description:Cyprinus carpio 'Songpu mirror carp' Genome sequencing
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Project description:Purpose:In order to elucidate the molecular mechanism of the effects of different diets on the antioxidant capacity of fish, three groups of adult common carp (Cyprinus carpio) (initial weight 517.8 ±50 g) were fed with earthworm, earthworm + duckweed and duckweed, respectively, which were performed by miRNA sequencing. Methods:MiRNA profiles of common carp fed with earthworm, earthworm + duckweed and duckweed were generated by deep sequencing, in duplicate, using Illumina Hiseq 2500 platform. qRT–PCR validation was performed using SYBR Green assays Results: We built microRNA libraries by using total RNA and contained filtered 20,868,000, 18,984,242, 22,300,487, 19,538,683, 17,110,676 and 14,747,090 high-quality reads that were obtained from sample A1, A2, M1, M2, P1 and P2 respectively.In total, we discovered 236 known carp miRNAs (225, 225, 222, 227, 228 and 219 in A1, A2, M1, M2, P1and P2, respectively).For the known miRNA, 9 differentially expressed miRNAs (DEM) were found between A and M and 8 known miRNAs differentially expressed between P and M, and 11 of these were validated with qRT–PCR. The expression level of 11 known microRNAs via miRNA-seq had highly similar with the relative expression level of 11 known microRNAs via qRT-PCR. Conclusions: In present study, we demonstrated the transcriptional profiles, identification of 5 differentially expressed miRNAs be reported related to oxidative stress, including miR-137-3p, miR-143-3p, miR-146a-5p, miR-21-5p and miR-125b-5p. For omnivorous fish, feed a single bait may might cause oxidative stress inordinately.
2018-07-14 | GSE117059 | GEO
Project description:Cyprinus carpio carpio breed:Yellow River carp | cultivar:Huanghe carp Raw sequence reads
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Project description:The Cyprinus carpio is one of the most important food fish with over hundred varieties in the world. It shows many morphological and genetic variations after selection breeding. It is also considered an alternative vertebrate fish model to zebrafish. MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) have been suggested to have a crucial role in embryonic development. However, systemic research on the lncRNAs and miRNAs during embryonic development of C. carpio has not been reported yet. In this study, we investigated the miRNA, lncRNA and mRNA expression profiles during six main embryonic development stages (cleavage (2 hours post-fertilization hpf)), blastocyst (6 hpf), gastrulation (12 hpf), organ formation (20 hpf), hatching (64 hpf) and 1 day post-hatching). A total of 9,888,123 clean reads were obtained frommiRNA library. After filtering, 2886 miRNAs were identified. The results would open the way for future genetic, genomic, and evolutionary studies and enable better understanding of gene regulation during embryonic development of C. carpio.
2019-03-26 | GSE128806 | GEO
Project description:Genome-wide analysis of skin color-related lncRNA and mRNA expression in Koi carp, Cyprinus carpio L. LncRNAs information linked to fish skin color regulation is over-limited. In this study, Illumina sequencing and bioinformatics were primarily conducted on black, white and red skin colors of Koi carp. A total of 590,415,050 clean reads, 446,614 putative transcripts, 4,252 known and 72,907 novel lncRNAs were simultaneously obtained, respectively. Out of these genes, 92 significant differentially expressed lncRNAs and 722 mRNAs were excavated. Ccr_lnc5622441, Ccr_lnc765201 were found up-regulated in black and red skins; Ccr_lnc14074601 were up-regulated in white skin; and premelanosome proteins a (Pmela), tyrosinase (Tyr) were up-regulated in black skin, etc. Quantitative real-time PCR (qRT-PCR) further validated 12 differentially expressed genes were consistent with RNA-seq. Moreover, 70 lncRNAs on 107 target mRNAs in cis and 79 lncRNAs on 41,625 target mRNAs in trans were investigated, the networks revealed one lncRNAs can connected with numerous mRNAs, vice versa. These findings broadened the lncRNAs landscape of skin colors and provided new insights into the mechanisms underlying lncRNAs mediated pigmentation and differentiation in Koi carp.
2019-01-15 | GSE125039 | GEO
Project description:ZnO nanoparticles (NPs) are widely used in industrial and consumer products. Thus, understanding their interaction with biological systems is the key for their safe application. The aim of present study was to evaluate the toxicological effects on the intestine of common carp, Cyprinus carpio, after dietary exposure to ZnO NPs. To assess the toxicity of ZnO NPs and of their toxic mechanism to gastrointestinal tract, we applied label free protein quantification on carp intestine considering the fact that fish are on the top of food chain in aquatic ecosystems. Even though carp and zebrafish do not have five intestinal segments like mammals (Brugman, 2016), previous studies have revealed that intestinal anatomy and architecture in cyprinid teleost fish is closely related to mammals with functional homology (Curry, 1939). Therefore, the findings can also provide beneficial information to understand the mechanisms underlying NPs toxicity in mammals.
2017-09-25 | PXD006867 | Pride
Project description:The Cyprinus carpio is one of the most important food fish with over hundred varieties in the world. It shows many morphological and genetic variations after selection breeding. It is also considered an alternative vertebrate fish model to zebrafish. MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) have been suggested to have a crucial role in embryonic development. However, systemic research on the lncRNAs and miRNAs during embryonic development of C. carpio has not been reported yet. In this study, we investigated the miRNA, lncRNA and mRNA expression profiles during six main embryonic development stages (cleavage (2 hours post-fertilization hpf)), blastocyst (6 hpf), gastrulation (12 hpf), organ formation (20 hpf), hatching (64 hpf) and 1 day post-hatching). A total of 323.43 Gb high-quality reads were obtained from lncRNA library. After filtering, 51,979 lncRNAs were identified. The results would open the way for future genetic, genomic, and evolutionary studies and enable better understanding of gene regulation during embryonic development of C. carpio.
2020-12-31 | GSE150036 | GEO