Cyprinus carpio 'Songpu mirror carp'
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ABSTRACT:
PROVIDER: PRJNA202478 | ENA |
REPOSITORIES: ENA
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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: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: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 carpio breed:Yellow River carp | cultivar:Huanghe carp Raw sequence reads
| PRJNA493161 | ENA
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: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:Growth and reproduction are two major physiological processes that are closely related in vertebrates, and IGFs are key factors that regulate the growth and reproduction axis. As a novel IGF system member, igf3 plays an important role in gonadal development of teleost fish. Although studies have reported the abnormal expression of igf3 in fish gonad, whether the igf3 regulates the expression of long noncoding RNAs (lncRNAs) in gonad remains unknown. In this study, a igf3 knockdown common carp (Cyprinus carpio) model was established by RNA interference. Than RNA sequencing of transcriptome in C. carpio after igf3 knockdown was performed. A total of 327,169,410 and 306,305,018 clean reads were identified from control and igf3-dsRNA group, respectively. After a stringent filtering, RNA-seq yielded 14199 lncRNA and 106932 mRNA transcripts with 124 and 353 differentially expressed lncRNAs and mRNAs. Gene Ontology analysis revealed that the target genes of differentially expressed lncRNAs and mRNAs mainly regulated male genitalia development, female gonad development, cellular response to gonadotropin-releasing hormone, insulin-like growth factor-activated receptor activity and insulin-like growth factor binding. Kyoto Encyclopedia of Genes and Genomes analysis showed that the target genes of differentially expressed lncRNAs and mRNAs mainly involved in pathways associated with insulin signaling pathway, GnRH signaling pathway, Wnt signaling pathway, PI3K-Akt signaling pathway and TGF-beta signaling pathway. The lncRNA-mRNA co-expression network highlight the inter-regulation of the differentially expressed lncRNAs and mRNAs in gonad. Our results provide essential data regarding differentially expressed lncRNAs and mRNAs after igf3 knockdown, which may be useful to elucidate the role of igf3 in the gonadal development of C. carpio.
2018-10-27 | GSE121692 | 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
Project description:fermented common carp (Cyprinus carpio L.) Raw sequence reads
| PRJNA778028 | ENA