Cyprinus carpio breed:Three strains including Hebao red carp, Huanghe carp and Songpu mirror carp
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA562102 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10023508_1.fastq.gz | Fastqsanger.gz | |||
| SRR10023508_2.fastq.gz | Fastqsanger.gz | |||
| SRR10023509_1.fastq.gz | Fastqsanger.gz | |||
| SRR10023509_2.fastq.gz | Fastqsanger.gz | |||
| SRR10023510_1.fastq.gz | Fastqsanger.gz |
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Project description:Cyprinus carpio 'Songpu mirror carp' Genome sequencing
| PRJNA202478 | ENA
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:Using a combination of protein fractionation by one-dimensional gel electrophoresis and high performance liquid chromatography - electrospray ionization tandem mass spectrometry, we identified 348 proteins in carp spermatozoa, most of which were for the first time identified in fish. Dynein, tubulin, HSP90, HSP70, HSP60, adenosylhomocysteinase, NKEF-B, brain type creatine kinase, mitochondrial ATP synthase, and valosin containing enzyme represent high abundance proteins in carp spermatozoa. These proteins are functionally related to sperm motility and energy production as well as the protection of sperm against oxidative injury and stress. Moreover, carp sperm is equipped with functionally diverse proteins involved in signal transduction, transcription, translation, protein turnover and transport. About 15% of carp sperm proteins identified here were also detected in seminal plasma which may be a result of leakage from spermatozoa into seminal plasma, adsorption of seminal plasma proteins on spermatozoa surface, and expression in both spermatozoa and cells secreting seminal plasma proteins. The availability of a catalogue of carp sperm proteins provides substantial advances for an understanding of sperm function and for future development of molecular diagnostic tests of carp sperm quality, the evaluation of which is currently limited to certain parameters such as sperm count, morphology and motility or viability.
2014-10-13 | PXD000877 | Pride
Project description:Cyprinid herpesvirus 3 (CyHV-3), also known as koi herpesvirus (KHV), is the aetiological agent of an emerging and lethal disease in common and koi carp. In this work we studied the immune response of two genetically different lines of common carp (Polish K and Polish R3) infected with CyHV-3 by immersion. The two carp lines presented a 20% difference in survival rate and, furthermore, significant difference in virus loads measured at day 3 post infection (p.i.). Microarray analysis revealed that 581 genes in line K (330 up-regulated, 251 down-regulated) and 107 genes in line R3 (77 up-regulated, 30 down-regulated), were at least 2-fold differentially expressed at day 3 p.i. compared to day 0. Genes which were at least 4-fold differentially expressed in both lines were selected as potential markers of an infection of common carp by CyHV-3. This group includes 17 up-regulated and only 1 down-regulated genes. In addition, microarray analysis revealed no significant differences in gene expression between line K and R3 at day 0. At day 3 p.i. there were, however, 76 genes that were at least 2-fold differentially expressed between the two lines. The kinetics of expression of T cell markers and selected cytokines indicate for higher activation of immune response in more resistant R3 line. Thus, our study revealed that differences in resistance to CyHV-3 between two carp lines can be correlated with differentially expressed immune-related genes. The experiment included four biological replicates with no dye swaps for (i) each strain (K and R3) and (ii) each condition (day 0 and day 3).
2012-01-05 | E-GEOD-30426 | biostudies-arrayexpress
Project description:Cyprinid herpesvirus 3 (CyHV-3), also known as koi herpesvirus (KHV), is the aetiological agent of an emerging and lethal disease in common and koi carp. In this work we studied the immune response of two genetically different lines of common carp (Polish K and Polish R3) infected with CyHV-3 by immersion. The two carp lines presented a 20% difference in survival rate and, furthermore, significant difference in virus loads measured at day 3 post infection (p.i.). Microarray analysis revealed that 581 genes in line K (330 up-regulated, 251 down-regulated) and 107 genes in line R3 (77 up-regulated, 30 down-regulated), were at least 2-fold differentially expressed at day 3 p.i. compared to day 0. Genes which were at least 4-fold differentially expressed in both lines were selected as potential markers of an infection of common carp by CyHV-3. This group includes 17 up-regulated and only 1 down-regulated genes. In addition, microarray analysis revealed no significant differences in gene expression between line K and R3 at day 0. At day 3 p.i. there were, however, 76 genes that were at least 2-fold differentially expressed between the two lines. The kinetics of expression of T cell markers and selected cytokines indicate for higher activation of immune response in more resistant R3 line. Thus, our study revealed that differences in resistance to CyHV-3 between two carp lines can be correlated with differentially expressed immune-related genes.
2012-01-05 | GSE30426 | GEO
Project description:In this study, the complete mitochondrial genome sequences of Cyprinus carpio (strain Songpu) were reported for the first time. The genome is found to be 16 582 bp in length accurately using the next-generation sequencing technology and bioinformatics tools, and it has a base composition of A (31.9%), G (15.7%), C (27.5%) and T (24.9%), indicating that the percentage of A + T (56.8%) was higher than G + C (43.2%). The whole genome contains a typically conserved structure, which includes 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one control region (D-loop). To obtain the phylogenetic relationship between Songpu mirror carp and other species, 11 mitochondrial genomes were used for phylogenetic analysis. The result shows the Songpu mirror carp is closely related to Cyprinu carpio carpio that is also a member of the genus Cyprinu.
| S-EPMC7800881 | biostudies-literature
Project description:We report RNA-seq data of several tissue types in the european common carp.
2018-09-25 | GSE73429 | 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: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:Cyprinus carpio carpio breed:Yellow River carp | cultivar:Huanghe carp Raw sequence reads
| PRJNA493161 | ENA