Pig backfat miRNA profiling
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA763511 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15904200.fastq.gz | Fastqsanger.gz | |||
| SRR15904201.fastq.gz | Fastqsanger.gz | |||
| SRR15904202.fastq.gz | Fastqsanger.gz | |||
| SRR15904203.fastq.gz | Fastqsanger.gz | |||
| SRR15904204.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: Analysis of the effect of different fats and amonut of cDDGS in the feedstuff on miRNA expression in porcine backfat Methods: miRNA-seq analysis was performed on backfat samples collected from 24 male and female crossbred fatteners originating from sows (Polish Landrace × White Large Polish) mated with a boar (Duroc × Pietrain) divided into four dietary groups: 7-cDDGS+rapeseed oil (group I), n=6 (+cDDGS+rapeseed oil -group II), n= 6 (+cDDGS+beeftallow -group III),n=5 (+cDDGS+coconut oil -group IV). The miRNA libraries were constructed from total RNA using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) according to the manufacturer protocol. The quantification of the obtained libraries was performed on a Qubit 2.0 spectrophotometer (Invitrogen, Life Technologies), while a quality control on a TapeStation 2200 instrument (D1000 ScreenTape; Agilent). 100 single-end cycle sequencing was performed on the HiScanSQ platform (Illumina) with the use of TruSeq SR Cluster Kit v3- CBOT-HS and TruSeq SBS Kit v 3 - HS (Illumina). MicroRNA differentially expressed between dietary groups were identified with the DESeq2 software. Results: The comparison of miRNA profiles between dietary groups showed The highest number of miRNAs with altered expression was identified in the comparison of animals fed the diet containing cDDGS and coconut oil (group IV) with animals from the –cDDGS + rapeseed oil (group I) (37 miRNA, p adjusted <0.01). Moreover, in comparison between the group IV and groups III and II , 29 (12 upregulated and 17 downregulated in +cDDGS+coconut oil group) and 28 (10 upregulated and 18 downregulated in +cDDGS+coconut oil group) miRNAs were identified, respectively (p adjusted <0.1) Conclusions: Obtained results suggest that coconut oil induces changes in miRNA profile of backfat in pigs.
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Project description:We report the application of Illumina short RNA sequencing for characterization and discovery of miRNAs and moRNAs in two Italian Large White pig backfat tissue.
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Project description:We report the application of Illumina RNA sequencing for characterization and discovery of genes and transcripts in Italian Large Whtie pig backfat tissue.
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Project description:We report the application of Illumina RNA sequencing for characterization and discovery of genes and transcripts in Italian Large Whtie pig backfat tissue. RNAs sequencing for long RNA quantification, discovery, characterisation and differential expression evaluation.
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Project description:The objective of this study was to identify key genes associated with porcine muscle growth and adipose metabolism which different expression in porcine backfat tissue between Fat Type Pig(Taihu pig) and Lean Type Pig (Landrace), among developmental phases(Month 1,2,3,4,5). The gene expression analyses will increase understanding of impact factors of pork quality by identifying key genes and pathways controlling backfat development. Relative real-time RT-PCR was used to confirm differential expression of 3 different expression genes(ME,SCD and UCP3) which normalized by 3 housekeep genes(ACTB, TBP and TOP2B). Keywords: time course and breed comparison
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Project description:We report the significant role methylation in differentially expressed genes in backfat and liver tissue of Nanchukmacdon pig
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Project description:The identification of the molecular mechanisms regulating pathways associated to the potential of fat deposition in pigs can lead to the detection of key genes and markers for the genetic improvement of fat traits. MicroRNAs (miRNAs) interactions with target RNAs regulate gene expression and modulate pathway activation in cells and tissues. In pigs, miRNA discovery is well far from saturation and the knowledge of miRNA expression in backfat tissue and particularly of the impact of miRNA variations are still fragmentary. We characterized by RNA-seq the small RNAs (sRNAs) expression profiles in Italian Large White pig backfat tissue. Comparing two groups of pigs divergent for backfat deposition, we detected 31 significant differentially expressed (DE) sRNAs, 14 up-regulated (including ssc-miR-132 ,ssc-miR-146b, ssc-miR-221-5p, ssc-miR-365-5p, and the moRNA ssc-moR-21-5p) and 17 down-regulated (including ssc-miR-136, ssc-miR-195, ssc-miR-199a-5p, and ssc-miR-335). To understand the biological impact of the observed miRNA expression variations, we used the expression correlation of DE miRNA target transcripts expressed in the same samples to define a regulatory network of 193 interactions between DE miRNAs and 40 DE target transcripts showing opposite expression profiles and being involved in specific pathways. Several miRNAs and mRNAs in the network resulted to be expressed from backfat related pig QTLs. These results are informative on the complex mechanisms influencing fat traits, shed light on a new aspect of the genetic regulation of fat deposition in pigs, and facilitate the perspective implementation of innovative strategies of pig genetic improvement based on genomic markers.
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Project description:Purpose: The aim of present research was to characterize miRNA profile of the pig brain tissue and identify miRNAs potentially connected with brain functioning. Methods: miRNA-seq analysis was performed on brain samples collected from 21 male and female pigs belonging to the Polish 990 synthetic line. The miRNA libraries were constructed from total RNA using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) according to the manufacturer protocol. The quantification of the obtained libraries was performed on a Qubit 2.0 spectrophotometer (Invitrogen, Life Technologies), while a quality control on a TapeStation 2200 instrument (D1000 ScreenTape; Agilent). 100 single-end cycle sequencing was performed on the HiScanSQ platform (Illumina) with the use of TruSeq SR Cluster Kit v3- CBOT-HS and TruSeq SBS Kit v 3 - HS (Illumina). MicroRNA differentially expressed between males and females were identified with the DESeq2 software, while validation was carried out with RT-qPCR. Results: miRNA-seq approach allowed the identification of 237 known and 286 potentially novel miRNAs. The comparison of miRNA profiles between females and males showed differential expression of 38 microRNAs. Pathway analysis (DIANA mirPath v.3 tool) confirmed that detected miRNAs are engaged in estrogen signaling pathway, prolactin signaling pathway, long-term depression, axon guidance according to KEGG Database, and response to stress, immune system process, catabolic process according to GO. Conclusions: Obtained results enabled us to characterize the miRNA profile of the pig brain tissue of males and females, with particular emphasis on the influence of sex. Moreover, they can be the basis for future studies in terms of search of candidate miRNAs related with important processes occuring in the brain and its diseases.
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