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Series GSE184177 Query DataSets for GSE184177
Status Public on Sep 17, 2021
Title Pig backfat miRNA profiling
Organism Sus scrofa
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary 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.
Overall design MicroRNA next generation sequencing of 24 pig backfat samples collected from castrated males and females was performed using Illumina HiScan SQ.
Contributor(s) Pawlina-Tyszko K, Oczkowicz M
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Submission date Sep 15, 2021
Last update date Sep 19, 2021
Contact name Klaudia Pawlina-Tyszko
Organization name National Research Institute of Animal Production
Department Deaprtment of Animal Genomics and Molecular Biology
Lab Laboratory of Genomics
Street address Krakowska 1
City Balice near Krakow
ZIP/Postal code 32-083
Country Poland
Platforms (1)
GPL21186 Illumina HiScanSQ (Sus scrofa)
Samples (24)
GSM5579621 49s
GSM5579622 52s
GSM5579623 53s
BioProject PRJNA763511
SRA SRP337223

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE184177_RAW.tar 2.9 Mb (http)(custom) TAR (of FA)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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