NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE107207 Query DataSets for GSE107207
Status Public on Dec 01, 2017
Title Whole transcriptome and miRNAome analysis of porcine muscle tissue in the terms of muscle growth and development
Organism Sus scrofa
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: The aim of present research was to identify genes potentially related with muscle growth in pig
Methods: RNA-seq analysis was performed on longissimus lumborum samples collected from 13 pigs representing two sire-line breeds – Pietrain and Hampshire. Base on dissection data, pigs were selected from a larger population in terms of weight of loin muscle to obtain the most extreme groups in each breed The cDNA libraries were constructed form 300 ng of total RNA with the use TruSeq RNA Sample Prep Kit v2 kit (Illumina) according to the protocol. The quantification of obtained libraries was performed on Qubit 2.0 (Invitrogen, Life Technologies) and TapeStation 2200 (D1000 ScreenTape; Agilent). The RNA-seq was performed in 101 single-end cycles on HiScanSQ platform (Illumina) with the use of ruSeq SR Cluster Kit v3- CBOT-HS and TruSeq SBS Kit v 3 - HS (Illumina). Each library was sequences in 4 technical replications. The DEGs were detected using DESEq2 software and validation was performed by qPCR.
Results: RNA-seq approach allowed to identify 627 and 416 DEGs between pig groups with different loin weight (pvalue <0.05; fold change≤1.5) for Pietrain and Hampshire; respectively. Next, the comparison of obtained genes sets showed 43 genes identified in both breeds. The Gene Ontology analysis (Panther software) confirmed that detected genes were involved in regulation of metabolic process (18 genes), developmental growth or skeletal system development (PCOLCE; BBS2; TBX2; RBBP6; ATAF5). According to David software these genes belong to PI3K-Akt signaling, Focal adhesion and ECM-receptor interaction pathways.
Conclusions: Obtained results allow to propose the panel of genes, which can be related with porcine muscle growth and development. Such analysis can be the basis of future research in terms of identification of candidate genes related with important production traits in pigs.
 
Overall design The muscle (longissimus dorsi) transcriptome sequencing was performed for 13 samples collected form pigs representing two breeds - Pietrain and Hampshare, using Illumina HiScan SQ in 101 single-end cycles and in 4 technical repetitions repetitions.
 
Contributor(s) Ropka-Molik K, Pawlina K, Żukowski K, Piórkowska K, Żak G, Derebecka N, Wesoły J
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Nov 21, 2017
Last update date May 15, 2019
Contact name Kacper Zukowski
E-mail(s) zukowski.kacper@gmail.com
Organization name National Research Institute of Animal Production
Street address Krakowska 1 Street
City Balice
ZIP/Postal code 32-083
Country Poland
 
Platforms (1)
GPL21186 Illumina HiScanSQ (Sus scrofa)
Samples (13)
GSM2862765 d - low weight of loin - 1hp
GSM2862766 a - high weight of loin - 1p
GSM2862767 d - low weight of loin - 2hp
Relations
BioProject PRJNA419312
SRA SRP125390

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
GSE107207_raw.genes.hampshire.csv.gz 222.4 Kb (ftp)(http) CSV
GSE107207_raw.genes.pietrain.csv.gz 242.3 Kb (ftp)(http) CSV
GSE107207_res.genes.hampshire.c-d.csv.gz 241.1 Kb (ftp)(http) CSV
GSE107207_res.genes.pietrain.a-b.csv.gz 349.3 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap