20.500.12556/DiRROS-28453 Effect of rearing systems and dietary protein levels on the skeletal muscle histomorphology and transcriptome profiles in indigenous Krškopolje Pig expression profiling by high throughput sequencing Platforms (1) GPL26351 Illumina NovaSeq 6000 (Sus scrofa) RNA-sequencing was performed to compare the effects of production systems (conventional indoor, vs. outdoor) and diets (standard protein, HP, vs. low protein, LP) within each rearing system on the transcriptomic profiles of two skeletal muscles, longissimus thoracis et lumborum (LL) and semispinalis capitis (SSC). Differentially expressed genes (DEGs) were identified with |log2FC| > 1 and q-value < 0.005. The effect of rearing system (indoor vs. outdoor) resulted in 354 DEGs in LL and 334 DEGs in SSC. The effect of diet within individual rearing system was less pronounced. In LL, HP vs. LP resulted in 23 DEGs under indoor and none under outdoor rearing system. In SSC, HP vs. LP resulted in 28 DEGs under indoor and 30 DEGs under outdoor rearing system. Pathway enrichment analysis revealed 42 pathways significantly enriched for HP vs. LP in the outdoor rearing system (across both muscles); additionally, 11 pathways were altered specifically in SSC for HP vs. LP under indoor rearing system, and 27 pathways were altered specifically in LL for HP vs. LP under outdoor rearing system RNA sequences pigs adipose tissue high throughput sequencing RNA transcriptome profiles gene expression locel breeds hybrid breeds data data set RNK sekvence prašiči režim prehranjevanja nivo proteinov v krmi histomorfološke lastnosti skeletno mišičan muskulatura visokozmogljivo sekvenciranje RNK profili transkriptomoov izražanje genov lokalne pasme sodobne pasme vsebnost beljakovin v prehrani podatki podatkovni set Sus scrofa true false true Gene Expression Omnibus (GEO) Angleški jezik Slovenski jezik Neznano 2026-03-20 08:34:59 2026-03-20 08:34:59 2026-03-26 03:47:05 0000-00-00 00:00:00 2026 0 Bethesda 2026 Bethesda Nasl. z. nasl. zaslona; Opis vira z dne 20. 3. 2026; 1 spletni vir 0000-00-00 Zaloznikova Objavljeno NiDoloceno 0000-00-00 0000-00-00 2026-02-20 2030-02-20 636 272369923 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE320088 Podatki nedostopni, 20. 3. 2026, dostopni po 20. 2. 2030 1 4fa566fc-242f-11f1-b469-001a4af901a5 https://dirros.openscience.si/Dokument.php?lang=slv&id=42151 Vrecl_Series_GSE320088_2026.pdf Vrecl_Series_GSE320088_2026.pdf 1 969957605D665B3927658E5566FBD90F 9d0375e6df65a2d63927c0b5874ad2a1c6e0bdf254d8b540ce76acdc6704f32a 6c0b3115-242f-11f1-b469-001a4af901a5 https://dirros.openscience.si/Dokument.php?lang=slv&id=42152 Kmetijski inštitut Slovenije 0 0 0