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| Status |
Public on Oct 14, 2015 |
| Title |
Genome-wide RNA-Seq analysis of breast muscles of two broiler chicken groups differing in shear force |
| Organism |
Gallus gallus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: Next-generation sequencing (NGS) was used to select genes potentially associated with the level of meat tenderness in broiler chickens.
Methods: Chicken mRNA profiles of 6-weeks-old characterized by low (n=4) and high (n=4) shear force of pectoralis musle were generated by deep sequencing, using Illumina HiScan SQ. The alignment and estimation of gene level expression was made using the RSEM package and TopHat splice junction mapper, each supported by a Bowtie2 aligner. Differentially expressed genes (DEG) and their corresponding p-values were determined using the Cufflinks package, edgeR and DESeq2. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: A total of 11,560 transcripts and 9,824 genes per sample were identified. In the low shear force chicken group 19 genes were up-regulatated and 49 genes were down regutated. The up-regulated gene group included the ASB2 gene, which is probably involved in the meat conversion process, as its product results in the degradation of filamins, proteins which form muscle fibres. In the down-regulated gene group, genes which play a role in lipogenesis (THRSP, PLIN1) and in collagen synthesis (P4HA3, LEPREL4, PCOLCE2, COL16A1, COL20A1, VWA1) were detected.
Conclusions: Results obtained in our study sugest the involvement of the extracellular matrix in the determination of meat tenderness. In this study were identified a pool of genes that may participate in the tenderisation process in broiler chickens.
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| Overall design |
Chicken mRNA profiles of 6-weeks-old characterized by low (n=4) and high (n=4) shear force of pectoralis musle were generated by deep sequencing, using Illumina HiScan SQ in in two technical repetitions
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| Contributor(s) |
Piórkowska K, Żukowski K, Nowak J, Połtowicz K, Ropka-Molik K, Gurgul A |
| Citation(s) |
26592359 |
| BioProject |
PRJNA297364 |
| |
| Submission date |
Oct 13, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Katarzyna Piorkowska |
| E-mail(s) |
katarzyna.piorkowska@izoo.krakow.pl
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| Organization name |
National Research Institute of Animal Production
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| Department |
Animal Genomics and Molecular Biology
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| Lab |
Laboratory of Genomics
|
| Street address |
Krakowska 1
|
| City |
Balice |
| ZIP/Postal code |
32-083 |
| Country |
Poland |
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| Platforms (1) |
| GPL21018 |
Illumina HiScanSQ (Gallus gallus) |
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| Samples (8)
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| Relations |
| SRA |
SRP064441 |
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