Transcriptome Profile Analysis of Mammary Gland Tissue from Two Breeds of Lactating Sheep
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. Experimental Animals and RNA Preparation
2.3. cDNA Library Construction and RNA-Seq
2.4. Mapping of Sequencing Reads and Identification of DEGs
2.5. GO and KEGG Pathway Analyses
2.6. Validation of DEGs by Reverse Transcription-Quantitative PCR
3. Results
3.1. RNA-Seq Reads and Mapping to the Reference Genome
3.2. Identification of DEGs
3.3. GO Enrichment and KEGG Pathway Analyses
3.4. Validation of Selected DEGs Using RT-qPCR
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Gene | Forward (5′→3′) | Reverse (5′→3′) |
---|---|---|
NOD2 | GAATTACCGGTCCCATTGGC | ACACTTCTTCCAGGCACAGA |
PLA2G2D | AACCCAGAGATGCCACAGAC | AAGCCAACGTCTTGTCACAG |
LEPR | TGTTGCTTTGGAGTGAGGA | TCCAGTGTGCACCTGTTTGT |
NEU2 | GACGAGCAAGAAGGATGAGC | CGGGGATGGCAATGAAGAAG |
CDKN1A | GAGAGCGATGGAACTTCGAC | AGTGGTCCTCCTGAGACGTG |
COL6A5 | GAGACCATCGCAGGGGATAA | ACCATGTCAGAGCCATCACA |
RELN | ACTCTGGGCCAAACTGCTAT | TTGTCTCACTGTGGATCCCC |
MYLK-3 | GCTGGCCAGAAGATACAAGC | CGGGAACGAGACAAACTCAT |
GR1N3A | GCAAATATGGAGCCTGGAAA | CTGGCTTCGTGCAGTATTGA |
PAH | CGCTGTCCAGGAGTATACGA | TTGTGGCAGCAAAGTTCCTC |
CACNA1D | TTCCCAGCTCAACAAATGCC | TGCCCGTTTTCAGACACAAG |
GDF-5 | GGGCTGGGATGACTGGATTA | GGCTGAGTCGATGAAGAGGA |
CD19 | AGATGCAGCTGAAGGTCACT | CAGGGAAGTCAGGCAGAAGA |
β-actin | AGCCTTCCTTCCTGGGCATGGA | GGACAGCACCGTGTTGGCGTAGA |
GAPDH | ATCTCGCTCCTGGAAGATG | TCGGAGTGAACGGATTCG |
Sample | Useful Reads | Map Event | Map Reads | Map Reads (%) | Multiple Reads | Multiple Reads (%) | Unique Reads | Unique Reads (%) |
---|---|---|---|---|---|---|---|---|
GAM-1 | 141244574 | 119373530 | 110324120 | 78.11 | 3934715 | 3.57 | 106389405 | 96.43 |
GAM-2 | 139563102 | 118260385 | 107968116 | 77.36 | 4219681 | 3.91 | 103748435 | 96.09 |
GAM-3 | 139407058 | 117075040 | 106817466 | 77.62 | 4707008 | 4.41 | 102110458 | 95.59 |
STH-1 | 140828556 | 117044888 | 108043045 | 76.72 | 3664975 | 3.39 | 104378070 | 96.61 |
STH-2 | 136465766 | 113483944 | 103333734 | 75.72 | 4688735 | 4.54 | 98644999 | 95.46 |
STH-3 | 136990336 | 111826264 | 103170887 | 75.31 | 3926392 | 3.81 | 99244495 | 96.19 |
KEGG Pathway 1 | Upregulated Genes | Down-Regulated Genes | Corrected p-Value |
---|---|---|---|
Hematopoietic cell lineage | CD22, CD19, CD13 | 0.012 | |
Oxytocin signaling pathway | MYLK-3, CDKN1A | RGS2, CACNA1D | 0.018 |
Neuroactive ligand-receptor interaction | GIPR, LEPR, GRIN3A | HTR4, LPAR4 | 0.031 |
Phenylalanine, tyrosine and tryptophan biosynthesis | PAH | 0.034 | |
cAMP signaling pathway | GIPR, GRIN3A | CACNA1D, HTR4 | 0.048 |
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Hao, Z.; Zhou, H.; Hickford, J.G.H.; Gong, H.; Wang, J.; Hu, J.; Liu, X.; Li, S.; Zhao, M.; Luo, Y. Transcriptome Profile Analysis of Mammary Gland Tissue from Two Breeds of Lactating Sheep. Genes 2019, 10, 781. https://doi.org/10.3390/genes10100781
Hao Z, Zhou H, Hickford JGH, Gong H, Wang J, Hu J, Liu X, Li S, Zhao M, Luo Y. Transcriptome Profile Analysis of Mammary Gland Tissue from Two Breeds of Lactating Sheep. Genes. 2019; 10(10):781. https://doi.org/10.3390/genes10100781
Chicago/Turabian StyleHao, Zhiyun, Huitong Zhou, Jon G.H. Hickford, Hua Gong, Jiqing Wang, Jiang Hu, Xiu Liu, Shaobin Li, Mengli Zhao, and Yuzhu Luo. 2019. "Transcriptome Profile Analysis of Mammary Gland Tissue from Two Breeds of Lactating Sheep" Genes 10, no. 10: 781. https://doi.org/10.3390/genes10100781