Expression patterns of housekeeping genes and tissue-specific genes in black goats across multiple tissues

Zeder, M. A. & Hesse, B. The initial domestication of goats (Capra hircus) in the Zagros Mountains 10,000 years ago. Science. 287, 2254–2257 (2000).ADS 
CAS 
PubMed 

Google Scholar 
Saleh, A. A., Rashad, A. M. A., Hassanine, N. N. A. M., Sharaby, M. A. & Zhao, Y. Evaluation of morphological traits and physiological variables of several Chinese goat breeds and their crosses. Trop. Anim. Health Prod.53, 74 (2021).PubMed 

Google Scholar 
Naderi, S. et al. The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals. Proc. Natl. Acad. Sci. USA. 105, 17659–17664 (2008).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Sacarrão-Birrento, L. & de Almeida, A. M. The Portuguese Serrana goat breed: a review. Trop. Anim. Health Prod.53, 114 (2021).PubMed 

Google Scholar 
van Leeuwen, S. S. et al. Goat milk oligosaccharides: their diversity, quantity, and functional properties in comparison to human milk oligosaccharides. J. Agric. Food Chem.68, 13469–13485 (2020).PubMed 
PubMed Central 

Google Scholar 
Bertolini, F. et al. Signatures of selection and environmental adaptation across the goat genome post-domestication. Genet. Sel. Evol. GSE. 50, 57 (2018).PubMed 

Google Scholar 
Saleh, A. A., Rashad, A. M. A., Hassanine, N. N. A. M., Sharaby, M. A. & Zhao, Y. Assessment of hair and cashmere properties and their genetic background of several goat breeds in Southwest China. Sci. Rep.12, 11135 (2022).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Gawat, M., Boland, M., Singh, J. & Kaur, L. Goat meat: production and quality attributes. Foods Basel Switz.12, 3130 (2023).CAS 

Google Scholar 
MacHugh, D. E. & Bradley, D. G. Livestock genetic origins: goats buck the trend. Proc. Natl. Acad. Sci. USA.98, 5382–5384 (2001).Stark, R., Grzelak, M. & Hadfield, J. RNA sequencing: the teenage years. Nat. Rev. Genet.20, 631–656 (2019).CAS 
PubMed 

Google Scholar 
Wu, C., Qin, C., Fu, X., Huang, X. & Tian, K. Integrated analysis of lncRNAs and mRNAs by RNA-Seq in secondary hair follicle development and cycling (anagen, catagen and telogen) of Jiangnan cashmere goat (Capra hircus). BMC Vet. Res.18, 167 (2022).CAS 
PubMed 
PubMed Central 

Google Scholar 
Shen, J. et al. Deep small RNA sequencing reveals important miRNAs related to muscle development and intramuscular fat deposition in longissimus dorsi muscle from different goat breeds. Front. Vet. Sci.9, 911166 (2022).ADS 
PubMed 
PubMed Central 

Google Scholar 
Poklukar, K. et al. Adipose tissue gene expression of entire male, immunocastrated and surgically castrated pigs. Int. J. Mol. Sci.22, 1768 (2021).CAS 
PubMed 
PubMed Central 

Google Scholar 
La, Y. et al. Identification and characterization of Piwi-interacting RNAs for early testicular development in Yak. Int. J. Mol. Sci.23, 12320 (2022).CAS 
PubMed 
PubMed Central 

Google Scholar 
Zhang, M. et al. Transcriptome analysis reveals the molecular regulatory network of muscle development and meat quality in Sunit lamb supplemented with dietary probiotic. Meat Sci.194, 108996 (2022).CAS 
PubMed 

Google Scholar 
Yao, Y. C. et al. Transcriptome analysis of sheep follicular development during prerecruitment, dominant, and mature stages after FSH superstimulation. Domest. Anim. Endocrinol.74, 106563 (2021).CAS 
PubMed 

Google Scholar 
Zhen, H. et al. Characteristics and expression of circ_003628 and its promoted effect on proliferation and differentiation of skeletal muscle satellite cells in goats. Anim. Open. Access. J. MDPI. 12, 2524 (2022).
Google Scholar 
Hou, B. et al. Transcriptome analysis reveals mRNAs and long non-coding RNAs associated with fecundity in the hypothalamus of high-and low-fecundity goat. Front. Vet. Sci.10, 1145594 (2023).PubMed 
PubMed Central 

Google Scholar 
Li, L. et al. The novel RNA-RNA activation of H19 on MyoD transcripts promoting myogenic differentiation of goat muscle satellite cells. Int. J. Biol. Macromol.253, 127341 (2023).CAS 
PubMed 

Google Scholar 
Levy, B. & Dixon, G. H. Diversity of sequences of polyadenylated cytoplasmic RNA from rainbow trout (Salmo gairdnerii) testis and liver. Biochemistry. 16, 958–964 (1977).CAS 
PubMed 

Google Scholar 
Eisenberg, E. & Levanon, E. Y. Human housekeeping genes, revisited. Trends Genet. TIG. 29, 569–574 (2013).CAS 
PubMed 

Google Scholar 
Chang, C. W. et al. Identification of human housekeeping genes and tissue-selective genes by microarray meta-analysis. PLoS ONE. 6, e22859 (2011).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Pseudogenes as weaknesses of ACTB (Actb). and GAPDH (gapdh) used as reference genes in reverse transcription and polymerase chain reactions – PubMed. https://pubmed.ncbi.nlm.nih.gov/22927912/Pan, X. et al. Expression profile of housekeeping genes and tissue-specific genes in multiple tissues of pigs. Animals. 12, 3539 (2022).PubMed 
PubMed Central 

Google Scholar 
Joshi, C. J., Ke, W., Drangowska-Way, A., O’Rourke, E. J. & Lewis, N. E. What are housekeeping genes? PLoS Comput. Biol.18, e1010295 (2022).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Gong, H. et al. Evaluation of candidate reference genes for RT-qPCR studies in three metabolism related tissues of mice after caloric restriction. Sci. Rep.6, 38513 (2016).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Zhao, X. et al. The selection and identification of compound housekeeping genes for quantitative real-time polymerase chain reaction analysis in rat fetal kidney. J. Appl. Toxicol. JAT. 42, 360–370 (2022).CAS 
PubMed 

Google Scholar 
Sullivan-Gunn, M., Hinch, E., Vaughan, V. & Lewandowski, P. Choosing a stable housekeeping gene and protein is essential in generating valid gene and protein expression results. Br. J. Cancer. 104, 1055 (2011). author reply 1056.CAS 
PubMed 
PubMed Central 

Google Scholar 
Blotas, C., Férec, C. & Moisan, S. Tissue-specific regulation of CFTR gene expression. Int. J. Mol. Sci.24, 10678 (2023).CAS 
PubMed 
PubMed Central 

Google Scholar 
Ryaboshapkina, M. & Hammar, M. Tissue-specific genes as an underutilized resource in drug discovery. Sci. Rep.9, 7233 (2019).ADS 
PubMed 
PubMed Central 

Google Scholar 
Sonawane, A. R. et al. Understanding tissue-specific gene regulation. Cell. Rep.21, 1077–1088 (2017).CAS 
PubMed 
PubMed Central 

Google Scholar 
Zhang, L. & Li, W. H. Mammalian housekeeping genes evolve more slowly than tissue-specific genes. Mol. Biol. Evol.21, 236–239 (2004).PubMed 

Google Scholar 
Zhang, S. et al. Screening of bovine tissue-specific expressed genes and identification of genetic variation within an adipose tissue-specific lncRNA gene. Front. Vet. Sci.9, 887520 (2022).PubMed 
PubMed Central 

Google Scholar 
Rogala, S. et al. The lncRNA Sweetheart regulates compensatory cardiac hypertrophy after myocardial injury in murine males. Nat. Commun.14, 7024 (2023).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Langfelder, P. & Horvath, S. W. G. C. N. A. An R package for weighted correlation network analysis. BMC Bioinf.9, 559 (2008).
Google Scholar 
Nangraj, A. S. et al. Integrated PPI- and WGCNA-retrieval of hub gene signatures shared between barrett’s esophagus and esophageal adenocarcinoma. Front. Pharmacol.11, 881 (2020).CAS 
PubMed 
PubMed Central 

Google Scholar 
Feng, S. et al. Integrative analysis from multicenter studies identifies a WGCNA-derived cancer-associated fibroblast signature for ovarian cancer. Front. Immunol.13, 951582 (2022).CAS 
PubMed 
PubMed Central 

Google Scholar 
Luo, D. et al. Long RNA profiles of human brain extracellular vesicles provide new insights into the pathogenesis of alzheimer’s disease. Aging Dis.14, 229–244 (2023).ADS 
PubMed 
PubMed Central 

Google Scholar 
Yu, T. et al. Transcriptome, proteome and metabolome analysis provide insights on fat deposition and meat quality in pig. Food Res. Int. Ott. Ont.166, 112550 (2023).CAS 

Google Scholar 
Silva-Vignato, B. et al. Gene co-expression networks associated with carcass traits reveal new pathways for muscle and fat deposition in Nelore cattle. BMC Genom. 20, 32 (2019).
Google Scholar 
Wang, J., Chen, H. & Zeng, X. Identification of hub genes associated with follicle development in multiple births sheep by WGCNA. Front. Vet. Sci.9, 1057282 (2022).PubMed 
PubMed Central 

Google Scholar 
Finucane, H. K. et al. Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types. Nat. Genet.50, 621–629 (2018).CAS 
PubMed 
PubMed Central 

Google Scholar 
Zhang, T. et al. Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle. BMC Biol.20, 79 (2022).PubMed 
PubMed Central 

Google Scholar 
de Jonge, H. J. M. et al. Evidence based selection of housekeeping genes. PLoS ONE. 2, e898 (2007).ADS 
PubMed 
PubMed Central 

Google Scholar 
Friedrichs, V., Balkema-Buschmann, A., Dorhoi, A. & Pei, G. Selection and stability validation of reference gene candidates for transcriptional analysis in Rousettus aegyptiacus. Sci. Rep.11, 21662 (2021).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Gentile, A. M. et al. RPL13A and EEF1A1 are suitable reference genes for qPCR during adipocyte differentiation of vascular stromal cells from patients with different BMI and HOMA-IR. PLoS ONE. 11, e0157002 (2016).PubMed 
PubMed Central 

Google Scholar 
Zhao, J. et al. Genome-wide identification of reference genes for reverse-transcription quantitative PCR in goat rumen. Anim. Open. Access. J. MDPI. 11, 3137 (2021).
Google Scholar 
Bansal, R., Haviland, D. R. & Hunter, W. B. Selection and validation of reference genes for quantifying gene expression in the Gill’s mealybug. J. Econ. Entomol.116, 2166–2172 (2023).CAS 
PubMed 

Google Scholar 
Ma, K. S. et al. Identification and validation of reference genes for the normalization of gene expression data in qRT-PCR analysis in Aphis gossypii (Hemiptera: Aphididae). J. Insect Sci. Online. 16, 17 (2016).
Google Scholar 
Mogilicherla, K., Athe, R. P., Chatterjee, R. N. & Bhattacharya, T. K. Identification of suitable reference genes for normalization of quantitative real-time PCR-based gene expression in chicken (Gallus gallus). Anim. Genet.53, 881–887 (2022).CAS 
PubMed 

Google Scholar 
Min, Q., Yang, L., Wang, Y., Liu, Y. & Jiang, M. Transcriptome-based evaluation of optimal reference genes for quantitative real-time PCR in yak stomach throughout the growth cycle. Anim. Open. Access. J. MDPI. 13, 925 (2023).
Google Scholar 
Jiang, X. et al. Evaluation of reference gene suitability for quantitative expression analysis by quantitative polymerase chain reaction in the mandibular condyle of sheep. Mol. Med. Rep.12, 5633–5640 (2015).CAS 
PubMed 
PubMed Central 

Google Scholar 
Arukwe, A. Toxicological housekeeping genes: do they really keep the house? Environ. Sci. Technol.40, 7944–7949 (2006).ADS 
CAS 
PubMed 

Google Scholar 
Li, B. et al. A comprehensive mouse transcriptomic bodymap across 17 tissues by RNA-seq. Sci. Rep.7, 4200 (2017).ADS 
PubMed 
PubMed Central 

Google Scholar 
Fang, L. et al. Comprehensive analyses of 723 transcriptomes enhance genetic and biological interpretations for complex traits in cattle. Genome Res.30, 790–801 (2020).CAS 
PubMed 
PubMed Central 

Google Scholar 
Zhang, J. Y. et al. Long noncoding RNA AFAP1-AS1 indicates a poor prognosis of hepatocellular carcinoma and promotes cell proliferation and invasion via upregulation of the RhoA/Rac2 signaling. Int. J. Oncol.48, 1590–1598 (2016).CAS 
PubMed 

Google Scholar 
Saito, N. et al. Macrophage ubiquitin-specific protease 2 modifies insulin sensitivity in obese mice. Biochem. Biophys. Rep.9, 322–329 (2017).PubMed 
PubMed Central 

Google Scholar 
Itoh, T. et al. Identification of a novel aquaporin, AQP12, expressed in pancreatic acinar cells. Biochem. Biophys. Res. Commun.330, 832–838 (2005).CAS 
PubMed 

Google Scholar 
Bockerstett, K. A. et al. Single cell transcriptional analyses identify lineage-specific epithelial responses to inflammation and metaplastic development in the gastric corpus. Gastroenterology. 159, 2116–2129e4 (2020).CAS 
PubMed 

Google Scholar 
Zhong, Y., Di, R., Yang, Y., Liu, Q. & Chu, M. Transcriptome analysis of neuroendocrine regulation of ovine hypothalamus-pituitary-ovary axis during ovine anestrus and the breeding season. Genes. 12, 1861 (2021).CAS 
PubMed 
PubMed Central 

Google Scholar 
Ueno, A. et al. Lrit1, a retinal transmembrane protein, regulates selective synapse formation in cone photoreceptor cells and visual acuity. Cell. Rep.22, 3548–3561 (2018).CAS 
PubMed 

Google Scholar 
Ping, X. et al. Rapamycin relieves the cataract caused by ablation of Gja8b through stimulating autophagy in zebrafish. Autophagy. 17, 3323–3337 (2021).CAS 
PubMed 
PubMed Central 

Google Scholar 
Liu, Y., Jia, Y., Liu, C., Ding, L. & Xia, Z. RNA-Seq transcriptome analysis of breast muscle in Pekin ducks supplemented with the dietary probiotic Clostridium butyricum. BMC Genom. 19, 844 (2018).CAS 

Google Scholar 
Zhu, J. et al. Identification of tissue-specific protein-coding and noncoding transcripts across 14 human tissues using RNA-seq. Sci. Rep.6, 28400 (2016).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Perreault, L. R., Le, T. T., Oudin, M. J. & Black, L. D. RNA sequencing indicates age-dependent shifts in the cardiac fibroblast transcriptome between fetal, neonatal, and adult developmental ages. Physiol. Genom. 53, 414–429 (2021).CAS 

Google Scholar 
Wang, G., Zhao, D., Yan, C. & Lin, P. Exon skipping caused by splicing mutation in TNNT1 nemaline myopathy. J. Hum. Genet.68, 97–101 (2023).CAS 
PubMed 

Google Scholar 
Mansur, A. et al. Dynamic regulation of inter-organelle communication by ubiquitylation controls skeletal muscle development and disease onset. eLife12, e81966 (2023).Dietlein, F. et al. Genome-wide analysis of somatic noncoding mutation patterns in cancer. Science. 376, eabg5601 (2022).CAS 
PubMed 
PubMed Central 

Google Scholar 
Yin, Y. et al. HRG inhibits liver cancer lung metastasis by suppressing neutrophil extracellular trap formation. Clin. Transl Med.13, e1283 (2023).CAS 
PubMed 
PubMed Central 

Google Scholar 
Zhao, L. et al. Ovine ELOVL5 and FASN genes polymorphisms and their correlations with sheep tail fat deposition. Gene. 807, 145954 (2022).CAS 
PubMed 

Google Scholar 
Li, H. et al. Comparison of long non-coding RNA expression profiles of cattle and buffalo differing in muscle characteristics. Front. Genet.11, 98 (2020).PubMed 
PubMed Central 

Google Scholar 
Chen, S., Zhou, Y., Chen, Y. & Gu, J. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinforma Oxf. Engl.34, i884–i890 (2018).
Google Scholar 
Kim, D., Langmead, B. & Salzberg, S. L. HISAT: A fast spliced aligner with low memory requirements. Nat. Methods. 12, 357–360 (2015).CAS 
PubMed 
PubMed Central 

Google Scholar 
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinforma Oxf. Engl.25, 2078–2079 (2009).
Google Scholar 
Pertea, M. et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol.33, 290–295 (2015).CAS 
PubMed 
PubMed Central 

Google Scholar 
Sherman, B. T. et al. A web server for functional enrichment analysis and functional annotation of gene lists (2021 update). Nucleic Acids Res.50, W216–W221 (2022).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Huang, D. W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc.4, 44–57 (2009).CAS 
PubMed 

Google Scholar 
Dennis, G. et al. Database for annotation, visualization, and integrated discovery. Genome Biol.4, P3 (2003).PubMed 

Google Scholar 
Szklarczyk, D. et al. The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res.51, D638–D646 (2023).CAS 
PubMed 

Google Scholar 
Juengel, J. L., Meberg, B. M., Turzillo, A. M., Nett, T. M. & Niswender, G. D. Hormonal regulation of messenger ribonucleic acid encoding steroidogenic acute regulatory protein in ovine corpora lutea. Endocrinology. 136, 5423–5429 (1995).CAS 
PubMed 

Google Scholar 
Zhao, Y. et al. A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome. Nat. Commun.12, 2217 (2021).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar