Identification of differentially expressed genes through RNA sequencing in goats (Capra hircus) at different postnatal stages

Lin, Yaqiu; Zhu, Jiangjiang; Wang, Yong; Li, Qian; Lin, Sen

doi:10.1371/journal.pone.0182602

Cited by 24 publications

(31 citation statements)

References 43 publications

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“…The cDNA was sequenced by Sangon Biotech (Shanghai, China). The expected value of FPKM (fragments per kilobase of transcript sequence per million base pairs sequenced) was used for expression normalization [17, 18]. The relationship analysis of the FPKM value of a gene between different organs and the pathway analysis associated with related genes [15] were also made by Sangon Biotech.…”

Section: Methodsmentioning

confidence: 99%

What Is the Biological Function of Uric Acid? An Antioxidant for Neural Protection or a Biomarker for Cell Death

Liu

Yang

et al. 2019

Disease Markers

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The main aim of the present study was to investigate the biological function of uric acid. The level of uric acid in different organs in normal male rats was determined with uric acid assay kits, and the expression level of genes in the organs was determined by RNA quantitative sequencing. The correlation analysis between uric acid in the organs and gene expression (measured by FPKM value) was made. Serum uric acid (SUA) in patients with breast cancer or with breast benign tumor was assayed when the diagnosis was made, and SUA in patients with breast cancer was also assayed just after chemotherapy. There were 1937 mRNAs whose expression level significantly correlated with the level of uric acid, and most of which were associated with purine or nucleoside metabolism, cellular metabolism, cell cycles, and cell death pathways. Further analysis showed that the level of uric acid was highly correlated with cell death rather than cell viability. The level of SUA in patients with breast cancer was higher than that in patients with breast benign tumor, and the SUA increased after chemotherapy. All the results suggested that uric acid was mainly synthesized from local nucleosides degraded from dead cells, and uric acid could be an important biomarker for cell death rather than an antioxidant for neural protection.

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Section: Methodsmentioning

confidence: 99%

What Is the Biological Function of Uric Acid? An Antioxidant for Neural Protection or a Biomarker for Cell Death

Liu

Yang

et al. 2019

Disease Markers

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“…The cDNA was sequenced by Sangon Biotech (Shanghai, China). Expected value of FPKM (fragments per kilobase of transcript sequence per million base pairs sequenced) was used for expression normalization [ 19 , 20 ]. The analysis of the FPKM of a gene between different intestinal tissues was also made by Sangon Biotech.…”

Section: Methodsmentioning

confidence: 99%

Intestinal tract is an important organ for lowering serum uric acid in rats

Yin

Gao

et al. 2017

PLoS ONE

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The kidney was recognized as a dominant organ for uric acid excretion. The main aim of the study demonstrated intestinal tract was an even more important organ for serum uric acid (SUA) lowering. Sprague-Dawley rats were treated normally or with antibiotics, uric acid, adenine, or inosine of the same molar dose orally or intraperitoneally for 5 days. Rat’s intestinal tract was equally divided into 20 segments except the cecum. Uric acid in serum and intestinal segment juice was assayed. Total RNA in the initial intestinal tract and at the end ileum was extracted and sequenced. Protein expression of xanthine dehydrogenase (XDH) and urate oxidase (UOX) was tested by Western blot analysis. The effect of oral UOX in lowering SUA was investigated in model rats treated with adenine and an inhibitor of uric oxidase for 5 days. SUA in the normal rats was 20.93±6.98 μg/ml, and total uric acid in the intestinal juice was 308.27±16.37 μg, which is two times more than the total SUA. The uric acid was very low in stomach juice, and attained maximum in the juice of the first segment (duodenum) and then declined all the way till the intestinal end. The level of uric acid in the initial intestinal tissue was very high, where XDH and most of the proteins associated with bicarbonate secretion were up-regulated. In addition, SUA was decreased by oral UOX in model rats. The results suggested that intestinal juice was an important pool for uric acid, and intestinal tract was an important organ for SUA lowering. The uric acid distribution was associated with uric acid synthesis and secretion in the upper intestinal tract, and reclamation in the lower.

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“…Total RNA from rat kidney was also sequenced with the second generation of high throughput sequencing technique by Sangon Biotech. Expected values of fragment per kilobases of exon model per million mapped reads (FPKM) were calculated from mapped reads, and were used for normalization of gene expression level (Lin et al, 2017;Trapnell et al, 2010). Values of FPKM were used to evaluate the level of gene expression associated with urate excretion or reclamation in kidney.…”

Section: Rt-pcr and High Throughput Sequencingmentioning

confidence: 99%

Uricase-deficient rat is generated with CRISPR/Cas9 technique

Zhang

Dong

et al. 2020

PeerJ

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Urate oxidase (uricase, Uox) is a big obstacle for scientists to establish stable animal models for studying hyperuricemia and associated disorders. Due to the low survival rate of uricase-deficient mice, we generated a Uox-knockout model animal from Sprague Dawley (SD) rats using the CRISPR/Cas9 technique by deleting exons 2 to 4 of the Uox gene. The uricase-deficient rats were named “Kunming-DY rats”, and were apparently healthy with more than a 95% survival up to one year. The male rats’ serum uric acid (SUA) increased to 48.3 ± 19.1 µg/ml, significantly higher than those of wild-type rats. Some indexes of the blood fat like total triglyceride, low density lipoprotein, and renal function indexes including blood urea nitrogen and serum creatinine were significantly different from those of wild-type rats, however, all the indexes were close to or in normal ranges. Histological renal changes including mild glomerular/tubular lesions were observed in these uricase-deficient rats. Thus, “Kunming-DY rats” with stable uricase-deficiency were successfully established and are an alternative model animal to study hyperuricemia and associated diseases mimicking human conditions.

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Identification of differentially expressed genes through RNA sequencing in goats (Capra hircus) at different postnatal stages

Cited by 24 publications

References 43 publications

What Is the Biological Function of Uric Acid? An Antioxidant for Neural Protection or a Biomarker for Cell Death

What Is the Biological Function of Uric Acid? An Antioxidant for Neural Protection or a Biomarker for Cell Death

Intestinal tract is an important organ for lowering serum uric acid in rats

Uricase-deficient rat is generated with CRISPR/Cas9 technique

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