identifier	taxonID	type	CVterm	format	language	title	description	additionalInformationURL	UsageTerms	rights	Owner	contributor	creator	bibliographicCitation
260D50077C1E3A7DFCE00EE02CD3F835.text	260D50077C1E3A7DFCE00EE02CD3F835.taxon	http://purl.org/dc/dcmitype/Text	http://rs.tdwg.org/ontology/voc/SPMInfoItems#GeneralDescription	text/html	en	Toxoplasma Nicolle & Manceaux 1909	<div><p>Expression of small RNAs in serum from both Toxoplasma -infected and normal rabbits</p><p>To explore small RNA profiles in serum and urine during toxoplasmosis progression, RNA sequencing was used to analyze sRNA expression in serum and urine from oocysts-infected and non-infected rabbits. After removing low-quality reads,&gt; 19.78 million high-quality clean reads were obtained. Te read quality is shown in Additional file 1: Table S 1. Of the filtered clean reads, 76.50–91.50% detected in serum were mapped to the reference Oryctolagus cuniculus genome. Te first residue at the 5 ′ terminus of the 20–26 nt known miRNAs is predominantly uridine (U) (Fig. 2a), while the first residue at the 5 ′ terminus of the predicted miRNAs is predominantly cytosine (C) (Fig. 2b). As shown in Fig. 2c, the first residue at the 5 ′ terminus of the 18–45 nt predicted piRNAs is predominantly cytosine (C). To explore the similarity of serum samples, we performed Pearson correlation analysis, principal component analysis (PCA) and hierarchical clustering analysis. As shown in Fig. 3a, a Pearson correlation matrix separated the AI samples from the other samples, as illustrated by the heatmap correlation matrices (Spearman correlations [r] = 0.898 –0.968), showing a high level of correlation within Con samples ([r] = 0.934 –0.972). As shown in Fig. 3b, PCA score plots did not clearly differentiate chronically infected rabbits from uninfected control rabbits. However, hierarchical clustering displayed that the sRNA expression pattern in acutely infected rabbits was distinguishable compared to that of chronically infected rabbits and uninfected control rabbits (Fig. 3c).</p></div>	https://treatment.plazi.org/id/260D50077C1E3A7DFCE00EE02CD3F835	Public Domain	No known copyright restrictions apply. See Agosti, D., Egloff, W., 2009. Taxonomic information exchange and copyright: the Plazi approach. BMC Research Notes 2009, 2:53 for further explanation.		Plazi	Xie, Shi-Chen;Zhou, Chun-Xue;Zhai, Bin-Tao;Zheng, Wen-Bin;Liu, Guo-Hua;Zhu, Xing-Quan	Xie, Shi-Chen, Zhou, Chun-Xue, Zhai, Bin-Tao, Zheng, Wen-Bin, Liu, Guo-Hua, Zhu, Xing-Quan (2022): A combined miRNA-piRNA signature in the serum and urine of rabbits infected with ToxoplaSMa gondii oocysts. Parasites & Vectors (490) 15 (1): 1-12, DOI: 10.1186/s13071-022-05620-0, URL: http://dx.doi.org/10.1186/s13071-022-05620-0
260D50077C193A7BFF5A0E9B2D22F8FC.text	260D50077C193A7BFF5A0E9B2D22F8FC.taxon	http://purl.org/dc/dcmitype/Text	http://rs.tdwg.org/ontology/voc/SPMInfoItems#GeneralDescription	text/html	en	Toxoplasma gondii	<div><p>DE miRNAs and DE piRNAs in serum and urine following T. gondii infection</p><p>Ten, the volcano plots were used to analyze DE miRNAs and DE piRNAs in serum and urine from uninfected, acutely infected and chronically infected rabbits. In serum, 210 upregulated and 968 downregulated miRNAs were identified between acutely infected rabbits and control groups (Fig. 6a). Comparison between chronically infected and control rabbits showed more dysregulated miRNAs, including 414 upregulated and 903 downregulated miRNAs (Fig. 6b). As shown in Fig. 6d, 107 miRNAs were shared among the three comparison groups. Compared to the control group, the majority of DE piRNAs were common in both the acute and chronic infection groups. More DE piRNAs (n = 1814) were found in CI versus Con (Fig. 7d). Compared with serum, there are fewer DE miRNAs identified in urine. As shown in Fig. 8a, b, there are 311 and 294 DE miRNAs in AI versus Con and CI versus Con, respectively. Moreover, there are 226 common DE miRNAs in both AI versus Con and CI versus Con (Fig. 8d). Meanwhile, there are 597 and 708 DE piRNAs in AI versus Con and CI versus Con, respectively (Fig. 9a, b). Tere are 431 common DE piRNAs in both AI versus Con and CI versus Con (Fig. 9d).</p><p>Furthermore, there are 88 common DE miRNAs found in both serum and urine samples of infected rabbits, which include 20 known miRNAs and 68 novel miRNAs (Fig. 10a). A complete list of the above-mentioned DE miRNAs is available in Additional file 3: Table S3. It is worth mentioning that the majority of the common DE miRNA were downregulated in all infected sera (78/88) and infected urine samples (73/88). However, two miRNAs (miR-138-5p and miR-509c-5p) in infected sera and miR-191-3p in urine were up-expressed during the whole toxoplasmosis progression. As shown in Fig. 10b, a total of 120 DE novel piRNAs were identified in all infected serum and urine samples, of which 110 piRNAs were downregulated in infected sera and 98 piRNAs were downregulated in the infected urine. Detailed information of the common DE piRNAs are shown in Additional file 4: Table S4.</p></div>	https://treatment.plazi.org/id/260D50077C193A7BFF5A0E9B2D22F8FC	Public Domain	No known copyright restrictions apply. See Agosti, D., Egloff, W., 2009. Taxonomic information exchange and copyright: the Plazi approach. BMC Research Notes 2009, 2:53 for further explanation.		Plazi	Xie, Shi-Chen;Zhou, Chun-Xue;Zhai, Bin-Tao;Zheng, Wen-Bin;Liu, Guo-Hua;Zhu, Xing-Quan	Xie, Shi-Chen, Zhou, Chun-Xue, Zhai, Bin-Tao, Zheng, Wen-Bin, Liu, Guo-Hua, Zhu, Xing-Quan (2022): A combined miRNA-piRNA signature in the serum and urine of rabbits infected with ToxoplaSMa gondii oocysts. Parasites & Vectors (490) 15 (1): 1-12, DOI: 10.1186/s13071-022-05620-0, URL: http://dx.doi.org/10.1186/s13071-022-05620-0
