The expression of <i>c-Kit</i> gene in black and white feather bulb samples from different plumage types.

<p>The expression of <i>c-Kit</i> gene in black and white feather bulb samples from different plumage types.</p

The expression of <i>Tyrp1</i>, <i>Tyr</i>, <i>c-Kit</i> and <i>Mitf</i> genes in retina samples from black plumage and white plumage ducks.

<p>The expression of <i>Tyrp1</i>, <i>Tyr</i>, <i>c-Kit</i> and <i>Mitf</i> genes in retina samples from black plumage and white plumage ducks.</p

Primers used in Semi-RT-PCR and qPCR.

<p>Note: AT = Annealing temperature.</p

RNA-Seq data summary and annotation results.

<p>Note: DCT- distinct clean tag; TDCT- Total distinct clean tag; Chicken- <i>Gallus gallus</i>; Duck<i>- Anas platyrhynchos</i>.</p

Additional file 1: of miR-124 attenuates Japanese encephalitis virus replication by targeting DNM2

The pathways of predicted target genes of miR-124. (XLSX 19 kb

The expression of <i>Mitf</i> gene in black and white feather bulb samples from different plumage types.

<p>The expression of <i>Mitf</i> gene in black and white feather bulb samples from different plumage types.</p

DataSheet_1_Comparative transcriptome analysis of T lymphocyte subpopulations and identification of critical regulators defining porcine thymocyte identity.zip

IntroductionThe development and migration of T cells in the thymus and peripheral tissues are crucial for maintaining adaptive immunity in mammals. However, the regulatory mechanisms underlying T cell development and thymocyte identity formation in pigs remain largely underexplored. MethodHere, by integrating bulk and single-cell RNA-sequencing data, we investigated regulatory signatures of porcine thymus and lymph node T cells. ResultsThe comparison of T cell subpopulations derived from porcine thymus and lymph nodes revealed that their transcriptomic differences were influenced more by tissue origin than by T cell phenotypes, and that lymph node cells exhibited greater transcriptional diversity than thymocytes. Through weighted gene co-expression network analysis (WGCNA), we identified the key modules and candidate hub genes regulating the heterogeneity of T cell subpopulations. Further, we integrated the porcine thymocyte dataset with peripheral blood mononuclear cell (PBMC) dataset to systematically compare transcriptomic differences between T cell types from different tissues. Based on single-cell datasets, we further identified the key transcription factors (TFs) responsible for maintaining porcine thymocyte identity and unveiled that these TFs coordinately regulated the entire T cell development process. Finally, we performed GWAS of cell type-specific differentially expressed genes (DEGs) and 30 complex traits, and found that the DEGs in thymus-related and peripheral blood-related cell types, especially CD4_SP cluster and CD8-related cluster, were significantly associated with pig productive and reproductive traits. DiscussionOur findings provide an insight into T cell development and lay a foundation for further exploring the porcine immune system and genetic mechanisms underlying complex traits in pigs.</p

Cross reaction (%) of each let-7 miRNAs by specific pincer probe real-time PCR assays.

<p>Cross reaction (%) of each let-7 miRNAs by specific pincer probe real-time PCR assays.</p

Quantification of Mature MicroRNAs Using Pincer Probes and Real-Time PCR Amplification

<div><p>The robust and reliable detection of small microRNAs (miRNAs) is important to understand the functional significance of miRNAs. Several methods can be used to quantify miRNAs. Selectively quantifying mature miRNAs among miRNA precursors, pri-miRNAs, and other miRNA-like sequences is challenging because of the short length of miRNAs. In this study, we developed a two-step miRNA quantification system based on pincer probe capture and real-time PCR amplification. The performance of the method was tested using synthetic mature miRNAs and clinical RNA samples. Results showed that the method demonstrated dynamic range of seven orders of magnitude and sensitivity of detection of hundreds of copies of miRNA molecules. The use of pincer probes allowed excellent discrimination of mature miRNAs from their precursors with five Cq (quantification cycle) values difference. The developed method also showed good discrimination of highly homologous family members with cross reaction less than 5%. The pincer probe-based approach is a potential alternative to currently used methods for mature miRNA quantification.</p></div

Principal Component Analysis (PCA) plot of microarray data in porcine endometrium.

<p>In each case, three replicates from each gestational day cluster together. Clustering of the samples according to gestational day is shown. The red, blue and green circles stand for three different gestational days. D15: gestational day 15; D26: gestational day 26; D50: gestational day 50.</p