Project description:The cattle industry is the largest of the agricultural commodities in the United States and generated over $101 billion in farm cash receipts during 2016; 28% of all US farm cash receipts. Although the sequence of the bovine reference genome has been publicly available since 2009, annotation of functional genome elements is largely incomplete, resulting in limitations for exploiting the genome to phenome relationship. This project generate high-quality detailed transcript and miRNA status datasets from a comprehensive set of bovine tissues, developmental stages, and cells through a set of rationally selected assays.
Project description:We investigate if the differences in phenotype and transcriptome over age might be explained by an underlying change on the epigenetic level. We performed single-cell ATAC sequencing using the 10x Chromium platform. We profiled 2259 nuclei prepared from 3 young liver tissues and 2490 nuclei from 3 old liver tissues.
Project description:We investigate if the differences in phenotype and transcriptome over age might be explained by an underlying change on the epigenetic level. We performed single-cell ATAC sequencing using the 10x Chromium platform. We profiled 4838 nuclei prepared from 3 young liver tissues and 3361 nuclei from 3 old liver tissues.
Project description:Plasmodium-specific CD4+ T cells from mice infected with Plasmodium chabaudi chabaudi AS parasites were recovered at Days 0, 4, 7, and 32 to undergo processing and to generate scATAC-seq dataset. At Day 7, CXCR5+ and CXCR6+ cells were recovered separately. At Day 32, mice were administered with either saline or artesunate (intermittent artesunate therapy - IAT). scATAC-seq dataset was analysed to investigate epigenomic landscapes of CD4+ T cells from effector to memory states.
Project description:Human and mouse monocytes can be divided into 2 different sub-populations, using CD14-CD16 and Ly6C-CX3CR1 respectively. We investigated the pig monocytes sub-populations and found that all porcine monocyte express CD16 and CD172M-NM-1 but can be divided into 2 subpopulation using CD14 and the scavenger receptor CD163. The CD14hi-CD163low population resemble to the inflammatory monocytes whereas the CD14low-CD163hi display more a resident monocyte type. Pig monocyte can be differentiated into macrophages when cultured with rhCSF-1 and show an increase in size, granularity and autofluorescence, and express the common macrophage markers CD14, CD16 and CD172M-NM-1. Gene expression in these 2 sub-populations was profiled using the newly-developed and annotated pig whole genome snowball microarray, showing a distinct pattern between inflammatory and resident monocytes but this difference would be more a maturation process instead of two separate subsets. Furthermore, the expression of certain genes such as CD36, CLEC4E or TREM-1 proved to share the same pattern as human monocytes, quite different from mouse monocytes. These results emphasize the potential role of the pigs as a model for human inflammatory disease and will improved our knowledge on the mononuclear phagocyte system development. Porcine PBMCs were isolated from the blood of three seperate pigs, FACS sorted on expression of CD14 and CD163 and RNA isolated from each sample, a total of 6 microarrays were hybridised
Project description:The objective of this experiment was to use transcriptional profiling of skeletal muscle and adipose tissue to develop a better understanding of the metabolic basis for poor weaned-pig transition. A total of 1,054 pigs were reared in commercial conditions and weighed at birth, weaning, and 3 weeks post- weaning. Transition average daily gain (tADG) was calculated as the average daily gain for the 3-week period post-weaning. Nine pigs from each of the lowest 10th percentile (low tADG) and the 60th-70th percentile (high tADG) were harvested at 3 weeks post-weaning. Differential expression analysis was conduced in both tissues using RNA-Seq methodology mRNA profiling in two different tissues (skeletal muscle and adipose tissue) harvested at 3 weeks post-weaning
Project description:Purpose: evaluate if different proestrus-estrus concentrations of estradiol (E2) and metestrus progesterone (P4) concentrations specifically regulate oviductal gene expression. Methods: ampulla and isthmus samples of animals whit a large pre-ovulatory follicle and a large CL (LF/LCL) and animals whit a small pre-ovulatory follicle and a small CL (SF/SCL) were collected after slaughter at day four of the estrous cycle. Total RNA was extracted and RNA sequencing was performed using the Illumina HiScanSeq (ampulla samples) and the Illumina HiSeq 2500 (isthmus samples) platforms. Results: After using HTSeq-count, approximately ~60% of the total reads uniquely mapped to the UMD 3.1 reference genome. In the ampulla samples, a total of 692 genes showed differential expression, of which 325 and 367 were up-regulated in the LF-LCL and SF-SCL samples, respectively. In the isthmus samples, a total of 590 genes showed differential expression, of which 274 and 316 were up-regulated in the isthmus of LF/LCL and SF/SCL samples, respectively. Conclusions: Our study represents the first detailed analysis of oviduct transcriptomes, generated by RNA-seq technology. Differential global gene expression profiles identified indicate that the biology of the bovine oviductal tissue is modulated by the periovulatory endocrine milieu. The LF-LCL group transcriptome may potentially reveal molecules associated with higher fertility. Oviductal mRNA profiles of cows whit different endocrine milleus were generated by next generation sequencing.
Project description:Purpose: evaluate if different proestrus-estrus concentrations of estradiol (E2) and metestrus progesterone (P4) concentrations specifically regulate oviductal gene expression. Methods: ampulla and isthmus samples of animals with a large pre-ovulatory follicle and a large CL (LF/LCL) and animals with a small pre-ovulatory follicle and a small CL (SF/SCL) were collected after slaughter at day four of the estrous cycle. Total RNA was extracted and RNA sequencing was performed using the Illumina HiScanSeq (ampulla samples) and the Illumina HiSeq 2500 (isthmus samples) platforms. Results: After using HTSeq-count, approximately ~60% of the total reads uniquely mapped to the UMD 3.1 reference genome. In the ampulla samples, a total of 692 genes showed differential expression, of which 325 and 367 were up-regulated in the LF-LCL and SF-SCL samples, respectively. In the isthmus samples, a total of 590 genes showed differential expression, of which 274 and 316 were up-regulated in the isthmus of LF/LCL and SF/SCL samples, respectively. Conclusions: Our study represents the first detailed analysis of oviduct transcriptomes, generated by RNA-seq technology. Differential global gene expression profiles identified indicate that the biology of the bovine oviductal tissue is modulated by the periovulatory endocrine milieu. The LF-LCL group transcriptome may potentially reveal molecules associated with higher fertility. Oviductal mRNA profiles of cows with different endocrine milleus were generated by next generation sequencing.