Project description:Background: The establishment of the anterior-posterior (A-P) axis is a crucial step during tissue repair and regeneration. Despite the association reported recently of N6-methyladenosine (m6A) with regeneration, the mechanism underlying the regulation of m6A in A-P axis specification during regeneration remains unknown. Herein, we deciphered the m6A landscape at a single-base resolution at multiple time points during A-P axis regeneration and constructed the de novo transcriptome assembly of the Dugesia japonica planarian.
Project description:The hippocampus supports many facets of cognition, including learning, memory, and emotional processing. Anatomically, the hippocampus runs along a longitudinal axis, posterior-to-anterior in primates (corresponding to dorsal-to-ventral in rodents). The structure, function, and connectivity of the hippocampus vary along this axis. In rodents, experiments have established the cellular, molecular, and functional heterogeneity along the hippocampal axis, resulting in comprehensive models of specialization that integrate these different types of information. In humans however, functional heterogeneity remains an active area of investigation, and structural heterogeneity has not been described. To better understand the cellular composition and molecular diversity along the hippocampal long axis in the human brain and define distinct molecular signatures corresponding to functional domains we performed single-nuclei RNA-sequencing on surgically resected human anterior and posterior hippocampus. Analysis of 131,325 nuclei revealed differentially expressed genes between the anterior and posterior human hippocampus at cellular resolution. We determine the program of these axis- and cell-type specific genes that are conserved in the mouse hippocampus, and we also identify patterns that are differential between the human and mouse. We further identify axis- and cell-type specific gene expression signatures that differentially intersect with human cognitive and neuropsychiatric genetic signals, identifying cell type-specific genes in the posterior hippocampus for cognitive function and in the anterior hippocampus for mood and affect. Our data illuminate a region- and cell-type-specific transcriptional landscape within the hippocampus. This data is accessible as a public resource through an interactive website (https://human-hippo-axis.cells.ucsc.edu/) and will act as a reference atlas for the human hippocampus.
Project description:The Del-Mar 14K chip was used to interrogate differential expression of transcripts in the white isthmus (WI) compared with the adjacent magnum (Mg) and uterine (Ut) segments of the hen oviduct. Differential expression of genes common to both comparisons (WI/Mg and WI/Ut) was detected for 204 annotated proteins. Of these, 58 genes were overexpressed in both WI/Mg and WI/Ut, and are therefore considered to be the most interesting candidates for WI - specific functions. Additionally, general analysis revealed 135 clones hybridizing to overexpressed transcripts (WI/Mg + WI/Ut), and corresponding to 102 NCBI annotatated non-redundant Gallus gallus gene ID~s. This combined analysis revealed that structural proteins highly over-expressed in white isthmus were collagen X (COL10A1), Fibrillin (FBN1) and Cysteine Rich Eggshell Membrane Protein (CREMP). In addition, genes encoding collagen-processing enzymes were over-expressed, as were proteins known to regulate disulfide cross-linking, suggesting that coordinated upregulation of gene networks in the white isthmus is associated with eggshell membrane fibre formation. IPA interactome analysis reinforces the key role of the estrogen receptor and SMAD3 in mediating gene regulation during eggshell membrane synthesis. These results will assist with development of selection strategies to improve eggshell quality and food safety of the table egg. Keywords: Laying hen, eggshell, oviduct, Isthmus expression, cDNA microarray, indirect cDNA labelling, Alexa Fluor dyes Keywords: Expression profiling by array
Project description:We report the transcriptomes of 10 different chicken (Gallus gallus) cell/tissue types. The goal of this project was to determine similarities and differences between different cell/tissue types, with respect to protein coding genes, lncRNA, isoform counts, and differential gene expression. We provide raw data and bigWig files for UCSC visualization. The findings described here will be useful towards a complete annotation of chicken tissue and cellular transcriptomes.