Similar Datasets
Project description:Comprehensive gene expression analysis of mouse brains in postnatal maturation stages using Transcriptome Tomography
| PRJNA948677 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below.
2025-12-05 | GSE228206 | GEO
Project description:Comprehensive gene expression analysis of Huntington disease model mouse brains using Transcriptome Tomography
| PRJNA948676 | ENA
Project description:Changes in the foveal anatomy during infancy are an important component in early development of spatial vision. The present longitudinal study in rhesus monkeys was undertaken to characterize the postnatal maturation of the fovea. Starting at four weeks after birth, the retinas of the left eyes of sixteen infant monkeys were imaged using spectral domain optical coherence tomography (SD OCT). Retinal scans were repeated every 30 days during the first year of life and every 60 days thereafter. Volume scans through the fovea were registered, scaled using a three surface schematic eye, and analyzed to measure foveal pit parameters. The individual layers of the retina were manually segmented and thicknesses were measured over a transverse distance of 1250 microns from the center of the foveal pit. Based on infrared scanning laser ophthalmoscope (IR SLO) images acquired with the SD OCT system, there were significant changes in the extent of the retina scanned as the eyes matured. Using a three-surface schematic eye, the length of each scan could be computed and was validated using image registration (R2 = 0.88, slope = 1.003, p < 0.05). Over the first 18 months of life, the mean retinal thickness at the pit center had increased by 21.4% with a corresponding 20.3% decrease in pit depth. The major changes occurred within the first 120 days, but did not stabilize until a year after birth. In Macaca mulatta infants, the primary anatomical maturation of the fovea occurs within the first few months of life, as determined by longitudinal data from SD OCT measurements. The timelines for maturation of the fovea correspond well with the normal development of the lateral geniculate nucleus, cortical neurophysiology, and spatial resolution in monkeys.
| S-EPMC5628152 | biostudies-literature
Project description:During development, brain regions follow encoded growth trajectories. Compared to classical brain growth charts, high-definition growth charts could quantify regional volumetric growth and constituent cell types, improving our understanding of typical and pathological brain development. Here, we create high-resolution 3D atlases of the early postnatal mouse brain, using Allen CCFv3 anatomical labels, at postnatal days (P) 4, 6, 8, 10, 12, and 14, and determine the volumetric growth of different brain regions. We utilize 11 different cell type-specific transgenic animals to validate and refine anatomical labels. Moreover, we reveal region-specific density changes in γ-aminobutyric acid-producing (GABAergic), cortical layer-specific cell types, and microglia as key players in shaping early postnatal brain development. We find contrasting changes in GABAergic neuronal densities between cortical and striatal areas, stabilizing at P12. Moreover, somatostatin-expressing cortical interneurons undergo regionally distinct density reductions, while vasoactive intestinal peptide-expressing interneurons show no significant changes. Remarkably, microglia transition from high density in white matter tracks to gray matter at P10, and show selective density increases in sensory processing areas that correlate with the emergence of individual sensory modalities. Lastly, we create an open-access web-visualization (https://kimlab.io/brain-map/epDevAtlas) for cell-type growth charts and developmental atlases for all postnatal time points.
| S-EPMC10690281 | biostudies-literature
Project description:The purpose of this study was to identify the major molecular components in the secretory and maturation stages of amelogenesis through transcriptome analyses. Ameloblasts (40 sections per age group) were laser micro-dissected from Day 5 (secretory stage) and Days 11-12 (maturation stage) first molars. PolyA+ RNA was isolated from the lysed cells, converted to cDNA, and amplified to generate a cDNA library. DNA sequences were obtained using next generation sequencing and analyzed to identify genes whose expression had increased or decreased at least 1.5-fold in maturation stage relative to secretory stage ameloblasts. Among the 9198 genes that surpassed the quality threshold, 373 showed higher expression in secretory stage, while 614 genes increased in maturation stage ameloblasts. The results were cross-checked against a previously published transcriptome generated from tissues overlying secretory and maturation stage mouse incisor enamel and 34 increasing and 26 decreasing expressers common to the two studies were identified. Expression of F2r, which encodes protease activated receptor 1 (PAR1) that showed 10-fold higher expression during the secretory stage in our transcriptome analysis, was characterized in mouse incisors by immunohistochemistry. PAR1 was detected in secretory, but not maturation stage ameloblasts. We conclude that transcriptome analyses are a good starting point for identifying genes/proteins that are critical for proper dental enamel formation and that PAR1 is specifically expressed by secretory stage ameloblasts.
| S-EPMC4252044 | biostudies-literature
Project description:The mouse posterior primitive streak at neural plate/headfold stages (NP/HF, ~7.5 dpc-8 dpc) represents an optimal window from which hemangioblasts can be isolated. We performed immunohistochemistry on this domain using established monoclonal antibodies for proteins that affect blood and endothelial fates. We demonstrate that HoxB4 and GATA1 are the first set of markers that segregate independently to endothelial or blood populations during NP/HF stages of mouse embryonic development. In a subset of cells, both proteins are co-expressed and immunoreactivities appear mutually excluded within nuclear spaces. We searched for this particular state at later sites of hematopoietic stem cell emergence, viz., the aorta-gonad-mesonephros (AGM) and the fetal liver at 10.5-11.5 dpc, and found that only a rare number of cells displayed this character. Based on this spatial-temporal argument, we propose that the earliest blood progenitors emerge either directly from the epiblast or through segregation within the allantoic core domain (ACD) through reduction of cell adhesion and pSmad1/5 nuclear signaling, followed by a stochastic decision toward a blood or endothelial fate that involves GATA1 and HoxB4, respectively. A third form in which binding distributions are balanced may represent a common condition shared by hemangioblasts and HSCs. We developed a heuristic model of hemangioblast maturation, in part, to be explicit about our assumptions.
| S-EPMC3322272 | biostudies-literature
Project description:The testis is a highly specialized tissue that plays dual roles in ensuring fertility by producing spermatozoa and hormones. Spermatogenesis is a complex process, resulting in the production of mature sperm from primordial germ cells. Significant structural and biochemical changes take place in the seminiferous epithelium of the adult testis during spermatogenesis. The gene expression pattern of testis in Chinese mitten crab (Eriocheir sinensis) has not been extensively studied, and limited genetic research has been performed on this species. The advent of high-throughput sequencing technologies enables the generation of genomic resources within a short period of time and at minimal cost. In the present study, we performed de novo transcriptome sequencing to produce a comprehensive transcript dataset for testis of E. sinensis. In two runs, we produced 25,698,778 sequencing reads corresponding with 2.31 Gb total nucleotides. These reads were assembled into 342,753 contigs or 141,861 scaffold sequences, which identified 96,311 unigenes. Based on similarity searches with known proteins, 39,995 unigenes were annotated based on having a Blast hit in the non-redundant database or ESTscan results with a cut-off E-value above 10(-5). This is the first report of a mitten crab transcriptome using high-throughput sequencing technology, and all these testes transcripts can help us understand the molecular mechanisms involved in spermatogenesis and testis maturation.
| S-EPMC3307765 | biostudies-literature
Project description:We developed a novel framework to assess comprehensive endogenous gene expression maps in a broad and isotropic 3D-anatomical context using a relatively small number of original data points: transcriptome tomography. Using this method, we produced a dataset of gene expression maps of the whole mouse brain, computationally reconstructed from fraction data.
2012-09-21 | GSE36408 | GEO
Project description:Current functional neuroimaging methods are not adequate for high-resolution whole-brain visualization of neural activity in real time. Here, we show imaging of fast hemodynamic changes in deep mouse brain using fully noninvasive acquisition of five-dimensional optoacoustic data from animals subjected to oxygenation stress. Multispectral video-rate acquisition of three-dimensional tomographic data enables simultaneous label-free assessment of multiple brain hemodynamic parameters, including blood oxygenation, total hemoglobin, cerebral blood volume, oxygenized and deoxygenized hemoglobin, in real time. The unprecedented results indicate that the proposed methodology may serve as a powerful complementary, and potentially superior, method for functional neuroimaging studies in rodents.
| S-EPMC4420890 | biostudies-literature