Similar Datasets
Project description:single cell transcriptome profiling for palm and hip skin
| PRJNA742431 | ENA
Project description:We aim to investigate chromatin accessibility in the keratinocytes of hip and palm
2023-05-03 | GSE226926 | GEO
Project description:Palmoplantar skin is structurally and functionally unique, but the transcriptional programs driving this specialization are unknown. Here, we exploit bulk and single-cell RNA-sequencing of human palm, sole, and hip skin to describe the distinguishing characteristics of palmoplantar and non-palmoplantar skin while also uncovering previously unappreciated differences between palmar and plantar sites. Our approach reveals downregulation of diverse immunological processes and decreased immune cell populations in palmoplantar skin, highlighting an altered immune environment in the skin of the palms and soles. Further, we identify specific palmoplantar and non-palmoplantar fibroblast populations that appear to orchestrate key differences in cell-cell communication in palm, sole, and hip. Dedicated analysis of epidermal keratinocytes highlights major differences in basal cell fraction among the three sites and validates the presence of a more differentiated, cycling basal population. Finally, our data demonstrate the existence of two spinous keratinocyte populations that constitute two parallel, site-selective epidermal differentiation trajectories. Together, these results provide a deep characterization of the highly adapted palmoplantar skin and contribute new insights into the fundamental biology of human skin.
2023-01-05 | GSE193101 | GEO
Project description:Palmoplantar skin is structurally and functionally unique, but the transcriptional programs driving this specialization are unknown. Here, we exploit single-cell RNA-sequencing of human palm, sole, and hip skin to describe the distinguishing characteristics of palmoplantar and non-palmoplantar skin while also uncovering previously unappreciated differences between palmar and plantar sites. Our approach reveals downregulation of diverse immunological processes and decreased immune cell populations in palmoplantar skin, highlighting an altered immune environment in the skin of the palms and soles. Further, we identify specific palmoplantar and non-palmoplantar fibroblast populations that appear to orchestrate key differences in cell-cell communication in palm, sole, and hip. Dedicated analysis of epidermal keratinocytes highlights major differences in basal cell fraction among the three sites and validates the presence of a more differentiated, cycling basal population. Finally, our data demonstrate the existence of two spinous keratinocyte populations that constitute two parallel, site-selective epidermal differentiation trajectories. Together, these results provide a deep characterization of the highly adapted palmoplantar skin and contribute new insights into the fundamental biology of human skin.
2023-01-11 | GSE202352 | GEO
Project description:The pathogenesis of necrosis of femoral head (NFH) remains elusive now. Limited studies were conducted to investigate the molecular mechanism of hip articular cartilage damage of NFH. We conducted a genome-wide gene expression profiling of hip articular cartilage with NFH.
2016-06-01 | GSE74089 | GEO
Project description:The pathogenesis of necrosis of femoral head (NFH) remains elusive now. Limited studies were conducted to investigate the molecular mechanism of hip articular cartilage damage of NFH. We conducted a genome-wide gene expression profiling of hip articular cartilage with NFH. Hip articular cartilage specimens were collected from 12 NFH patients and 12 healthy controls. Gene expression profiling of NFH articular cartilage was carried out by Agilent Human 4x44K Gene Expression Microarray chip. Differently expressed genes were identified using the Significance Analysis of Microarrays (SAM) software.
2016-06-01 | E-GEOD-74089 | biostudies-arrayexpress
Project description:The aim of this study was to characterise the genome-wide DNA methylation profile of osteoathritis (OA) chondrocytes from both knee and hip cartilage, providing the first comparison of DNA methylation between OA and non-OA hip cartilage, and between OA hip and OA knee cartilage. The study was performed using the Illumina Infinium HumanMethylation450 BeadChip array. Genome-wide methylation was assesed in chondrocyte DNA extracted from 23 OA hip, 73 OA knee and 21 healthy hip controls (NOF - neck of femure samples). Keywords: Methylation profiling by array
2015-09-02 | GSE63695 | GEO
Project description:To determine the mechanisms of fleshy fruit abscission of the monocot oil palm (Elaeis guineensis Jacq.) compared with other abscission systems, we performed multi-scale comparative transcriptome analyses on fruit targeting the developing primary AZ and adjacent tissues. Combining between-tissue developmental comparisons with exogenous ethylene treatments, and naturally occurring abscission in the field, RNAseq analysis revealed a robust core set of 168 genes with differentially regulated expression, spatially associated with the ripe fruit AZ, and temporally restricted to the abscission timing. The expression of a set of candidate genes was validated by qRT-PCR in the fruit AZ of a natural oil palm variant with blocked fruit abscission, which provides evidence for their functions during abscission. Our results substantiate the conservation of gene function between dicot dry fruit dehiscence and monocot fleshy fruit abscission. The study also revealed major metabolic transitions occur in the AZ during abscission, including key senescence marker genes and transcriptional regulators, in addition to genes involved in nutrient recycling and reallocation, alternative routes for energy supply and adaptation to oxidative stress. The study provides the first reference transcriptome of a monocot fleshy fruit abscission zone and provides insight into the mechanisms underlying abscission by identifying key genes with functional roles and processes, including metabolic transitions, cell wall modifications, signalling, stress adaptations and transcriptional regulation, that occur during ripe fruit abscission of the monocot oil palm. The transcriptome data comprises an original reference and resource useful towards understanding the evolutionary basis of this fundamental plant process.
2021-02-08 | GSE166314 | GEO
Project description:Spatial genome organization is essential to direct fundamental DNA-templated biological processes (e.g. transcription, replication, and repair), but the 3D in situ nanometer-scale structure of accessible cis-regulatory DNA elements within the crowded nuclear environment remains elusive. Here, we combined the recently developed Assay for Transposase-Accessible Chromatin with visualization (ATAC-see), PALM super-resolution imaging and lattice light-sheet microscope (a method termed 3D ATAC-PALM) to selectively image and quantitatively analyze key features of the 3D accessible genome in single cells. 3D ATAC-PALM reveals that accessible chromatin are non-homogeneously organized into spatially segregated clusters or accessible chromatin domains (ACDs). To directly link imaging and genomic data, we optimized multiplexed imaging of 3D ATAC-PALM with Oligopaint DNA-FISH, RNA-FISH and protein fluorescence. We found that ACDs colocalize with active chromatin and enclose transcribed genes. By applying these methods to analyze genetically purterbed cells, we demonstrated that genome architectural protein CTCF prevents excessive clustering of accessible chromatin and decompacts ACDs. These results highlight the 3D ATAC-PALM as a useful tool to probe the structure and organizing mechanism of the genome.
2020-01-29 | GSE126112 | GEO
Project description:We provide data that compares global gene expression in dysplastic hip compared to control hip tissue in dogs.
2018-11-27 | GSE112874 | GEO