The Transcriptome of Basilar Papilla Hair Cell Regeneration in the Avian Inner Ear
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ABSTRACT: A comprehensive transcriptome profile of chicken basilar papilla hair cell across a 7 days regenerative time course. Compare gene expression changes in chicken basilar papilla treated with streptomycin to the control. A total of 60 samples were collected from 8 different time points. Each time point contains 2 biological samples.
Project description:In chick basilar papilla, hair cells can be regenerated after gentamicin treatment. To identify genes and pathways involved in this process, we performed microarray analysis on the basilar papilla 0, 48 and 72 hours after gentamicin.
Project description:Precise frequency discrimination is a hallmark of auditory function in birds and mammals. In the cochlea, tuning and spectral separation result from longitudinal differences in basilar membrane stiffness and numerous individual gradiations in sensory hair cell phenotypes, but it is unknown what patterns those phenotypes. Hypothesizing that morphogen levels might differ along the longitudinal axis of the developing cochlea, we sequenced the transcriptomes of the proximal, middle, and distal thirds of the chicken cochlea at E6.5, when postmitotic hair cells first form. Embryonic day 6.5 chicken cochlea were dissected. Three samples were collected from each cochlear duct by cutting the duct into three approximately equal sized pieces to produce proximal, middle, and distal pieces. Each sample contained a portion of the future tegmentum vasculosum and the basilar papilla sensory epithelium. The distal piece also contained the region fo the future lagena.
Project description:We investigated the role of AMPK activation in the progression of senescence in HFDPCs. The anti-senescence effects of adenine, a recently identified AMPK activator, were determined in a comparison with AICAR, a pharmacological AMPK activator, in HFDPCs. The results showed that either adenine or AICAR induced phosphorylation of Thr172 of AMPK in HFDPCs. As revealed by microarray analysis, significant changes of gene expression pattern were observed in the high-passage HFDPCs compared with that at lower passage level. A chip study using total RNA recovered from three separate wild-type cultures of Human follicle dermal papilla cells (HFDPCs) and three separate cultures of a triple adenine-treated cells.
Project description:In order to gain insight into the molecular events which underlie auditory hair cell regeneration in chicken, we compared gene expression in chicken basilar papillae after 24, 48, and 72 hours in culture with or without forskolin (100uM).<br><br>Under sterile conditions, cochlear ducts containing the basilar papillae were carefully dissected out of ~4-day-old chicks and then individually cultured in DMEM with 10% fetal bovine serum with or without forskolin (final concentration 100 ?M, delivered in 1% DMSO) for either 24, 48, or 72 hours at 37ï¾°C. Control samples received DMSO at 1% as a vehicle control. At the end of 3 days, the tegmentum vasculosum was dissected off to expose the auditory epithelium, which was delicately freed from the underlying cartilaginous plates. All explants were kept in culture for 3 days because new hair cells are first seen in basilar papillae treated with forskolin after ~3 days of exposure to the drug [19]. Therefore, at even earlier time points in culture the molecular events that subserve hair cell proliferation are well underway. Each sample was comprised of 3 auditory epithelia from 3 different chicks which were put in ~100 ?L of DMEM and then immediately frozen at -80ï¾°C until RNA isolation could be performed. There were a total of 24 samples in this experiment: six 72-hour forskolin, six 72-hour control, three 48-hour forskolin, three 48-hour control, three 24-hour forskolin, and three 24-hour control.
Project description:scRNAseq of chicken basilar papilla at P7 and P11 as controls, and 12, 16, 20, 24, 30, 38, 48, and 96 hours post sisomicin administration. Cells were isolated using FACS and underwent Smartseq-2 protocol for single cell RNA seq with paired-end sequencing. Processed data file contains SingleCellExperiment object with all metadata. The dataset has undergone quality control using scater package in R, normalized using SCnorm, and normalized counts were log2 transformed (found in RDS file here). Only genes expressed in at least 3 cells are included for a total of 16,302 genes. A total of 2,625 high quality cells are in the normalized dataset. Raw sequence data for all 3,831 sequenced cells pre-quality control is also included.
Project description:A comprehensive transcriptome profile of chicken utricle hair cell across a 7 days regenerative time course. Compare gene expression changes in chicken utricle treated with streptomycin to the control. A total of 60 samples were collected from 11 different time points. Each time point contains at least 2 biological samples.
Project description:High-flow causes the remodeling of arteries, in which smooth muscle cells play an important role. To know the profile of smooth muscle gene expression under high-flow conditions in vivo, flow of rabbit basilar artery was increased by ligation of both common carotid arteries. Microarrays were performed to profile the gene expression of smooth muscle cells isolated from rabbit basilar artery. Expression profiles indicate 43603 differentially expressed genes in smooth muscle cells exposed to high-flow insult compared with the sham control, of which 1470 genes were upregulated and 780 genes downregulated using 2 fold-changes and P<0.05 as a cut-off. Bilateral common carotid arteries of female New Zealand White rabbits were ligated to increase vascular flow.The control group was performed the same procedure to expose the CCAs without ligation. Rabbits were euthanized at day 5 after ligation or exposure of bilateral CCAs in both groups (n=3 for each group). The rabbits used and all procedures in this study were approved by the local Institutional Animal Care and Use Committee. Smooth muscle cells were isolated. After euthanization of rabbits, the whole basilar arteries were removed. The arteries were cleaned in PBS buffer,cannulated and perfused at a constant flow with a cocktail which contains PBS and 0.4 mg/ml elastase (Sigma) and 1 mg/ml collagenase (type 1A, Sigma). After an incubation time of 45 min, the tissue left was removed and stored in PBS. SMCs were released from the artery by trituration. Then Total RNA was extracted and gene chip tests were performed.
Project description:Hair Follicle regeneration relies on both epithelial components (bulge and hair germ cells) and a mesenchymal one (dermal papilla cells). We used microarrays to detail the global programme of gene expression underlying organ regeneration at the transition between quiescent stages (early and middle telogen) and the initiation of a new growth (late telogen). Experiment Overall Design: These microarray at the 3 different stages were designed to identify signals released by the mesenchymal dermal papilla cells to activate epithelial growth, their target genes in the hair germ and bulge compartments, and to get at gene signature differences and similarities between hair germ and bulge cells.