Project description:In order to identify protein involved in sensing DNA double strand breaks and recruiting the repair machinry, we performed in vitro assembly of chromatin on small circular and linear DNA templates, respectively. Proteins involved in chromatin assembly and sensing of free DNA ends were isolated and subjected to proteomics analysis.
Project description:Planarian flatworms can regenerate every organ after amputation. Adult pluripotent stem cells drive the ability to regenerate, but how injury activates these cells and directs them into the appropriate lineages is not understood. To study the regeneration response in a simplified context, we selectively induced the ejection of the planarian pharynx by briefly exposing animals to sodium azide followed by microarray analysis. Tissue surrounding the wound site was examined at 6, 12, 18, 24, 48, and 72 hours post amputation by comparison to tissue isolated immediately after amputation (time zero). Stem cells are required for the regeneration process, and can be eradicated by exposure to radiation. A parallel time course was also performed on worms that had been irradiated with 10k rads of gamma irradiation. Two time courses consisting of irradiated or unirradiated worms following chemical amputation of the pharynx. Tissue samples taken at 6, 12, 18, 24, 48 and 72 hours are each compared to a reference sample at time zero. The experiment was performed in triplicate for a total of 42 samples on 36 arrays.
Project description:The goal of the study was to identify genes expressed in the proliferative cell population (neoblasts) of adult planarians. Proliferating cells are rapidly and specifically eliminated following lethal irradiation. Genes expressed by neoblasts, therefore, were expected to show decreased level of expression following 6,000 rads, relative to control animals. Total RNA was collected from control (unirradiated) animals and from animals 6, 12, 24, and 48 hours following 6,000 rads irradiation. Between three and five replicates were used for each sample
Project description:Transcriptional profiling of Schmidtea mediterranea planarians that have been amputated transversely and left to regenerate for different time points (UNIRR); the same experiment was performed on irradiated - neoblast depleted animals (IRR). The purpose of this experiment was to identify transcriptional changes that are induced within the first 12h following amputation. In order to distinguish between gene expression changes in the differentiated tissue and the neoblasts, a second set of time course data was created from irradiated animals Two-color experiment, 3 replicates per condition (including 10 animals/replica)
Project description:Positional RNA-sequencing of isolated Hydra body pieces and RNA-sequencing of fully regenerated Hydra animal was combined with RNA-sequencing of actively regenerating spheroids (see submission E-MTAB-9672) in order to elucidate the role of tissue stretching on regeneration and body pattern formation.
Project description:Analysis of gene expression level changes during the regeneration of the hemichordate posterior during the first 96 hours of regeneration. Animals were bisected, then collected at eight experimental timepoints - 2 hours, 4 hours, 6 hours, 12 hours, 24 hours, 48 hours, 72 hours, 96 hours, with a minimum of four replicates for each timepoint. Additionally, four healthy and intact animals were bisected and immediately collected to serve as reference controls.
Project description:The goal of this study was to identify genes that were expressed in the protonephridial system. Because Six1/2(RNAi) and POU2/3(RNAi) animals lose the tubules, flame cells and accessory cells, these animals were expected to show decreased levels of the genes expressed in the nephridial system relative to control RNAi animals. RNA from Six1/2(RNAi) and POU2/3(RNAi) animals was harvested with Trizol at days 8 and 15 after RNAi initiation for the former and days 15 and 21 for the latter. Three biological replicates were used. RNA from the four samples were competetively hybridized on a microarray with RNA from control RNAi animals of the corresponding days.
Project description:Microarray analysis indicated many changes in gene expression, including genes related the the Notch signaling system, during oral siphon regeneration in adult Ciona. Subsequent qPCR gene expression and inhibitor of experiments confirm a role of the Notch system, probably in the formation of a regeneration blastema. To identify the genes defferentially expressed in degenerating siphone, gene expressions in intact siphones and excised siphones (after 3 days, 6 days and 9 days) were examined.
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:Our objective is to identify new miRNAs and their target mRNAs involved in arterial stenosis, especially pathological changes of smooth muscle cells. To this end, the balloon injury model was used to induce the activation of smooth muscle cells by damaging arterial endothelial cells. The balloon-injured rat carotid arteries were isolated and subjected to the RNA-Seq.