GNPS_Ancient DNA teeth
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Homo Sapiens (ncbitaxon:9606)
SUBMITTER: 
Pieter Dorrestein
PROVIDER: MSV000083264 | GNPS | Wed Dec 19 13:49:00 GMT 2018
REPOSITORIES: GNPS
Similar Datasets
Project description:The data set contains MS/MS data on teeth extracts for Ancient DNA teeth samples ran in both positive and Negative ionization modes
2018-12-19 | MSV000083264 | MassIVE
Project description:PITX1 had a significantly higher expression in the lower teeth compared to the upper teeth and this difference in PITX1 level was more evident in the molars compared to premolars, consistent with data in mouse developing teeth. These show that the differential gene expression during odontogenesis can continue to exist in mature teeth. We suggest that an in vitro study of dental pulp cells should take the differential gene profiles between the mandibular and maxillary teeth into consideration. The knowledge about gene profiling and pathways in mature teeth paves a way to explore a more precise treatment approach in regenerative dentistry.
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Project description:This dataset contains LC-MS/MS data from > 800 samples with different staining of human teeth
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Project description:In order to research the variation in protein distribution in teeth, proteins were extracted from archaeological (15-18th century, Netherlands) and modern teeth and identified using LC-MS/MS. Of the recovered proteins we then visualised the distribution of collagen type I (both the alpha-1 and -2 chains), alpha-2-HS-glycoprotein, haemoglobin subunit alpha and myosin light polypeptide 6 using MALDI-MSI. We found distinct differences in the spatial distributions of different proteins as well as between some peptides of the same protein. The reason for these differences in protein spatial distribution remain unclear, yet this study highlights the ability of MALDI-MSI for visualisng the spatial distribution of proteins in archaeological biomineralised tissues. Therefore MALDI-MSI might prove a useful tool to improve our understanding of protein preservation as well as aid in deciding sampling strategies.
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Project description:LC-MS/MS spectra were collected from the extracts of 92 human teeth powders.
2022-02-28 | MSV000088933 | MassIVE
Project description:Deciduous and permanent human teeth represent a model system to study ageing of mesenchymal populations. Aging is tightly connected to self-renewal and proliferation and thus, mapping potential molecular differences in these characteristics between populations constitutes an important task. Specifically designed microarray panels were used. We have detected a number of molecules that were differentially expressed in dental pulp mesenchyme from deciduous and permanent teeth extracted from young children and adults, respectively. Among the differentially regulated genes HMGA2, a stem cell-associated marker, stood out as a remarkable example with a robust expression in deciduous pulp cells. In addition to this, we discovered that several proliferation-related genes, including CDC2A and CDK4, were up-regulated in deciduous pulp cells, while matrix genes COL1A1, fibronectin and several signaling molecules, such as VEGF, FGFr-1 and IGFr-1 were up-regulated in the pulp cells from permanent teeth. Taken together, our data suggest that deciduous pulp cells are more robust in self- renewal and proliferation, whereas adult dental pulp cells are more capable of signaling and matrix synthesis.
2014-09-01 | GSE58668 | GEO
Project description:Deciduous and permanent human teeth represent a model system to study ageing of mesenchymal populations. Aging is tightly connected to self-renewal and proliferation and thus, mapping potential molecular differences in these characteristics between populations constitutes an important task. Specifically designed microarray panels were used. We have detected a number of molecules that were differentially expressed in dental pulp mesenchyme from deciduous and permanent teeth extracted from young children and adults, respectively. Among the differentially regulated genes HMGA2, a stem cell-associated marker, stood out as a remarkable example with a robust expression in deciduous pulp cells. In addition to this, we discovered that several proliferation-related genes, including CDC2A and CDK4, were up-regulated in deciduous pulp cells, while matrix genes COL1A1, fibronectin and several signaling molecules, such as VEGF, FGFr-1 and IGFr-1 were up-regulated in the pulp cells from permanent teeth. Taken together, our data suggest that deciduous pulp cells are more robust in self- renewal and proliferation, whereas adult dental pulp cells are more capable of signaling and matrix synthesis. The deciduous teeth were collected from 3-12-year-old children (N=8), whereas the permanent teeth were collected from adults, 19-52 years of age (N=8). The tooth was mechanically separated into two halves to remove all soft tissue in the pulp. The pulp tissue was digested and the dissociated cells were passed through cell strainer and plated with culture medium. The cells were then passaged at 90% confluency to a 10 cm dish for expansion. RNA was extracted from passage one cells with the Qiagen RNeasy Mini Kit. Microarray analysis was performed using PIQORTM Stem Cell Microarray chip (Miltenyi Biotech), which is comprised of 942 relevant genes for stem/progenitor cells and key genes for cell differentiation, to identify gene sets that are differentially expressed between cells in the deciduous and adult teeth. A total of 1 μg RNA for each sample was used for amplification and further analysis with the PIQORTM stem cell microarray chip (Miltenyi Biotec), followed by detection with a laser scanner (Agilent Technologies). In total, 8 comparisons were performed with dataset consisting of two microarrays, each containing a total of 11 slides with signal intensities within the R/Bioconductor statistical framework. The Linear Model for Microarray Data package (Limma) was used to pre-process the raw data, perform quality controls and estimate statistical significance. Expression intensities were background-corrected using a convolution of normal and exponential distributions with an offset of 50, which were then normalized within every slide using loess normalization. We analyzed the red and green channels separately using the mixed model method and different groups were quantile-normalized separately. The correlation was computed between the two channels for the same spot. Differentially expressed genes were identified by computing the contrasts, fitting to a linear model, performing the hypothesis tests, and correcting for multiple testing by performing the false discovery rate using the Benjamini-Hochberg correction.
2014-09-01 | E-GEOD-58668 | biostudies-arrayexpress
Project description:Human deciduous and permanent teeth exhibit different developmental processes, morphologies, histological characteristics and life cycles. In addition their pulp tissues react differently to external stimuli, such as the pulp sensitivity test, dental trauma and pulp therapy materials. These differences are attributable to their genetic backgrounds. Therefore the purpose of this study is to compare the differences of dental pulp in deciduous and permanent teeth. Pulp samples were obtained from permanent premolars (n=6, aged 11-14 years) and deciduous teeth (n=6, aged 11-14 years). Comparative cDNA microarrary analysis revealed several differences in gene expression between the deciduous and permanent pulp tissues. Each GSM record represents a pulp sample pooled from two teeth samples.
2014-08-21 | E-GEOD-51449 | biostudies-arrayexpress
Project description:Limpets are marine mollusks using mineralized teeth, one of the hardest and strongest biomaterials, to feed on algae on intertidal rocks. However, most of studies only focuses on the ultrastructure and chemical composition of the teeth while the molecular information is largely unknown, limiting our understanding of this unique and fundamental biomineralization process. In this study, we investigated the teeth of limpet Cellana toreuma from three perspectives: 1) by using electron microscopy to observe the microstructure of the teeth; 2) by using proteomics and RNA-seq to investigate the proteins involved in the limpet teeth and 3) by in vitro crystallization experiment combined with Raman spectroscopy to investigate the effects of proteins and chitin framework on crystal formation. It is found that the limpets formed alternatively tricuspid teeth and unicuspid teeth. Small nanoneedles were densely packed at the tips or leading regions of the cusps. In contrast, big nanoneedles resembling chemical synthesized goethite were loosely packed in the trailing regions of the cusps. Proteins extracted from the whole teeth such as ferritin, peroxiredoxin, arginine kinase, GTPase-Rabs and clathrin were identified by proteomics. Goethite-binding experiment coupled with proteomics and RNA-seq highlighted six chitin-binding proteins (CtCBPs). Furthermore, these proteins or the framework chitin only induced packing of crystals without affecting their crystal polymorphs in vitro. Taken together, the limpets formed hierarchical teeth across different length scales through preformed framework and secreted complex proteins; in addition, the chitin could also be an important player in controlling crystallinity and crystal packing in vivo. This study provides insight into the unique biomineralization process in the limpet teeth at the molecular levels, which may guide biomimetic strategies aimed at designing hard materials at room temperature.
2019-03-26 | PXD010113 | Pride