Quantitative proteomic analysis of oxaliplatin induced peripheral neurotoxicity
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Fusion Lumos
ORGANISM(S): Mus Musculus (mouse)
TISSUE(S): Nerve Cord
SUBMITTER: 
Linlin YANG
LAB HEAD: Ruibing Chen
PROVIDER: PXD031322 | Pride | 2022-07-11
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| OFL001513-YLL-GPF-15K-1.raw | Raw | |||
| OFL001513-YLL-GPF-15K-2.raw | Raw | |||
| OFL001513-YLL-GPF-15K-3.raw | Raw | |||
| OFL001513-YLL-GPF-15K-4.raw | Raw | |||
| OFL001513-YLL-GPF-15K-5.raw | Raw |
Items per page: 5 1 - 5 of 22 |
Similar Datasets
Project description:We evalueted gene expression in dorsal root ganglion (DRG) over-expressing NRG1 typeIII ICD (Intra Cellular Domain). DRG were infected with a lentivirus expressing ICD and compared to not infected DRG or DRG infected with a lentivirus expressing EGFP.
2014-12-14 | E-MTAB-2131 | biostudies-arrayexpress
Project description:Expression profiling of L4 and L5 Dorsal Root Ganglion (DRG) in the spinal nerve ligation model of neuropathic pain. The goal of the study was to identify genes involved in neuropathic pain This series of samples comprises of contralateral and ipsilateral L4 and L5 DRG tissue collected 4 weeks after rats underwent a L5 spinal nerve ligation (SNL) or a sham operation with no L5 spinal nerve ligation. This defines 8 groups (i) contralateral L4 DRG from the sham cohort (n=5), (ii) ipsilateral L4 DRG from sham cohort (n=5), (iii) contralateral L4 DRG from SNL cohort (n=5), (iv) ipsilateral L4 DRG from the SNL chort (n=5), (v) contralateral L5 DRG from the sham cohort (n=5), (vi) ipsilateral L5 DRG from sham cohort (n=5), (vii) contralateral L5 DRG from SNL cohort (n=5), (viii) ipsilateral L5 DRG from the SNL cohort (n=5)
2011-10-17 | E-GEOD-24982 | biostudies-arrayexpress
Project description:Treatment strategies of critical nerve injuries involving nerve gaps more than 3 cm are still not optimal. The need for an alternative to the standard autologous nerve grafts has led to the exploration of adipose derived stem cells (ASC) seeded in bioartificial nerve conduits for enhancement of peripheral nerve regeneration. ASC can be differentiated into Schwann cell like cells, which is believed to improve their neurotrophic potency. Nevertheless, the differentiation process requires several weeks and there is no evidence that the cells maintain their differentiated phenotype in vivo. Thus, the present study evaluated the synergistic effect of undifferentiated ASC with exogenously added growth factors in vitro with the aim to improve the neurotrophic potency of undifferentiated ASC through short ex-vivo stimulation with growth factors. The study furthermore provides a comparative in vitro assay of the six well-known neurotrophic factors NGF, GDNF, BDNF, CNTF, NT3 and NT4. ASC were cultured and thus stimulated in the presence of the respective exogenous growth factor for three days and resulting conditioned medium was evaluated in an in vitro axonal outgrowth assay. In addition, also unstimulated ASC’s conditioned medium was tested in combination with the respective exogenous growth factor for the same assay, which was perfomed on dorsal root ganglion (DRG) explants from 10 days old embryonic chicken. DRG explants from most promising conditions were further analyzed for upregulated STAT-3 and GAP-43 by qRT-PCR. Furthermore, also proteomics and phosphoproteomics were performed for ASC and DRG explants using mass spectrometry. The quantity of selected proteins contained in the ASC’s conditioned medium was investigated by ELISA. Combination of ASC’s conditioned medium with growth factors generally resulted in significantly enhanced axonal outgrowth when compared with their control of DRG explants cultured with the respective growth factor only. Specifically, conditioned medium derived from NT3-stimulated as well as ASC’s conditioned medium supplemented with NT3 or BDNF elicited significant axonal outgrowth from DRG explants in contrast to all other experimental conditions. Significant upregulation of STAT-3 and GAP-43 was evidenced for DRG explants grown in NT3-stimulated ASC’s conditioned medium and to a certain extent also for DRG cultured in ASC’s conditioned medium supplemented with NT3.
2021-09-09 | PXD019015 | Pride
Project description:Inflammation plays a role in neuropathic pain conditions as well as in pain induced solely by an inflammatory stimulus. Robust mechanical hyperalgesia and allodynia can be induced by locally inflaming the L5 dorsal root ganglion (DRG) in rat. This model allows investigation of the contribution of inflammation per se to chronic pain conditions. Most previous microarray studies of DRG gene expression have investigated neuropathic pain models involving axon transection. To examine the role of inflammation, we used microarray methods to examine gene expression 3 days after local inflammation of the L5 DRG in rat. We observed significant regulation in a large number of genes (23% of observed transcripts), and examined 221 (3%) with a fold-change of 1.5-fold or more in more detail. Immune-related genes were the largest category in this group and included members of the complement system as well as several pro-inflammatory cytokines. However, these upregulated cytokines had no prior links to peripheral pain in the literature other than through microarray studies, though most had previously described roles in CNS (especially neuroinflammatory conditions) as well as in immune responses. The L5 dorsal root ganglion (DRG) was locally inflamed with zymosan/Incomplete Freund's Adjuvant. DRG were isolated 3 days later. Each sample was RNA extracted from a single DRG. 6 samples from rats with local DRG inflammation were compared with 6 samples from sham-operated rats.
2012-06-21 | E-GEOD-38859 | biostudies-arrayexpress
Project description:Transcriptional analysis of identified DRG subpopulations. Cell-type specific intrinsic programs instruct neuronal subpopulations before target-derived factors influence later neuronal maturation. Retrograde neurotrophin signaling controls neuronal survival and maturation of dorsal root ganglion (DRG) sensory neurons, but how these potent signaling pathways intersect with transcriptional programs established at earlier developmental stages remains poorly understood. Here we determine the consequences of genetic alternation of NT3 signaling on genome-wide transcription programs in proprioceptors, an important sensory neuron subpopulation involved in motor reflex behavior. We find that the expression of many proprioceptor-enriched genes is dramatically altered by genetic NT3 elimination, independent of survival-related activities. Combinatorial analysis of gene expression profiles with proprioceptors isolated from mice expressing surplus muscular NT3 identifies an anticorrelated gene set with transcriptional levels scaled in opposite directions. Voluntary running experiments in adult mice further demonstrate the maintenance of transcriptional adjustability of genes expressed by DRG neurons, pointing to life-long gene expression plasticity in sensory neurons. We combined a mouse line expressing GFP under the control of the TrkC promoter (BAC transgene approach) with various NT3 signaling mutants in order to identify the transcriptional changes in identified subpopulations of dorsal root ganglia (DRG) neurons. Sorted cells were processed for RNA extraction and hybridization on Affymetrix microarrays. Analysis was performed a postnatal (p) day p0. Subsequent analysis focused on the transcriptional profile of DRG neuron subpopulations at specific lumbar levels. Additional work addressed the transcriptional changes in whole DRG in adult mice with and without physical exercise.
2012-08-23 | E-GEOD-38074 | biostudies-arrayexpress
Project description:This program addresses the gene signature associated with DRG in the Chung rat model for neuropathic pain. The Chung neuropathic pain profiling data was analyzed by identifying genes that were up- and down-regulated at selected p value and fold change in DRG of the Sprague Dawley rats following spinal nerve ligation compared to the sham-operated controls.
2013-03-22 | E-GEOD-38038 | biostudies-arrayexpress
Project description:Schwann cells and macrophages were dissociated from normal DRGs and 1- and 7-month-old neurofibroma. Schwann cells from neurofibroma have Nf1-/- phenotypes. All macrophages have Nf1+/+ phenotypes. We used microarrays (Affymetrix MoGene 2.0 ST GeneChip) to detect transcriptomal changes between 7-month-old neurofibroma Schwann cells (or macrophages) versus 1-month-old wild-type (or neurofibroma) Schwann cells (or macrophages). Expression data of three sets of cells: (1)Schwann cells and macrophages from 1-month-old wild-type mouse dorsal root ganglia, (2) Schwann cells (Nf1-/-) and macrophages (Nf1+/+) from 1-month-old neurofibroma, (3) Schwann cells (Nf1-/-) and macrophages (Nf1+/+) from 7-month-old neurofibroma We chopped mouse DRG/neurofibromas into 1-3 mm^3 pieces and plated them in dissociation medium containing 20mL L-15 (Mediatech), 0.5 mg/mL collagenase type 1 (Worthington; Lakewood, NJ), and 2.5 mg/mL dispase protease type II (Cambrex; East Rutherford, NJ) at 37°C for 4-6 hours with shaking. The dissociation reaction was stopped by adding DMEM +10%FBS. Undigested DRG/tumors were excluded by 100µM cell strainer. Cells were collected by centrifugation. For each microarrays (Schwann cell, macrophage), Affymetrix GeneChip Command Console (v4.0.0) was used to create .chp files. All the probe sets on Affymetrix Mouse Gene 2.0 ST array (Mogene-2_0-st-v1.na33.2.mm10) were summarized by Affymetix Expression Console program using robust multi-chip average (RMA) method . After preprocessing steps, data from two batches were combined and their batch effects were corrected using ComBat method Please note that [1] all MP samples are Nf1+/+ (no mutation on Nf1 gene) and the only difference is their ages (1month, 7month) and [2] the 'nf1' in sample title reperesents "neurofibroma type1 disease", not "Nf1 gene".
2017-05-01 | E-GEOD-78901 | biostudies-arrayexpress
Project description:The vast majority of cold sensitive DRG neurons from mice do not express the voltage-gated sodium channel NaV1.8. Therefore, we aimed to compare the molecular profiles of NaV1.8 and non-NaV1.8-expressing neurons using microarray analysis. Fluorescent activated cell sorting was performed at 4 degrees centigrade on acutely dissociated DRG neurons from mice expressing NaV1.8-Cre, Pirt-GCaMP3 and a Cre-dependent global reporter (td tomato). NaV1.8-expressing neurons were sorted based on their reporter fluorescence (td tomato; red) and putative cold sensing neurons were sorted based on their GCaMP3 fluorescence at 4 degrees centigrade and absence of Cre-dependent reporter fluorescence. A total of three mice were used (samples one, two and three) with GCaMP3 only and NaV1.8-expressing neurons forming two relative populations within each sample (eg. GC3 one is the experimental counterpart of Tom one).
2019-07-01 | E-MTAB-7070 | biostudies-arrayexpress
Project description:The goal of this study was to analyze global gene expression in specific populations of somatosensory neurons in the periphery, including major, non-overlapping populations that include nociceptors, pruriceptors, and prorioceptors. The mammalian somatosensory nervous system encodes the perception of specific environmental stimuli. The dorsal root ganglion (DRG) contains distinct somatosensory neuron subtypes that innervate diverse peripheral tissues, mediating the detection of thermal, mechanical, proprioceptive, pruriceptive, and nociceptive stimuli. We purified discrete subtypes of mouse DRG somatosensory neurons by flow cytometry using fluorescently labeled mouse lines (SNS-Cre/TdTomato, Parv-Cre/TdTomato) in combination with Isolectin B4-FITC surface staining (IB4). This allowed identification of transcriptional differences between these major populations, revealing enrichment of voltage-gated ion channels, TRP channels, G-protein coupled receptors, transcription factors, and other functionally important classes of genes within specific somatosensory neuron subsets. SNS-Cre mice were bred with Rosa26-TdTomato mice to generate SNS-Cre/TdTomato reporter mice. Parv-Cre mice were bred with Rosa26-TdTomato mice to generate Parv-Cre/TdTomato mice. Isolectin B4-FITC was used to stain the surface of SNS-Cre/TdTomato reporter mice. We used these strategies of fluorescent labeling to purify distinct murine sensory neuron subsets from the dorsal root ganglia (DRG) by fluorescence activated cell sorting (FACS). Neurons were sorted directly in Qiazol for total RNA extraction and microarray analysis. Whole DRG tissue was also included for transcriptome analysis to compare with purified neuronal populations.
2014-12-23 | E-GEOD-55114 | biostudies-arrayexpress
Project description:We have undertaken a genome-wide study of transcriptional activity in embryonic superior cervical ganglia (SCG) and dorsal root ganglia (DRG) during a time course of neurite outgrowth in vitro. Gene expression observed in these models likely includes both developmental gene expression patterns and regenerative responses to axotomy, which occurs as the result of tissue dissection. Comparison across both models revealed many genes with similar gene expression patterns during neurite outgrowth. These patterns were minimally affected by exposure to the potent inhibitory cue Semaphorin3A, indicating that this extrinsic cue does not exert major effects at the level of nuclear transcription. We also compared our data to several published studies of DRG and SCG gene expression in animal models of regeneration, and found the expression of a large number of genes in common between neurite outgrowth in vitro and regeneration in vivo. Experiment Overall Design: We wished to determine the transcriptional profiles of neurons undergoing neurite outgrowth in vitro. We were particularly interested in finding genes whose expression is generally associated with the process of neurite outgrowth, rather than with cell type-specific effects. Thus, in order to avoid focusing on transcripts unique to one tissue type versus another, we used a comparative strategy to look for effects that were common to two tissue types and therefore more likely to be involved in the general process of neurite outgrowth. While these explants contain multiple cell types, we felt this was preferable to the more disruptive conditions required to dissociate neurons or obtain a pure neuron population. To this end, we monitored gene expression in cultured explants from SCG and DRG using DNA microarrays. We initiated our studies by culturing embryonic day 13 (E13) mouse SCG in vitro and harvesting tissue for RNA isolation at time points from 2 to 65 hours. Time points were selected to detect both fast, short-term responses (2, 5 and 12 hours), as well as sustained, long-term changes (24, 40, and 65 hours). Samples were hybridized to Affymetrix MG-U74v2 A and B microarrays, with RNA from acutely dissected explants serving as a baseline reference. We followed these experiments with a parallel analysis of a more heterogeneous tissue type, the DRG, which is more frequently used than SCG for in vivo studies of neurite regeneration. Cervical and upper thoracic DRG from E12 embryos were cultured with NGF (the same trophic support as in SCG cultures), harvested at time points from 2 to 40 hours, and hybridized to Affymetrix MOE 430A microarrays.
2008-06-16 | E-GEOD-9739 | biostudies-arrayexpress