Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Differential quantitative proteome analysis of cerebellar flocculus on oculomotor behavior training mouse model

ABSTRACT: Oculomotor behavior model system is commonly employed to study the neural circuits and the cellular mechanisms underlying neural integration related to motor behavior. The flocculus is a small lobe at the posterior border of the middle cerebellar and involved in motor control to aid in the oculomotor system in the brain. However, only several studies have investigated the molecular mechanism of learning and memory in flocculus region using another approach than proteomics.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Brain, Granule Cell, Purkinje Cell

SUBMITTER: Jongmin Woo

LAB HEAD: Youngsoo Kim

PROVIDER: PXD008433 | Pride | 2020-03-20

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20160519_Flocculus_TMT_ALL-01.pep.xml	Pepxml
	20160519_Flocculus_TMT_ALL-01_PSMs.txt	Txt
	20160519_Flocculus_TMT_ALL-01_PeptideGroups.txt	Txt
	20160519_Flocculus_TMT_ALL-01_Proteins.txt	Txt
	20160519_Flocculus_TMT_ALL.msf	Msf

Items per page:

1 - 5 of 44

Publications

Quantitative Proteomics Reveals Distinct Molecular Signatures of Different Cerebellum-Dependent Learning Paradigms.

Kim Yong Gyu YG Woo Jongmin J Park Joonho J Kim Sooyong S Lee Yong-Seok YS Kim Youngsoo Y Kim Sang Jeong SJ

Journal of proteome research 20200330 5

The cerebellum improves motor performance by adjusting motor gain appropriately. As de novo protein synthesis is essential for the formation and retention of memories, we hypothesized that motor learning in the opposite direction would induce a distinct pattern of protein expression in the cerebellum. We conducted quantitative proteomic profiling to compare the level of protein expression in the cerebellum at 1 and 24 h after training from mice that underwent different paradigms of cerebellum-de ...[more]

PMID: 32181667

Similar Datasets

Aplysia Pleural Ganglia 24 Hours After Long-Term Habituation Training

Project description:We used a custom-designed microarray and qPCR to characterize the persistent transcriptional response to long-term habituation training in the marine mollusk Aplysia californica. Aplysia were exposed to either 3 days of spaced long-term habituation training (10 rounds of stimulation/day; each round = 15 min brushing at a 10s ISI; 15 min rest between rounds); a matched set of controls was not exposed to any brushing (n = 8/group). While reflex responsiveness remained stable in controls, trained animals exhibited a large reduction in siphon-withdrawal duration that was evident at stimulation sites across the entire dorsal surface of the body (head, tail, and siphon). This habituation was retained for at least 24 hours after the end of training. Immediately after 24 hour retention tests, pleural ganglia were harvested from each trained animal and its matched control. The pleural ganglia contain the VC nociceptors, which we confirmed are activated by the brush stimulus used to produce habituation. Microarray analysis from 8 biological replicates suggests that long-term habituation training persistently regulates 21 transcripts. We used qPCR to test a subset of these transcripts and found persistent regulation of an putative Aplysia cornichon homolog. Between-subjects comparison of a trained animal to a matched control (matching based on duration of pre-test responsiveness). Conducted with 8 biological replicates, meaning 8 arrays, each comparing 1 trained and 1 matched control.

2014-07-16 | E-GEOD-59448 | biostudies-arrayexpress

Transcription profiling of soleus muscle from lean and obese Zucker rats following exercise training

Project description:Endurance exercise training has been shown to decrease whole-body and skeletal muscle insulin resistance and increase glucose tolerance in conditions of both pre-diabetes and overt type 2 diabetes. However, the adaptive responses in skeletal muscle at the molecular and genetic level for these beneficial effects of exercise training have not been clearly established in an animal model of pre-diabetes. The present study identifies alterations in skeletal muscle gene expression that occur with exercise training in pre-diabetic, insulin-resistant obese Zucker (fa/fa) rats and insulin-sensitive lean Zucker (Fa/-) rats. Treadmill running for up to 4 weeks caused significant enhancements of glucose tolerance as assessed by the integrated area under the curve for glucose (AUCg) during an oral glucose tolerance test in both lean and obese animals. Using microarray analysis, a set of only 12 genes was identified as both significantly altered (>1.5-fold change relative to sedentary controls; p<0.05) and significantly correlated (p<0.05) with the AUCg. Two of these genes, peroxisome proliferator-activated receptor-g coactivator 1a (PGC-1a) and the z-isoform of protein kinase C (PKC-z), have known involvement in the regulation of skeletal muscle glucose transport. We confirmed that protein expression levels of PGC-1a and PKC-z were positively correlated with the mRNA expression levels for these two genes. Overall, this study has identified a limited number of genes in soleus muscle of lean and obese Zucker rats that are associated with decreased insulin resistance and increase glucose tolerance following endurance exercise training. These findings could guide the development of pharmaceutical M-^Sexercise mimeticsM-^T in the treatment of insulin-resistant, pre-diabetic or overtly type 2 diabetic individuals.

2009-11-16 | E-TABM-213 | biostudies-arrayexpress

Prosit: Proteome-wide prediction of peptide tandem mass spectra by deep learning

Project description:In this study, we extended the ProteomeTools peptide library (PROPEL, see PXD004732 and PXD010595) to train a deep neural network resulting in chromatographic retention time and fragment ion intensity predictions for (tryptic) peptides that exceed the quality of the experimental data.

2019-05-30 | PXD010871 | Pride

Rat DNA methylation in the Nucleus Accumbens in Incubation of Cocaine Craving

Project description:DNA methylation profiling of nucleus Accumbens of rats that self administered cocaine and were subjected to 1 or 30 withdrawal days with or without extinction tests. The groups consist of 1. Saline rats (Sal.) 2. Rats that self-administered cocaine for 10 days and that were subjected to a withdrawal period of 1 day (1W) 3. Rats that self-administered cocaine for 10 days and that were subjected to a withdrawal period of 1 day and to an extinction test for assessment of cue-induced cocaine-seeking behavior (1C) 4. Rats that self-administered cocaine for 10 days and that were subjected to a withdrawal period of 30 days (30W) 5. Rats that self-administered cocaine for 10 days and that were subjected to a withdrawal period of 30 days and to an extinction test for assessment of cue-induced cocaine-seeking behavior (30C)

2015-02-27 | E-GEOD-66348 | biostudies-arrayexpress

Rat gene expression in the Nucleus Accumbens in Incubation of Cocaine Craving

Project description:Gene expression profiling of nucleus Accumbens of rats that self administered cocaine and were subjected to 1 or 30 withdrawal days with or without extinction tests. The groups consist of 1. Saline rats (Sal.) 2. Rats that self-administered cocaine for 10 days and that were subjected to a withdrawal period of 1 day (1W) 3. Rats that self-administered cocaine for 10 days and that were subjected to a withdrawal period of 1 day and to an extinction test for assessment of cue-induced cocaine-seeking behavior (1C) 4. Rats that self-administered cocaine for 10 days and that were subjected to a withdrawal period of 30 days (30W) 5. Rats that self-administered cocaine for 10 days and that were subjected to a withdrawal period of 30 days and to an extinction test for assessment of cue-induced cocaine-seeking behavior (30C)

2015-02-27 | E-GEOD-66349 | biostudies-arrayexpress

Microarray dataset of gene transcription in mouse microglia and peripheral monocytes in contextual fear conditioning

Project description:Using Illumina MouseWG-6v2 microarrays, we investigated the gene transcription changes in microglia and peripheral monocytes after contextual fear conditioning of C57BL/6J mice. Mice were trained with or without a single minimized footshock stimulation (0-s or 2-s, 0.4 mA) and re-exposed to the training context without footshock for three different durations 24 h later: 0 min (FS0), 3 min (FS3), or 30 min (FS30). Whole brain microglia and peripheral monocytes were prepared 24 h after re-exposure using a neural tissue dissociation kit, including non-footshock controls for two re-exposure durations (Con3 and Con30). The data can be valuable for researchers interested in glial cells and neurotransmission studies and are related to the research article “Contextual fear conditioning regulates synapse-related gene transcription in mouse microglia”.

2022-10-28 | E-MTAB-12361 | biostudies-arrayexpress

Wild-type Zebrafish subjected to swim-training

Project description:Genome-wide microarray analysis of the effects of swim-training on zebrafish larval development. Zebrafish were subjected to swim-training from 5 days post fertilization (dpf) until 10 dpf. Subsequently, we performed a genome-wide microarray analysis of trained and control fish at 10 dpf. The goal of the project was to investigate the effects of swim-training on the gene expression level during zebrafish larval development Two-condition experiment: control vs trained fish. RNA was isolated from 10 control fish and from 10 trained fish. Subsequently, each sample was labeled with Cy3 and Cy5 in order to correct for dye bias. Control-Cy3 and Trained-Cy5 were hybridized on array 1 and Trained-Cy5 and Control-Cy3 were hybridized on array 2.

2014-07-17 | E-GEOD-42967 | biostudies-arrayexpress

Genome-wide changes in DNA methylation in response to physical exercise

Project description:Here we describe a genome-wide analysis of DNA-methylation in muscle of trained mice. In comparison to sedentary controls 2762 genes exhibited differentially methylated CpGs in their putative promoter regions. The majority of these genes were related to muscle growth and differentiation and a minor fraction involved in metabolic regulation. These findings suggest that DNA-methylation is involved in the regulation of muscle adaptation to regular exercise training. Reduced representation bisulfite sequencing of murine quadriceps muscle

2015-02-01 | E-GEOD-54277 | biostudies-arrayexpress

The blood transcriptional signature of recombinant human erythropoietin administration and implications for anti-doping strategies

Project description:Scottish trained individuals (SCO; n = 18) living and training at or near sea-level and Kenyan runners (KEN; n = 20) living and training at ~2,150 m received rHuEPO injections of 50 IUâ kg-1 body mass every two days for four weeks. Blood was collected at baseline, during rHuEPO administration and for four weeks after administration. Eight time points per subject were selected for gene expression analysis; two baseline samples, then one sample at two days, two weeks and four weeks after the first rHuEPO injection and one week, two weeks and four weeks after ceasing rHuEPO administration. RNA was extracted from blood stabilized in Tempus Blood RNA tubes (Life Technologies), amplified, labelled and hybridized to Illumina HumanHT-12v4 Expression BeadChips (Illumina). Expression data was analysed using Rank Products with a Benjamini-Hochberg 5% false discovery rate and an additional 1.5 fold-change threshold. The expression profiles of a subset of target genes was further confirmed using QuantiGene Plex assay (Affymetrix) and Limma (linear models for microarray).

2015-07-07 | E-MTAB-2874 | biostudies-arrayexpress

Longitudinal SLE study with clinical parameters

Project description:Goal of the study was to compare transcriptomes of SLE patients at various stages of the disease, as well as to evaluate the transcriptome for individual patients over time while taking a large number of clinical parameters into account. 996 samples analyzed of which 72 are Healthy controls and 924 are SLE; 24 technical replicates of healthy samples are included and were used for batch correction purposes.

2016-03-31 | E-GEOD-65391 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data