Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The Aged Neuronal Aggregome Identified by BONCAT

ABSTRACT: Aggregating neuronal proteins. The identification of neuronal proteins contributing to aged protein aggregates was enabled by labeling the neuronal proteome with BONCAT technology, enrichment of insoluble protein aggregates, and affinity enrichment for the tagged proteins.

INSTRUMENT(S):

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Brain

SUBMITTER: Ian Guldner

LAB HEAD: Tony Wyss-Coray

PROVIDER: PXD066053 | Pride | 2025-11-07

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	250603_Stanford_AgedAgg.sne	Other
	HyStarMetadata.xml	Xml
	InstrumentSetup.isset	Other
	Maldi.method	Other
	SampleInfo.xml	Xml

Items per page:

1 - 5 of 83

Similar Datasets

BONCAT Model Comparison in Camk2a+ Neurons

Project description:Comparison of three different BONCAT models (MetRS, PheRS, TyrRS) driven by Camk2a promoter to drive BONCAT machinery in excitatory neurons.

2025-11-07 | PXD057020 | Pride

Brain Region Camk2a Neuronal Protein Analaysis

Project description:Analysis of Camk2a+ neuronal proteome by brain region (hippocampus, striatum, cortex) by BONCAT labeling of Camk2a+ neurons, subsequent regional dissection, labeled-protein enrichment, and analysis by LC-MS.

2025-11-07 | PXD057261 | Pride

Comparison of Transgenic and Viral Labeling

Project description:Comparison of BONCAT labeling in Camk2aCre;PheRS* transgenic mice to mice injected with AAV-Camk2a;PheRS*.

2025-11-07 | PXD057456 | Pride

CMVCreBONCAT Proteome Coverage Comparison

Project description:Comparing proteome coverage between different BONCAT lines crossed to a CMV-Cre driver.

2025-11-06 | PXD056569 | Pride

Neuron-Microglia Protein Transfer

Project description:Analysis of BONCAT-labeled, Neuron-derived proteins inside of microglia.

2025-11-07 | PXD066030 | Pride

Aged vs Young Camk2a+ Neuron Proteome

Project description:Comparison of aged and young Camk2a+ neuronal proteome by transduction of mice with AAV-Camk2a;PheRS+ followed by AzF administration for BONCAT labeling of neuronal proteomes.

2025-11-07 | PXD057488 | Pride

Pseudomonas aeruginosa BONCAT biofilms

Project description:Cell-selective BONCAT analysis of proteins synthesized by a P. aeruginosa biofilm subpopulation throughout treatment with ciprofloxacin.

2017-10-24 | PXD007261 | Pride

Enrichment and quantitation of newly secreted proteins under serum condition by combining BONCAT and pulsed SILAC

Project description:Despite the increasing interest of secretome involved in paracrine/autocrine mechanisms, the majority of the mass spectrometric cell secretome studies have been performed using serum-free medium (SFM), due to low-abundance of secreted proteins and high-abundance of contaminating fetal bovine serum (FBS) proteins in serum-containing medium (SCM). In this study, through the combination of bioorthogonal non-canonical amino acid tagging (BONCAT) and pulsed-SILAC (pSILAC), the low-abundant secreted proteins were captured selectively and quantified. We set up the combined BONCAT-pSILAC method by optimizing capturing condition and by using a composite human-FBS database, and applied it to the analysis of differentially secreted proteins between SFM and SCM. The amount of secreted proteins for 24 h in SCM was much bigger than that from SFM for U-87MG glioblastoma cells (1.28-fold) and mesenchymal stem cells from human umbilical cord blood (hUCB-MSCs; 2.01-fold). The proteins secreted more in SCM were predominantly predicted to be truly secretory. Therefore, this study suggests the analysis of the secretome should be processed in serum-containing medium that promotes cell proliferation and secretion.

2019-03-13 | PXD007529 | Pride

Gene expression profiling in an induced pluripotent stem cell model of the developing human telencephalon: effect of heat shock and its potential impact on the development of neuropsychiatric disorders

Project description:Schizophrenia (SZ) and autism spectrum disorders (ASD) are highly heritable neuropsychiatric/neurodevelopmental disorders, although environmental factors, such as maternal immune activation (MIA), play a role as well. Inflammatory cytokines appear to mediate the effects of MIA on neurogenesis and behavior in animal models. However, drugs and cytokines that trigger MIA can also induce a febrile reaction, which could have independent effects on neurogenesis through heat shock (HS)-regulated cellular stress pathways. However, this has not been well-studied. As a first step towards addressing the role of fever in MIA, we used a recently described model of human brain development in which induced pluripotent stem cells (iPSCs) differentiate into 3-dimensional neuronal aggregates that resemble a first trimester telencephalon. RNA-seq was carried out on aggregates that were heat shocked at 39oC for 24 hours, along with their control partners maintained at 37oC. Overall, 186 genes showed significant differences in expression following HS (p<0.05), including known HS-inducible genes, as expected, as well as those coding for NGFR and a number of SZ and ASD candidates, including SMARCA2, DPP10, ARNT2, AHI1 and ZNF804A. The degree to which the expression of these genes decrease or increase during HS is similar to that found in copy loss and copy gain CNVs, although the effects of HS are likely to be more transient. RNA-seq was carried out on neuronal aggregates as described by Mariani et al. with slight modification (PMID:22761314). For the heat shock experiment, a group of 49 day old aggregates was placed in an incubator set at 39C for 24 hours, while control sets of aggregates were maintained at 37C. The incubator conditions were otherwise unchanged. After detaching the aggregates, total cellular RNA was isolated using the miRNeasy Kit (Qiagen) according to the manufacturer’s protocol. Lastly, RNAseq profiles of HS and Control were compared

2014-06-01 | E-GEOD-53667 | biostudies-arrayexpress

Transcriptome profiling of human neural progenitor cells and neurons with DISC1 interruption

Project description:Purpose: Genetic and clinical association studies have identified disrupted-in-schizophrenia 1 (DISC1) as a candidate risk gene for major mental illness. DISC1 is interrupted by a balanced chr(1;11) translocation in a Scottish family, in which the translocation predisposes to psychiatric disorders. We investigate the consequences of DISC1 interruption in human neural cells using TALENs or CRISPR-Cas9 to target the DISC1 locus. We sought to compare the gene expression profiles of human neural progenitor cells (NPCs) and neurons with interruption of the DISC1 gene in exon 2 (affecting all known coding transcripts) or exon 8 (near the site of the Scottish translocation, affecting longer transcripts). Methods: Wild-type and DISC1-targeted iPSCs (wild-type = "WT", exon 8 single allelic frameshift mutant = "ex8_wm", exon 8 biallelic frameshift mutant = "ex8_mm", exon 2 biallelic frameshift mutant = "ex2mm") were differentiated to NPCs and neurons using an embryoid aggregate method. NPC or neuronal cultures were used for RNA harvest and subsequent paired-end stranded sequencing of >50M reads/sample and 3-6 biological replicates per group. Results: We find that a subset of genes related to neuronal differentiation and development are dysregulated with DISC1 disruption at the NPC timepoint, whereas expression of genes related to neuronal function and signaling are altered at the neuronal timepoint. This study implicates DISC1 as a regulator of neuronal development. mRNA profiles of wild-type and DISC1-targeted human iPSC-derived neural progenitor cells (day 17) and neurons (day 50) by paired-end sequencing, with 3-6 biological replicates, using Illumina HiSeq

2015-09-14 | E-GEOD-71289 | 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