Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Translational profiling of hypothalamic and midbrain neurons that project to the nucleus accumbens.

ABSTRACT: Neuroanatomical methods enable high-resolution mapping of neural circuitry, but do not allow systematic molecular profiling of neurons based on their connectivity. Here, we report the development of a novel approach for molecularly profiling projective neurons. We show that ribosomes can be labeled with a camelid nanobody raised against GFP and that this system can be engineered to selectively capture translating mRNAs from cells expressing GFP. We generated a transgenic mouse encoding a nanobody-ribosomal protein fusion (Syn-NBL10) and used a retrograde virus (CAV) encoding GFP to immunoprecipitate ribosomes from projection neurons. This enabled us to profile neurons projecting to the nucleus accumbens. The current method provides a new means for profiling neurons based on their projections.

ORGANISM(S): Mus musculus

PROVIDER: GSE55800 | GEO | 2014/05/22

SECONDARY ACCESSION(S): PRJNA241023

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Translational profiling of hypothalamic and midbrain neurons that project to the nucleus accumbens.

Project description:Neuroanatomical methods enable high-resolution mapping of neural circuitry, but do not allow systematic molecular profiling of neurons based on their connectivity. Here, we report the development of a novel approach for molecularly profiling projective neurons. We show that ribosomes can be labeled with a camelid nanobody raised against GFP and that this system can be engineered to selectively capture translating mRNAs from cells expressing GFP. We generated a transgenic mouse encoding a nanobody-ribosomal protein fusion (Syn-NBL10) and used a retrograde virus (CAV) encoding GFP to immunoprecipitate ribosomes from projection neurons. This enabled us to profile neurons projecting to the nucleus accumbens. The current method provides a new means for profiling neurons based on their projections. Translating mRNAs immunoprecipitated from neurons projecting to the nucleus accumbens. Each Input and IP sample corrspond to a pooled group of 6 mice.

2014-05-22 | E-GEOD-55800 | biostudies-arrayexpress

Mouse psd95 coimmunoprecipitation from excitatory or inhibitory neurons and mass spectrometry

Project description:We used a psd95-GFP cre dependent KI mouse to label PSD95 with GFP specifically in excitatory (CaMK) or inhibitory (vGAT) neurons. PSD95 was pulled down with a GFP nanobody and the resulting complex was used for massspectrometry analysis.

2023-06-03 | PXD041635 | Pride

Molecular profiling of reticular gigantocellularis neurons

Project description:we used technique that allows the molecular characterization of particular neuronal subpopulations based on their neuroanatomical projections and the locations of their cell bodies. This ‘retro-TRAP’ (translating ribosome affinity purification from retrogradely labeled neurons) approach relies on viral injection into an anatomical area targeted by the neurons of interest, followed by selective precipitation of ribosomes from retrogradely labeled cell bodies, and subsequent RNAseq analysis.

2018-11-01 | GSE115526 | GEO

RNP immunoprecipitation of fission yeast using Rng3p myosin-specific chaperones to investigate if the association of Rng3p with RNAs occurs on ribosomes

Project description:Ribonucleoprotein immunoprecipitation microarray (RIp-chip) study using the Rng3p myosin-specific chaperones from the fission Schizosaccaromyces pombe. Rng3p associates with RNAs encoding myosins. To investigate if the association of Rng3p with these RNAs occurs on ribosomes, Rng3-purified fractions were immunoprecipitated with antibodies against a ribosomal RNA or an unrelated antibody. The RNAs present in the second immunoprecipitate were analysed using DNA microarrays

2008-12-23 | E-TABM-564 | biostudies-arrayexpress

Identification of tissue-specific SPD-5 and PLK-1 proximity interactors by direct and indirect TurboID

Project description:In this set of proof of principle experiments we compare the proximity interactomes obtained for two C. elegans centrosomal proteins, SPD-5 and PLK-1, by direct TurboID and indirect, GFP nanobody-targeted, TurboID in a range of different tissues, embryos, germ cell precursors and ciliated neurons.

2022-04-01 | PXD031970 | Pride

Antibody RING-Mediated Destruction (ARMeD) of endogenous proteins

Project description:To understand the cellular function of a gene the encoding DNA or mRNA transcript can be manipulated and the consequences observed. However, these approaches do not have a direct effect on the protein product of the gene, which is either permanently abrogated or depleted at a rate defined by the half-life of the protein. Therefore, complete gene deletions and RNA interference of proteins with a very long half-life risk obscuring the direct consequences via compensatory or secondary cellular responses. We therefore sought to develop a single-component system that could induce the rapid degradation of the specific endogenous protein itself. A genetically introduced inducible construct of the RING domain of the ubiquitin E3 ligase RNF4 with a protein-specific camelid nanobody mediates destruction of the target by the ubiquitin proteasome system, a process we describe as Antibody RING-Mediated Destruction (ARMeD). The technique is acutely specific as we observed no off-target protein destruction. Furthermore, bacterially produced nanobody-RING fusion proteins electroporated into cells induce degradation of target within minutes. With the increasing availability of protein-specific nanobodies this method will allow the rapid and specific degradation of a wide range of endogenous proteins.

2020-05-29 | PXD018113 | Pride

BacTRAP-based ribosome profiling of murine hypothalamic PNOC neurons

Project description:We performed a BacTRAP-based ribosome profiling of PNOC-expressing cells in the hypothalamus of mice. Therefore, we employed mice, which express a fusion protein of the ribosomal L10a protein with EGFP (L10a-EGFP) under control of the PNOC promoter (Doyle et al., 2008). Precipitation of ribosomes of hypothalamic PNOC neurons with anti-GFP antibodies and subsequent mRNA sequencing of associated mRNAs allowed for assessment of an in-depth translational profile of these cells. Affinity purification of translating ribosomes was performed as described by (Heiman et al., 2014) with minor modifications.

2020-04-16 | GSE137626 | GEO

Vector-transduced neurons transcriptome profiles

Project description:With the goal of specifically dissecting the toxicogenomic signatures of the helper-dependent (HD) human (HAd5) and canine (CAV-2) adenovirus, the VSV-G-pseudotyped SIN HIV-1 (LV) and the Adenoviral-associated vector 2/9 for human neurons (AAV2/9), we transduced a bona fide human neuronal system with HD-HAd5, HD-CAV-2, LV and AAV2/9, we analysed the transcriptional response of more than 47,000 transcripts using gene chips. Chip data showed that HD-CAV-2 and LV vectors both activated the innate arm of the immune response, including Toll-like receptors and hyaluronan circuits. LV vector induced as well an IFN response. Moreover, HD-CAV-2 and LV vectors affected DNA damage pathways - at 5 days in opposite directions - suggesting a differential response of the p53 and ATM pathways to the vector genomes. As a general response to the vectors, human neurons activated pro-survival genes and neuron morphogenesis. Total RNAs extracted from transduced hmNPCs cells at 2 h and 5 days post-infection with HD-HAd, HD-CAV-2, LV and AAV2/9 vectors were hybridizated on Affymetrix microarrays and paired pair wise comparisons were performed between the mock and vector transduced hmNPCs cells. Each condition was tested in three replicates.

2013-05-22 | E-GEOD-47130 | biostudies-arrayexpress

greenCUT&RUN: a rapid and efficient genome profiling approach for transcription and chromatin regulatory proteins

Project description:Chromatin modifiers, transcription factors and cofactors regulate gene expression through engagement with chromatin and DNA, which can be detected by a variety of genomic techniques. Here, we describe a novel method ‘greenCUT&RUN’ for genome-wide profiling of transcription regulatory factors, which has higher sensitivity, resolution, accuracy and reproducibility than existing methods, whilst assuring specificity as assessed for the gene specific transcription factors NFY and c-FOS, and for the basal transcription factor TBP. Our strategy begins with tagging the protein of interest with GFP and utilizes a GFP-specific nanobody fused to MNase to profile genome-wide binding events. Since the nanobody targets GFP, the greenCUT&RUN approach eliminates dependency on protein-specific antibodies, which makes it widely applicable. To examine, if GFP-tagged proteins form complex with known interactors and GFP did not interfere in the formation of protein complex, mass spectrometry was performed.

2021-01-13 | PXD021089 | Pride

Translation deficits drive C9orf72 associated poly-GR/PR toxicity

Project description:Frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) patients with the C9orf72 mutation show predominantly cytoplasmic aggregates of poly-GR and poly-PR proteins that are acutely toxic in various model systems. To identify the molecular mediators of neurotoxicity of poly-GR/PR, we analyzed their interactomes in primary neurons. GFP-(GR)149 and (PR)175-GFP preferentially interacted with RNA-binding proteins, including stress granule-associated and nucleolar proteins, as well as ribosomes. Overexpression of the poly-GR/PR interactors Staufen 1/2 (STAU1/2) and YBX1 led to cytoplasmic aggregation of poly-GR/PR into large stress granule-like inclusions, while the poly-GR/PR interactor nucleophosmin (NPM1) recruited poly-GR into the nucleolus. In addition, poly-PR expression reduced ribosome levels and translation, which is consistent with the widespread reduction of synaptic proteins detected by proteomics. Surprisingly, only GFP-(GR)53, but not GFP-(GR)149, localized to the nucleolus and reduced ribosome levels and translation in neurons, suggesting impaired ribosome biogenesis is driving the acute toxicity commonly observed in vitro. In C9orf72 patient brains, we detected co-aggregation of poly-GR/PR inclusions with ribosomes, but not stress granules. Partial sequestration of ribosomes may chronically impair protein synthesis and contribute to C9orf72 ALS/FTD pathogenesis.

2018-06-27 | PXD008691 | Pride

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