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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Identification of molecular controls of Corticothalamic projection neurons differentiatiion

ABSTRACT: Molecular mechanisms controlling specification and differentiation of distinct neuron subtypes in the cerebral cortex are not well understood. Corticothalamic projection neurons (CThPN) are a diverse set of neurons, critical for function of the neocortex, but little is known about the molecular mechansims controlling their development. We used microarrays to detail CThPN gene expression at 3 developmental time points. We then compared CThPN gene expression, with the gene expression of other neuron subtypes in the cerebral cortex at the same stages (previously described in Arlotta et a., 2005) CThPN were retrogradely label with fluorescent microespheres injected into the thalamus, and were FACS purified at 3 developmental stages for RNA extraction and hybridization on Affymetrix microarrays.

ORGANISM(S): Mus musculus

SUBMITTER: Vibhu Sahni

PROVIDER: E-GEOD-61711 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Identification of molecular controls of Corticothalamic projection neurons differentiatiion

Project description:Molecular mechanisms controlling specification and differentiation of distinct neuron subtypes in the cerebral cortex are not well understood. Corticothalamic projection neurons (CThPN) are a diverse set of neurons, critical for function of the neocortex, but little is known about the molecular mechansims controlling their development. We used microarrays to detail CThPN gene expression at 3 developmental time points. We then compared CThPN gene expression, with the gene expression of other neuron subtypes in the cerebral cortex at the same stages (previously described in Arlotta et a., 2005)

2016-06-28 | GSE61711 | GEO

Transcription profiling of mouse FACS-purified cortical projection neurons using Affymetrix 430 2.0 microarrays

Project description:3 subtypes of cortical projection neurons were purified by fluorescence-activated cell sorting (FACS) at 4 different stages of development from mouse cortex. A detailed description of the data set is described in Arlotta, P et al (2005) and Molyneaux, BJ et al (2009). The hybridization cocktails used here were originally applied to the Affymetrix mouse 430A arrays and submitted as GEO accession number GSE2039. The same hybridization cocktails were then applied to the Affymetrix mouse 430 2.0 arrays, and those data are contained in this series. Experiment Overall Design: Three subtypes of cortical neurons were purified by FACS at multiple stages of mouse brain development. The neuron subtypes are: corticospinal motor neurons (CSMN), callosal projection neurons (CPN), and corticotectal projection neurons (CTPN). The stages of development included embryonic day 18 (E18), postnatal day 3 (P3), postnatal day 6 (P6), and postnatal day 14 (P14). CSMN and CPN were analyzed at all four stages, while CTPN were only analyzed at P14. The replicates included in the data set are all true biological replicates with independent sample collection for each.

2009-10-09 | E-GEOD-17783 | biostudies-arrayexpress

FACS purified cortical projection neurons

Project description:3 subtypes of cortical projection neurons were purified by fluorescence-activated cell sorting at 4 different stages of development from mouse cortex. A detailed description of the data set is described in Arlotta, P et al (2005). Keywords = corticospinal motor neuron callosal corticotectal cortex development FACS

2005-01-19 | GSE2039 | GEO

Cortical somatostatin long-range projection neurons and interneurons exhibit divergent developmental trajectories

Project description:The mammalian cerebral cortex contains an extraordinary diversity of cell types that emerge through the implementation of different developmental programs. Delineating when and how cellular diversification occurs is particularly challenging for cortical inhibitory neurons, as they represent a relatively small proportion of all cortical cells, migrate tangentially from their embryonic origin to the cerebral cortex, and have a protracted development. Here we combine single-cell RNA sequencing and spatial transcriptomics to characterize the emergence of neuronal diversity among somatostatin-expressing (SST+) cells, the most diverse subclass of inhibitory neurons in the mouse cerebral cortex. We found that SST+ inhibitory neurons segregate during embryonic stages into long-range projection (LRP) neurons and two types of interneurons, Martinotti cells and non-Martinotti cells, following distinct developmental trajectories. Two main subtypes of LRP neurons and several subtypes of interneurons are readily distinguishable in the embryo, although interneuron diversity is further refined during early postanal life. Our results suggest that the timing for cellular diversification is unique for different subtypes of SST+ neurons and particularly divergent for LRP neurons and interneurons. Thus, the diversification of SST+ inhibitory neurons involves a temporal cascade of unique molecular programs driving their divergent developmental trajectories.

2023-11-01 | GSE217065 | GEO

Transcription profiling of mouse FACS-purified cortical projection neurons

Project description:This SuperSeries is composed of the following subset Series:; GSE2039: FACS purified cortical projection neurons; GSE17783: Analysis of gene expression in FACS-purified cortical projection neurons using Affymetrix 430 2.0 microarrays Experiment Overall Design: Refer to individual Series

2009-10-10 | E-GEOD-17784 | biostudies-arrayexpress

Transcription profiling of mouse FACS purified cortical projection neurons

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RNA sequencing of corticospinal neurons and control callosal projection neurons purified from the cerebral cortex of adult wild-type and Sod1G86R mice, a model of amyotrophic lateral sclerosis, at four disease-relevant ages.

Project description:Amyotrophic Lateral Sclerosis is clinically defined as the combined degeneration of the corticospinal and corticobulbar neurons (CSN) along with the bulbar and spinal motor neurons (SMN). While a growing body of evidence points to the motor cortex, where CSN are located, as the potential initiation site of ALS, little is known about how CSN degenerate. To gain insights into the molecular mechanisms behind CSN selective degeneration, we first developed an approach to purify this neuronal population from the cerebral cortex of adult wild-type and Sod1G86R mice, combining retrograde labelling and Fluorescence Activated Cell Sorting. In parallel, a second population of cortical neurons, the callosal projection neurons (CPN) located in the layers II/III of the cerebral cortex were also purified. CPN and CSN are both cortical excitatory projection neurons but as opposed to CSN, CPN do not degenerate in Sod1G86R mice, and served as control population. CSN and CPN were purified from same animals, at two presymptomatic ages (3 and 60 days) and two symptomatic ages, 90 and 105 days. A total of 57 samples were further processed and analysed (CSN: 30d: n=4 WT and 3 Sod1G86R; 60d: n=4 WT and 4 Sod1G86R; 90d: n=4 WT and 4 Sod1G86R; 105d: n=4 WT and 2 Sod1G86R; CPN: 30d: n=4 WT and 3 Sod1G86R; 60d: n=2 WT and 3 Sod1G86R; 90d: n=4 WT and 4 Sod1G86R; 105d: n=4 WT and 4 Sod1G86R).

2020-12-30 | E-MTAB-7876 | biostudies-arrayexpress

High-throughput mapping of single-neuron projection and molecular features by retrograde barcoded labelling [scRNA-seq]

Project description:Deciphering patterns of connectivity between neurons in the mammalian brain is a critical step toward understanding brain function. Conventional imaging based neuroanatomical tracing methods identify area-to-area or sparse neuron-to-neuron connectivity patterns, but with extremely limited throughput. Recently developed barcode-based connectomics methods can efficiently map large numbers of single-neuron projections, but linking these data to single-cell transcriptomics remains a challenge. Here, we established a retro-AAV barcode-based multiplexed tracing method called MERGE-seq (Multiplexed projection neuRons retroGrade barcodE sequencing), which is capable of simultaneously characterizing the projectome and transcriptome at the single neuron level. We uncovered dedicated and collateral projection patterns of ventromedial prefrontal cortex (vmPFC) neurons to five downstream targets (AI, DMS, BLA, MD and LH). We found that projection-defined vmPFC neurons are molecularly heterogeneous, which are composed of different neuronal subtypes. We further identified transcriptional signatures of various dedicated and bifurcated vmPFC neurons, and verified Pou3f1 as the marker gene of neurons sending collateral axons to DMS and LH. Finally, we fitted our single-neuron connectome/transcriptome data into a machine learning-based model and revealed groups of genes that were predictive of certain projection pattern. In summary, we have developed a new multiplexed technique whose paired connectome and gene expression data can help reveal organizational principles that form neural circuits and process information.

2024-02-25 | GSE210172 | GEO

High-throughput mapping of single-neuron projection and molecular features by retrograde barcoded labelling [bulk RNA-seq]

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Single cell RNA-seq analysis of human embryonic cortex

Project description:Many studies have been launched to investigate cellular and molecular regulation regarding human neural system development, yet there is hardly any regional characterization on the whole developmental human cerebral cortex. We found that inhibitory neuron subtypes possibly originated from MGE and CGE. The molecular regulation of excitatory neuron maturation in vivo showed differences to that in rodent. Different regions appeared to have distinct cell type diversities with pons proceeding to show astrocyte explosion. Generally neurons of the same subtype were more uniform in gene expression inside each region except for those in parietal lobe.

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