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Single cell deletion of the transcription factors Sox9 and Trps1 reveals novel functions in adult cortical astrocytes [Spatial transcriptomics]

ABSTRACT: Single cell deletion of the transcription factors Sox9 and Trps1 reveals novel functions in adult cortical astrocytes [Spatial transcriptomics]

PROVIDER: PRJNA1174069 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR31023785_1.fastq.gz	Fastqsanger.gz
	SRR31023785_2.fastq.gz	Fastqsanger.gz
	SRR31023786_1.fastq.gz	Fastqsanger.gz
	SRR31023786_2.fastq.gz	Fastqsanger.gz
	SRR31023787_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Single cell deletion of the transcription factors Sox9 and Trps1 reveals novel functions in adult cortical astrocytes [Spatial transcriptomics]

Project description:Astrocytes play key roles in brain function but it is still poorly understood how these are orchestrated by pan-astrocyte transcriptions factors (TFs). Here we examined the function of the well-known pan-astrocyte TF Sox9 and the novel astrocyte TF Trps1 (Transcriptional Repressor GATA Binding 1) by Cas9-mediated in vivo deletion using Mokola-pseudotyped lentiviral delivery into the adult cerebral cortex. The consequences of deleting either Sox9 or Trps1 alone or simultaneously were explored at single cell level (by patch-based single cell transcriptomics) and tissue level (by spatial transcriptomics). This revealed TF-specific functions in astrocytes, like synapse maintenance and immune response, as well as non-cell-autonomous effects on the surrounding cells such as on oligodendrocytes and other immune cells. Interestingly, deleting both factors cancels out some effects, suggesting that they antagonize each other’s function to some extent. Taken together, this study reveals a novel role of Trps1 and Sox9 in adult astrocytes and their communication with other glial and immune cells.

2025-02-10 | GSE279676 | GEO

Single cell deletion of the transcription factors Sox9 and Trps1 reveals novel functions in adult cortical astrocytes [RNA-seq]

Project description:Purpose of the study is to evaluate the impact of Sox9 and Trps1 knock-down in vivo at single cell level

2025-02-10 | GSE279677 | GEO

Single cell deletion of the transcription factors Sox9 and Trps1 reveals novel functions in adult cortical astrocytes [RNA-seq]

Project description:Single cell deletion of the transcription factors Sox9 and Trps1 reveals novel functions in adult cortical astrocytes [RNA-seq]

| PRJNA1174066 | ENA

Single Cell Deletion of the Transcription Factors Trps1 and Sox9 in Astrocytes Reveals Novel Functions in the Adult Cerebral Cortex.

Project description:Astrocytes play key roles in brain function, but how these are orchestrated by transcription factors (TFs) in the adult brain and aligned with astrocyte heterogeneity is largely unknown. Here we examined the localization and function of the novel astrocyte TF Trps1 (Transcriptional Repressor GATA Binding 1) and the well-known astrocyte TF Sox9 by Cas9-mediated deletion using Mokola-pseudotyped lentiviral delivery into the adult cerebral cortex. Trps1 and Sox9 levels showed heterogeneity among adult cortical astrocytes, which prompted us to explore the effects of deleting either Sox9 or Trps1 alone or simultaneously at the single-cell (by patch-based single-cell transcriptomics) and tissue levels (by spatial transcriptomics). This revealed TF-specific functions in astrocytes, such as synapse maintenance with the strongest effects on synapse number achieved by Trps1 deletion and a common effect on immune response. In addition, spatial transcriptomics showed non-cell-autonomous effects on the surrounding cells, such as oligodendrocytes and other immune cells with TF-specific differences on the type of immune cells: Trps1 deletion affecting monocytes specifically, while Sox9 deletion acting mostly on microglia and deletion of both TF affecting mostly B cells. Taken together, this study reveals novel roles of Trps1 and Sox9 in adult astrocytes and their communication with other glial and immune cells.

| S-EPMC11845849 | biostudies-literature

Olfactory bulb gene expression profiling upon loss of Sox9 in adult astrocytes

Project description:The goal of this study is to determine how the loss of the transcription factor Sox9 affects the molecular profiles of adult astrocytes from the olfactory. We performed RNA-sequencing on wildtype and Sox9 knockout (KO) astrocytes from the olfactory bulb and analyzed the molecular signatures of Sox9 KO astrocytes compared to the wildtype control.

2021-07-28 | GSE180841 | GEO

RNA-seq investigating the influence of astrocytes on developing cortical neurons

Project description:Astrocytes are implicated in neuronal development, particularly excitatory synaptogenesis, but their genome-wide impact is unclear. Using cell-type specific RNA-seq we show that cortical astrocytes induce widespread transcriptomic changes in developing cortical neurons. Rat cortical neurons were maintained in the presence or absence of mouse astrocytes, RNA-seq performed, and mixed-species RNA-seq reads sorted according to species. Cultures were also treated with TTX to abolish neuronal firing activity, to investigate the effects of the presence or absence activity-dependent signalling.

2024-05-14 | E-MTAB-14070 | biostudies-arrayexpress

GNPS - Human NVU - Cortical Astrocytes

Project description:Cortical human fetal astrocytes, density 8-15000 cells/cm2 ( ScienCell, San Diego, CA, USA) seeded in Astrocyte medium (ScienCell, San Diego, CA, USA). Further info in "Proteomic and metabolomic characterization of human neurovascular unit cells in response to methamphetamine" Herland et al Adv Biosystems 2020

2020-07-23 | MSV000085817 | GNPS

ChIP-seq investigating the influence of astrocytes on the epigenetic landscape of developing cortical neurons

Project description:Astrocytes are implicated in neuronal development, particularly excitatory synaptogenesis, but their genome-wide impact is unclear. Using cell-type specific ChIP-seq we show that cortical astrocytes induce widespread changes in developing cortical neurons in histone marks associated with active open chromatin and repressed/condensed chromatin. Rat cortical neurons were maintained in the presence or absence of mouse astrocytes, ChIP-seq performed, and mixed-species ChIP-seq reads sorted according to species.

2024-05-16 | E-MTAB-14081 | biostudies-arrayexpress

A single-cell transcriptomic dataset of pluripotent stem cell-derived astrocytes via NFIB/SOX9 overexpression

Project description:Astrocytes, the predominant glial cells in the central nervous system, play essential roles in maintaining brain function. Reprogramming induced pluripotent stem cells (iPSCs) to become astrocytes through overexpression of the transcription factors, NFIB and SOX9, is a rapid and efficient approach for studying human neurological diseases and identifying therapeutic targets. However, the precise differentiation path and molecular signatures of induced astrocytes remain incompletely understood. Accordingly, we performed single-cell RNA sequencing analysis on 64,736 cells to establish a comprehensive atlas of NFIB/SOX9-directed astrocyte differentiation from human iPSCs. Our dataset provides detailed information about the path of astrocyte differentiation, highlighting the stepwise molecular changes that occur throughout the differentiation process. This dataset serves as a valuable reference for dissecting uncharacterized transcriptomic features of NFIB/SOX9-induced astrocytes and investigating lineage progression during astrocyte differentiation. Moreover, these findings pave the way for future studies on neurological diseases using the NFIB/SOX9-induced astrocyte model.

2024-06-15 | GSE245169 | GEO

Transcriptional targets of Trps1 in vibrissae

Project description:Mutations in TRPS1 cause trichorhinophalangeal syndrome types I and III, which are characterized by sparse scalp hair in addition to craniofacial and skeletal abnormalities. Trps1 is a vertebrate transcription factor containing nine zinc-finger domains, including a GATA-type zinc finger through which it binds DNA. Mice in which the GATA domain of Trps1 has been deleted (Trps1∆gt/∆gt) have a reduced number of pelage follicles and lack vibrissae follicles postnatally. To identify the transcriptional targets of Trps1 in the developing vibrissa follicle, we performed microarray hybridization analysis comparing expression patterns in the whisker pads of wild-type versus Trps1∆gt/∆gt embryos. We identified a number of transcription factors and Wnt inhibitors among transcripts downregulated in the mutant embryos, and several extracellular matrix proteins there were upregulated in the mutant samples. Whole whisker pads were dissected from E12.5 embryos and total RNA was isolated using the RNeasy Mini Kit (Qiagen). Triplicate RNA samples from three independent embryos of each genotype were amplified and labeled for hybridization to Affymetrix GeneChip MOE430A microarrays using Affymetrix reagents and protocols. The data output was analyzed using GeneSpring GX 10.0 commercial software (Agilent Technologies). P-values were calculated using an unpaired t-test. Expression values with a p-value less than or equal to 0.05 and a fold difference of at least 1.5 relative to wild-type baseline expression levels were considered significant.

2011-12-22 | E-GEOD-33766 | biostudies-arrayexpress

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