Multiomic sequencing of the MGE
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ABSTRACT:
PROVIDER: PRJNA693284 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Single-cell multiomic sequencing (RNA+ATAC in the same cells) of the E13.5 medial ganglionic eminence (MGE).
2021-09-22 | GSE165114 | GEO
Project description:Purpose: Understand the cues that orchestrate the expansion or differentiation of medial ganglionic eminence (MGE) progenitors no matter in vivo or in vitro. Methods: Total RNA from each sample was used to prepare the library. Then the libraries were sequenced at 50bp single read on an Illumina HiSeq 2500 platform. Sequencing reads from each sample were mapped to the mouse reference genomes mm10 by using TopHat v2.1.1. The mapped reads were further analyzed by cufflinks v1.3.0 and the expression levels for each transcript were quantified as Fragments Per Kilobase of transcript per Million mapped reads (FPKM). For differential expression analysis, sequencing counts at the gene level were obtained using HTSeq v 0.9.1. R package DESeq2 was then used to identify differential expressed genes between different conditions. Results: Transcriptome profiling reveals that ablation of β-catenin in MGE cells leads to advanced neuronal differentiation, while activation of Wnt/β-catenin signaling keeps the MGE cells in an undifferentiated progenitor state. Conclusions: Wnt signaling is a key player in governing self-renewal vs. terminal differentiation of MGE progenitors both in vivo and in vitro.
2021-08-17 | GSE130320 | GEO
Project description:The Otx2 homeobox transcription factor is essential for gastrulation and early neural development. We generated Otx2 conditional knockout (cKO) mice to investigate its roles in telencephalon development after E9.0. We conducted transcriptional profiling and in situ hybridization to identify genes de-regulated in Otx2 cKO ventral forebrain. In parallel, we used ChIP-seq to identify enhancer elements, OTX2 binding motif, and which de-regulated genes are likely direct targets of Otx2 transcriptional regulation. We found that Otx2 was essential in septum specification; regulation of Fgf signaling in the rostral telencephalon; and medial ganglionic eminence (MGE) patterning, neurogenesis, and oligodendrogenesis. Within the MGE, Otx2 was required for ventral but not dorsal identity; this is the first demonstration of a transcription factor that contributes to regional patterning within the MGE. Microdissected subpallium (septum, MGE, and LGE ) from wildtype E12.5 CD-1 embryos was used in three independentanti-OTX2 ChIP-seq experiments.
2015-06-10 | E-GEOD-69724 | biostudies-arrayexpress
Project description:Here, we used joint single-nuclei RNA-sequencing (snRNA-seq) and single-nuclei ATAC sequencing (scATAC) to profile freshly isolated crypts from the human fetal intestine and matched intestinal epithelial only organoids (also known as enteroids) derived from these crypts after one passage of in vitro growth. Organoids were grown in the standard 25% LWRN media with either 100 ng/ml of EGF or 1 ng/ml of EREG added. Fresh crypts were not placed in culture but rather immediately frozen for multiomic processing.
2022-07-16 | E-MTAB-11908 | biostudies-arrayexpress
Project description:Purpose: Understand the cues that orchestrate the expansion or differentiation of medial ganglionic eminence (MGE) progenitors no matter in vivo or in vitro. Methods: Total RNA from each sample was used to prepare the library. Then the libraries were sequenced at 50bp single read on an Illumina HiSeq 2500 platform. Sequencing reads from each sample were mapped to the human reference genomes (hg38 version) by using TopHat v2.1.1. The mapped reads were further analyzed by cufflinks v1.3.0 and the expression levels for each transcript were quantified as Fragments Per Kilobase of transcript per Million mapped reads (FPKM). For differential expression analysis, sequencing counts at the gene level were obtained using HTSeq v 0.9.1. R package DESeq2 was then used to identify differential expressed genes between different conditions.Statistically enriched functional categories of genes were identified using DAVID 6.8. PPI networks were constructed by using STRING v10.0 . Results: Transcriptome profiling reveals that ablation of β-catenin in MGE cells leads to advanced neuronal differentiation, while activation of Wnt/β-catenin signaling keeps the MGE cells in an undifferentiated progenitor state. Conclusions: Wnt signaling is a key player in governing self-renewal vs terminal differentiation of MGE progenitors both in vivo and in vitro.
2019-06-01 | GSE112714 | GEO
Project description:This study aimed to understand the role of the transcriptional regulator Prdm16 in the development of cortical interneurons in the mouse. Prdm16 was knocked out in cells derived from the medial ganglionic eminence (MGE) by using an Nkx2.1-Cre driver line in combination with a line carrying floxed Prdm16 alleles and with a Cre-dependent tdTomato reporter line (Ai14). The sequencing data compares the gene expression profiles of dissected MGEs at embryonic day 14 (E14), a stage when cortical interneurons are being generated from MGE progenitors.
2020-10-22 | GSE159728 | GEO
Project description:The Dlx homeodomain transcription factors are implicated in regulating the function of inhibitory GABAergic interneurons; therefore understanding their functions will provide insights into disorders such as epilepsy, mental retardation and autism. Identifying genes that are downstream of Dlx1/2 function and are relevant for the differentiation and survival of GABAergic interneurons. During embryonic development, cortical GABAergic interneurons are generated in the proliferative zone of the medial ganglionic eminence (MGE), from where they migrate to reach their final positions in the cortex. The differentiation of these interneuron precursors is dependent on Dlx genes, as shown by Dlx1/Dlx2 double mutants, which have a block in GABAergic cell differentiation and in cell migration. When interneuron progenitors are isolated from the mutant MGE and growth in culture, they are able to proceed along their differentiation program. However, mutant cells growth in vitro show defects in cell morphogenesis and increased cell apoptosis. We hypothesize that Dlx transcription factors regulate important aspects of GABAergic neuron differentiation such as the formation and growth of axon and dendrites, and the formation of inhibitory synapses. We generated E15.5 mouse embryos that are Dlx1/2 -/- or Dlx1/2 +/?. Genotype was confirmed by PCR. A total of 8 litters were used. For each experiment, we pooled tissue from at least 6 different embryos of the same genotype. We dissected the ventricular and subventricular zones of the MGE (rostral part). This area contains ~1 million of progenitor cells per embryo. We isolated total RNA using the Stratagene RNA Miniprep kit (these samples are called MGE+/ and MGE-/- in our proposal). In addition, we used the same area (ventricular and subventricular zones of the rostral MGE) to perform primary neuronal cultures. Cells were maintained 3 days in vitro. After that, we isolated total RNA using the Stratagene RNA Miniprep kit (samples called primary cells+/ and primary cells-/- in our proposal). We would like to perform gene expression comparison between: 1) MGE+/ and MGE-/-, and 2) primary cells+/ and primary cells-/-.
2008-06-16 | E-GEOD-8311 | biostudies-arrayexpress
Project description:This study used single-cell RNA sequencing to characterize early transcriptional alterations in medial ganglionic eminence (MGE) development caused by mutant huntingtin expression in a Huntington’s disease mouse model. Single-cell transcriptomes were generated from fluorescence-activated cell sorted (FACS) Dlx1-eGFP–positive MGE cells isolated from embryonic day 12.5 (E12.5) BACHD and wild-type control embryos. To control for biological variability, MGE tissue from eight embryos per genotype was collected and pooled into two independent biological replicates per condition, with each replicate consisting of four paired MGEs. Following dissociation and sorting, each replicate was processed independently for single-cell library preparation using the Chromium Next GEM Single Cell 3′ v3.1 platform (10x Genomics). Libraries were sequenced on an Illumina NextSeq 2000, yielding an average depth of approximately 26,000 reads per cell. Single-cell transcriptomic profiling was used to (i) resolve the cellular composition of the E12.5 MGE, (ii) define major progenitor and precursor populations along the MGE neurogenic trajectory, and (iii) assess genotype-dependent transcriptional changes using pseudobulk differential expression approaches. Particular emphasis was placed on basal GABAergic progenitors and postmitotic precursor cells. Together, this scRNA-seq dataset provides a high-resolution framework for interrogating how mutant huntingtin perturbs early progenitor states and downstream lineage programs during ventral telencephalic development, particularly the MGE.
2026-02-15 | GSE316394 | GEO