GEO DataSets

(Submitter supplied) Diversity of cortical radial glia cells (RGCs) and their complex relationships to generate neurons in species with expanded germinal zones and a folded cortex, remains unclear. We used TrackerSeq, a technique that integrates DNA barcodes into the genome of electroporated RGCs, to identify the distinct cell lineages that shape ferret cortex.

Organism:

Mustela putorius furo

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28629

8 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) Cortical neurogenesis follows a simple lineage: apical Radial Glia Cells (RGC) generate basal progenitors, and these produce neurons. How this occurs in species with expanded germinal zones and a folded cortex, like human, remains unclear. We used single-cell RNA sequencing from individual cortical germinal zones in ferret, and barcoded lineage tracking, to determine the molecular diversity of progenitor cells and their lineages. more...

Organism:

Mustela putorius; Mustela putorius furo

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28629 GPL32908

26 Samples

Download data: MTX, TSV

(Submitter supplied) Diversity of cortical radial glia cells (RGCs) and their complex relationships to generate neurons in species with expanded germinal zones and a folded cortex, remains unclear. We used single-cell RNA sequencing (scRNA-seq) of microdissected cortical germinal layers (ventricular zone (VZ) and outer subventricular zone (OSVZ)), from two cortical regions (splenial gyrus (SG) and neighboring lateral sulcus (LS)) at two critical time points for ferret cortex development (embryonic day (E) 34 and postnatal day (P) 1) to distinguish the molecular diversity of progenitors and newborn neurons, and study their transcriptomic trajectories.

Organism:

Mustela putorius

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32908

18 Samples

Download data: MTX, TSV

(Submitter supplied) Our brains accommodate a largely folded cerebral cortex that associates to our advanced brain functions. Several theories have been proposed to explain the cortical folding process, reasoning the mechanical forces as neuronal tension in underlying layers, cellular expansion and glial progenitor’s diversity in the OSVZ; but the mechanistic insights and underlying genomics changes causing the appearance of cortical folds is still illusive. more...

Organism:

Mustela putorius furo

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL28629 GPL25735 GPL28369

49 Samples

Download data: CSV, H5AD, MTX

(Submitter supplied) Gyrencephalic species develop folds in the cerebral cortex in a stereotypic manner, but the genetic mechanisms underlying this unique patterning process are unknown. We present a large-scale transcriptomic analysis of individual germinal layers in the developing cortex of the gyrencephalic ferret, comparing between regions prospective of fold and fissure. We find unique transcriptional signatures in each germinal compartment, indicating that thousands of genes are differentially expressed between regions, including ~80% of genes mutated in human cortical malformations. more...

Organism:

Mustela putorius furo

Type:

Expression profiling by array

Platform:

GPL19111

19 Samples

Download data: TXT

(Submitter supplied) Heterogeneity of meningeal cortical cells was deciphered on the molecular level using single cell RNA seq

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

179 Samples

Download data: CSV

(Submitter supplied) Glial cells distribute extensively in the brain and execute important functions. However, their developmental process and molecular features are still not fully explored in human, especially for fetal astrocytes. It is known that EGFR is involved in glial development and we found that the emergence of EGFR+ cells are near the start of gliogenesis and majority of those co-expressed SOX2 during human cerebral cortex development at midgestation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

41 Samples

Download data: TXT

(Submitter supplied) Conditional deletion of Geminin from the entire hematopoietic compartment using Vav1:iCre mice led to defective hematopoiesis/dyserythropoiesis in E15.5 mouse embryos. The present data set includes data from lineage-negative cells isolated from homogenized livers that were dissected from E15.5.dpc embryos. The two conditions compared were wild-type versus Geminin-KO Lin- cells. The cells were collected from littermates.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

6 Samples

Download data: CEL

(Submitter supplied) As described in our paper "Aspm knockout ferret reveals an evolutionary mechanism governing cerebral cortical size" (Johnson et al., Nature 2018), we used the standard Drop-seq method and analysis of Macosko et al. (2015) to capture, sequence, and analyze mRNA from single cells from Aspm wild-type, heterozygous, and knock-out littermate ferrets at embryonic day 35. Bulk reference samples were processed using standard Illumina mRNA-seq library prep and sequencing protocols, and the samples were described previously (Johnson, Wang et al., Nature Neurosci 2015)

Organism:

Mustela putorius furo

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24172

12 Samples

Download data: TXT

(Submitter supplied) Purpose:To asses changes in gene expression profiles of single cell from the E39 Ferret Cortex. Mouse E18 littermate controls cortex, and Smo CKO (SmoF/F hGFAP-Cre) mice. Methords: E39 ferret cortex, E18 wild type and Smo CKO cortices were carefully dissected under a fluorescent stereoscope, and incubated in 4 ml of papain solution for 20 min at 37℃, The cortical tissues were gently triturated, filtered through a 40 mm strainer, and washed with HBSS to obtain the single cell suspension. more...

Organism:

Mustela putorius furo; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21273 GPL29836

4 Samples

Download data: CSV

(Submitter supplied) A hallmark of cortical evolution is the high dynamic subventricular zone (SVZ) expansion, where basal progenitors (BPs) amplify and neuronal transcriptional programs unfold. How non-coding molecular factors such as microRNAs influence these developmental trajectories and regulate the acquisition of cortical type identities is largely unknown. Here we demonstrate that miR-137 and miR-122 regulate the positioning and identity features of superficial layer cortical neurons by acting at distinct steps of their developmental trajectories. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

2524 Samples

Download data: TSV

(Submitter supplied) The Outer Subventricular Zone (OSVZ) is a germinal layer playing key roles in the development of the neocortex, with particular relevance in gyrencephalic species like human and ferret where it contains abundant basal Radial Glia Cells (bRGCs) that promote cortical expansion. Here we identify a brief period in ferret embryonic development when apical RGCs generate a burst of bRGCs that become founders of the OSVZ. more...

Organism:

Mustela putorius furo

Type:

Expression profiling by array

Platform:

GPL19111

11 Samples

Download data: TXT

(Submitter supplied) Increased cortical size is essential to the enhanced intellectual capacity of primates during mammalian evolution. The mechanisms that control cortical size are largely unknown. Here, we show that mammalian BAF170, a subunit of the chromatin remodeling complex mSWI/SNF, is an intrinsic factor that controls cortical size. We find that the conditional deletion of BAF170 promotes indirect neurogenesis by increasing the pool of intermediate progenitors (IPs) and results in an enlarged cortex, whereas cortex-specific BAF170 over-expression results an opposing phenotype. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

6 Samples

Download data: TXT

(Submitter supplied) Although technological advances now allow increased tumor profiling, a detailed understanding of the mechanisms leading to the development of different cancers remains elusive. Our approach towards understanding the molecular events that lead to cancer is to characterize changes in transcriptional regulatory networks between normal and tumor tissue. Because enhancer activity is thought to be critical in regulating cell fate decisions, we have focused our studies on distal regulatory elements and transcription factors that bind to these elements. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL11154 GPL18573

29 Samples

Download data: TXT

(Submitter supplied) We used massively parallel tagging of progenitors to track clonal relationships and transcriptomic signatures during murine forebrain development. We found several examples of clonal divergence and convergence in both neurons and glia, and examined the processes that led to clonal divergence of GABAergic neurons. Immediately after exiting the cell-cycle, GABAergic neurons originating from the same mitotic progenitor diverged into different trajectories, suggesting that differentiation into subtypes is initiated as a lineage-dependent processes at the progenitor cell level.

Organism:

Mus musculus

Type:

Other

Platforms:

GPL19057 GPL24247

63 Samples

Download data: RDS

(Submitter supplied) Ptf1a has been shown to be necessary for determining an inhibitory interneuronal fate in many regions of the nervous system. In this study, we aim to investigate the sufficiency of Ptf1a to cell-autonomously promote a specific neuronal identity by misexpressing it in developing excitatory cortical pyramidal cells and studying its impact on pyramidal cell features, such as its gene expression profile. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

5 Samples

Download data: TXT

(Submitter supplied) We performed ATAC-seq for microdissected lens epithelium and fiber from E14.5 and P0.5 mouse lenses.Through investigating dynamics of chromatin changes during mouse lens fiber and epithelium differentiation, we identified spatial-temporal differential accessible regions and the enriched known and novel motifs. We also discovered some novel and known enhancers for the transcription factors and structural genes that are important in lens development. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

8 Samples

Download data: NARROWPEAK

(Submitter supplied) The human cerebral cortex depends for its normal development and size on a precisely controlled balance between self-renewal and differentiation of diverse neural progenitor cells. Specialized progenitors that are common in humans, but virtually absent in rodents, called ‘outer radial glia’ (ORG), have been suggested to be crucial to the evolutionary expansion of the human cortex. We combined cell type-specific sorting with transcriptome-wide RNA-sequencing to identify genes enriched in human ORG, including targets of the transcription factor Neurogenin, and previously uncharacterized, evolutionarily dynamic, long noncoding RNAs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

9 Samples

Download data: FPKM_TRACKING

(Submitter supplied) We report the transcriptomes of mouse E12.5 cortical radial glial cells and the changes caused by inhibition of the canonical BMP signalling effectors SMAD1/5, whose expression levels are reduced by 50% in the SmadNes mutants.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: TXT, XLSX

(Submitter supplied) The cerebral cortex is a cellularly-complex structure comprised of a rich diversity of neuronal and glial cell types. Cortical neurons can be broadly categorized into two classes—glutamatergic excitatory neurons and GABAergic inhibitory interneurons. Previous developmental studies in rodents have led to the prevailing model that while excitatory neurons are born from progenitors located in the cortex, cortical interneurons are born from a separate population of progenitors located outside of the developing cortex in the ganglionic eminences1-5. more...

Organism:

Synthetic plasmid

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30924 GPL30925

2 Samples

Download data: TSV