GEO DataSets

(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) 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) Gene expression profiles of Cep135 wildtype and knockout E14.4 and E11.5 mouse embryonic neocortices. Gene expression profiles of in vitro E14.5 cortices-derived primary neurospheres are also included; in vitro samples listed as "12h" or "24h" depending on the duration of the in vitro culture from NPs isolation for incipient neurosphere formation and RNA isolation for RNAseq.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

24 Samples

Download data: TXT

(Submitter supplied) Here, we performed RNA-seq to analyze the transcriptome changes on Cenpj depletion cortices at E15.5.RNA-Seq correlation test shows the similarity of the expression patterns between Cenpj+/+ and CenpjCKO was high.By comparing gene expression levels in Cenpj+/+ and CenpjCKO samples, GO term analysis of down-regulated genes in E15.5 CenpjCKO samples showed a significant enrichment of terms related to cell cycle, cell migration, neurogenesis, neuron differentiation and axongenesis, while the up-regulated genes were enriched in cell death, cilium assembly.KEGG signaling pathway analysis revealed that the differentially expressed genes are predicted to be involved in Wnt, MAPK, Hippo, AMPK, Notch, etc. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

2 Samples

Download data: XLS

(Submitter supplied) A massively expanded outer subventricular zone (OSVZ) in the primate and human has been proposed for generating majority of neocortical neurons, which consists of basally located radial glia cells. Previous studies with various strategies have tried to recognize genes specifically expressed in those cells; however, the molecular and cellular features of these cells still remain uncertain. By profiling gene expression across single cells isolated from cellular anatomy location and subtype sorting, we identified a primate-specific gene TMEM14B as a novel marker for basally located radial glia. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL16791

46 Samples

Download data: XLSX

(Submitter supplied) The neocortex, the center for higher brain function, first emerged in mammals and has become massively expanded and folded in humans, constituting almost half the volume of the human brain. Primary microcephaly, a developmental disorder in which the brain is smaller than normal at birth, mainly results from there being fewer neurons in the neocortex because of defects in neural progenitor cells (NPCs). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

19 Samples

Download data: TXT

(Submitter supplied) To identify DDX3X-dependent translation targets in the developing mouse cortex, we used E11.5 cortices from both sexes of wildtype and conditional Ddx3x knockout mice (driven by Emx1-Cre). We performed RNAseq and Riboseq on these samples in parallel.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24247

22 Samples

Download data: XLSX

(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) We report that miR3607 controls the embryonic cerebral cortex development by regulating neurogenesis, neuron migration and axon growth in a bCatenin signaling pathway dependent manner.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: TXT

(Submitter supplied) The coordination of cellular behaviors during neurodevelopment is critical for determining the form, function, and size of the central nervous system. Mutations in the vertebrate Abnormal Spindle-Like, Microcephaly Associated (ASPM) gene and its Drosophila melanogaster ortholog abnormal spindle (asp) lead to microcephaly, a reduction in overall brain size whose etiology remains poorly defined. Here we provide the neurodevelopmental transcriptional landscape for a Drosophila model for autosomal recessive primary microcephaly-5 (MCPH5) and extend our findings into the functional realm to identify the key cellular mechanisms responsible for Asp-dependent brain growth and development. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25244

36 Samples

Download data: TXT

(Submitter supplied) Organoid transcriptomes were mapped onto brain development trajectories using bulk RNA sequencing (RNAseq) at seven successive developmental times from day-17 (2 weeks) today-158 (11 weeks)

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

21 Samples

Download data: CSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

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

Platforms:

GPL9250 GPL1261

15 Samples

Download data: BEDGRAPH, CEL, EXP

(Submitter supplied) The progression from stem cell to differentiated neuron is associated with extensive chromatin remodeling that controls gene expression, but the mechanisms that connect chromatin to gene expression are not well defined. Here we show that mutation of ZNF335 causes severe human microcephaly ("small brain"), small somatic size, and neonatal death. Germline Znf335 null mutations are embryonically lethal in mice, whereas RNA-interference studies and postmortem human studies show that Znf335 is essential for neural progenitor self-renewal, neurogenesis, and neuronal differentiation. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9250

3 Samples

Download data: BEDGRAPH

(Submitter supplied) The progression from stem cell to differentiated neuron is associated with extensive chromatin remodeling that controls gene expression, but the mechanisms that connect chromatin to gene expression are not well defined. Here we show that mutation of ZNF335 causes severe human microcephaly ("small brain"), small somatic size, and neonatal death. Germline Znf335 null mutations are embryonically lethal in mice, whereas RNA-interference studies and postmortem human studies show that Znf335 is essential for neural progenitor self-renewal, neurogenesis, and neuronal differentiation. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

12 Samples

Download data: CEL, EXP

(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 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) 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 GPL28369 GPL25735

49 Samples

Download data: CSV, H5AD, MTX

(Submitter supplied) Cerebral organoids exhibit broad regional heterogeneity accompanied by limited cortical cellular diversity under a variety of derivation methods, suggesting inadequate patterning of early neural stem cell (NSC) starting populations. Here we show that a short combined Dual SMAD/WNT inhibition course during early organoid establishment is sufficient for yielding robust and lasting cortical identity with efficient suppression of non-cortical fates in organoid NSCs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL24676

70 Samples

Download data: TXT, XLSX

(Submitter supplied) The cerebral cortex is a pivotal structure that is integral to advanced brain functions within the mammalian central nervous system. Patterns of DNA methylation and hydroxymethylation play important roles in regulating cerebral cortex development. However, it remains unclear whether abnormal cerebral cortex development, such as microcephaly, could rescale the epigenetic landscape, potentially contributing to dysregulated gene expression during brain development. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL17021

36 Samples

Download data: COV