GEO DataSets

(Submitter supplied) The mammalian neocortex comprises an enormous diversity regarding cell types, morphology, and connectivity. In this work, we discover a post-transcriptional mechanism of gene expression regulation, protein translation, as a determinant of cortical neuron identity. We find specific upregulation of protein synthesis in the progenitors of later-born neurons and show that translation rates and concomitantly protein half-lives are inherent features of cortical neuron subtypes. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24247 GPL21103

20 Samples

Download data: CSV

(Submitter supplied) Precise spatiotemporal control of mRNA translation machinery is essential to proper development of highly complex systems like the neocortex. Here, we show that an RNA-binding protein, Hu antigen R (HuR), regulates both neocorticogenesis and specificity of neocortical translation machinery in a developmental stage-dependent manner in mice. Neocortical absence of HuR alters the phosphorylation states of the initiation and elongation factors of the core translation machinery. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

31 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21103 GPL21626

26 Samples

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(Submitter supplied) We perform Ribosome Profiling (Riboseq) analysis of mouse Neuro2a neuronal cultures in Ebp1-siRNA knockdown vs. scrambled-siRNA control conditions in biological triplicate to assess the translation-specific function of Ebp1

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

12 Samples

Download data: TSV

(Submitter supplied) We perform Selective Ribosome Profiling (SeRP) analysis of mouse Neuro2a neuronal cultures with Ebp1-immuno-precipitation in biological duplicate to assess the translation-specific function of Ebp1

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

4 Samples

Download data: CSV

(Submitter supplied) We report the quantification of steady-state mRNA coding for ribosomal proteins, translation-associated proteins, and Ebp1 (Pa2g4) in mouse total neocortex brain lysates at embryonic days 12.5, 14, 15.5, 17 and postnatal day 0

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

10 Samples

Download data: TSV

(Submitter supplied) Neuronal development requires a complex choreography of transcriptional decisions to obtain specific cellular identities. Realizing the ultimate goal of identifying genome-wide signatures that define and drive specific neuronal fates has been hampered by enormous complexity in both time and space during development. Here, we have paired high-throughput purification of pyramidal neuron subclasses with deep profiling of spatiotemporal transcriptional dynamics during corticogenesis to resolve lineage choice decisions. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

24 Samples

Download data: TXT

(Submitter supplied) Intrinsic molecular pathways in the central nervous system dictate neuronal cell fate during development. However, interplay of RNA binding proteins (RBPs) dictating mRNA translation, and their spatiotemporal extracellular regulators in neocortical neural stem cells during neurogenesis are poorly understood. Using an unbiased RNAseq screen of polysomes between early and mid-neurogenesis, we identified functionally related mRNA groups and their isoforms are regulated translationally in prenatal neocortices, including mRNAs encoding RBPs. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

18 Samples

Download data: CSV

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

Organism:

Mus musculus

Type:

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

Platform:

GPL9250

8 Samples

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(Submitter supplied) The goal of the study was to compare gene expression of P0 wild-type and P0 Satb2-/- cortices. Total RNAs were isolated from P0 cortices dissected from wild-type and Satb2-/- mice (n=3 for each genotype), following Qiagen RNAeasy kit instruction.Sequence libraries were made following Illumina RNA TruSeq library preparation guide.The libaries were pair-end sequenced (50nt per end). Differentially expressed genes were identified by DESEQ.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9250

6 Samples

Download data: TXT

(Submitter supplied) The goal of the study was to identify the binding site of SATB2 in wild-ype cortex by performing ChIP-seq using SATB2 antibody. E15 cortical tissues were dissected, lysed and fixed. Chromatin was prepared by sonication. Sequences bound by SATB2 protein was precipitated using a SATB2 antibody. Sequencing was performed on Illumina Genome Analyzer II. SATB2 binding peaks were called using MACS.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9250

2 Samples

Download data: TXT

(Submitter supplied) Using an in vitro model of mouse corticogenesis from mouse embryonic stem cells (ESCs), we investigated the gene expression changes exerted by the inactivation of the Eutherian-specific microRNA miR-541. The microRNA mmu-miR-541-5p was inhibited by the transfection of an antago-miR into ESC-progenitors at 12 days of in vitro differentiation (DIV12) and and the cell transcriptome of transfected cells was compared to the transcriptome of control-transfected cells 5 days after transfection (DIV17). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: CSV

(Submitter supplied) We established an in vitro model of mouse corticogenesis starting from mouse embryonic stem cells (ESCs). We analyzed miRNAomes of dividing and post-mitotic ESC-cortical cells and miRNAomes of E12 and P0 mouse cortex. By comparing the microRNA expression profiles of progenitors and precursors at different times of in vitro differentiation to the microRNA expression profiles of E12 and P0 mouse cortex we validated the model of mouse in vitro corticogenesis and provided microRNA expression datasets of early mouse embryonic cerebral cortex. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16417

25 Samples

Download data: CSV

(Submitter supplied) Neocortical development is spatiotemporally regulated by exogenous factors, but the mechanism regulating timed specificity of neocortical mRNA translation is unknown. We find that active mRNA translation sites (polysomes) contain ribosomal protein subsets that undergo dynamic spatiotemporal rearrangements during mouse neocortical development.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6096

8 Samples

Download data: CEL, CHP

(Submitter supplied) qRT-PCR analysis of mouse brain neocortex during development at embyonic days 12.5, 14, 15.5, 17, and postnatal day 0 in biological duplicate

Organism:

Mus musculus

Type:

Expression profiling by RT-PCR

Platform:

GPL29919

10 Samples

Download data: TXT

(Submitter supplied) We perform Ribosome Profiling (Ribo-seq) analysis of mouse brain neocortex during development embyonic days 12.5, 14, 15.5, 17, and postnatal day 0 in biological duplicate

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL21103

10 Samples

Download data: TSV

(Submitter supplied) Forkhead-box domain (Fox) containing family members are known autism spectrum associated genes. Here we show that, within the developing neocortex, the distinct phospho-states of a single RNA-binding protein, Hu antigen R, dictate mRNA translation and are sufficient to define distinct Foxp-characterized subpopulations of neocortical projection neurons. This demonstrates the importance of HuR phospho-states within the framework of the developing brain and further confirms the role of mRNA translation in autism pathogenesis.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6096

11 Samples

Download data: CEL

(Submitter supplied) Radial glia (RG) in the neocortex sequentially generate distinct subtypes of projection neurons, accounting for the diversity and complex assembly of cortical neural circuits. Mechanisms that drive the rapid and precise temporal progression of RG are beginning to be elucidated. Here we reveal that the RG-specific transcriptional regulator PRDM16 promotes the transition of early to late phase of neurogenesis in the mouse neocortex. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL17021 GPL19057

22 Samples

Download data: BW, XLSX

(Submitter supplied) During CNS development, the nuclear protein SATB2 is expressed in superficial cortical layers and determines projection neuron identity. In the adult CNS, SATB2 is expressed in pyramidal neurons of all cortical layers and is a regulator of synaptic plasticity and long-term memory. Common variation in SATB2 locus confers risk of schizophrenia whereas rare, de novo structural and single nucleotide variants cause severe intellectual disability and absent or limited speech. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

12 Samples

Download data: TXT

(Submitter supplied) We show that the COMPASS family histone methyltransferase co-factor ASH2L is required in NPCs proliferation and upper layer cortical projection neurons production and position. Deletion of ASH2L impairs trimethylation of H3K4 and transcriptional machinery specifically for subsets of Wnt-β-catenin signaling, disrupting their transcription and consequently inhibiting the proliferation ability of NPCs in late stages of neurogenesis.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

6 Samples

Download data: TXT