Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Regulatory elements governing neurogenesis and proliferation in developing human neocortex

ABSTRACT: Non-coding regions compose most of the human genome, yet their functionality is poorly defined. In the developing human neocortex, non-coding regulatory elements tightly regulate expression to direct neural progenitor proliferation and neurogenesis. Here, we define thousands of non-coding elements involved in human neurogenesis by contrasting chromatin accessibility via ATAC-seq from the germinal zone and cortical plate.

ORGANISM(S): Homo sapiens

PROVIDER: GSE95023 | GEO | 2018/01/11

SECONDARY ACCESSION(S): PRJNA375750

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Bulk RNA-seq of the human fetal neocortex, lateral ganglionic eminence and medial ganglionic eminence at 7, 9, 11 and 20 post-conceptional weeks

Project description:Deep transcriptional profiling of the human neocortex, lateral ganglionic eminence (LGE) and medial ganglionic eminences (MGE), from 7 to 20 post-conceptional weeks (pcw), for de novo lincRNAs discovery and to establish a unique coding and non-coding gene signature for the three different regions.

2021-05-13 | E-MTAB-8893 | biostudies-arrayexpress

Chromatin Accessibility in Developing Human Brain

Project description:<p>Non-coding regions comprise most of the human genome and harbor a significant fraction of risk alleles for neuropsychiatric diseases, yet their functions remain poorly defined. We created a high-resolution map of non-coding elements involved in human cortical neurogenesis by contrasting chromatin accessibility and gene expression in the germinal zone and cortical plate of the developing cerebral cortex. To obtain a high resolution depiction of chromatin structure and gene expression in developing human fetal cortex, we dissected the post-conception week (PCW) 15-17 human neocortex into two major anatomical divisions to distinguish between proliferating neural progenitors and post mitotic neurons: (1) GZ: the neural progenitor-enriched region encompassing the ventricular zone (VZ), subventricular zone (SVZ), and intermediate zone (IZ) and (2) CP: the neuron-enriched region containing the subplate (SP), cortical plate (CP), and marginal zone (MZ). Tissues were obtained from three independent donors and three to four technical replicates from each tissue were processed for ATAC-seq to define the landscape of accessible chromatin and RNA-seq for genome-wide gene expression profiling.</p>

| phs001438 | dbGaP

Homo sapiens

Project description:Regulatory elements governing neurogenesis and proliferation in developing human neocortex

| PRJNA375750 | ENA

Alzheimer disease neocortex LC-MSMS

Project description:Alzheimer’s disease (AD) is a progressive neurodegenerative disorder that is pathologically characterized by amyloid β-peptide (Aβ)-containing plaques and the generation of neurofibrillary tangles (NFTs). Although proteome profile changes have been reported in AD brains, it is unclear whether they represent a continuous process from mild to severe changes or whether there is a sequence, with step-by-step involvement of proteins. To address this we analyzed neocortex samples of 19 control cases without signs of neurodegeneration (nonAD), 17 pathologically-diagnosed preclinical AD (p-preAD), and 17 symptomatic AD cases by mass spectrometry after homogenization and separation into soluble, dispersible, membrane-associated, and plaque-associated fractions. Here, we show three classes of proteins exhibiting changed levels during the pathogenesis and progression of AD from the AD pathology-free to the symptomatic stage: five early- and 24 late-responding proteins and 17 gradually changing proteins. The identified proteins and hierarchy point to endocytosis/synaptic vesicle cycle-related processes as key elements in the initiation of AD pathology in the neocortex, while later changes document the resulting neurodegenerative process.

2021-06-21 | PXD020020 | Pride

Human temporal neocortex brain LC-MS

Project description:We used label-free shotgun mass spectrometry to analyze temporal neocortex samples from AD brain, other neurological disorders and non-demented controls, in order to identify additional proteins thatare altered in AD. The mass spectrometry results were then verified by antibody suspension bead arrays.

2016-09-29 | PXD004499 | Pride

Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion

Project description:The evolutionary expansion of the human neocortex reflects increased amplification of basal progenitors in the subventricular zone, producing more neurons during fetal corticogenesis. Here, we analyze the transcriptomes of distinct progenitor subpopulations isolated by a novel approach from developing mouse and human neocortex. We identify 56 genes preferentially expressed in human apical and basal radial glia that lack mouse orthologs. Among these, ARHGAP11B has the highest degree of radial glia-specific expression. ARHGAP11B arose from partial duplication of the Rho GTPase-activating-protein–encoding ARHGAP11A on the human lineage after separation from the chimpanzee lineage. Expression of ARHGAP11B in embryonic mouse neocortex promotes basal progenitor generation and self-renewal, and can increase cortical plate area and induce gyrification. Hence, ARHGAP11B may have contributed to evolutionary expansion of human neocortex. Gene expression profiles of mouse and human purified neocortical progenitor types and neurons were generated by RNA-seq and analyzed including inter- and intra-species comparison.

2015-03-02 | E-GEOD-65000 | biostudies-arrayexpress

RNA-Seq analysis of total mouse neocortex during development

Project description: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

2021-03-23 | GSE136199 | GEO

SRSF10 regulates proliferation of neural progenitor cells and affects neurogenesis in the developing mouse neocortex

Project description:To identify the potential functions of SRSF10 in neural progenitor cells and neocortex development, we constructed SRSF10 flox/flox mice, and conditionally knock out the SRSF10 in the neural progenitor cells by breeding with Nestin-Cre mice.

2023-05-30 | GSE225647 | GEO

Temporal neocortex mesial temporal lobe epilepsy

Project description:Ion channel splice array data collected from temporal neocortex brain tissue collected from patients with mesial temporal lobe epilepsy. Temporal cortex samples from control subjects were compared to temporal neocortex of patients with mesial temporal lobe epilepsy

2010-06-11 | E-GEOD-6773 | biostudies-arrayexpress

Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion

2015-03-02 | GSE65000 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data