GEO DataSets

(Submitter supplied) Studies in animal models have been fundamental for understanding brain development but only a fraction of these findings have been validated in a human context. Here, we tissue-engineered a model (MiSTR) of human neural tube regionalization based on human embryonic stem cells (hESCs) and microfluidic cell culturing. By exposing differentiating hESCs to a WNT signalling gradient we mimicked early rostro-caudal neural patterning, and with >80% reproducibility generated a coherent tissue with progressive caudalization from forebrain over midbrain to hindbrain, including formation of isthmic organiser characteristics. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL18573

10 Samples

Download data: MTX, TSV

(Submitter supplied) We analyzed scRNA-seq data in human pluripotent stem cells derived neural tube models. This in vitro system recapitulates some key aspects of neural patterning in the entire neural tube, including both brain and SC regions, along both rostral-caudal and dorsal-ventral axes

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: MTX, RDS, TSV

(Submitter supplied) Generation of brain region-specific progenitors from human embryonic stem cells (hESCs) is critical for their application. However, transcriptional regulation of neural regionalization in human embryos is poorly understood. Here, we report that transcription factor SOX21 is required for telencephalic fate specification from hESCs. SOX21 knockout (KO) impairs telencephalic fate specification, concomitant with the activation of diencephalic genes and Wnt signaling. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

38 Samples

Download data: CSV

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL15520 GPL20795

56 Samples

Download data: BW

(Submitter supplied) To understand how SOX21 regulates neural fate specification, we differentiated wild type and SOX21 knockout hESC into neural epithelial cells (NECs) using dual SMAD inhibition protocol. We collected cells at neural differentiation day 5 and performed SOX21 ChIP-seq to investigate the genome-wide binding profiles. Meanwhile, we also carried out b-catenin ChIP-seq in wild type and SOX21 knockout NECs to dissect the role of SOX21 in Wnt signaling inhibition, thus providing important information for the mechanism underlying SOX21's functions in early neural fate specification.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20795

6 Samples

Download data: BW

(Submitter supplied) Generation of brain region-specific progenitors from human embryonic stem cells (hESCs) is critical for their application. However, transcriptional regulation of neural regionalization in human embryos is poorly understood. Here, we report that transcription factor SOX21 is required for telencephalic fate specification from hESCs. SOX21 knockout (KO) impairs telencephalic fate specification, concomitant with the activation of diencephalic genes and Wnt signaling. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20795 GPL15520

12 Samples

Download data: CSV

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

4556 Samples

Download data

(Submitter supplied) Anterior-posterior (A-P) specification of the neural tube involves initial acquisition of anterior fate followed by the induction of posterior characteristics in the primitive anterior neuroectoderm. Several morphogens have been implicated in the regulation of A-P neural patterning; however, our understanding of factors regulating these morphogens remains incomplete. Here we show that the Krüppel-like zinc finger transcription factor GLI-Similar 3 (GLIS3) directs differentiation of human embryonic stem cells into posterior neural progenitor cells in lieu of the default anterior pathway. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL18573 GPL16791

15 Samples

Download data: BW, TXT

(Submitter supplied) NPCs adhesion affinity along the AP axis is under the control of Wnt/RA molecular networks Caudal NPCs express a high amount of ECM genes compare to rostral-NPCs.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16570

6 Samples

Download data: CEL

(Submitter supplied) The neuroectoderm is patterned along a rostral-caudal axis in response to localized factors in the embryo, but exactly how these factors act as positional information for this patterning is not yet fully understood. Here, using the self-organizing properties of mouse embryonic stem cell (ESC), we report that ESC-derived neuroectoderm self-generates a Six3+ rostral and a Irx3+ caudal bipolarized patterning. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

4 Samples

Download data: CEL

(Submitter supplied) To determine the in vivo cellular identity of BMP-treated human embryonic stem cells (hESCs), we performed bulk RNA sequencing data of hESCs under pluripotency and BMP-treated conditions. Our analyses show that BMP-treated hESCs resemble human trophoblast cells in vivo.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: XLSX

(Submitter supplied) The earliest aspects of human embryogenesis remain mysterious. To model patterning events in the human embryo we used colonies of human embryonic stem cells (hESCs) grown on micropatterned substrate and differentiated with BMP4. These recapitulate the embryonic arrangement of the mammalian germ layers and provide an assay to assess the structural and signaling mechanisms patterning the human gastrula. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

4 Samples

Download data: TXT

(Submitter supplied) Identify gene expression patterns of isthmic organizer (IsO) like cells derived from human embryonic stem cells.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10904

6 Samples

Download data: TXT

(Submitter supplied) The post-implantation embryo is subject to extensive growth, morphogenetic changes and lineage decisions that take place in utero and are therefore difficult to deconstruct in vivo. A robust in vitro culture system that mimics post-implantation mouse development would pave the path towards understanding the dynamics of these processes and how they are coupled. Small aggregates of mouse embryonic stem cells (mESCs) can undergo gastrulation-like events and elongation in vitro, resulting in aggregates with gene expression domains that reflect the post-occipital embryo (gastruloids1–3). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19057 GPL24247

20 Samples

Download data: TAR, TSV

(Submitter supplied) RNA-seq transcriptome analysis identified a functional requirement for zebrafish Rfx4 in the developing neural floor plate and roof plate.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

11 Samples

Download data: TXT

(Submitter supplied) Self-elongating neural tube organoids recapitulate key aspects of the morphology, anterior-posterior patterning, neural crest emergence and neural differentiation of mouse embryo in vivo by self-organization. We used single-cell RNA sequencing (scRNA-seq) to analyse the cell types and to reveal the sequence of transcriptional events in the emergence of neural crest cells and neural differentiation.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24247 GPL21103

6 Samples

Download data: MTX, TSV

(Submitter supplied) Here we describe an approach to generate gastruloids that have a more complete antero-posterior development. We used bioengineered hydrogel microwell arrays to promote the robust derivation of mouse ESCs into post-implantation epiblast-like (EPI) aggregates in a reproducible and scalable manner. These EPI aggregates break symmetry and axially elongate without external chemical stimulation. Inhibition of WNT signaling in early stages of development leads to the formation of gastruloids with anterior neural tissues.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

40 Samples

Download data: TSV

(Submitter supplied) Differentiation of hESCs to neural lineages was used as a model for early embryonic brain development in order to assess the effect of their exposure to low (17 mGy) and high (572 mGy) doses of radiation on gene expression. Exposure of hESC to the low dose did not result in changes in gene expression at any of the time points, whereas exposure to the high dose resulted in downregulation of some major neurodifferentiation markers on days 6 and 10. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

26 Samples

Download data: TXT

(Submitter supplied) Thousands of transcriptome data sets are available, but approaches for their use in dynamic cell response modelling are sparse, especially for processes affected simultaneously by two orthogonal influence variables. We approached this problem for neuroepithelial development of human pluripotent stem cell (differentiation variable), in the presence or absence of valproic acid (signaling variable). Using few basic assumptions (sequential differentiation states of cells; discrete on/off states for individual genes in these states), and time-resolved transcriptome data, a comprehensive model of spontaneous and perturbed gene expression dynamics was developed. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

140 Samples

Download data: CEL