GEO DataSets

(Submitter supplied) The goals of this study are to compare transcriptome profiling (mRNA level) and singnaling pathways between slc30a1 mutant zebrafish and their siblings. We found pathways in cell differentiation and migration were different between these two groups, and the stem markers of nueral crest progenitors were upregulated in mutants.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

8 Samples

Download data: TXT

(Submitter supplied) Analyses of the effect of CRISPR/CAS9 mediated knock out of the EMT-transcription factor SNAI2 on the mRNA expression profile of human neuroblastoma SH-SY5Y cells to identify genes that are differentially expressed upon loss of SNAI2. Results provide insight into genes that are repressed by SNAI2 in neuroblastoma cells under normal culture conditions, where loss of SNAI2 enhances the expression of genes involved in biological processes such as neuron development and neuron differentiation.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

9 Samples

Download data: TXT

(Submitter supplied) Bone marrow (BM) mesenchymal stem and progenitor cells (MSPCs) are a critical constituent of the hematopoietic stem cell (HSC) niche. Previous studies have suggested that the zinc-finger epithelial-mesenchymal transition transcription factor Snai2 (also known as Slug) regulated HSCs autonomously. Here, we show that Snai2 expression in the BM is restricted to the BM stromal compartment where it regulates the HSC niche. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: TXT

(Submitter supplied) The specification of cartilage requires Sox9, a transcription factor with broad roles for organogenesis outside the skeletal system. How Sox9 gains selective access to cartilage-specific cis-regulatory regions during skeletal development had remained unclear. By analyzing chromatin accessibility during the differentiation of neural crest cells into chondrocytes of the zebrafish head, we find that cartilage-associated chromatin accessibility is dynamically established. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25922

16 Samples

Download data: NARROWPEAK

(Submitter supplied) Craniofacial development depends on cell-cell interactions, coordinated cellular movement and differentiation under the control of regulatory gene networks, which include the distal-less (Dlx) gene family. However, the functional significance of Dlx5 in patterning the oropharyngeal region has remained unknown. Here we show that loss of Dlx5 leads to a shortened soft palate and an absence of the levator veli palatini, palatopharyngeus, and palatoglossus muscles that are derived from the 4th pharyngeal arch (PA), but the tensor veli palatini, derived from the 1st PA, is unaffected. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: TXT

(Submitter supplied) We report the ChIP-Seq results of SNAI2 in several different conditions which include: SNAI2 binding in both control and SNAI2 knockdown cells to demonstrate specificity of the binding. SNAI2 ChIP-Seq was also performed in SNAI2 or control LACZ overexpressing cells cultured in growth medium as well as LACZ or SNAI2 overexpressing cells in differentiation medium.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

18 Samples

Download data: TXT

(Submitter supplied) 1. Keratinocytes infected with retroviruses expressing control or SNAI2 shRNAs were cultured in growth medium and Affymetrix HG-U133 plus 2.0 arrays were used to determine global gene expression profiles. 2. Keratinocytes infected with retroviruses overexpressing LACZ or SNAI2 were cultured in growth medium and Affymetrix HG-U133 plus 2.0 arrays were used to determine global gene expression profiles.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

8 Samples

Download data: CEL, CHP

(Submitter supplied) CRISPR/Cas9-mediated ablation of two Alas2 intronic cis-elements in G1E-ER-GATA1 cells strongly reduced GATA-1-induced Alas2 transcription, heme biosynthesis, and GATA-1 regulation of other vital constituents of the erythroid cell transcriptome. Bypassing Alas2 function in Alas2 cis-element-mutant (double mutant) cells by providing its catalytic product 5-aminolevulinic acid (5-ALA) rescued heme biosynthesis and a subset of GATA-1-dependent genetic network. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

18 Samples

Download data: BW

(Submitter supplied) Analysis of the effect of shRNA-mediated knockdown of TRPM7 on gene expression levels in SH-SY5Y and SH-EP2 human neuroblastoma cells. Results were used for the identification of neural-crest-associated transcription factors that were affected by TRPM7 knockdown.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10904

8 Samples

Download data: TXT

(Submitter supplied) Distinct shaping of the upper versus lower facial skeleton is essential for function of the vertebrate jaw and middle ear, yet the cellular mechanisms by which this occurs have remained unclear. Here, we show that Endothelin1 (Edn1) signaling accelerates mesenchymal condensation and subsequent cartilage formation in the lower face through antagonism of Jagged-Notch signaling and Prrx1 transcription factors. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20828 GPL14875

13 Samples

Download data: CSV

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

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18413 GPL24995

13 Samples

Download data

(Submitter supplied) We have performed single-cell RNA-seq of cranial NC cells in zebrafish over several stages during their migration

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

7 Samples

Download data: CSV

(Submitter supplied) The purpose of this study was to obtain an unbiased list of wnt-regulated genes in zebrafish neural crest.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

6 Samples

Download data: TXT

(Submitter supplied) Investigation of the transcriptional profile of TGF-β1-induced EMT in HaCaT cells.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL21185

2 Samples

Download data: TXT

(Submitter supplied) Investigation of the transcriptional profile of SNAI2-overexpressing HaCaT cells.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL21185

2 Samples

Download data: TXT

(Submitter supplied) We analyzed, by HTA 2.0, colorectal adenocarcinoma samples and matched normal colonic tissues in order to determine the whole transcriptome expression levels. Three widely used colorectal cancer cell lines were also analyzed. Results provided insights into the regulation, at transcript level, of genes involved in copper homeostasis.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

15 Samples

Download data: CEL, CHP

(Submitter supplied) We analyzed, by HTA 2.0, colorectal adenocarcinoma samples and matched normal colonic tissues in order to determine the whole transcriptome expression levels. Three widely used colorectal cancer cell lines (Caco-2, HT-29,HCT-116), one human breast adenocarcinoma cell line (MCF-7) and one human prostate adenocarcinoma cell line (PC3) were also analyzed. Results provided insights into the regulation, at transcript level, of genes involved in copper homeostasis.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

96 Samples

Download data: CEL, CHP

(Submitter supplied) The neural crest (NC) is a transient embryonic stem cell population characterised by its multipotency and broad developmental potential. Here, we perform NC-specific transcriptional and epigenomic profiling of foxd3-mutant versus wild-type cells in vivo to define the gene regulatory circuits controlling NC specification. Together with global binding analysis obtained by foxd3 biotin-ChIP and single cell profiles of foxd3-expressing premigratory NC, our analysis shows that during early steps of NC formation, foxd3 acts globally as a pioneer factor to prime the onset of genes regulating NC specification and migration by re-arranging the chromatin landscape, opening cis-regulatory elements and reshuffling nucleosomes. more...

Organism:

Danio rerio

Type:

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

Platforms:

GPL20828 GPL18413 GPL14875

151 Samples

Download data: BED, BW, TXT, WIG