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SRP102493
Danio rerio
17 Downloadable Samples
IlluminaHiSeq2000
Description
Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic, hormonal and environmental factors can influence sexual development. 17 alpha-methyltestosterone (MT), a synthetic androgen, induces female-to-male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all-male populations. However, the molecular mechanisms underlying 17 alpha-methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study, we analysed gonad transcriptomes of zebrafish treated with 17 alpha-methyltestosterone during gonadal development (from 20 dpf to 40 dpf and 60 dpf) and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.
Publication Title
Histological and transcriptomic effects of 17α-methyltestosterone on zebrafish gonad development.
Sample Metadata Fields
No sample metadata fields
View Samples- Danio rerio
- 24 Downloadable Samples
- IlluminaHiSeq2000
Description
During embryogenesis the heart forms as a linear tube that then undergoes multiple simultaneous morphogenetic events to obtain its mature shape. To understand the gene regulatory networks (GRNs) driving this phase of heart development, during which many congenital heart disease malformations likely arise, we conducted an RNA-seq timecourse in zebrafish from 30 hpf to 72 hpf and identified 5861 genes with altered expression. We clustered the genes by temporal expression pattern, identified transcription factor binding motifs enriched in each cluster, and generated a model GRN for the major gene batteries in heart morphogenesis.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Differentiation assays with neural progenitor cells of the enteric nervous system (ENS) showed elongated neurite outgrowth under influence of 3,5,3'-Triiodothyronine (concentrations 50 nm and 100 nm). For analysis, neural cells were stained with TUJ1 (beta-Tubulin III). Microarray analysis should enlighten these results on a genetical basis and give hints about the regulation pathways.
Publication Title
Molecular and cell biological effects of 3,5,3'-triiodothyronine on progenitor cells of the enteric nervous system in vitro.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Postnatal neural progenitors of the enteric nervous system are a potential source for future cell replacement therapies of developmental dysplasia like Hirschsprung's disease. However, little is known about the molecular mechanisms driving the homeostasis and differentiation of this cell pool. In this work, we conducted Affymetrix gene chip experiments to identify differences in gene regulation between proliferation and early differentiation of enteric neural progenitors. We detected a total of 1333 regulated genes that were linked to different groups of cellular mechanisms involved in cell cycle, apoptosis, neural proliferation, and differentiation. As expected, we found a strong inhibition of cell cycle progression as well as an enhanced expression of neuronal and glial markers. We further found a marked inactivation of the canonical Wnt pathway during the beginning of cellular differentiation. Taken together, this data illustrated the various mechanisms taking place during the proliferation and early differentiation of enteric neural progenitor cells.
Publication Title
Comparative Microarray Analysis of Proliferating and Differentiating Murine ENS Progenitor Cells.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
The ventrolateral hypothalamic parvafox (formerly called PV1-Foxb1) nucleus is an anatomical entity of recent discovery and unknown function. With a view to gaining an insight into its putative functional role(s), we conducted a gene-microarray analysis.
Publication Title
Parvalbumin-Neurons of the Ventrolateral Hypothalamic Parvafox Nucleus Receive a Glycinergic Input: A Gene-Microarray Study.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
Masseter and Tibialis anterior muscles from adult female control mice to determine expression differences between muscle groups
Publication Title
Expression profiling reveals heightened apoptosis and supports fiber size economy in the murine muscles of mastication.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 42 Downloadable Samples
- Illumina HiSeq 1500
Description
Nuclear reprogramming is an inefficient process with only a small proportion of cells successful converting into induced pluripotent stem (iPS) cells. However, in order to molecularly understand the process these rare intermediates need to be identified and isolated for profiling. In the context of this project we purified the rare reprogramming for three cell types (Fibroblasts, Neutrophils and Keratinocytes) by fluorescent activated cell sorting and submitted them, together with the resulting iPS cells, to RNA sequencing.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Cell line
View Samples- Mus musculus
- 25 Downloadable Samples
- Affymetrix Mouse Gene 1.1 ST Array (mogene11st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Lhx5 controls mamillary differentiation in the developing hypothalamus of the mouse.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 25 Downloadable Samples
- Affymetrix Mouse Gene 1.1 ST Array (mogene11st)
Description
Lhx5 mutant mouse embryos show loss of a neuronal nucleus of the brain called the mamillary body and essential for the formation of memories. We wanted to identify the genes that are responsible for the normal development of the mammillary body.
Publication Title
Lhx5 controls mamillary differentiation in the developing hypothalamus of the mouse.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 15 Downloadable Samples
- Illumina HiSeq 2000
Description
The isolation of pure populations of mouse intestinal stem cells (ISCs) is essential to facilitate functional studies of tissue homeostasis, tissue regeneration and intestinal diseases. However, the purification of ISCs has relied predominantly on the use of transgenic reporter alleles in mice. Here, we introduce a new combinational cell surface marker mediated strategy that allows the isolation of an ISC population transcriptionally and functionally equivalent to the gold standard Lgr5-GFP ISCs. We tested the ability of three cell surface marker mediated isolated strategies (termed SM2, SM4 and SM6 according to the number of key cell surface markers used) to purify ISCs and transcriptionally compared them to established standards, Lgr5-GFP high cells and cells negative for any ISC markers (Negative). The best cell surface marker mediated strategy (SM6) allowed the isolation of ISCs from reporter free mice (SM6-WT) that were functionally and transcriptionally distinct from cells isolated from transgenic mice (SM6-TG) due to Lgr5 haploinsufficiency. Overall design: To adequately benchmark the quality of our method with the existing methods, we performed first RNA sequencing with the Lgr5-GFP strain (C57/Bl6 background) on 5 FACS purified groups: SM2, SM4, SM6, Lgr5-GFPhigh reference population and cells negative or low for all of the cell surface markers used. We also performed RNA sequencing of SM6-TG and SM6-WT cells to investigate in detail potential transcriptional differences between them.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Cell line
View Samples