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GSE2429
Homo sapiens
2 Downloadable Samples
Affymetrix Human Genome U133A Array (hgu133a)
Description
Fresh Atypical ductal hyperplasia (ADH) tissue collected from breast of a women who either (1) had no prior history of breast cancer and had not developed breast cancer in five years after diagnosis, (2) had cancer before ADH, or had cancer at the time as ADH or developed cancer after ADH diagnosis
Publication Title
Identification of MMP-1 as a putative breast cancer predictive marker by global gene expression analysis.
Sample Metadata Fields
No sample metadata fields
View Samples- Danio rerio
- 6 Downloadable Samples
IlluminaHiSeq2000
Description
The optic vesicle comprises a pool of bi-potential progenitor cells from which the retinal pigment epithelium (RPE) and neural retina fates segregate during ocular morphogenesis. Several transcription factors and signaling pathways have been shown to be important for RPE maintenance and differentiation, but an understanding of the initial fate specification and determination of this ocular cell type is lacking. We show that Yap/Taz-Tead activity is necessary and sufficient for optic vesicle progenitors to adopt RPE identity in zebrafish. A Teadresponsive transgene is expressed within the domain of the optic cup from which RPE arises, and Yap immunoreactivity localizes to the nuclei of prospective RPE cells. yap (yap1) mutants lack a subset of RPE cells and/or exhibit coloboma. Loss of RPE in yap mutants is exacerbated in combination with taz (wwtr1) mutant alleles such that, when Yap and Taz are both absent, optic vesicle progenitor cells completely lose their ability to form RPE. The mechanism of Yap dependent RPE cell type determination is reliant on both nuclear localization of Yap and interaction with a Tead co-factor. In contrast to loss of Yap and Taz, overexpression of either protein within optic vesicle progenitors leads to ectopic pigmentation in a dosagedependent manner. Overall, this study identifies Yap and Taz as key early regulators of RPE genesis and provides a mechanistic framework for understanding the congenital ocular defects of Sveinsson’s chorioretinal atrophy and congenital retinal coloboma. Overall design: 60 pooled eyes from 36 hpf wild type or vsx2:Gal4/dsRed:14xUAS:YapS87A embryos were pooled for one sample. Three wild type and three vsx2:Gal4/dsRed:14xUAS:YapS87A pools were analyzed for RNA.
Publication Title
Yap and Taz regulate retinal pigment epithelial cell fate.
Sample Metadata Fields
No sample metadata fields
View Samples- Triticum aestivum
- 32 Downloadable Samples
- Affymetrix Wheat Genome Array (wheat)
Description
The aim of the experiment is provide a reference dataset for placing wheat grain transcriptome experiments in a developmental context. RNA was isolated from whole grain tissue of replicate wheat cv. Hereward plants at 6, 8, 10, 12, 14, 17, 21, 28, 35 and 42 days after anthesis (daa). Also supplied are array data for grain sampled at 14, 21 and 28 daa under control, hot, dry and hot&dry conditions to illustrate the importance of developmental context in interpretation.
Publication Title
Transcriptome analysis of grain development in hexaploid wheat.
Sample Metadata Fields
Age, Specimen part, Time
View Samples- Gallus gallus
- 9 Downloadable Samples
- Affymetrix Chicken Genome Array (chicken)
Description
We used microarrays to detail the global program of gene expression underlying gonadotropin-releasing hormone (GnRH) generation and delamination from the olfactory placode.
Publication Title
Serotonin Receptor 1A (HTR1A), a Novel Regulator of GnRH Neuronal Migration in Chick Embryo.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 34 Downloadable Samples
- Illumina HiSeq 1500
Description
In mammals, chromosomes are partitioned into megabase-sized topologically associating domains (TADs). TADs can be in either A (active) or B (inactive) subnuclear compartments, which correspond to early (E) and late (L) replicating timing (RT) domains, respectively. Here, we show that RT changes are tightly correlated with A/B compartment changes during mouse embryonic stem cell (mESC) differentiation. A/B compartments changed mostly by a “boundary shift,” frequently causing compartment switching of single TADs, which coincided with or preceded RT changes. Upon differentiation, mESCs acquired an A/B compartment organization that closely resembled EpiSCs (epiblast-derived stem cells), suggesting that accumulation of compartment boundary repositioning eventually led to naïve-to-primed pluripotency transition in A/B compartment organization. We propose that large-scale reorganization of A/B compartments, which is reflected in RT domain reorganization, represents major cell fate changes. Collectively, our data provides valuable insights into the regulatory principles of 3-dimensional (3D) genome organization during early embryonic stages. Overall design: RNA-Seq: 9 cell types, with a total of 34 individual replicates.
Publication Title
Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization.
Sample Metadata Fields
Specimen part, Subject
View Samples- Saccharomyces cerevisiae
- 14 Downloadable Samples
- Affymetrix Yeast Genome S98 Array (ygs98)
Description
Raw expression values (CHP data) for transcriptional profiling of the response of Saccharomyces cerevisiae to challenges with various weak organic acids
Publication Title
Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
A number of inhibitors of chemokine CCL2 and its receptor CCR2 are in development and may find application for treating a range of inflammatory conditions, including autoimmune and viral arthritides. Herein we sought to determine the effect of CCR2 deficiency on arthritis caused by an arthritogenic alphavirus, Chikungunya virus.
Publication Title
CCR2 deficiency promotes exacerbated chronic erosive neutrophil-dominated chikungunya virus arthritis.
Sample Metadata Fields
Sex, Specimen part
View Samples- Staphylococcus aureus
- 11 Downloadable Samples
- Affymetrix S. aureus Genome Array (saureus)
Description
The S. aureus transcriptome was assessed for strains Newman (wild type) and Newman (sarZ) during both exponential (2hr) and early stationary (5hr) cell growth.
Publication Title
A new oxidative sensing and regulation pathway mediated by the MgrA homologue SarZ in Staphylococcus aureus.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Osteoarthritis (OA) is a common degenerative disease of the joint. Data from our lab indicates that Hedgehog (Hh) signaling is activated in human OA and murine models of OA (Lin et al., 2009, Nature Medicine). To identify Hh target genes, microarray analyses were performed to detect changes in gene expression when the Hh pathway was inhibited in human OA cartilage samples.
Publication Title
Regulation of Cholesterol Homeostasis by Hedgehog Signaling in Osteoarthritic Cartilage.
Sample Metadata Fields
Sex, Specimen part, Treatment
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Transcription factor ID2 prevents E proteins from enforcing a naïve T lymphocyte gene program during NK cell development.
Sample Metadata Fields
Specimen part
View Samples