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GSE6741
Pseudomonas aeruginosa
8 Downloadable Samples
Affymetrix Pseudomonas aeruginosa Array (paeg1a)
Description
In order to understand how Pseudomonas aeruginosa responds to low oxygen we grew strain PAO1 with 3 different oxygen concentrations: 2%, 0.4% and 0% supplemented with nitrate as an electron acceptor. Gene expression under these conditions was compared to that of cells grown with 20% oxygen.
Publication Title
Responses of Pseudomonas aeruginosa to low oxygen indicate that growth in the cystic fibrosis lung is by aerobic respiration.
Sample Metadata Fields
No sample metadata fields
View Samples- Drosophila melanogaster
- 9 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
Nutrient-responsive oogenesis in Drosophila is a complex and dynamic process regulated, in part, by members of the Pc and Trx complexes. The recent finding that O-GlcNAc Transferase (ogt/sxc) is essential for Pc repression raises the question of whether this nutrient-sensing pathway plays a role in regulating oogenesis. OGT transfers O-GlcNAc to key transcriptional regulators in response to graded levels of the nutrient-derived precursor UDP-GlcNAc; O-GlcNAcase (OGA) catalyzes the removal of O-GlcNAc. Here we produced a null allele of oga (oga1) in Drosophila to examine its in vivo function. We found that oga mutant flies were viable, but that females displayed greatly reduced fecundity. The ovaries from the female OGA knockout exhibited a starvation-like phenotype, even under well-fed conditions. Germline stem cell division was slowed in the germarium of OGA knockout fly ovarioles. Ovaries from the oga1 mutants displayed significantly decreased H3K4 monomethylation in germline stem cells. The Trithorax family members Trx and Ash1 and Compass member Set1 histone methyltransferases are O-GlcNAc modified in oga1 mutant ovaries. Our results suggest that the loss of OGA disrupts oogenesis at least in part by interfering with H3K4 monomethylation in germ cells in the ovary. The findings also suggest that O-GlcNAc cycling is an essential part of the nutrient-responsive epigenetic machinery regulating Drosophila oogenesis in response to a changing nutrient supply.
Publication Title
Drosophila O-GlcNAcase Deletion Globally Perturbs Chromatin O-GlcNAcylation.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Single O-GlcNAc modification orchestrate by O-GlcNAc Transferase (OGT) and O-GlcNAcase (OGA alias MGEA5) enzymes, affects signal transduction and gene expression by chromatin modulation. We developed Oga deleted MEF (mouse embryonic fibroblast) cells to investigate effects of O-GlcNAc modification in mice. RNA isolated from Mouse Embryonic Fibroblast cells generated from Oga Knock out (KO) Heterozygous (Het) and wild type (WT) cells and subjected to microarray analysis.
Publication Title
Conditional knock-out reveals a requirement for O-linked N-Acetylglucosaminase (O-GlcNAcase) in metabolic homeostasis.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 38 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Cutaneous squamous cell carcinoma (cSCC) is one of the most common malignancies in fair skinned populations worldwide and its incidence is increasing. Despite previous observations of multiple genetic abnormalities in cSCC, the oncogenic process remains elusive. The purpose of this study was to investigate the transcriptomes of cSCC and actinic keratoses (AK), to elucidate key differences between precursor AK lesions and invasive carcinoma.
Publication Title
Key differences identified between actinic keratosis and cutaneous squamous cell carcinoma by transcriptome profiling.
Sample Metadata Fields
Sex, Specimen part, Subject
View Samples- Bos taurus
- 1 Downloadable Sample
Illumina Genome Analyzer II
Description
The aim of this study was to identify and quantify microRNAs and other small regulatory RNAs expressed in primary retinal microvascular endothelial cells (RMECs) using deep sequencing. RMECs were isolated, RNA extracted, a small RNA library prepared and deep sequencing performed. A total of 6.8 million reads were mapped to 250 known microRNAs in miRBase (release 16). Several novel microRNAs and multiple new members of the miR-2284/2285 family were detected. Several ~30 nucleotide sno-miRNAs were identified, with the most highly expressed being derived from snoRNA U78. Highly expressed microRNAs previously associated with endothelial cells included miR-126 and miR-378, but the most highly expressed was miR-21, comprising more than one third of all mapped reads. The independence from prior sequence knowledge provided by deep sequencing facilitates analysis of novel microRNAs and other small RNAs. This approach also enables quantitative evaluation of microRNA expression, which has highlighted the predominance of a small number of microRNAs in RMECs. Further characterisation of the functions of the highly expressed microRNAs will provide insights into endothelial biology. Overall design: Single sample of primary cell culture
Publication Title
Deep sequencing reveals predominant expression of miR-21 amongst the small non-coding RNAs in retinal microvascular endothelial cells.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st), Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Chromatinized protein kinase C-θ directly regulates inducible genes in epithelial to mesenchymal transition and breast cancer stem cells.
Sample Metadata Fields
Cell line, Treatment
View Samples- Homo sapiens
- 4 Downloadable Samples
Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Epithelial to mesenchymal transition (EMT) is activated during cancer invasion and metastasis, enriches for cancer stem cells (CSCs), and contributes to therapeutic resistance and disease recurrence. The epithelial cell line MCF7, can be induced to undergo EMT with the induction of PKC by PMA. 5-10% of the resulting cells have a CSC phenotype. This study looks at the transcriptome of these cells and how it differs from cells with a non-CSC phenotype.
Publication Title
Chromatinized protein kinase C-θ directly regulates inducible genes in epithelial to mesenchymal transition and breast cancer stem cells.
Sample Metadata Fields
Cell line, Treatment
View Samples- Mus musculus
- 48 Downloadable Samples
- Illumina HiSeq 2500
Description
Transcriptome profiling of radial glia, intermediate progenitors, and cortical neurons in WT and Prdm16 conditional knock-out (cKO) mouse (Emx1Ires-Cre; Prdm16flox/flox) at embryonic day 15.5. Overall design: Sorting of PAX6+ radial glia, TBR2+ intermediate progenitors and Pax6-TBR2- neurons from WT and Prdm16 cKO embryonic cerebral cortex was followed by library preparation and RNA-seq of 4 biological replicates per cell type and genotype.
Publication Title
The Epigenetic State of PRDM16-Regulated Enhancers in Radial Glia Controls Cortical Neuron Position.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 19 Downloadable Samples
- Illumina HiSeq 2500
Description
Early innate lymphoid progenitors (EILP) have recently been identified in the mouse adult bone marrow as a multipotential progenitor population committed to ILC lineages, but their relationship with other described ILC progenitors is still unclear. In this study, we examine the progenitor-successor relationships between EILP, IL-7R+ common lymphoid progenitors (ALP), and ILC precursors (ILCp). Bioinformatic, phenotypical, functional, and genetic approaches collectively establish EILP as an intermediate progenitor between ALP and ILCp. Our work additionally provides new candidate regulators of ILC development and clearly defines the stage of requirement of transcription factors key for early ILC development. Overall design: transcriptional profiling of early ILC progenitors (EILP, ILCp), and common lymphoid progenitors (ALP) was performed by RNA sequencing
Publication Title
Development and differentiation of early innate lymphoid progenitors.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Membrane estrogen receptor (ER) alpha stimulates AMP kinase to suppress SREBP1 processing and lipids in liver
Publication Title
Estrogen reduces lipid content in the liver exclusively from membrane receptor signaling.
Sample Metadata Fields
Specimen part
View Samples