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GSE110986
Mus musculus
6 Downloadable Samples
Illumina HiSeq 2000, Affymetrix Mouse Gene 1.1 ST Array (mogene11st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Loss of the Hematopoietic Stem Cell Factor GATA2 in the Osteogenic Lineage Impairs Trabecularization and Mechanical Strength of Bone.
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 6 Downloadable Samples
Affymetrix Mouse Gene 1.1 ST Array (mogene11st)
Description
GATA2 is a transcription factor that is required for hematopoietic stem cell (HSC) differentiation. GATA2 is also expressed in mesenchymal cells and blocks differentiation of both white and brown adipocytes by interfering with C/EBP activity and PPAR expression. By studying genome-wide binding sites of endogenous GATA2 in mesenchymal stem cells (MSC), we discovered a previously unrecognized function of GATA2 in the regulation of skeletal development-related genes. In contrast to hematopoietic stem cells, canonical GATA2 binding motifs in MSCs co-localized with motifs for transcription factors of the FOX and HOX family, known regulators of skeletal development. Consistently, ectopic GATA2 expression in MSCs regulated many osteoblast-related genes. Ectopic GATA2 blocked, whereas GATA2 deletion enhanced differentiation of osteoblastic precursors. GATA2 expression inhibited bone morphogenetic protein (BMP)-2 induced SMAD1/5/8 activity, a pathway that drives osteoblastogenesis. MSC-specific deletion of GATA2 in mice affected both numbers and osteogenic potential of bone-residing precursors without disturbing normal skeletal development. In adult mice, MSC-specific GATA2 deficiency affected trabecular bone structure and its mechanical properties. blood phenotype? In summary, our study identified GATA2 as a novel regulator of osteoblast differentiation and bone morphology, suggesting a role of GATA2 in MSC lineage determination that goes beyond adipocyte differentiation.
Publication Title
Loss of the hematopoietic stem cell factor GATA2 in the osteogenic lineage impairs trabecularization and mechanical strength of bone.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 24 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Global gene experssion study of the HAEC transcriptional response to artificial chlyomicron remnant-like particles (A-CRLPs) prepared with triglycerides extracted from four natural dietary oils: fish, DHASCO, corn and palm oils. We hypothesised that A-CRLPs could differentially regulate HAEC gene expression according to thier triglyceride content. These data provide an important starting point for investigations into the effects of A-CRLPs on endothelial cells, particulary genes involved in redox balance and inflammatory processes.
Publication Title
Endothelial HO-1 induction by model TG-rich lipoproteins is regulated through a NOX4-Nrf2 pathway.
Sample Metadata Fields
Specimen part
View Samples- Hordeum vulgare
- 22 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
Malting is seed germination under strictly controlled environmental conditions. Malting quality is a complex phenotype that combines a large number of interrelated components, each of which shows complex inheritance. Currently, only a few genes involved in determining malting quality have been characterized. This study combined transcript profiling with phenotypic correlations to identify candidate genes for malting quality.
Publication Title
Differentially expressed genes during malting and correlation with malting quality phenotypes in barley (Hordeum vulgare L.).
Sample Metadata Fields
No sample metadata fields
View Samples- Rattus norvegicus
- 128 Downloadable Samples
- IonTorrentProton
Description
The current study employed next-generation RNA sequencing to examine gene expression related to brain aging and cognitive decline. Young and aged rats were trained on a spatial episodic memory task. Hippocampal regions CA1, CA3 and the dentate gyrus (DG) were isolated. Poly-A mRNA was examined using two different platforms, Illumina and Ion Proton. The Illumina platform was used to generate lists of genes that were differentially expressed across regions, ages, and in association with cognitive function. The gene lists were then retested using the Ion Proton platform. The results describe regional differences in gene expression and point to regional differences in vulnerability to aging. Aging was associated with increased expression of immune response related genes, particularly in the dentate gyrus. Finally, for the memory task used, impaired performance of aged animals was linked to the regulation of Ca2+ and synaptic function in region CA1. Overall design: The study contains a total of 10 young (5-6 months) and 24 aged (17-22 months) Fischer 344 male rats which were used to investigate expression patterns associated with aging and behavior. Prior to gene analysis, the animals were characterized on an episodic memory task across two academic institutions to test the reliability of the task (University of Florida: 5 young rats and 13 aged rats; University of Arizona: 5 young rats and 11 aged rats). Following total RNA isolation for the CA1, CA3 and DG regions, next-generation sequencing (NGS) libraries were prepared for two platforms, Illumina and Ion Proton. For both platforms, poly-A selection of mRNA was performed followed by library preparation protocols for each NGS system. In addition, whole transcriptome sequencing in Illumina was also performed using the ribominus method to investigate differential expression of additional RNA species across the hippocampus. This Series includes only the samples examined using the Ion Proton platform.
Publication Title
Hippocampal Transcriptomic Profiles: Subfield Vulnerability to Age and Cognitive Impairment.
Sample Metadata Fields
No sample metadata fields
View Samples- Rattus norvegicus
- 92 Downloadable Samples
- Illumina HiSeq 2500
Description
The current study employed next generation RNA sequencing using two different platforms (Illumina and Ion Proton) to examine gene expression differences related to brain aging, cognitive decline, and hippocampus subregions (CA1, CA3, DG). Young and aged rats were trained on a spatial episodic memory task. The results describe regional differences in gene expression and point to regional differences in vulnerability to aging. Aging was associated with increased expression of immune response related genes, particularly in the dentate gyrus. For the memory task, impaired performance of aged animals was linked to the regulation of Ca2+ and synaptic function in region CA1. Finally, we provided a transcriptomic characterization of the three subregions regardless of age or cognitive status, highlighting and confirming a correspondence between cytoarchitectural boundaries and molecular profiling. Overall design: Male Fisher 344 rats of two ages, young (5-6 months, total n = 10; n = 5 AZ, n = 5 FL) and aged (17-22 months, total n = 24; n = 11 AZ, n = 13 FL) were obtained from National Institute on Aging''s colonies (Taconic, FL; Charles River, AZ). Animals were maintained on a 12:12 hour light/dark schedule, and provided ad libitum access to food and water prior to the set shifting task. The Morris Water Maze test was conducted, and behavioural data were acquired with either Noldus EthoVision computer tracking software (Noldus Information Technology, (Leesburg, VA) in FL or AnyMaze (Wood Dale, IL) in AZ) and included path-length and time in the goal and opposite quadrants. Two weeks following water maze testing, rats were anesthetized with isoflurane (Piramal Healthcare), decapitated and the brain was rapidly removed. The hippocampus was isolated, a 1-2 mm slice was removed from the dorsal hippocampus, and the CA1, CA3 and dentate gyrus (DG) regions were dissected [1, 8]. The collected tissue was immediately frozen in liquid nitrogen and stored in -80ºC until processed.
Publication Title
Hippocampal Transcriptomic Profiles: Subfield Vulnerability to Age and Cognitive Impairment.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 18 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
Staphylococcus aureus produces the cyclic dipeptides tyrvalin and phevalin (aureusimine A and B, respectively).
Publication Title
Phevalin (aureusimine B) production by Staphylococcus aureus biofilm and impacts on human keratinocyte gene expression.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 4 Downloadable Samples
- Illumina HiSeq 2000
Description
Analysis of mouse primary natural killer (NK) cells and NK cells treated with DKK2 for 24 hours.Sequencing of the mRNAs from DKK2-treated primary NK cells in comparison of those from mock-treated cells suggest an alteration in STAT signaling. Overall design: Mouse primary NK cells were isolated from the spleens and cultured in the presence of 50 ng/ml recombinant murine IL-15 for 24 hours. And then NK cells were treated with mock or 200ng/ml DKK2 for another 24 hours before mRNA was isolated and purified by using RNeasy Plus Mini Kit (Qiagen). A total of two groups of Control NK cells and two groups of DKK2-treated NK cells were individually micromanipulated.
Publication Title
DKK2 imparts tumor immunity evasion through β-catenin-independent suppression of cytotoxic immune-cell activation.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Subject
View Samples- Homo sapiens
- 159 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Molecular profiling of 159 lung cancers of different histological subtypes. A primary objective is to identify gene expression differences between histological subtypes. Sample overlap exist with GSE60644
Publication Title
Gene Expression Profiling of Large Cell Lung Cancer Links Transcriptional Phenotypes to the New Histological WHO 2015 Classification.
Sample Metadata Fields
Sex, Age
View Samples- Mus musculus, Homo sapiens
- 75 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a), (ffymetrixgenechipmousegenome4302.0array[cdf:mmentrezg10)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Cross-species transcriptional network analysis defines shared inflammatory responses in murine and human lupus nephritis.
Sample Metadata Fields
Specimen part, Disease, Subject
View Samples