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Mus musculus
47 Downloadable Samples
Affymetrix Mouse Gene 2.1 ST Array (mogene21st)
Description
Expression data from 4T1 subclones derived from mammary fat pad tumors (MFP), axillary lymph node tumors (AxLN), and axillary lymph node-derived lung metastases (AxLN-LuM). In parallel, expression data, in the same subclones, of tail vein-derived (TV) lung metastases.
Publication Title
Histone deacetylase 11 inhibition promotes breast cancer metastasis from lymph nodes.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 60 Downloadable Samples
Illumina HiSeq 2500
Description
Background and Purpose—Analyzing genes involved in development and rupture of intracranial aneurysms can enhance knowledge about the pathogenesis of aneurysms, and identify new treatment strategies. We compared gene expression between ruptured and unruptured aneurysms and control intracranial arteries. Methods—We determined expression levels with RNA sequencing. Applying a multivariate negative binomial model, we identified genes that were differentially expressed between 44 aneurysms and 16 control arteries, and between 22 ruptured and 21 unruptured aneurysms. The differential expression of 8 relevant and highly significant genes was validated using digital polymerase chain reaction. Pathway analysis was used to identify enriched pathways. We also analyzed genes with an extreme pattern of differential expression: only expressed in 1 condition without any expression in the other. Results—We found 229 differentially expressed genes in aneurysms versus controls and 1489 in ruptured versus unruptured aneurysms. The differential expression of all 8 genes selected for digital polymerase chain reaction validation was confirmed. Extracellular matrix pathways were enriched in aneurysms versus controls, whereas pathways involved in immune response and the lysosome pathway were enriched in ruptured versus unruptured aneurysms. Immunoglobulin genes were expressed in aneurysms, but showed no expression in controls. Conclusions—For rupture of intracranial aneurysms, we identified the lysosome pathway as a new pathway and found further evidence for the role of the immune response. Our results also point toward a role for immunoglobulins in the pathogenesis of aneurysms. Immune-modifying drugs are, therefore, interesting candidate treatment strategies in the prevention of aneurysm development and rupture. Overall design: RNA sequencing of 44 intracranial aneurysm samples (including 21 unruptured, 22 ruptured and 1 undetermined) and 16 control samples of the intracranial cortical artery
Publication Title
RNA Sequencing Analysis of Intracranial Aneurysm Walls Reveals Involvement of Lysosomes and Immunoglobulins in Rupture.
Sample Metadata Fields
Sex, Age, Subject
View Samples- Mus musculus
- 34 Downloadable Samples
- Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
The goal of this study was to identify the transcriptional mechanisms involved in the activation of the immune system by QS-21, a triterpene glycoside purified from the bark of Quillaja saponaria which has adjuvant activity in vivo. Saponins represent a promising class of vaccine adjuvant. Together with the TLR4-ligand MPL, QS-21 is part of the Adjuvant System AS01, a key component of the Malaria and Zoster candidate vaccines that display demonstrated clinical efficacy. However, the mechanism of action of QS-21 in this liposomal formulation is poorly understood. Upon intra-muscular immunisation, we observed that QS-21 rapidly accumulated in CD169+ resident macrophages of the draining lymph node where it elicited a local innate immune response. Depletion of these cells abrogated QS-21-mediated innate cell recruitment to the lymph node, dendritic cell (DC) phenotypic maturation as well as the adjuvant effect on T cell and antibody responses to co-administered antigens. DCs rather than lymph node-resident macrophages were directly involved in T cell priming by QS-21 as revealed by the decrease in antigen-specific T cell response in Batf3/ mice. Further analysis showed that the adjuvant effect of QS-21 depended on the integration of Caspase-1 and MyD88 pathways, at least in part through the local release of HMGB1. Taken together, this work unravels the key role of lymph node sentinel macrophage in controlling the adjuvant effect of a molecule proven to improve vaccine response in humans
Publication Title
Central Role of CD169<sup>+</sup> Lymph Node Resident Macrophages in the Adjuvanticity of the QS-21 Component of AS01.
Sample Metadata Fields
Specimen part
View Samples
GSE82173- Homo sapiens
- 146 Downloadable Samples
Affymetrix HT HG-U133+ PM Array Plate (hthgu133pluspm), Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Phosphoserine aminotransferase 1 is associated to poor outcome on tamoxifen therapy in recurrent breast cancer.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 128 Downloadable Samples
- Affymetrix HT HG-U133+ PM Array Plate (hthgu133pluspm), Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Expression data were used to predict the activity status of diverse pathways, which were compared to Tamoxifen response
Publication Title
Phosphoserine aminotransferase 1 is associated to poor outcome on tamoxifen therapy in recurrent breast cancer.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 18 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Expression data were used to predict the activity status of diverse pathways, which were compared to Tamoxifen response
Publication Title
Phosphoserine aminotransferase 1 is associated to poor outcome on tamoxifen therapy in recurrent breast cancer.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
FoxO6 is expressed in the brain, craniofacial region and somite, but the precise role of FoxO6 in craniofacial development remain unknown. We found that FoxO6 is expressed specifically in craniofacial tissues and FoxO6-/- mice undergo expansion of the face, frontal cortex, olfactory component and skull.
Publication Title
FoxO6 regulates Hippo signaling and growth of the craniofacial complex.
Sample Metadata Fields
Specimen part
View Samples SRP043544- Mus musculus
- 9 Downloadable Samples
- Illumina HiSeq 2000
Description
This experiment seeks to ascertain the transcriptional changes in the adult mouse hippocampus (CA1 subregion) that occur following viral knockdown of the histone variant H2A.Z. We are especially interested in understanding the role of this histone variant in memory formation and memory maintenance in the adult central nervous system. Overall design: This experiment includes 3 groups, each with 3 biological replicates. Samples S108, S109, and S110 are from controls infected with an AAV expressing a scrambled shRNA control. Samples A100, A101, A102, A104, A106, and A107 were infected with an AAV expressing an shRNA against H2A.Z. Samples A100, A101, and A102 were naive animals, whereas samples A104, A106, and A107 were trained in contextual fear conditioning.
Publication Title
Histone H2A.Z subunit exchange controls consolidation of recent and remote memory.
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