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SRP149576
Mus musculus
43 Downloadable Samples
NextSeq 500
Description
We report the RNA-Seq data of microglia from CK-p25 mice visual cortex Overall design: Summary of mice and treatments included in this series: CK-p25 mice - in which the expression of the Cdk5 activator p25 is driven by the excitatory neuron-specific CaMKIIa promoter in an inducible manner (CaMKIIa promoter- tTA x TetO- p25+GFP) (Cruz et al., 2003). Following withdrawal of doxycycline from the diet, CK-p25 exhibit progressive neuronal and synaptic loss with cognitive impairment, which is severe by 6 weeks of p25 induction (Cruz et al., 2003). Tau P301S mice, which express high levels of humanized mutant microtubule-associated protein tau and have tau aggregates that are associated with frontotemporal dementia as early as 5 months of age (Yoshiyama et al., 2007). 8 months old P301S mice, at which age they have synaptic and neuronal loss and cognitive deficits. CK = wild type control mice; CK-p25 + No Stim = CK-p25 mice that did not under go any stimulation; CK-p25 +GENUS = Ck-p25 mice that was stimulated with 40 Hz visual stimulation WT = wild type control mice; P301S + No Stim = P301S mice that did not under go any stimulation; P301S +GENUS = P301S mice that was stimulated with 40 Hz visual stimulation
Publication Title
Gamma Entrainment Binds Higher-Order Brain Regions and Offers Neuroprotection.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
Gamma oscillations (20-50Hz) are a common local field potential signature in many brain regions that are generated by a resonant circuit between fast-spiking parvalbumin (PV)-positive interneurons and pyramidal cells. Changes in the magnitude and frequency of gamma have been observed in several neuropsychiatric disorders. However, it is unclear how disruptions in gamma oscillations affect cellular pathologies seen in these disorders. Here, we investigate this using the 5XFAD mouse model of Alzheimer’s disease (AD) and find reduced power and magnitude of behaviorally driven gamma oscillatory activity — even before the onset of plaque formation or measurable cognitive decline. Because of the early onset, we aimed to determine if exogenous manipulations of gamma could influence the progression of disease pathology. We find that driving PV-positive neurons at gamma frequency (40Hz) using channelrhodopsin-2 reduced total levels of amyloid-ß (Aß) 40 and 42 isoforms in the hippocampus of 5XFAD mouse. Driving PV-positive neurons at other frequencies, or driving excitatory neurons, did not reduce Aß levels. Furthermore, driving PV-positive neurons reduced enlarged endosomes in hippocampal neurons and cleavage intermediates of APP in 5XFAD mouse. Gene expression profiling revealed a neuroprotective response with morphological transformation of microglia and markedly increased phagocytosis of Aß by microglia. Inspired by these observations, we designed a non-invasive light-flickering paradigm that drives 40Hz gamma activity in mouse visual cortex. The light-flickering paradigm profoundly reduced Aß40 and Aß42 levels in the visual cortex of pre-symptomatic mice and greatly mitigated plaque load in the visual cortex of aged, symptomatic mice. This reduction was completely blocked by a GABA-A antagonist, providing further support for an essential role of GABAergic signaling in mediating neuroprotective gamma activity. Overall, our findings uncover a dramatic and previously unappreciated function of the brain’s endogenous gamma rhythms in reducing the production and increasing the clearance of Aß peptides, whose accumulation is believed to drive the pathogenesis of AD. Overall design: Two to four weeks following virus injection and implant placement, hippocampal CA1 neurons were optigenetically manipulated. During the experiment, 1mW of optical stimulation was delivered for 1h using a 40Hz stimulation protocol.
Publication Title
Gamma frequency entrainment attenuates amyloid load and modifies microglia.
Sample Metadata Fields
Age, Specimen part, Cell line, Subject
View Samples- Mus musculus
- 6 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The ectopic expression of a Col10a1-13del transgene in osteocytes induced ER stress, compromising their differentiation and expression of Sclerostin, resulting in generalized bone overgrowth resembling human crainodiaphyseal chondrodysplasia (CCD).
Publication Title
Activating the unfolded protein response in osteocytes causes hyperostosis consistent with craniodiaphyseal dysplasia.
Sample Metadata Fields
Specimen part
View Samples- Hordeum vulgare
- 12 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
Transcriptional changes were monitored in the barley cultivar Golden Promise 24 hours post inoculation (hpi) with the bacteria Pseudomonas syringae pv. tomato DC3000 avrRpm1 (PstavrRpm1) using the Affymetrix Barley genome array GeneChip. Seedlings of Golden Promise were grown to growth stage 12-13 (Zadoks et al., 1974) before inoculating with either PstavrRpm1 or water (for the mock inoculation control) by infiltration. Plants were grown under a 18 C / 16 h light period; 12 C / 8 h dark period, with artificial lighting (100 mol m-2 s-1) and a relative humidity of 75 85 %. Leaf samples from three seedlings were collected 24 hpi for RNA extraction and transcriptomics analysis from the area infiltrated (local) and from the area next to the infiltrated region (adjacent) from three biological replicates. Leaf tissue was ground under liquid nitrogen and total RNA extracted using the RNeasy miniprep kit (Qiagen), following the manufacturers instructions. RNA was DNase treated using Turbo DNase (Ambion) according to the manufacturer instructions. RNA integrity was confirmed using the Agilent 2100 Bioanalyzer (Agilent). The two cycle-target labeling method was used following the Affymetrix protocol. Affymetrix GeneChip processing, including RNA quality control, microarray hybridisation and data acquisition was performed through contract research services by Cogenics (North Carolina, U.S.A.). A total of twelve hybridisations were performed. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Ellen Colebrook. The equivalent experiment is BB92 at PLEXdb.]
Publication Title
Broad-spectrum acquired resistance in barley induced by the Pseudomonas pathosystem shares transcriptional components with Arabidopsis systemic acquired resistance.
Sample Metadata Fields
Specimen part
View Samples- Triticum aestivum
- 12 Downloadable Samples
- Affymetrix Wheat Genome Array (wheat)
Description
Transcriptional changes were monitored in the wheat cultivar Renan 24 hours post i noculation with adapted and non-adapted Magnaporthe isolates using the Affymetrix wheat genome array GeneChip. Wheat plants cv. Renan were grown in a peat and sand (1:1) mix at 23 C in a Sanyo Fitotron growth cabinet (Sanyo Gallenkamp PLC, Loughborough, U.K.) with a 16/8 h, light/dark cycle. Three Magnaporthe isolates were used in this expt, two wheat-adapted isolates (BR32, BR37) and one wheat non-adapted isolate (BR29). Magnaporthe isolates were grown for eleven days on Complete Media Agar at 25 C under a 16/8h, light/dark cycle. Conidia were harvested by flooding the plates with 5 mL of sterile inoculation solution [0.25% (w/v) gelatine and 0.01% (v/v) Tween 20] and scraping the conidia from the surface using a sterile glass rod. Conidia were filtered through sterile miracloth and the density adjusted to 1 x 10 5 conidia mL-1 with inoculation solution. Fourteen day old wheat seedlings mist inoculated with 4 mL of a Magnaporthe conidia suspension and plants were sealed in plastic propagators to maintain relative humidity c.100% and kept at 25 C in the dark for the first 24 hours post inoculation (hpi). Inoculation solution without Magnaporthe conidia was used as a mock-inoculation control. Leaf samples were collected 24 hpi for transcriptomics analysis from three independent biological experiments. Leaf tissue was ground under liquid nitrogen and total RNA extracted using a QIAquick RNeasy Plant Extraction Kit (Qiagen, Hilden, Germany), followed by TURBO DNaseTM (Ambion, Texas, U.S.A.) treatment. RNeasy Mini Spin column purification (Qiagen) was used to further purify RNA samples for array hybridisation. RNA quality checks, cRNA conversion and Affymetrix genome array hybridisation was carried out by the Nottingham Arabidopsis Stock Centre (NASC) array hybridisation service (http://affymetrix.arabidopsis.info/). ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Graham McGrann. The equivalent experiment is TA24 at PLEXdb.]
Publication Title
Wheat blast: histopathology and transcriptome reprogramming in response to adapted and nonadapted Magnaporthe isolates.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 11 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Human intervertebral disc tissue was obtained from patients (average age 51 yrs) undergoing surgery for lumbar interbody fusion (n=3) or lumbar disc herniation (n=1). Cells were isolated by sequential pronase-collagenase digestion [3]. Cells were passaged twice in monolayer and suspended at a density of 2 x 106 cells/ml in 1.2% alginate (low viscosity, Sigma Chemical, St Louis, MO) dissolved in 150 mM NaCl. Alginate beads were formed by dropwise addition of the alginate from a 22 gauge needle into 102 mM CaCl2, followed by 10 minutes of curing, as described previously [13, 27]. Cell-gel beads were incubated in cell culture media consisting of Hams F-12 medium (Gibco BRL, Grand Island, NY), supplemented with 10% FBS (HyClone, Logan, UT), 25 g/ml ascorbic acid (Sigma, St. Louis, MO), 100 U/ml penicillin, 100 g/ml streptomycin, and 1 g/ml Fungizone at 5% CO2 and 37 C.
Publication Title
Osmolarity regulates gene expression in intervertebral disc cells determined by gene array and real-time quantitative RT-PCR.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 2 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
Gene expression studies from hematopoietic stem cell (HSC) populations purified to variable degrees have defined a set of stemness genes. The present study describes the construction and comparative molecular analysis of l-phage cDNA libraries from highly purified primitive HSCs (PHSCs) which retained their long term repopulating activities (LTRAs), and from maturing HSCs (MHSCs) which were largely depleted of LTRAs. Library inserts were amplified and tagged by a T7 RNA polymerase promoter and used to generate biotinylated cRNA for Microarray hybridization. Microarray analysis of the libraries confirmed previous results but also revealed an unforseen preferential expression of translation and metabolism associated genes in the PHSCs. Therefore these data indicate that HSCs are quiescent only in regard of proliferative activities, but are in a state of readiness to provide the metabolic and translational activities required following induction of proliferation by factors which induce differentiation and exit from the HSC pool.
Publication Title
Gene expression profiles in murine hematopoietic stem cells revisited: analysis of cDNA libraries reveals high levels of translational and metabolic activities.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 58 Downloadable Samples
- Affymetrix Human Genome U95 Version 2 Array (hgu95av2)
Description
PURPOSE:
Publication Title
Unique gene expression profile based on pathologic response in epithelial ovarian cancer.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 3 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Human pluripotent stem cells (hPSC) generate hematopoietic progenitor cells (HPC), but fail to engraft xenograft models, which is a hallmark feature of adult/somatic hematopoietic stem cells (HSC) from human donors. Progress to derive hPSC-derived HSCs has relied on cell autonomous approaches that force expression of transcription factors (TF), however the role of bone marrow (BM) niche remains poorly understood. Here, we quantified a failure of hPSC-HPCs to survive even in the first 24 h upon transplantation into the BM. Across several hPSC-HPC differentiation methodologies, we identified the lack of CXCR4 expression and network function. Ectopic CXCR4 conferred CXCL12-dependent signaling of hPSC-HPCs in biochemical assays and increased migration/chemotaxis and progenitor capacity, as well as survival and proliferation following transplantation in vivo. In addition, hPSC-HPCs forced to express CXCR4 demonstrated a transcriptional shift toward somatic HPCs, but this approach failed to produce long-term HSC engraftment. Our results reveal that independent of differentiation methods, networks involving CXCR4 should be targeted to generate HSCs with in vivo function from hPSCs.
Publication Title
CXCL12/CXCR4 Signaling Enhances Human PSC-Derived Hematopoietic Progenitor Function and Overcomes Early In Vivo Transplantation Failure.
Sample Metadata Fields
Specimen part
View Samples- Caenorhabditis elegans
- 8 Downloadable Samples
- Affymetrix C. elegans Genome Array (celegans)
Description
We used gene expression profiling to address several specific questions that arose in a study of repair of ultraviolet C radiation in C elegans, as well as to generate hypotheses regarding the possible mechanism(s) of decreased DNA repair observed in old adults in that study. This analysis was performed in order to analyze gene expression in the strain (JK1107) and experimental conditions that we used for our DNA repair studies.
Publication Title
Decline of nucleotide excision repair capacity in aging Caenorhabditis elegans.
Sample Metadata Fields
No sample metadata fields
View Samples