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GSE51379
Citrus sinensis
20 Downloadable Samples
Affymetrix Citrus Genome Array (citrus)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Identification of putative TAL effector targets of the citrus canker pathogens shows functional convergence underlying disease development and defense response.
Sample Metadata Fields
Age, Specimen part, Time
View Samples- Citrus sinensis
- 12 Downloadable Samples
- Affymetrix Citrus Genome Array (citrus)
Description
Microarray analyses of sweet orange epicotyls transiently transfected with the pthA2, pthA4 or pthC1 gene, relative to epicotyls transfected with the uid gene (GUS)
Publication Title
Identification of putative TAL effector targets of the citrus canker pathogens shows functional convergence underlying disease development and defense response.
Sample Metadata Fields
Age, Specimen part, Time
View Samples- Citrus sinensis
- 8 Downloadable Samples
- Affymetrix Citrus Genome Array (citrus)
Description
Microarray analyses of sweet orange leaves infiltrated with Xc in the presence or absence of Ch, or Ch alone
Publication Title
Identification of putative TAL effector targets of the citrus canker pathogens shows functional convergence underlying disease development and defense response.
Sample Metadata Fields
Specimen part, Time
View Samples- Gossypium barbadense, Gossypium hirsutum
- 2 Downloadable Samples
- Affymetrix Cotton Genome Array (cotton)
Description
affy_cotton_2011_12 - affy_cotton_2011_12 - In this study we characterized the fiber transcriptomes of the two species, Gossypium hirsutum and Gossypium barbadense that were parental genotypes of a RIL mapping population used previously for phenotypic QTL and expression QTL mapping., We used 454 deep pyrosequencing to characterize cDNAs from developing fibers at two key developmental time-points; 10 and 22 days post anthesis. A unigene set was assembled and annotated, and differential digital gene expression was assessed from the different time-point and genotype representations of the reads within assembled contigs. As a complementary approach, we conducted microarray-based hybridization profiling using the cotton Affymetrix gene chip and labeled cDNAs from fibers at 11 dpa and for the same two genotypes and compared differentially expressed genes identified by the two platforms. The 454 unigenes were also mined for the presence of microsatellite repeats and SNPs that will be useful markers for mapping and marker-assisted selection in cotton improvement.-Total RNA was extracted from 11 dpa-old fibers from the two genotypes, Guazuncho 2 (Gossypium hirsutum) and VH8-4602 (G. barbadense), and included two replicates of each. RNA was checked for quality and quantity using an Agilent Bioanalyser 2100 (Agilent Technologies, Santa Clara, CA, USA, http://www.home.agilent.com) following the manufacturers recommendations. The RNA was sent to the Australian Genome Research Facility Ltd. (http://www.agrf.org.au, Melbourne, Victoria, Australia) for labeling and hybridization to the Affymetrix Genechip Cotton Genome Array (21,854 genes) (Affymetrix, http://www.affymetrix.com/). -
Publication Title
Deep sequencing reveals differences in the transcriptional landscapes of fibers from two cultivated species of cotton.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 52 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Untreated HIV-1 infection progresses through acute and asymptomatic stages to AIDS. While each of the three stages has well-known clinical, virologic and immunological characteristics, much less is known of the molecular mechanisms underlying each stage. Here we report lymphatic tissue microarray analyses revealing for the first time stage-specific patterns of gene expression during HIV-1 infection. We show that while there is a common set of key genes with altered expression throughout all stages, each stage has a unique gene-expression signature. The acute stage is most notably characterized by increased expression of hundreds of genes involved in immune activation, innate immune defenses (e.g.MDA-5, TLR-7 and -8, PKR, APOBEC3B, 3F, 3G), adaptive immunity, and in the pro-apoptotic Fas-Fas-L pathway. Yet, quite strikingly, the expression of nearly all acute-stage genes return to baseline levels in the asymptomatic stage, accompanying partial control of infection. In the AIDS stage, decreased expression of numerous genes involved in T cell signaling identifies genes contributing to T cell dysfunction. These common and stage-specific, gene-expression signatures provide new insights into the molecular mechanisms underlying the host response and the slow, natural course of HIV-1 infection.
Publication Title
Microarray analysis of lymphatic tissue reveals stage-specific, gene expression signatures in HIV-1 infection.
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Disease stage, Race, Subject
View Samples- Rattus norvegicus
- 17 Downloadable Samples
- Affymetrix Rat Gene 1.0 ST Array (ragene10st)
Description
Frequent hemodialysis is associated with improvement in myocardial mechanics and cardiac gene expression profile
Publication Title
Impact of frequent nocturnal hemodialysis on myocardial mechanics and cardiomyocyte gene expression.
Sample Metadata Fields
Age, Specimen part
View Samples- Drosophila melanogaster
- 16 Downloadable Samples
Illumina HiSeq 2000
Description
Samples 1-8: Tissue-specific RNA sequencing (Illumina) using dissected ring glands isolated from TWO different time points of control (phm>w1118) third instar larvae. Time points are: light phase zt0-4 (which corresponde to 2-4 hours from second to third instar larvae molt); and dark phase zt18-22 (which corresponde to 16-20 hours from second to third instar larvae molt) Samples 9-32: Tissue-specific gene expression (RNA seq Illumina) using dissected ring glands isolated from TWO different time points of third instar larvae. Genotypes were Timeless-RNAi (phm>tim-RNAi), Period-RNAi (phm>per-RNAi), UAS-TimcDNA (phm>UAS-Tim) and UAS-TimcDNA;UAS-PercDNA (phm>UAS-TimcDNA;UAS-PercDNA). Goal was to identify circadin pathway dependent gene sets in the ring gland. Time points were 2-4 hours and 18-20 hours after L2-L3 molt. Overall design: This study comprises two parts: First, Next generation sequencing was used to determine transcriptional profiles from Drosophila ring glands at ZT0-4 versus ZT18-22 in control larvae. Encore Complete RNA-Seq IL Multiplex System 1-8 (Nugen Part No. 0312) and Encore Complete RNA-Seq IL Multiplex System 9-16 (Nugen Part No. 0313) was used for barcoding and multiplex sequencing. Library prep was based on total RNA isolated from dissected ring glands at two different time points during the third instar (the last larval stage of Drosophila development). Libraries were sequenced on a High-Seq Illumina platform. The second part examined gene expression changes in ring glands where we altered circadian signaling by genetic means. Encore Complete RNA-Seq IL Multiplex System was used to prep the cDNA library from total RNA isolated from ring glands of controls, ring gland-specific Timeless-RNAi (phm>tim-RNAi), Period-RNAi (phm>per-RNAi), UAS-Tim-cDNA (phm>UAS-Tim) and UAS-Tim-cDNA; UAS-Per-cDNA (phm>UAS-Tim-cDNA;UAS-Per-cDNA) larvae at two different time points in the day (ZT0-4 and ZT18-22) for the first three genotypes and exclusively at ZT18-22 for the last two genotypes. Each condition was measured by using two biological samples.
Publication Title
The Circadian Clock Is a Key Driver of Steroid Hormone Production in Drosophila.
Sample Metadata Fields
Specimen part, Subject
View Samples- Arabidopsis thaliana
- 13 Downloadable Samples
- Affymetrix Arabidopsis Genome Array (ag)
Description
10 day old seedlings were treated with 5uM of the cytokinin Benzyladenine(BA)or DMSO at 15min, 45min, 120min, 480min and 1440min
Publication Title
Expression profiling of cytokinin action in Arabidopsis.
Sample Metadata Fields
Age, Compound, Time
View Samples- Mus musculus
- 24 Downloadable Samples
- Illumina MouseRef-8 v2.0 expression beadchip
Description
Treatments that stimulate neuronal excitability enhance motor performance after stroke.cAMP-response-element binding protein (CREB) is a transcription factor that plays a key rolein neuronal excitability. Increasing the levels of CREB with a viral vector in a small pool ofmotor neurons enhances motor recovery after stroke, while blocking CREB signaling preventsstroke recovery. Silencing CREB-transfected neurons in the peri-infarct region with thehM4di-DREADD blocks motor recovery. Reversing this inhibition allows recovery to continue,demonstrating that it is possible to turn off and on stroke recovery by manipulating theactivity of CREB-transfected neurons. CREB transfection enhances re-mapping of injuredsomatosensory and motor circuits, and induces the formation of new connections withinthese circuits. CREB is a central molecular node in the circuit responses after stroke that leadto recovery from motor deficits.
Publication Title
CREB controls cortical circuit plasticity and functional recovery after stroke.
Sample Metadata Fields
Specimen part
View Samples- Macaca mulatta
- 15 Downloadable Samples
- Affymetrix Rhesus Macaque Genome Array (rhesus)
Description
Systemic vaccination with the attenuated virus SIVmac239-Nef provides sterilizing or partial protection to rhesus monkeys challenged with WT SIV strains, providing important opportunities to study key immunological components of a protective host response. Here we show that intravenous vaccination with SIVmac239-Nef provides two potentially crucial immunological barriers localized at mucosal surfaces that correlate with the vaccines protective effects against WT SIVmac251 vaginal challenge: 1) a conditioned and coordinated response from the mucosal epithelium that blunts the early inflammatory and chemotactic signalling cascade that aids virus propagation and expansion; 2) early on-site generation/diversification of SIV-specific Abs from ectopic germinal center-like lymphoid aggregates. This unique host response to WT SIVmac251 in the female reproductive tract of SIVmac239-Nef-vaccinated animals points to a multi-layered strategy for a protective host response during immunodeficiency virus exposurerapid induction of humroal immunity at mucosal surfaces without the deleterious inflammatory side effects tied to innate recognition of virus. This vaccine-induced host response highlights potential key protective mechanisms needed for an effective HIV vaccine
Publication Title
Live simian immunodeficiency virus vaccine correlate of protection: immune complex-inhibitory Fc receptor interactions that reduce target cell availability.
Sample Metadata Fields
Sex, Specimen part
View Samples