Filters
Technology
Platform
SRP149997
Saccharomyces cerevisiae
4 Downloadable Samples
Illumina HiSeq 2000
Description
Transcriptome study of 2 Saccharomyces cerevisiae W303 derivatives, one carrying GFP (control) and one carrying aSyn-GFP
Publication Title
Different 8-hydroxyquinolines protect models of TDP-43 protein, α-synuclein, and polyglutamine proteotoxicity through distinct mechanisms.
Sample Metadata Fields
Specimen part, Disease, Cell line
View Samples- Hordeum vulgare
- 108 Downloadable Samples
Affymetrix Barley Genome Array (barley1)
Description
A large-scale parallel expression analysis was conducted to elucidate Mla-specified responses to powdery mildew infection using 22K Barley1 GeneChip probe arrays. Our goal was to identify genes differentially expressed in incompatible (resistant) vs. compatible (susceptible) and Mla-specified Rar1-dependent vs. -independent interactions. A split-split-plot design with 108 experimental units (3 replications x 2 isolates x 3 genotypes x 6 time points) was used to profile near-isogenic lines containing the Mla1, Mla6, and Mla13 resistance specificities in response to inoculation with the Blumeria graminis f. sp. hordei (Bgh) isolates 5874 (AvrMla1, AvrMla6) and K1 (AvrMla1, AvrMla13). ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Rico Caldo. The equivalent experiment is BB4 at PLEXdb.]
Publication Title
Interaction-dependent gene expression in Mla-specified response to barley powdery mildew.
Sample Metadata Fields
Specimen part, Time
View Samples- Hordeum vulgare
- 72 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
Time-course expression profiles of Bgh challenged barley cultivar C.I. 16151 (harboring the Mla6 powdery mildew resistance allele) and its fast-neutron-derived "Bgh-induced tip cell death1" mutant, bcd1, were compared using the 22K Barley1 GeneChip. Planting, stage of seedlings, harvesting, and experimental design were part of a larger experiment described by Caldo et al. (2004). PLEXdb BB4. Experiment Design: C.I. 16151 (wildtype) and bcd1 (mutant) were planted in separate 20 x 30-cm flats using sterilized potting soil. Each experimental flat consisted of six rows of 15 seedlings, with rows randomly assigned to one of six harvest time points (0, 8, 16, 20, 24, and 32 hai). Seedlings grown to the 1st leaf stage with 2nd leaf unfolded were inoculated with a high density of fresh conidiospores (84 +/- 19 spores/mm2). Groups of flats were placed at 18C (8-hour darkness, 16-hour light) in separate controlled growth chambers corresponding to the Bgh isolates. Rows of plants were harvested at each assigned time points and snap frozen in liquid nitrogen. The entire experiment was repeated three times in a standard split-split-plot design with 72 experimental units (2 genotypes x 2 pathogen isolates x 6 time points x 3 replications). Treatment Description: The samples constituted pairwise combinations of the the cultivar C.I. 16151(containing the Mla6 resistance allele), and its fast-neutron-derived "Bgh-induced tip cell death1" mutant, bcd1 with the two Bgh (Blumeria graminis f. sp. hordei) isolates, 5874 (AvrMla6, AvrMla1) and K1 (AvrMla13, AvrMla1). For each replication, individual genotypes were planted in separate 20 x 30 cm flats using sterilized potting soil. Each experimental flat consisted of six rows of 15 seedlings, with rows randomly assigned to one of six harvest times (0, 8, 16, 20, 24, and 32 hai). Seedlings were grown to the 2nd-leaf stage with 1st leaf unfolded, and inoculation was performed at 4 PM Central Standard Time by tipping the flats at 45oC and dusting the plants with a high density of fresh conidiospores [84 +/- 19 spores/mm2]. This procedure was repeated from the opposite angle to ensure that a high proportion of the cells are in contact with the fungus. This conidial density per unit leaf area routinely results in greater than 50% of epidermal cells that are successfully infected. Groups of flats were placed at 18oC (8 hours darkness, 16 hours light, 8 hours darkness) in separate controlled growth chambers corresponding to the Bgh isolate. Rows of plants were harvested at their assigned harvest times and flash-frozen in liquid nitrogen. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Roger P Wise. The equivalent experiment is BB46 at PLEXdb.]
Publication Title
Interaction-dependent gene expression in Mla-specified response to barley powdery mildew.
Sample Metadata Fields
Age, Specimen part, Time
View Samples- Hordeum vulgare
- 1 Downloadable Sample
- Affymetrix Barley Genome Array (barley1)
Description
A large-scale parallel expression analysis was conducted to elucidate Mla-specified responses to powdery mildew infection using 22K Barley1 GeneChip probe arrays. Our goal was to identify genes differentially expressed in incompatible (resistant) vs. compatible (susceptible) and Mla-specified Rar1-dependent vs. -independent interactions. A split-split-plot design with 108 experimental units (3 replications x 2 isolates x 3 genotypes x 6 time points) was used to profile near-isogenic lines containing the Mla1, Mla6, and Mla13 resistance specificities in response to inoculation with the Blumeria graminis f. sp. hordei (Bgh) isolates 5874 (AvrMla1, AvrMla6) and K1 (AvrMla1, AvrMla13).
Publication Title
Interaction-dependent gene expression in Mla-specified response to barley powdery mildew.
Sample Metadata Fields
Age, Specimen part, Disease, Disease stage, Cell line, Time
View Samples- Saccharomyces cerevisiae
- 8 Downloadable Samples
- Illumina HiSeq 2500
Description
DHPM-thiones rescue Ab-mediated toxicity in a metal-dependent manner that strongly synergizes with clioquinol, a known metal-binding and cytoprotective compound. RNA-seq experiments reveal a modest, yet specific effect on metal-responsive genes that do not change with the inactive control compound. Overall design: Treatment of biological replicates with DMSO, 0.8 uM clioquinol, or 20 uM 10{3,3,1} (DHPM-thione) for ~6 hours prior to harvesting of cells and isolation of total RNA.
Publication Title
Dihydropyrimidine-Thiones and Clioquinol Synergize To Target β-Amyloid Cellular Pathologies through a Metal-Dependent Mechanism.
Sample Metadata Fields
Cell line, Subject
View Samples- Hordeum vulgare
- 180 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
A large-scale time course expression profiling of wild type (Mla12/Rar1/Rom1) and mutants (mla12-M66, M82 (rar1-1), M100 (rar1-2) and rom1) of barley cultivar Sultan 5 was conducted to understand the molecular mechanisms of delayed powdery mildew resistance. Barley plants were inoculated with powdery mildew pathogen isolate 5874. First leaves of inoculated and non-inoculated plants were harvested at six time points after pathogen inoculation. The experiment was laid out in split-split-plot design with 180 experimental units (3 replications x 2 treatments (inoculated and non-inoculated) x 5 genotypes x 6 time points).
Publication Title
Stage-specific suppression of basal defense discriminates barley plants containing fast- and delayed-acting Mla powdery mildew resistance alleles.
Sample Metadata Fields
Age, Specimen part, Time
View Samples- Mus musculus
- 20 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
In an accompanying paper we found specific localization of diabetogenic T cells only to islets of Langerhans bearing the specific antigen. Instrumental in the specific localization was the presence of intra-islet dendritic cells bearing the -cell-peptide-MHC complex. Here we report that the entry of diabetogenic CD4 T cells very rapidly triggered inflammatory gene expression changes in islets and vessels by up-regulating chemokines and adhesion molecules. VCAM-1 expression was notable in blood vessels and so was ICAM-1. ICAM-1 was also found on -cells. These expression changes induced the entry of non-specific T cells that otherwise did not localize to the islets. In contrast to the entry of diabetogenic CD4 T cells, the entrance of non-specific T cells required a chemokine response and VCAM-1 expression by the islets. Interferon-gamma was important for the early gene expression changes in the islets. By microarray analysis we detected up-regulation of a group of interferon-inducible genes as early as 8 hours post T cell transfer. These studies provide a baseline to examine the development of therapeutics that can modulate islet localization of diabetogenic T cells to control this autoimmune disease.
Publication Title
Entry of diabetogenic T cells into islets induces changes that lead to amplification of the cellular response.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 57 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Type 1 diabetes (T1D) is an autoimmune disease triggered by T cell reactivity to protein antigens produced by the -cells. Here we present a chronological compendium of transcriptional profiles from islets of Langerhans isolated from non-obese diabetic (NOD) mice ranging from 2 wks up to diabetes and compared to controls. Parallel analysis was made of cellular components of the islets. Myeloid cells populated the islets early during development in all mouse strains. This was followed by a type I interferon signature detectable at 4-6 wks of age only in diabetes susceptible mice. Concurrently, CD4 T cells were found within islets, many in contact with intra-islet antigen presenting cells. Early cellular signs of islet reactivity were detected by six wks. By 8 wks, NOD islets contained all major leukocytes populations and an inflammatory gene signature. This work establishes the natural transcriptional signature of T1D and provides a resource for future research.
Publication Title
Defining the transcriptional and cellular landscape of type 1 diabetes in the NOD mouse.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
We demonstrate diverse roles of interferongamma (IFN-) in the induction and regulation of immune-mediated inflammation using a transfer model of autoimmune diabetes. The diabetogenic CD4+BDC2.5 (BDC) T cell clone upon transfer into NOD.scid mice induced destruction of islets of Langerhans leading to diabetes. Administration of a neutralizing antibody to IFN- (H22) resulted in long term protection (LTP) from diabetes, with inflammation but persistence of a significant, albeit decreased numbers of -cells. BDC T cells were a mixture of cells expressing high, intermediate and low levels of the T cell receptor. Clonotype-low BDC T cells were required for LTP. Furthermore, islet infiltrating leukocytes in the LTP mice contained Foxp3+CD4 T cells. Islet inflammation in both diabetic and LTP mice was characterized by heavy infiltration of macrophages. Gene expression profiles indicated that macrophages in diabetic mice were M1-type, while LTP mice contained M2-differentiated. The LTP was abolished if mice were treated with either an antibody depleting CD4 T cells, or a neutralizing antibody to CTLA-4, in this case, only at a late stage. Neutralization of IL-10, TGF-, GITR or CD25 had no effect. Transfer of only clonotype-high expressing BDC T cells induced diabetes but in contrast, H22 antibodies did not inhibit diabetes. While clonotype high T cells induced diabetes even when IFN- was neutralized, paradoxically, there was reduced inflammation and no diabetes if host myeloid cells lacked IFN- receptor. Hence, using monoclonal CD4 T cells, IFN- can have a wide diversity of roles, depending on the setting of the immune process.
Publication Title
IFN-gamma-dependent regulatory circuits in immune inflammation highlighted in diabetes.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 29 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Light initiates the seedling deetiolation transition by promoting major changes in gene expression mainly regulated by phytochrome (phy) photoreceptors. During the initial dark-to-light transition, phy photoactivation induces rapid changes in gene expression that eventually lead to the photomorphogenic development. Recent reports indicate that this process is achieved by phy-induced degradation of Phy-Interacting bHLH transcription Factors (PIFs) PIF1, PIF3 PIF4 and PIF5, which are partly redundant constitutive repressors of photomorphogenesis that accumulate in darkness. In order to test whether light/phy-regulated gene expression occurs through these PIFs, we have performed whole-genome expression analysis in the pif1pif3pif4pif5 quadruple mutant (pifq).
Publication Title
Definition of early transcriptional circuitry involved in light-induced reversal of PIF-imposed repression of photomorphogenesis in young Arabidopsis seedlings.
Sample Metadata Fields
No sample metadata fields
View Samples