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GSE24052
Arabidopsis thaliana
6 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Dicamba is an auxin-like herbicide that can stimulate the production of ethylene and ABA biosynthesis. The subsequent stomatal closure and build-up of reactive oxygen species is hypothesized to contribute to plant death.
Publication Title
Mutant analysis in Arabidopsis provides insight into the molecular mode of action of the auxinic herbicide dicamba.
Sample Metadata Fields
Specimen part
View Samples- Drosophila melanogaster
- 12 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
Innate immune responses contributed to the containment of intestinal microbes.
Publication Title
Constitutive Immune Activity Promotes Tumorigenesis in Drosophila Intestinal Progenitor Cells.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 9 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Rhizoctonia solani is an economically important soil-borne necrotrophic fungal pathogen, with a broad host range and for which little effective resistance exists in crop plants. Arabidopsis is resistant to the R. solani AG8 isolate but susceptible to R. solani AG2-1. Affymetrix microarray analysis was performed to determine genes that are affected in common and specifically by AG8 and AG2-1.
Publication Title
Genetic and genomic analysis of Rhizoctonia solani interactions with Arabidopsis; evidence of resistance mediated through NADPH oxidases.
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Mus musculus
- 9 Downloadable Samples
- Illumina MouseWG-6 v2.0 expression beadchip
Description
Comparative analysis of Endodermal-like cell lines with demonstrated ability to support myocardial differentiation
Publication Title
A comparative analysis of extra-embryonic endoderm cell lines.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus, Homo sapiens
- 37 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Cells were reprogrammed from cardiac fibroblasts to cardiomyocytes, in various conditions. These are the iCM cells (induced cardiomyocytes). There are both human and mouse arrays here, as seen below.
Publication Title
In vivo reprogramming of murine cardiac fibroblasts into induced cardiomyocytes.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 29 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
Toll like receptor 4 (TLR4), an innate immunity gene, is involved in responses to several pulmonary agonists including endotoxin (LPS; Poltorak et al.,1998), ozone (O3 ,Kleeberger et. al., 2001), Pseudomonas aeruginosa (Faure et al, 2004), and hyperoxia (Zhang et al, 2005). TLR4 appears to partially mediate the response to LPS- and O3-induced lung injury, however, TLR4 is protective for prevention of injury in Pseudomonas aeruginosa infection and against acute lung injury (hyperoxia). The mechanism behind this protection is unclear. We previously demonstrated that TLR4 was also protective against BHT-induced chronic inflammation and tumor promotion (Bauer et al, 2005). C.C3H-Tlr4Lps-d (BALBLps-d) mice, congenic for a 10 cM region of C3H/HeJ chromosome 4 that contains Tlr4 (Vogel et al, 1994), have a missence mutation that renders TLR4 dysfunctional. The Tlr4 mutation likely abrogates signaling by disrupting a direct point of contact with other signaling molecules (Akira S, Takeda K. Toll-like receptor signalling. Nat Rev Immunol 2004;4(7):499-511.). Bronchoalveolar lavage fluid (BALF) alveolar macrophages, lymphocytes, and total protein content were significantly elevated in BALBLps-d mice compared to BALB/c (BALB; Tlr4 sufficient) mice following chronic BHT (Bauer et al., 2005). BALBLps-d mice also had a significant increase in tumor multiplicity (60%) over that of BALB mice in response to an MCA/BHT tumor promotion protocol. While this was the first model to demonstrate a protective role for TLR4 in chronic lung inflammation and tumorigenesis, the downstream mechanism regulating this protective response remains unknown. Using Affymetrix microarray analysis followed by GeneSpring and Ingenuity pathway analyses, we herein identified known and novel downstream pathways and their interactions that may be involved in the protective mechanism elicited by TLR4. We therefore hypothesize that these pathways and interactions amongst the genes identified during the tumor promotion/chronic inflammation stage are in part influencing the differential strain response observed during tumorigenesis.
Publication Title
Transcriptomic analysis of pathways regulated by toll-like receptor 4 in a murine model of chronic pulmonary inflammation and carcinogenesis.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Reactive oxygen species such as hydrogen peroxide (H2O2) are important in biotic and abiotic stress responses in plants, but their source is often unclear. We have identified an Arabidopsis mutant that shows loss of stress responsive GSTF8 gene expression in response to the plant defence signal salicylic acid (SA) . The mutant showed increased susceptibility to both fungal and bacterial pathogens. The dsr1 mutation was mapped to mitochondrial succinate dehydrogenase (SDH1-1) and dsr1 had reduced SDH activity and a lowered mitochondrial H2O2 production.
Publication Title
Mitochondrial complex II has a key role in mitochondrial-derived reactive oxygen species influence on plant stress gene regulation and defense.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 2 Downloadable Samples
Illumina HiSeq 2000
Description
This project looks into experimentally identifying all minor introns by knocking down the minor spliceosome''s catalytic snRNP, U6atac. Overall design: Knockdown of U6atac by antisense morpholino followed by examining mRNA splicing by RNA-seq
Publication Title
Minor introns are embedded molecular switches regulated by highly unstable U6atac snRNA.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 98 Downloadable Samples
- IlluminaHiSeq2500, NextSeq500
Description
We performed single-cell and bulk transcriptome profiling in two different human cell lines. We performed single-cell RNA sequencing in live and fixed cells. Overall design: Single cell RNA sequencing of live and fixed cells, bulk RNA sequencing in two cell lines.
Publication Title
Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 90 Downloadable Samples
- Affymetrix HT HG-U133+ PM Array Plate (hthgu133pluspm)
Description
A673 cells were exposed in triplicate to three agrichemicals for 24hrs at 8 concentrations and a DMSO vehicle control (0.001, 0.003, 0.01, 0.03, 0.1, 0.3, 1, 3, and 10 M plus DMSO vehicle controls). While a common set of DMSO controls was used, these CEL files were RMA normalized independently with each of the chemical treated groups. Gene expression was measured on an Affymetrix GeneTitan system. The compounds used were fenbuconazole (a.k.a FENB, CAS # 114369-43-6) a triazole fungicide, imazalil (a.k.a. IMAZ, CAS # 35554-44-0), an azole pesticide, and 2,4-dichlorophenoxyacetic acid (a.k.a. 2,4-D or 2-4-D in file names, CAS # 94-75-7), a chlorophenoxy herbicide.
Publication Title
A Qualitative Modeling Approach for Whole Genome Prediction Using High-Throughput Toxicogenomics Data and Pathway-Based Validation.
Sample Metadata Fields
Specimen part, Cell line
View Samples