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GSE46184
Homo sapiens
73 Downloadable Samples
Affymetrix Human Genome U133A Array (hgu133a)
Description
Gene expression profiling of surgical biopsies from 74 breast cancer patients of different subtypes from Hamburg dataset.
Publication Title
Prognostic relevance of glycosylation-associated genes in breast cancer.
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 10 Downloadable Samples
Affymetrix Murine Genome U74A Array (mgu74a), Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2), Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Autoregulation of Th1-mediated inflammation by twist1.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2), Affymetrix Murine Genome U74A Array (mgu74a)
Description
Gene expression profiling of repeatedly activated compared to recently activated Th1 cells to identify genes that play a role in chronic inflammatory disorders and may qualify as diagnostic or therapeutic targets;
Publication Title
Autoregulation of Th1-mediated inflammation by twist1.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
The basic helix-loop-helix transcriptional repressor twist1, as an antagonist of nuclear factor B (NF-B)-dependent cytokine expression, is involved in the regulation of inflammation-induced immunopathology. We could show that twist1 is expressed by activated T helper (Th) 1 effector memory cells. Induction of twist1 in Th cells is dependent on NF-B, nuclear factor of activated T cells (NFAT), and interleukin (IL)-12 signaling via signal transducer and activator of transcription (STAT) 4. Expression of twist1 is transient following T-cell receptor engagement, and increases upon repeated stimulation of Th1 cells. Imprinting for enhanced twist1 expression is characteristic of repeatedly restimulated effector memory Th cells and thus of the pathogenic memory Th cells of chronic inflammation. Th lymphocytes from the inflamed joint or gut tissue of patients with rheumatic diseases, Crohns disease or ulcerative colitis express high levels of twist1. Expression of twist1 in Th1 lymphocytes limits the expression of the cytokines interferon-, IL-2 and tumor necrosis factor-, and ameliorates Th1-mediated immunopathology in delayed-type hypersensitivity and antigen-induced arthritis. In order to identify the effect of twist1 expression on the function of Th cells, twist1 was ectopically expressed and the transcriptome was compared to empty-virus infected control cells. In addition, this experiment allows for the identification of genes regulated by the transcription factor twist1.
Publication Title
Autoregulation of Th1-mediated inflammation by twist1.
Sample Metadata Fields
No sample metadata fields
View Samples- Drosophila melanogaster
- 4 Downloadable Samples
Illumina HiSeq 2500
Description
We have investigated the effect of RRP6 depletion on the transcriptome of S2 cells using Illumina deep RNA sequencing. We have also carried out Illumina ChIP-seq analysis of RRP6 genome occupancy in control S2 cells (GFP-KD) and in cells depleted of SU(VAR)3-9. Overall design: 8 samples total; 4 RNA-Seq samples (1 RRP6-KD and 1 GFP-KD, 2 biological replicates each); and 4 ChIP-Seq samples (RRP6 IP in GFP-KD and in Su(var)3-9-KD conditions; plus their respective Input samples).
Publication Title
An Interaction between RRP6 and SU(VAR)3-9 Targets RRP6 to Heterochromatin and Contributes to Heterochromatin Maintenance in Drosophila melanogaster.
Sample Metadata Fields
Subject
View Samples- Arabidopsis thaliana
- 18 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
The Arabidopsis thaliana defense regulator EDM2 was previously shown to be specifically required for disease resistance to the pathogenic oomycete Hyaloperonospora parasitica aradidopsis mediated by the R protein RPP7. We found EDM2 to have a promoting effect on several distinct developmental processes, such as leaf pavement cell development, vegetative phase change or the floral transition. We further identified the atypical protein kinase WNK8 to physically interact with EDM2 in nuclei.
Publication Title
Co-option of EDM2 to distinct regulatory modules in Arabidopsis thaliana development.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 23 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
DCA (3,5-Dichloroanthranilic acid) is a newly identified synthetic defense elicitor. To perform a comparative analysis of defense responses triggered by DCA and the structurally related defense inducer INA (2,6-Dichloroisonicotinic acid) Affymetrix chip experiments were performed with Arabidopsis thaliana seedlings treated with one of these two compounds.
Publication Title
The synthetic elicitor 3,5-dichloroanthranilic acid induces NPR1-dependent and NPR1-independent mechanisms of disease resistance in Arabidopsis.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 18 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Functional characterization of AtWRKY72 using Arabidopsis T-DNA insertion lines showed that this gene is important for basal defense to root-knot nematode (RKN) and Hyaloperonospora parasitica arabidopsis (Hpa), but not several tested R gene-mediated defenses.To profile transcriptional reprogramming associated with AtWRKY72-dependent basal defense we used Affymetrix ATH1 GeneChips representing ~24,000 Arabidopsis genes. Three independent biological replicates were performed with Col-0, wrky72-1 and wrky72-2 plants at 96 hpt with HpaNoco2 or mock treatment. Using a false discovery rate of less than 0.05 we identified for each of these three lines genes that showed significant transcriptional changes in response to HpaNoco2 compared to the mock-treated controls. Identification of downstream targets of WRKY72 in Arabidopsis by this microarray suggests that WRKY72 uses a unique signaling pathway that involves AP2/ERF TFs independent of the ethylene signaling pathway.
Publication Title
WRKY72-type transcription factors contribute to basal immunity in tomato and Arabidopsis as well as gene-for-gene resistance mediated by the tomato R gene Mi-1.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 6 Downloadable Samples
- IlluminaHiSeq2000
Description
We evaluated the transcriptome changes induced by infection with Salmonella (20 hpi, MOI 100). Overall design: Transcriptmic profiles of HeLa cells infected with Salmonella Typhimurium were generated by deep sequencing, using Illumina HiSeq 2000.
Publication Title
Functional high-throughput screening identifies the miR-15 microRNA family as cellular restriction factors for Salmonella infection.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 5 Downloadable Samples
- IlluminaHiSeq2000
Description
We identified miRNAs differentially regulated upon Salmonella infection by comparative deep-sequencing analysis of cDNA libraries prepared from the small RNA population (10–29 nt) of HeLa cells infected with Salmonella (20 hpi) and mock-treated cells. Considering that at a MOI of 25 Salmonella is internalized in only 10-15% of the HeLa cells, we separated the fraction of cells which had internalized Salmonella (Salmonella+) from the bystander fraction (Salmonella-) by fluorescence-activated cell sorting (FACS), and extended the analysis of miRNA changes to these samples. Interestingly, we observed that Salmonella infection induces a significant decrease in the expression of all the detected members of the miR-15 family Overall design: miRNA profiles of HeLa cells infected with Salmonella Typhimurium were generated by deep sequencing, using Illumina HiSeq2000.
Publication Title
Functional high-throughput screening identifies the miR-15 microRNA family as cellular restriction factors for Salmonella infection.
Sample Metadata Fields
No sample metadata fields
View Samples