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GSE79631
Mus musculus
2 Downloadable Samples
Affymetrix Mouse Gene 2.1 ST Array (mogene21st)
Description
Nlrp6-/- lamina propria Ly6C-hi monocytes in response to AOM/DSS have deficient TNF production, but increased production of other pro-inflammatory cytokines as compared to WT
Publication Title
NLRP6 function in inflammatory monocytes reduces susceptibility to chemically induced intestinal injury.
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 7 Downloadable Samples
- Affymetrix Rat Genome U34 Array (rgu34a)
Description
Chronic alcohol ingestion changes the alveolar landscape. We used microarrays to characterize the change in mRNA expression following chronic alcohol ingestion in male Sprague Dawley rates (EtOH 36% of calories)
Publication Title
Chronic ethanol exposure alters the lung proteome and leads to mitochondrial dysfunction in alveolar type 2 cells.
Sample Metadata Fields
Sex, Specimen part
View Samples- Drosophila melanogaster
- 4 Downloadable Samples
Illumina Genome Analyzer II
Description
We use mRNA-seq to transcriptionally profile larval salivary gland tissue from Drosophila third instar larvae. These data provide insights into tissue physiology and can be used to identify tissue specific transcripts. Overall design: Salivary glands were dissected from 200 wandering third instar larvae and the associated fat body was removed.Salivary glands were transferred to Graces unsupplemented medium on ice prior to RNA extraction with TRIzol reagent. mRNA-seq samples were prepared from 10 ug of total RNA and subject to Illumina based sequencing.
Publication Title
Developmental control of gene copy number by repression of replication initiation and fork progression.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 16 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
One of the most likely risks astronauts on long duration space missions face is exposure to ionizing radiation associated with highly energetic and charged heavy (HZE) particles. Since access to medical expertise on such a mission is limited at best, early diagnosis and mitigation of such exposure is critical. In order to accurately determine the dosage within 1 hour post-exposure, dose-dependent biomarkers are needed. Therefore, we performed a dose-course transcriptional analysis for radiation exposure at 0, 0.3, 1.5, and 3.0 Gy with corresponding time point at 1 hour (hr) post-exposure using Affymetrix GeneChip Human Gene 1.0 ST v1 Array chips. The analysis of our data suggests a set of sensitive genetic biomarkers specific to each radiation level as well as generic radiation response biomarkers. Upregulated biomarkers can then be used within lab-on-a-chip (LOC) systems to detect exposure to ionizing radiation.
Publication Title
Transcriptional profile of immediate response to ionizing radiation exposure.
Sample Metadata Fields
Specimen part, Time
View Samples- Homo sapiens
- 12 Downloadable Samples
- Illumina HiSeq 2500
Description
Using the recently described CD104+/CD44hi antigen combination we demonstrate that tumorigenicity depends on individual cells residing in a hybrid E/M state. Acquisition of this E/M hybrid state is facilitated by the differential expression of EMT- TFs, like Snail accompanied by the expression of adult stem-cell programs. Transition from the highly tumorigenic E/M state to a fully mesenchymal phenotype, achieved by constitutive ectopic expression of Zeb1, is sufficient to drive cells out of the E/M hybrid state into an extreme mesenchymal (xM) state, which is accompanied by a substantial loss of tumorigenicity and a switch from canonical to non-canonical Wnt signaling. Overall design: Performing RNASeq with HMLE (immortalized human mammary epithelial cells) in different EMT stages, either in the E state the hybrid E/M state or the extreme mesenchymal (xM) state as determined by sorting for CD104 and CD44. And performing RNASeq with HMLE cells locked in the xE state by Zeb1KO (xE-SCC-Zeb1KO), from there transferred to the hybrid E/M state by Snail overexpression (E-SCC-Zeb1KOSn) or rescued and transitioned to an xM state with CRISPR resistant Zeb1 wobble mutant (mt) (E-SCC-Zeb1KOSnZmt).
Publication Title
Acquisition of a hybrid E/M state is essential for tumorigenicity of basal breast cancer cells.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
For gene expression profiling, we used immortalized human mammary epithelial cells (HMLE) to isolate a pure epithelial fraction of cells by positive selection for CD24 expression using Magnetic Activated Cell Sorting (=24hi).
Publication Title
Paracrine and autocrine signals induce and maintain mesenchymal and stem cell states in the breast.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
Angiogenesis is essential for tissue development, wound healing and tissue perfusion, with its dysregulation linked-to tumorigenesis, rheumatoid arthritis and heart disease. Here we show pro-angiogenic stimuli couple to NADPH oxidase-dependent generation of oxidants that catalyse an activating intermolecular-disulphide between regulatory-RI subunits of protein kinase A (PKA), which stimulates PKA-dependent ERK signalling. This is crucial to blood vessel growth as 'redox-dead' Cys17Ser RI knock-in mice fully resistant to PKA disulphide-activation have deficient angiogenesis in models of hind limb ischaemia and tumour-implant growth. Disulphide-activation of PKA represents a new therapeutic target in diseases with aberrant angiogenesis.
Publication Title
Deficient angiogenesis in redox-dead Cys17Ser PKARIα knock-in mice.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 24 Downloadable Samples
- Illumina HiSeq 2000
Description
Acquired drug resistance prevents targeted cancer therapy from achieving stable and complete responses. Emerging evidence implicates a key role for nonmutational mechanisms including changes in cell state during early stages of acquired drug resistance. Targeting nonmutational resistance may therefore present a therapeutic opportunity to eliminate residual surviving tumor cells and impede relapse. A variety of cancer cell lines harbor quiescent, reversibly drug-tolerant “persister” cells which survive cytotoxic drugs including targeted therapies and chemotherapies. These persister cells survive drug through nonmutational mechanisms which are poorly understood. Specifically targeting persister cells is a promising strategy to prevent tumor relapse. We sought to identify therapeutically exploitable vulnerabilities in persister cells using the HER2-amplified breast cancer line BT474 as an experimental model. Similar to other persister cell models, upon treatment with the HER2 inhibitor lapatinib (2uM concentration) for nine or more days, the majority of BT474 cells die, revealing a small population of quiescent surviving persister cells. Removal of lapatinib allows the persister cells to regrow and to re-acquire sensitivity to lapatinib. Subsequent lapatinib treatment re-derives persister cells. The reversibility of persister cell drug resistance indicates a nonmutational resistance mechanism. Here we provide RNAseq gene expression profiling data generated from parental BT474 cells compared to BT474 persister cells generated from nine days of treatment with 2 uM lapatinib. These data can be used to identify genes and pathways which are upregulated in persister cells, revealing potential therapeutic targets. Overall design: 3 biological replicates of BT474 persister cells, two biological replicates of BT474 parental cells
Publication Title
Drug-tolerant persister cancer cells are vulnerable to GPX4 inhibition.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Drosophila melanogaster
- 9 Downloadable Samples
- Illumina HiSeq 2500
Description
The goal of this study was to identify ion channels, specifically transient receptor potential cation channel A (trpA1) channels, that were highly expressed and enriched in nociceptive sensory neurons of Drosophila larvae. In class IV da sensory neurons, we find that TrpA1 is the most highly expressed trpA1 channel of the 14 trpA1 channels in Drosophila, and that its expression is highly enriched when compared to the whole animal transcriptome. Overall design: Four biological replicates of 100 Drosophila melanogaster larval class IV dendritic arborization sensory neurons and five biological replicates of whole Drosophila melanogaster larvae were profiled by mRNA-Seq
Publication Title
TrpA1 activation in peripheral sensory neurons underlies the ionic basis of pain hypersensitivity in response to vinca alkaloids.
Sample Metadata Fields
Subject
View Samples- Mus musculus
- 5 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Dual oxidases play a role in innate host defense at barrier epithelia. We examined the effect of loss of dual oxidase function (duoxa-/-) on gene expression in the mouse terminal ileum at homeostasis. To control for cage/litter effects, duoxa-/- were cohoused with wild type littermate controls.
Publication Title
Increased Expression of DUOX2 Is an Epithelial Response to Mucosal Dysbiosis Required for Immune Homeostasis in Mouse Intestine.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples