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SRP135671
Homo sapiens
23 Downloadable Samples
Illumina HiSeq 2500
Description
Background: Diverticular disease is a significant healthcare burden in the United States. Younger diverticulitis patients are at increased risk for recurrence. How the molecular pathophysiology differs from those that develop disease at an older age is not understood. We aimed to profile the colonic transcriptome from younger versus older diverticulitis patients to identify differential biological pathways contributing to disease. Methods: We performed RNA-seq on full-thickness sigmoid colon tissue obtained at the time of surgery on diverticulitis patients (n=26) diagnosed at a younger age (<42 years old) or at an older age (>65 years old). Viral reads were identified from the RNA-seq dataset and associated with clinical metadata and the host transcriptome. HHV-6 positivity was evaluated in diverticulitis patients by PCR and immunofluorescence. Patient sera was profiled for HHV-6 using qPCR and ELISA to detect anti-HHV-6 antibodies. Results: Using RNA-seq, diverticulitis patients were profiled for differential expression associated with age of diagnosis. A subset of younger diverticulitis patients (diverticulitis colonic transcriptome-viral signature (DCT-VS)) demonstrated increased expression of anti-viral response genes. We identified viral transcripts in the RNA-seq dataset and found HHV-6 transcripts negatively correlated with DCT-VS. Younger patients more frequently displayed evidence of HHV-6 infection through DNA analysis and immunofluorescence of colonic tissue. During acute disease, HHV-6 DNA was detected in the serum but was absent during disease quiescence. Conclusions: Patients diagnosed with diverticulitis at a younger age demonstrate reactivation of HHV-6 in the sigmoid colon that remains persistent. Future studies to assess the role of pathogenicity and the use of anti-virals for acute uncomplicated diverticulitis should be considered. Overall design: Examination of full-thickness sigmoid colon tissue from 26 diverticulitis patients, including 13 diagnosed at an younger age (<42 years old) and 13 diagnosed at an older age (>65 years old)
Publication Title
A differential host response to viral infection defines a subset of earlier-onset diverticulitis patients.
Sample Metadata Fields
Sex, Specimen part, Race, Subject
View Samples- Mus musculus
- 6 Downloadable Samples
Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Epithelial-mesenchymal transition (EMT) and mesenchymal-epithelial transition (MET) facilitate breast cancer (BC) metastasis, however stable molecular changes that result as a consequence of these processes remain poorly defined. Therefore, we sought to identify molecular markers that could distinguish tumor cells that had completed the EMT:MET cycle in the hopes of identifying and targeting unique aspects of metastatic tumor outgrowth.Therefore, normal murine mammary gland (NMumG) cells transformed by overexpression of EGFR (NME) cells were cultured in the presence of TGF-beta1 (5 ng/ml) for 4 weeks, at which point TGF-beta1 supplementation was discontinued and the cells were allowed to recover for an additional 4 weeks (Post-TGF-Rec). Total RNA was prepared from unstimulated cells (Pre-TGF) of similar passage and compared by microarray analysis.
Publication Title
Fibroblast growth factor receptor splice variants are stable markers of oncogenic transforming growth factor β1 signaling in metastatic breast cancers.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 18 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
The pesticide rotenone, a neurotoxin that inhibits the mitochondrial complex I, and destabilizes microtubules (MT) has been linked to Parkinson disease (PD) etiology and is often used to model this neurodegenerative disease (ND). Many of the mechanisms of action of rotenone are posited mechanisms of neurodegeneration; however, they are not fully understood. Therefore, the study of rotenone-affected functional pathways is pertinent to the understanding of NDs pathogenesis. This report describes the transcriptome analysis of a neuroblastoma (NB) cell line chronically exposed to marginally toxic and moderately toxic doses of rotenone. The results revealed a complex pleiotropic response to rotenone that impacts a variety of cellular events, including cell cycle, DNA damage response, proliferation, differentiation, senescence and cell death, which could lead to survival or neurodegeneration depending on the dose and time of exposure and cell phenotype. The response encompasses an array of physiological pathways, modulated by transcriptional and epigenetic regulatory networks, likely activated by homeostatic alterations. Pathways that incorporate the contribution of MT destabilization to rotenone toxicity are suggested to explain complex I-independent rotenone-induced alterations of metabolism and redox homeostasis. The postulated mechanisms involve the blockage of mitochondrial voltage-dependent anions channels (VDACs) by tubulin, which coupled with other rotenone-induced organelle dysfunctions may underlie many presumed neurodegeneration mechanisms associated with pathophysiological aspects of various NDs including PD, AD and their variant forms. Thus, further investigation of such pathways may help identify novel therapeutic paths for these NDs.
Publication Title
Transcriptome analysis of a rotenone model of parkinsonism reveals complex I-tied and -untied toxicity mechanisms common to neurodegenerative diseases.
Sample Metadata Fields
Cell line, Treatment, Time
View Samples- Arabidopsis thaliana
- 24 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
The root epidermis of Arabidopsis provides a simple and experimentally useful model for studying the molecular basis of cell fate and differentiation. The goal of this study was to define the transcript changes in the root epidermis of mutants associated with root epidermis cell specification, including mutants that lack a visible phenotypic alteration (try, egl3, myb23, and ttg2). Transcript levels were assessed by purifying populations of root epidermal cells using fluorescence-based cell-sorting with the WER::GFP transgene. These microarray results were used to compare the effects of single and double mutants on the gene regulatory network that controls root epidermal cell fate and differentiation in Arabidopsis.
Publication Title
Tissue-specific profiling reveals transcriptome alterations in Arabidopsis mutants lacking morphological phenotypes.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 51 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Cell identity mediates the response of Arabidopsis roots to abiotic stress.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 36 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Cell-type specific transcriptional profiles were generated by FACS (Fluorescence Activated Cell Sorting) sorting of roots that express cell-type specific GFP-reporters. Six different GFP-reporter lines were utilized allowing us to obtain transcriptional profiles for cells in all radial zones of the root. FACS cell populations were isolated from roots grown under standard conditions or roots that had been transfered to media supplemented with 140 mM NaCl for 1 hour.
Publication Title
Cell identity mediates the response of Arabidopsis roots to abiotic stress.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 16 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
To gain a genome-scale understanding of the role that developmental processes play in regulating stimulus response, we examined the effect of salt stress on gene expression along the longitudinal axis of the root. Since roots grow from stem cells located near the tip, the position of cells along the longitudinal axis can be used as a proxy for developmental time, with distance from the root tip correlating with increased differentiation. To estimate the role developmental stage plays in regulating salt response, roots were dissected into four longitudinal zones (LZ data set) after transfer to standard or salt media and transcriptionally profiled.
Publication Title
Cell identity mediates the response of Arabidopsis roots to abiotic stress.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 16 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
We performed an expression analysis of the response of seedling root tips to 1 hour of treatment with 140mM NaCl using mutants defective in root hair patterning.
Publication Title
Cell identity mediates the response of Arabidopsis roots to abiotic stress.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 15 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Cell-type specific transcriptional profiles were generated by FACS (Fluorescence Activated Cell Sorting) sorting of roots that express cell-type specific GFP-reporters. Five different GFP-reporter lines were utilized allowing us to obtain transcriptional profiles for cells in all radial zones of the root. FACS cell populations were isolated from roots grown under standard conditions or roots that had been transfered to -Fe media for 24 hours.
Publication Title
Cell identity mediates the response of Arabidopsis roots to abiotic stress.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 16 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
To gain a genome-scale understanding of the role that developmental processes play in regulating stimulus response, we examined the effect of -Fe stress on gene expression along the longitudinal axis of the root. Since roots grow from stem cells located near the tip, the position of cells along the longitudinal axis can be used as a proxy for developmental time, with distance from the root tip correlating with increased differentiation. To estimate the role developmental stage plays in regulating salt response, roots were dissected into four longitudinal zones (LZ data set) after transfer to standard or -Fe media and transcriptionally profiled.
Publication Title
Cell identity mediates the response of Arabidopsis roots to abiotic stress.
Sample Metadata Fields
No sample metadata fields
View Samples