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SRP159291
Pseudomonas aeruginosa
10 Downloadable Samples
Illumina HiSeq 2500
Description
Purpose: The goal of this study was to use RNA Seq to explore whether and to what extent genetic heterogeneity would shape the transcriptional profile in the environment of the CF lung Methods : mRNA profiles were generated for Pseudomonas aerugionsa samples derived from explanted lung tissue or pure cultures isolated from the same lung regions by deep sequencing. To enrich the bacterial RNA MicrobeEnrich Kit (Ambion) was used. The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina) . The samples were sequenced in single end mode on an Illumina HiSeq 2500 device and mRNA reads were trimmed and mapped to the PAO1 NC_002516 reference genome from NCBI using Stampy pipeline with defaut settings. Overall design: mRNA profiles either from Pseudomonas aeruginosa containing explanted lung tissue from a single patient from various regions of the lung or pure P. aeruginosa liquid cultures grown in LB at 37C from the same lung regions as the ex vivo samples were generated and deep sequenced using Illumina HiSeq 2500.
Publication Title
Genetically diverse Pseudomonas aeruginosa populations display similar transcriptomic profiles in a cystic fibrosis explanted lung.
Sample Metadata Fields
Subject
View Samples- Escherichia coli
- 6 Downloadable Samples
Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
Mutation of marA, rob, and soxS causes a clinical strain of E.coli to be attenuated at d3 post-infection in a mouse model of pyelonephritis, here we extract RNA at d2 post infection to analyze transcriptional differences between the two strains.
Publication Title
SoxS increases the expression of the zinc uptake system ZnuACB in an Escherichia coli murine pyelonephritis model.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
F4/80+ macrophages treated with TGFb2 are potently tolerogenic. Our understanding of the molecular mechanisms mediating the development of these tolerogenic properties is incomplete.
Publication Title
FcγRI is required for TGFβ2-treated macrophage-induced tolerance.
Sample Metadata Fields
Sex, Specimen part, Treatment
View Samples- Mus musculus
- 30 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Identification of the cortical neurons that mediate antidepressant responses.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Molecular phenotyping of cell types and neural circuits underlying pathological neuropsychiatric conditions and their responses to therapy provides one avenue for the development of more specific and effective treatments. In this study, we identify a cell population in the cerebral cortex that shows robust and specific molecular adaptations following long-term SSRI treatment.
Publication Title
Identification of the cortical neurons that mediate antidepressant responses.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Molecular phenotyping of cell types and neural circuits underlying pathological neuropsychiatric conditions and their responses to therapy provides one avenue for the development of more specific and effective treatments. In this study, we identify a cell population in the cerebral cortex that shows robust and specific molecular adaptations following long-term SSRI treatment.
Publication Title
Identification of the cortical neurons that mediate antidepressant responses.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Molecular phenotyping of cell types and neural circuits underlying pathological neuropsychiatric conditions and their responses to therapy provides one avenue for the development of more specific and effective treatments. In this study, we identify a cell population in the cerebral cortex that shows robust and specific molecular adaptations following long-term SSRI treatment.
Publication Title
Identification of the cortical neurons that mediate antidepressant responses.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Molecular phenotyping of cell types and neural circuits underlying pathological neuropsychiatric conditions and their responses to therapy provides one avenue for the development of more specific and effective treatments. In this study, we identify a cell population in the cerebral cortex that shows robust and specific molecular adaptations following long-term SSRI treatment.
Publication Title
Identification of the cortical neurons that mediate antidepressant responses.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Molecular phenotyping of cell types and neural circuits underlying pathological neuropsychiatric conditions and their responses to therapy provides one avenue for the development of more specific and effective treatments. In this study, we identify a cell population in the cerebral cortex that shows robust and specific molecular adaptations following long-term SSRI treatment.
Publication Title
Identification of the cortical neurons that mediate antidepressant responses.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 29 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Breast cancer develops through the accumulation of genomic changes in the ductal epithelia cells of normal breast tissue. A determination of whether gene expression changes in ductal cells is associated with an increased risk for breast cancer is needed. We sought to determine if the global gene expression profiles of ductal cells of women at high risk for breast cancer or with cytologic ductal epithelial atypia differed from those of women at normal risk or without cytologic atypia.
Publication Title
Characteristics of Breast Ducts in Normal-Risk and High-risk Women and Their Relationship to Ductal Cytologic Atypia.
Sample Metadata Fields
Specimen part, Disease stage
View Samples