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E-MTAB-78
Saccharomyces cerevisiae
36 Downloadable Samples
Affymetrix Yeast Genome S98 Array (ygs98)
Description
A three-factor design was applied to study the relationship between specific growth rate and genome-wide gene expression in 36 steady-state chemostat cultures of Saccharomyces cerevisiae.
Publication Title
Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: a three factor design.
Sample Metadata Fields
No sample metadata fields
View Samples- Bos taurus
- 9 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
The bovine chromaffin cell (BCC) is a unique modela highly homogeneous and accessible neuroendocrine cellin which to study gene regulation through first messenger-initiated signaling pathways that are specific to post-mitotic cells. BCCs were treated with tumor necrosis factor (TNF) or pituitary adenylate cyclase activating polypeptide (PACAP), two critical regulators of neural cell transcriptional programming during inflammation that act on TNFR2 and PAC1 receptors, respectively, in post-mitotic neuroendocrine cells. Transcripts which were significantly up regulated by either or both first messenger were identified from microarray analysis using two bovine oligonucleotide arrays (Affymetrix and Agilent) followed by statistical analysis with Partek Genomic suite. Microarray data were combined from the two arrays using qRT-PCR sampling validation, and the first-messenger transcriptome derived from TNF and PACAP signaling were compared. More than 90 percent of the genes up regulated either by TNF or PACAP were specific to a single first messenger. BioBase suite, DIRE and Opossum were used to identify common promoter/enhancer response elements that control the expression of TNF- or PACAP-stimulated genes. Bioinformatic analysis revealed that distinct groups of transcription factors control the expression of genes up regulated by either TNF or PACAP . Most of the genes up regulated by TNF contained response elements for members of the Rel transcription factor family, suggesting TNF-TNFR2 signaling mainly through the NF-kB signaling pathway. On the other hand, the PACAP regulated genes showed no enrichment for any single response element, containing instead response elements for combinations of transcription factors allowing activation through multiple signaling pathways, including cAMP, calcium and ERK, in neuroendocrine cells. Pharmacological strategies for mimicking neuroprotection by either PACAP or TNF in the context of CNS injury or degeneration in disease might focus on individual downstream gene activation pathways to achieve greater specificity in vivo.
Publication Title
Neuropeptides, growth factors, and cytokines: a cohort of informational molecules whose expression is up-regulated by the stress-associated slow transmitter PACAP in chromaffin cells.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 12 Downloadable Samples
- Illumina MouseWG-6 v2.0 expression beadchip
Description
Analysis of gene expression profile in peritoneal macrophage extracted from LPS or PBS challenged DUSP3-/- and WT mice. DUSP3 deletion protects mice from sepsis and endotoxemia. We performed a microarray analysis to get insights into the differentially regulated pathways between WT and KO under inflammatory conditions.
Publication Title
DUSP3 Genetic Deletion Confers M2-like Macrophage-Dependent Tolerance to Septic Shock.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Macaca mulatta
- 16 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Rhesus monkey extraocular muscle. Data set includes: (a) whole medial and lateral rectus muscle and (b) global and orbital muscle layers separately microdissected using a Leica LSM. All samples were expression profiled here using the Affymetrix human U133 A&B arrays. Data form part of publication: Investigative Ophthalmology and Visual Science 45, 2004.
Publication Title
Genome-wide transcriptional profiles are consistent with functional specialization of the extraocular muscle layers.
Sample Metadata Fields
No sample metadata fields
View Samples- Bos taurus
- 3 Downloadable Samples
Illumina HiScanSQ
Description
We report RNAseq analysis of the transcriptome of 3 biological replicates of bovine retina Overall design: Examine retinal transcriptome of 3 biological replicates with tissue collected between 7:00 - 10:00AM
Publication Title
Argonaute high-throughput sequencing of RNAs isolated by cross-linking immunoprecipitation reveals a snapshot of miRNA gene regulation in the mammalian retina.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 9 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
We report RNA-Seq experiments of whole eye tissues from A/J, BALB/c, and C57BL/6 background mice. Overall design: Examine ocular tissue from 3 different background mice that display varying rates of retinal degeneration.
Publication Title
Transcriptome analysis reveals rod/cone photoreceptor specific signatures across mammalian retinas.
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Subject
View Samples- Mus musculus
- 9 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
We report RNA-Seq experiments of eye and retinal tissues from WT and RHO KO mice Overall design: Examine ocular tissue from different mouse genotypes
Publication Title
Transcriptome analysis reveals rod/cone photoreceptor specific signatures across mammalian retinas.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
The goal of this study is to determine whether A1 adenosine receptor (ADORA1) plays a role in atherosclerosis development and its possible mechanisms. This dataset compares gene expression (aortas) of ADORA1 knockout mice to ADORA1+APOE double-knockout mice.
Publication Title
A₁ adenosine receptor deficiency or inhibition reduces atherosclerotic lesions in apolipoprotein E deficient mice.
Sample Metadata Fields
Age, Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
We report RNA-Seq experiments of whole eye tissues from C57BL/6J background mice at 1.5 h and 9.0 h after light onset to better understand photoreceptor phagocytosis Overall design: Examine ocular tissue from mice at different time points
Publication Title
Transcriptome analysis reveals rod/cone photoreceptor specific signatures across mammalian retinas.
Sample Metadata Fields
Specimen part, Cell line, Subject, Time
View Samples- Macaca mulatta
- 19 Downloadable Samples
- Affymetrix Rhesus Macaque Genome Array (rhesus)
Description
Laser capture microdissection was used to obtain individual LGN layers for DNA microarray of Rhesus array in macaque monkeys that Monocular Visual Deprivation was generated by either opaque dark contact lens or tarsoraphoplasty at birth.
Publication Title
Monocular visual deprivation in macaque monkeys: a profile in the gene expression of lateral geniculate nucleus by laser capture microdissection.
Sample Metadata Fields
No sample metadata fields
View Samples