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SRP099448
Mus musculus
40 Downloadable Samples
Illumina HiSeq 2500
Description
We performed an RNA Sequencing experiment on dorsal hippocampal tissue from six groups of animals: Aging (18-20-month-old) HDAC3flox/flox homecage (H3F-HC); Aging (18-20-month-old) HDAC3flox/flox 60min post training (H3F-BV); Aging (18-20-month-old) wildtype homecage (OWT-HC); Aging (18-20-month-old) wildtype 60min post training (OWT-BV); Young (2-4-month-old) wildtype homecage (YWT-HC); Young (2-4-month-old) wildtype 60min post training (YWT-BV). Homecage animals were sacrificed directly from the animal's cage. Behavior animals were sacrificed sixty minutes following a 10min Object Location Memory training session. Overall design: The objective of this study was to examine activity regulated gene expression in the dorsal hippocampus following a learning event in young (~3-m.o.) and old (~18-m.o.) wildtype and HDAC3flox/flox mutant mice. HDAC3 was deleted in dorsal hippocampus tissue of HDAC3flox/flox mice using AAV-CaMKII-Cre before behavior.
Publication Title
Epigenetic regulation of the circadian gene Per1 contributes to age-related changes in hippocampal memory.
Sample Metadata Fields
Cell line, Subject, Time
View Samples- Drosophila melanogaster
- 41 Downloadable Samples
- Illumina HiSeq 2000
Description
Control of metazoan embryogenesis shifts from maternal to zygotic gene products as the zygotic genome becomes transcriptionally activated. In Drosophila, zygotic genome activation (ZGA) begins with a minor wave, but technical challenges have hampered the identification of early transcripts or obscured the onset of their transcription. Here, we develop an approach to isolate transcribed mRNAs and apply it over the course of the minor wave and the start of the major wave of Drosophila ZGA. Our results increase known genes of the minor wave by 10 fold and show that this wave is continuous and gradual. Transposable-element mRNAs are also produced, but discontinuously. Genes in the early and middle part of the minor wave are short with few if any introns, and their transcripts are frequently aborted and tend to have retained introns, suggesting that inefficient splicing as well as rapid cell divisions constrain the lengths of early transcripts. Overall design: The goal of this study is to use NGS to identify zygotic transcripts produced during early zygotic genome activation in Drosophila.
Publication Title
Early genome activation in <i>Drosophila</i> is extensive with an initial tendency for aborted transcripts and retained introns.
Sample Metadata Fields
Subject
View Samples- Homo sapiens
- 12 Downloadable Samples
Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Analysis of the human monocyte-derived macrophage (hMDM) transcriptional response to L. pneumophila infection at 8 hours post-infection
Publication Title
The transcriptome of Legionella pneumophila-infected human monocyte-derived macrophages.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 24 Downloadable Samples
- Illumina HiSeq 2500
Description
In cell stress, mRNA in the cytoplasm is sequestered to the insoluble ribonucleoprotein (RNP) compartments containing stress granules. These RNP granules are known to be involved in the control of mRNA processing and decay, but it has been elusive whether the mRNA redistribution in cell stress is universal or specific to a subset of transcripts. Here we provide a transcriptome-wide profiles of the RNP granules in cell stress and show that mRNA accumulation in stress granule differentially affects individual transcripts. mRNA species accumulated in stress granules are largely conserved across distinct stress types, such as in endoplasmic reticulum stress, heat shock and arsenic stress. Many mRNA species involved in cell survival and proliferation are more dynamically redistributed, suggesting that mRNA sequestration can be a specific response mechanism through which cells can reshape the landscape of their transcriptome and affect the cell fate determination in stress conditions . Overall design: 24 samples are analyzed, which include 3 replicates for control (DMSO) cytoplasmic fraction, 3 replicates of control (DMSO) RNP granule fraction, 3 replicates of Thapsigargin treated cytoplasmic fraction, 3 replicates of Thapsigargin treated RNP granule fraction, 2 replicates of control (H2O) cytoplasmic fraction, 2 replicates of control (H2O) RNP granule fractions, 2 replicates of heat shock (HS) treated cytoplsmic fraction (HS), 2 replicates of heat shock (HS) treated RNP granule fraction, 2 replicates of arsenite treated cytoplasmic fraction, and 2 replicates of arsenite treated RNP granule fraction.
Publication Title
Systematic Characterization of Stress-Induced RNA Granulation.
Sample Metadata Fields
Cell line, Treatment, Subject
View Samples- Mus musculus
- 7 Downloadable Samples
- Illumina Genome Analyzer II
Description
An immortalized multipotent otic progenitor (iMOP) cell was generated by transient expression of c-Myc in Sox2-expressing otic progenitor cells. The procedure activated endogenous c-Myc expression in the cells and amplified existing Sox2-dependent transcripts to promote self-renewal. Downregulation of c-Myc expression following growth factor withdrawal resulted in a molecular switch from self-renewal to otic differentiation. Overall design: Progenitor cells from embryonic inner ear that form otospheres were infected with a c-Myc retrovirus to promote self-renewal
Publication Title
SHIELD: an integrative gene expression database for inner ear research.
Sample Metadata Fields
No sample metadata fields
View Samples- Escherichia coli k-12
- 2 Downloadable Samples
- Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
Persister cells are a sub-population of all bacterial cultures which exhibit a non-inheritable, multi-drug tolerance when subjected to lethal antibiotic challenge. These persisters arise as a result of metabolic dormancy, and can resume growth subsequent to antibiotic challenge, leading to recalcitrance of bacterial infections.
Publication Title
Phosphodiesterase DosP increases persistence by reducing cAMP which reduces the signal indole.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The Lim1 gene has essential functions during several stages of kidney development. In particular, a tissue specific knockout in the early metanephric mesenchyme results in the formation of the earliest nephron precursor, the renal vesicle, but failure of this structure to progress to the next stage, the comma shaped body. To better understand the molecular nature of this developmental arrest we used a laser capture microdissection-microarray strategy to examine the perturbed gene expression pattern of the mutant renal vesicles. Among the genes found differently expressed were Chrdl2, an inhibitor of BMP signaling, the pro-apoptotic factor Bmf, as well as myob5, an atypical myosin which modulates chemokine and transferring signaling, and pdgfr1, which is important in epithelial folding. Of particular interest, the microarray data indicated that the Dkk1 gene, which encodes an inhibitor of Wnt signaling, was downregulated nine fold in mutants. This was confirmed by in situ hybridizations. It is interesting to note that Lim1 and Dkk1 mutant mice have striking similarities in phenotype. These results suggest that the Dkk1 gene might be a key downstream effector of Lim1 function.
Publication Title
Laser capture-microarray analysis of Lim1 mutant kidney development.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
BACKGROUND: Lim1 is a homeobox gene that is essential for nephrogenesis. During metanephric kidney development, Lim1 is expressed in the nephric duct, ureteric buds, and the induced metanephric mesenchyme. Conditional ablation of Lim1 in the metanephric mesenchyme blocks the formation of nephrons at the nephric vesicle stage, leading to the production of small, non-functional kidneys that lack nephrons.
Publication Title
Gene expression profiles in developing nephrons using Lim1 metanephric mesenchyme-specific conditional mutant mice.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 39 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
Background:Alternative splicing and isoform level expression profiling is an emerging field of interest within genomics. Splicing sensitive microarrays, with probes targeted to individual exons or exon-junctions, are becoming increasingly popular as a tool capable of both expression profiling and finer scale isoform detection. Despite their intuitive appeal, relatively little is known about the performance of such tools, particularly in comparison with more traditional 3 targeted microarrays. Here, we use the well studied Microarray Quality Control (MAQC) dataset to benchmark the Affymetrix Exon Array, and compare it to two other popular platforms: Illumina, and Affymetrix U133.
Publication Title
Gene expression and isoform variation analysis using Affymetrix Exon Arrays.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 20 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
Background:Alternative splicing and isoform level expression profiling is an emerging field of interest within genomics. Splicing sensitive microarrays, with probes targeted to individual exons or exon-junctions, are becoming increasingly popular as a tool capable of both expression profiling and finer scale isoform detection. Despite their intuitive appeal, relatively little is known about the performance of such tools, particularly in comparison with more traditional 3 targeted microarrays. Here, we use the well studied Microarray Quality Control (MAQC) dataset to benchmark the Affymetrix Exon Array, and compare it to two other popular platforms: Illumina, and Affymetrix U133.
Publication Title
Gene expression and isoform variation analysis using Affymetrix Exon Arrays.
Sample Metadata Fields
No sample metadata fields
View Samples