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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- Mus musculus
- 36 Downloadable Samples
Illumina MouseWG-6 v2.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Bromodomain-dependent stage-specific male genome programming by Brdt.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 36 Downloadable Samples
- Illumina MouseWG-6 v2.0 expression beadchip
Description
Male germ cell differentiation is a highly regulated multistep process initiated by the commitment of progenitor cells into meiosis and characterized by major chromatin reorganizations in haploid spermatids. We report here that a single member of the double bromodomain BET factors, Brdt, is a master regulator of both meiotic divisions and post-meiotic genome repackaging. Upon its activation at the onset of meiosis, Brdt drives and determines the developmental timing of a testis-specific gene expression program. In meiotic cells, Brdt initiates a genuine histone acetylation-guided programming of the genome by activating essential meiotic genes and repressing a progenitor cells gene expression program, while priming a post-meiotic gene group for further activation. At post-meiotic stages, a global chromatin hyperacetylation gives the signal for Brdts first bromodomain to direct the genome-wide replacement of histones by transition proteins. Brdt is therefore a unique and essential regulator of male germ cell differentiation, which, by using various domains in a developmentally controlled manner, first drives a specific spermatogenic gene expression program, and later controls the tight packaging of the male genome.
Publication Title
Bromodomain-dependent stage-specific male genome programming by Brdt.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Gene 2.1 ST Array (mogene21st)
Description
In vitro differentiated Th17 have a distinct expression profile compared to in vivo differentiated Th17
Publication Title
Inhibiting Oxidative Phosphorylation In Vivo Restrains Th17 Effector Responses and Ameliorates Murine Colitis.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 16 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
In order to establish a list of candidate direct COUP-TFI gene targets in the inner ear, we analyzed the differential gene expression profiles of the wild-type and the COUP-TFI/ P0 inner ears.
Publication Title
Genome-wide analysis of binding sites and direct target genes of the orphan nuclear receptor NR2F1/COUP-TFI.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Male patients (n=6, mean age 62 years) with NYHA III-IV and an left ventricular ejection fraction of <35% despite pharmacological therapy received 35 hours of enhanced external counterpulsation (EECP) over a period of 7 weeks.
Publication Title
Effects of enhanced external counterpulsation on skeletal muscle gene expression in patients with severe heart failure.
Sample Metadata Fields
Sex, Specimen part, Treatment, Subject
View Samples- Drosophila melanogaster
- 12 Downloadable Samples
- Affymetrix Drosophila Genome Array (drosgenome1)
Description
Cell migration contributes to normal development and homeostasis as well as to pathological processes such as inflammation and tumor metastasis. Previous genetic screens have revealed a few major signaling pathways that govern follicle cell migrations in the Drosophila ovary, several of which elicit transcriptional responses. However few downstream targets of the critical transcriptional regulators, such as the C/EBP homolog SLBO, have been identified. To characterize the gene expression profile of two migratory cell populations and identify SLBO targets, we employed a magnetic bead based cell separation approach to purify border cells and centripetal cells expressing the mouse CD8 antigen, and carried out whole genome microarray analysis.
Publication Title
Analysis of cell migration using whole-genome expression profiling of migratory cells in the Drosophila ovary.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 6 Downloadable Samples
- Illumina HiSeq 4000
Description
We have analyzed RNA-seq data to identify A-to-I editing sites in two groups of samples: one group isolated from human U87 cell line expressing an active ADAR3 mutant while the other isolated from U87 cell line expressing the inactive counterpart of the ADAR3 mutant. We compared these two groups of samples and identified sites whose editing levels are higher in the first group than in the second group. Overall design: Examine A-to-I editing sites in two group of samples.
Publication Title
RNA binding candidates for human ADAR3 from substrates of a gain of function mutant expressed in neuronal cells.
Sample Metadata Fields
Specimen part, Disease, Disease stage, Subject
View Samples- Homo sapiens
- 24 Downloadable Samples
- Ion Torrent Proton
Description
Cells can survive effector caspase (caspase 3/7) activation in response to transient apoptotic stimuli, a process named anastasis. To characterize the molecular events that occur during anastasis, we performed whole transcriptome RNA sequencing of untreated, apoptotic, and recovering cells. We found that anastasis is an active, two-stage program with unique transcriptional profiles in each stage. We also identified 10 genes that specific to the early stage of anastasis. Overall design: 3hr ethanol treatment was used to induce apoptosis in Hela cells. Ethanol was washed away after 3hr treatment to allow cells to recover. Total RNA was prepared from mock-treated cells, ethanol-treated cells and cells after 1hr, 2hr, 3hr, 4hr, 8hr, 12hr recovery, followed by ribosomal RNA depletion. 3 biological replicates were included for each group. Sequencing was done using Ion Proton.
Publication Title
A molecular signature for anastasis, recovery from the brink of apoptotic cell death.
Sample Metadata Fields
Cell line, Treatment, Subject
View Samples- Homo sapiens
- 73 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
The radiolabelled somatostatin analogue 177Lu-octreotate is a promising treatment option for malignant neuroendocrine tumors that overexpress somatostatin receptors. The human small intestine neuroendocrine tumor cell line GOT1 and Medullary thyroid carcinoma model GOT2 have shown promising treatment response to 177Lu-octreotate in xenografted mice. In clinical studies, however, only low cure rates have been achieved to date. In vitro and preclinical in vivo studies have shown that irradiation can up-regulate the expression of somatostatin receptors and thereby give an increased uptake of 177Lu-octreotate. The cellular processes that underlie positive treatment response to 177Lu-octreotate are otherwise largely unknown. Genome-wide analysis of tumor cell responses in this successful mouse model offers a venue to identify critical treatment parameters and to optimize clinical effectiveness of 177Lu-octreotate therapy. Combining 177Lu-octreotate with other anti-tumor agents has also been proposed as a strategy for optimization. Some studies have shown synergistic effects in tumor cell killing and volume reduction The hedgehog signaling pathway is involved in embryonic development and tissue regeneration and can be/is abnormally activated in various cancers. Inhibition of the hedgehog signaling pathway has yielded promising therapeutic effects on NE tumors and may potentially enhance the effects of 177Lu-octreotate treatment in patients.
Publication Title
Priming increases the anti-tumor effect and therapeutic window of <sup>177</sup>Lu-octreotate in nude mice bearing human small intestine neuroendocrine tumor GOT1.
Sample Metadata Fields
Time
View Samples