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SRP043525
Mus musculus
25 Downloadable Samples
Illumina HiSeq 2000
Description
To determine the temporal variation of mRNA levels, we collected and sequenced poly-adenylated RNA from all cell extracts, cytoplasmic and nuclear fractions of a conditional Dicer mutant [DTCM23/49 XY (Nesterova et al. 2008)] mouse Embryonic Stem Cells before induction of Dicer excision (day 0) and at days 4, 8, 10 and 12 following Dicer loss of function. coverage. Overall design: RNA from whole cell extracts was collected at days 0, 4, 8, 10 and 12 following loss of Dicer function and from the cytoplasmic and nuclear fractions of cell at day 0 and 12. Three biological replicates were obtained for all samples. Poly-adenylated directional 100 base paired-end sequencing libraries were prepared for all extracts and sequenced by BGI solutions (Hong Kong).
Publication Title
Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
These data show that Paupar, a CNS expressed long non-coding RNA (lncRNA), directly and functionally associates with KAP1, an essential epigenetic regulatory protein. Transcriptome profiling of N2A cells identified 1,913 differentially expressed genes whose expression significantly changed (at a 5% false discovery rate [FDR]) greater than 1.4-fold (log2 fold change 0.5) upon KAP1 depletion. Examination of the intersection of KAP1 and Paupar transcriptional targets showed that Paupar and KAP1 control expression of a shared set of target genes that are enriched for regulators of neuronal function and cell cycle in N2A cells. Furthermore, CHART-seq and ChIP-seq derived Paupar-KAP1 genome-wide co-occupancy maps revealed a 4-fold enrichment of overlap between Paupar and KAP1 bound sequences on chromatin. This study also indicates that Paupar promotes KAP1 chromatin occupancy and H3K9me3 deposition at a subset of distal targets, through formation of a ribonucleoprotein complex containing Paupar, KAP1 and the PAX6 transcription factor. These observations provide important conceptual insights into the trans-acting modes of lncRNA-mediated epigenetic regulation and the mechanisms of KAP1 genomic recruitment.
Publication Title
The long non-coding RNA <i>Paupar</i> promotes KAP1-dependent chromatin changes and regulates olfactory bulb neurogenesis.
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
The long non-coding RNA <i>Paupar</i> promotes KAP1-dependent chromatin changes and regulates olfactory bulb neurogenesis.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 191 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Normal children, children with SIRS, children with sepsis, and children with septic shock.
Publication Title
Genomic expression profiling across the pediatric systemic inflammatory response syndrome, sepsis, and septic shock spectrum.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 16 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Rationale: We previously generated genome-wide expression data in children with septic shock, based on whole blood-derive RNA, having the potential to lead the field into novel areas of investigation.
Publication Title
Validating the genomic signature of pediatric septic shock.
Sample Metadata Fields
Sex
View Samples- Mus musculus
- 15 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
The goal of this study was to gain insight into the molecular heterogeneity of capillary endothelial cells derived from different organs by microarray profiling of freshly isolated cells and identify transcription factors that may determine the specific gene expression profile of endothelial cells from different tissues. The study focused on heart endothelial cells and presents a validated signature of 31 genes that are highly enriched in heart endothelial cells. Within this signature 5 transcription factors were identified and the optimal combination of these transcription factors was determined for specification of the heart endothelial fingerprint.
Publication Title
Meox2/Tcf15 heterodimers program the heart capillary endothelium for cardiac fatty acid uptake.
Sample Metadata Fields
Sex, Specimen part
View Samples- Arabidopsis thaliana
- 24 Downloadable Samples
- Arabidopsis Gene 1.1 ST Array (aragene11st)
Description
Bearing in mind the prevalent occurrence of sulfur deficiency in soils, it is highly essential to comprehend the molecular processes of plant response to the changing conditions of sulfur nutrition. As there is an increasing understanding of ubiquitin-proteasomal protein degradation system participation in nutrient deficiency response, we could predict its input to the sulfur metabolism as well. Therefore, we decided to investigate the consequences of proteasome malfunction in Arabidopsis in sulfur deficient conditions.
Publication Title
Proteasomal Degradation of Proteins Is Important for the Proper Transcriptional Response to Sulfur Deficiency Conditions in Plants.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Objective Telmisartan, an angiotensin II type 1 (AT1) receptor blocker, and amlodipine, a calcium channel blocker, are antihypertensive agents clinically used as monotherapy or in combination. They exert beneficial cardiovascular effects independently of blood pressure lowering and classic mechanisms of action. In this study, we investigate molecular mechanisms responsible for the off-target effects of telmisartan and telmisartan-amlodipine in endothelial cells (EC), using an unbiased approach.
Publication Title
Telmisartan exerts pleiotropic effects in endothelial cells and promotes endothelial cell quiescence and survival.
Sample Metadata Fields
Specimen part, Disease, Treatment
View Samples- Mus musculus
- 36 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The goal of this experiment was to examine the innate immune response to helminth infection in the lung. Hookworms (like many other helminths) use an obligate migration pathway through the lung. Their infection has been characterized in the gut in detail, but early immune responses in the lung have not been fully characterized.
Publication Title
Innate immune responses to lung-stage helminth infection induce alternatively activated alveolar macrophages.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 55 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Goal of the experiment: To identify correlated genes, pathways and groups of patients with systemic inflammatory response syndrome and septic shock that is indicative of biologically important processes active in these patients.
Publication Title
Genome-level expression profiles in pediatric septic shock indicate a role for altered zinc homeostasis in poor outcome.
Sample Metadata Fields
No sample metadata fields
View Samples