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GSE42576
Homo sapiens
12 Downloadable Samples
Illumina HiSeq 2000, Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
CBFβ stabilizes HIV Vif to counteract APOBEC3 at the expense of RUNX1 target gene expression.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 12 Downloadable Samples
Illumina HiSeq 2000, Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
The HIV-1 accessory protein Vif hijacks a cellular
Publication Title
CBFβ stabilizes HIV Vif to counteract APOBEC3 at the expense of RUNX1 target gene expression.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 6 Downloadable Samples
Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
We used microarrays to detail the global programme of gene expression underlying the loss of CD28 co-receptor on primary human CD8+ T cells.
Publication Title
Metabolic reprogramming of human CD8<sup>+</sup> memory T cells through loss of SIRT1.
Sample Metadata Fields
Age, Specimen part
View Samples- Mus musculus
- 8 Downloadable Samples
- NextSeq 500
Description
To investigate the role of RPRD1B in regulating gene expression in NIH3T3 cells. Overall design: Examination of mRNA expression levels in cells with control or RPRD1B knockdown NIH3T3 cells
Publication Title
Crosstalk between RNA Pol II C-Terminal Domain Acetylation and Phosphorylation via RPRD Proteins.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Subject
View Samples- Mus musculus
- 4 Downloadable Samples
- Illumina HiSeq 2000
Description
We combine a genome-scale RNAi screen in mouse epiblast stem cells (EpiSCs) with genetic interaction, protein localization and “protein-level dependency” studies – a systematic technique that uncovers post-transcriptional regulation – to delineate the network of factors that control the expression of Oct4, a key regulator of pluripotency. Our data signify that there are similarities, but also fundamental differences in Oct4 regulation in EpiSCs vs. embryonic stem cells (ESCs). Through multiparametric data analyses we predict that Tox4 is associating with the Paf1C complex, which maintains cell identity in both cell types and validate that this protein-protein interaction exists in ESCs and EpiSCs. We also identify numerous knockdowns that increase Oct4 expression in EpiSCs, indicating that, in stark contrast to ESCs, Oct4 is under active repressive control in EpiSCs. These studies provide a framework for better understanding pluripotency and for dissecting the molecular events that govern the transition from the pre-implantation to the post-implantation state. Overall design: RNA-seq of Tox4 knockdown in mouse EpiSCs
Publication Title
Systems Analyses Reveal Shared and Diverse Attributes of Oct4 Regulation in Pluripotent Cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 22 Downloadable Samples
- Ion Torrent Proton
Description
We designed a study to investigate immunoediting of an epithelial cancer genome using wildtype and immunodeficient mice, NGS, and analytical pipelines to process and analyze the data. We carried out experiments with wildtype and immunodeficient RAG1-/- mice with transplanted tumors and analyzed longitudinal samples with respect to the genomic landscape and the immunophenotypes of the tumors. Finally, we performed also experiments with anti-PD-L1 antibodies and show how the activation of the PD1-PD-L1 axis modulates immunoediting. MC38 cells were subcutaneously injected into wild-type C57Bl/6 and immunodeficient Rag1-/- mice. Samples were taken at predefined time points and subjected to detailed analysis, including FACS, exome sequencing, RNA sequencing and SNP arrays. Overall design: Samples were taken at predifined time points, in triplicates and subjected to RNA sequencing using Ion Torrent Proton
Publication Title
Targeting immune checkpoints potentiates immunoediting and changes the dynamics of tumor evolution.
Sample Metadata Fields
Subject, Time
View Samples- Homo sapiens
- 34 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
A high-resolution time series study of transcriptome dynamics following antimiR--mediated inhibition of miR-9 in a Hodgkin lymphoma cell-line revealed both general and miR-9 specific aspects of the miRNA--mediated post--transcriptional dynamic response.MiR-9 inhibition induced a multiphasic gene response, with an initial direct response at approximately 4 hours and multiple later responses which showed transcription factor enrichments indicative of indirect causally downstream responses, and an overall shift of gene product function from predominantly mRNA processing at early time points to translation at later time points.
Publication Title
Transcriptome dynamics of the microRNA inhibition response.
Sample Metadata Fields
Cell line, Treatment, Time
View Samples- Homo sapiens
- 8 Downloadable Samples
- Ion Torrent S5
Description
We compared polyIC stimulated cells in the presence of either GFP or NS5 protein Overall design: A549 cells presence with GFP- or NS5-expressing plasmid using Polyjet (Signagen) according to manufacturer instructions, and 30 hours later stimulated with polyIC (Tocris) as previously described (Marazzi et al., 2012). At 12 hours post-stimulation, total cellular RNA was purified by RNeasy column (Qiagen).
Publication Title
Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
HSL is a key enzyme in in the mobilization of fatty acids from the triglyceride stores of white adipose tissue. In addition, it is expressed in mice liver. In the present microarray study, changes in the transcript profile of murine liver samples due to global HSL knockout were investigated.
Publication Title
Disturbed cholesterol homeostasis in hormone-sensitive lipase-null mice.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 33 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We used microarray to create a normal cell landscape for the myeloid arm of the hematopoietic system.
Publication Title
Comparing cancer vs normal gene expression profiles identifies new disease entities and common transcriptional programs in AML patients.
Sample Metadata Fields
Specimen part
View Samples