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GSE43998
Homo sapiens
8 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We defined the C/EBPa signature characterized by a set of genes which are upregulated upon C/EBPa activation. In order to identify the C/EBPa signature, we performed microarray gene expression analysis of K562 cells stably expressing p42-C/EBPa-ER after activating the C/EBPa construct to translocate to the nucleus for 6 hours with beta-estradiol.
Publication Title
The gene signature in CCAAT-enhancer-binding protein α dysfunctional acute myeloid leukemia predicts responsiveness to histone deacetylase inhibitors.
Sample Metadata Fields
Cell line, Treatment
View Samples- Homo sapiens
- 26 Downloadable Samples
Illumina HiSeq 2500
Description
Transcriptome levels of matched patient-derived xenograft (PDX) in vitro-in vivo models. Overall design: Comparison of gene expression levels between matched patient-derived xenograft in vitro-in vivo models.
Publication Title
Generation of matched patient-derived xenograft in vitro-in vivo models using 3D macroporous hydrogels for the study of liver cancer.
Sample Metadata Fields
Specimen part, Disease, Subject
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina MouseWG-6 v2.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
LPS independent activation of the pro-inflammatory receptor Trem1 by C/EBPε in granulocytes.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina MouseWG-6 v2.0 expression beadchip
Description
To identify target genes of C/EBPepsilon in differentiated granulocytes, total RNA were purified from sorted Gr-1intermediate/Mac-1+ and Gr-1hi/Mac-1+ cells of C/EBPepsilon knock out and C57BL/6 wild type mice using RNeasy Mini Kit (Qiagen). The differences of their expression pattern were compared with Illumina Mouse WG-6v2 Expression Chip platform. Raw Illumina BeadArray data in IDAT format were preprocessed using the open-source Bioconductor package illuminaio with the Illumina array design formation BGX file downloaded from NCBI, GEO accession: GPL6887. Following the preprocessing, the expression data were normalized by applying control background correction, log transformation and inter-quantile normalization using the neqc function from the limma bioconductor package. This allowed us to compare the transcriptomic consequences of C/EBPepsilon in two independent populations.
Publication Title
LPS independent activation of the pro-inflammatory receptor Trem1 by C/EBPε in granulocytes.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 2 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
DNMT1-interacting RNAs block gene-specific DNA methylation.
Sample Metadata Fields
Cell line, Treatment
View Samples- Homo sapiens
- 2 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
We used the microarray analysis to detail the gene expression profile from the leukemic cell line HL-60
Publication Title
DNMT1-interacting RNAs block gene-specific DNA methylation.
Sample Metadata Fields
Cell line
View Samples SRP009094- Homo sapiens
- 2 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
Identification of the all RNA species associated with DNMT1. Using a comparative genome-scale approach we identified and correlated the RNA species physically associated with DNMT1 and proximal to the annotated genes to the methylation status of the corresponding loci and expression levels of the respective genes. This comparative approach delineated the first -DNMT1 centered- 'epitranscriptome' map, a comprehensive map cross-referencing DNMT1-interacting transcripts to (i) DNA methylation and (ii) gene expression profile. Overall design: Relationship between DNMT1-RNA interactions, DNA methylation and gene expression
Publication Title
DNMT1-interacting RNAs block gene-specific DNA methylation.
Sample Metadata Fields
Cell line, Subject
View Samples- Rattus norvegicus
- 6 Downloadable Samples
- Affymetrix Rat Gene 1.0 ST Array (ragene10st)
Description
Complement protein C1q is induced after injury in the brain and during Alzheimer's disease and has been shown to protect against amyloid-beta induced neuronal death. In this study, we used microarray approach to identify the pathways modulated by C1q that are associated with neuroprotection.
Publication Title
C1q-induced LRP1B and GPR6 proteins expressed early in Alzheimer disease mouse models, are essential for the C1q-mediated protection against amyloid-β neurotoxicity.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 18 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Using the novel BTK inhibitor PF-303, we model the clinical phenotype of BTK inhibition by systematically examining the impact of PF-303 on the mature immune system in mice autoimmune indications. However, our current knowledge of the role of BTK in immune competence has been gathered in the context of genetic inactivation of btk in both mice and man. Using the novel BTK inhibitor PF-303, we model the clinical phenotype of BTK inhibition by systematically examining the impact of PF-303 on the mature immune system in mice. We implicate BTK in tonic BCR signaling, demonstrate dependence of the T3 B cell subset and IgM surface expression on BTK activity, and find that B1 cells survive and function independently of BTK. While BTK inhibition does not impact humoral memory survival, antigen-driven clonal expansion of memory B cells and antibody secreting cell generation are inhibited. These data define the role of BTK in the mature immune system and mechanistically predict the clinical phenotype of BTK inhibition.
Publication Title
Modeling the clinical phenotype of BTK inhibition in the mature murine immune system.
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 6 Downloadable Samples
- Affymetrix Rat Gene 1.0 ST Array (ragene10st)
Description
Identification of transcriptional profiles stimulated by the complement protein C1q in rat immature neurons associated with the C1q-dependent neuroprotection observed in vitro.
Publication Title
Complement protein C1q-mediated neuroprotection is correlated with regulation of neuronal gene and microRNA expression.
Sample Metadata Fields
Specimen part
View Samples