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GSE26624
Mus musculus
12 Downloadable Samples
Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Murine embryonic fibroblasts were isolated from WT and DGAT1,DGAT2-KO (D1D2KO) animals. mRNA was isolated from cells untreated (UNDIFF) or treated (DIFF) according to standard differentiation protocol for adipocytes (Harris, C, et al. JLR 2011).
Publication Title
DGAT enzymes are required for triacylglycerol synthesis and lipid droplets in adipocytes.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 457 Downloadable Samples
Illumina HiSeq 2000
Description
Transdifferentiation of fibroblasts into induced Neuronal cells (iNs) by neuronal-specific transcription factors Brn2, Myt1l and Ascl1 is a paradigmatic example of inter-lineage conversion across epigenetically distant cells. Despite tremendous progress on the transcriptional hierarchy underlying transdifferentiation, the enablers of the concomitant epigenome resetting remain to be elucidated. Here we investigated the role of KMT2A and KMT2B, two histone H3 lysine 4 methylases with cardinal roles in development, through individual and combined inactivation. We found that Kmt2b, whose human homologue's mutations cause dystonia, is selectively required for iN conversion through the suppression of the alternative myocyte program and the induction of neuronal maturation genes. Overall design: In order to study the role of KMT2A and KMT2B during transdifferentiation, we employed conditional mouse strains carrying: i) the exon 2 of Kmt2a and/or Kmt2b flanked by LoxP sites; ii) the knock-in of the YFP-coding gene into one Rosa26 allele, downstream of a LoxP-flanked transcription termination cassette (STOP cassette); and iii) the gene coding for the tamoxifen-inducible version of Cre recombinase knocked into the second Rosa26 allele (Glaser et al., 2006; Kranz et al., 2010; Testa et al., 2004). MEFs were derived from Kmt2a (and/or Kmt2b)fl/fl Cre+ YFP+ embryos and from Kmt2a+/+Kmt2b+/+ Cre+ YFP+ or Kmt2afl/+ Cre+ YFP+ for Kmt2a conditional KO (cKO) as controls (Figure 1A), and were subjected to transdifferentiation. After 13 days of BAM treatment, cells were FACS sorted for PSA-NCAM expression, and the transcriptome of positive and negative cells were independently profiled.
Publication Title
KMT2B Is Selectively Required for Neuronal Transdifferentiation, and Its Loss Exposes Dystonia Candidate Genes.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 10 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Induced pluripotent mesenchymal stromal cell clones retain donor-derived differences in DNA methylation profiles.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 10 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
The objective of this study was the assessment of transcriptional dysregulation in particular with regard to B-cell differentiation factors. Most studies focus on cross-section analyses of various leukemia subtypes to identify differentially regulated genes lacking suitable reference models. Here we applied comparative intraindividual transcriptome analysis of B-precursor ALL of childhood, which introduces a side-by-side analysis of leukemic cells and matched normal lymphoblasts from the same individual in complete continuous remission after the end of re-induction therapy. This approach reduces noise by eliminating interindividual variability.
Publication Title
Aberrant ZNF423 impedes B cell differentiation and is linked to adverse outcome of ETV6-RUNX1 negative B precursor acute lymphoblastic leukemia.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 5 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Reprogramming of somatic cells into induced pluripotent stem cells (iPSC) is an epigenetic phenomenon. We have reprogrammed mesenchymal stromal cells (MSC) from human bone marrow by retrovirus-mediated overexpression of OCT-3/4, SOX2, c-MYC, and KLF4. This series summarizes gene expression profiles of eight iP-MSC clones derived from three different donors. These datasets were subsequently used for PluriTest analysis (Muller FJ, Schuldt B et al., Nat. Methods 2011; 8: 315-317) demonstrating that all iP-MSC clones were clearly associated with pluripotent cells.
Publication Title
Induced pluripotent mesenchymal stromal cell clones retain donor-derived differences in DNA methylation profiles.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 12 Downloadable Samples
- Illumina HiSeq 4000
Description
We sequenced whole adipose tissue from control and LCMV infected mice 6dpi, in control vs T cell-specific IFNAR knockoutmice to understand the transcriptional changes in adipose tissue upon loss of type I IFN-T cell singaling axis, and how it contributes to cachexia. Overall design: inguinal fat pad (after removing iLN) was used for sequencing in control and infected mice (LCMV clone13 2x10^6PFU), this was done in two genotypes (IFNARfl/fl) as controls, vs (IFNARfl/fl-CD4cre/+) as T-cell specific IFNAR knockouts.
Publication Title
CD8<sup>+</sup> T cells induce cachexia during chronic viral infection.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 146 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This dataset encompassing the profiles of 150 lung cancer tumors was developed to serve as test dataset in the SBV IMPROVER Diagnostic Signature Challenge (sbvimprover.com). The aim of this subchallenge was to verify that it is possible to extract a robust diagnostic signature from gene expression data that can identify stages of different types of lung cancer. Participants were asked to develop and submit a classifier that can stratify lung cancer patients in one of four groups Stage 1 of Adenocarcinoma (AC Stage 1), Stage 2 of Adenocarcinoma (AC Stage 2), Stage 1 of Squamous cell carcinoma (SCC Stage 1) or Stage 2 of Squamous cell carcinoma (SCC Stage 2). The classifier could be built by using any publicly available gene expression data with related histopathological information and was tested on the independent dataset described here.
Publication Title
Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge.
Sample Metadata Fields
Sex, Specimen part, Disease stage, Race
View Samples- Homo sapiens
- 24 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Identification of relevant subgroups in childhood MDS patients by gene expression analysis and gene involve in progression into AML
Publication Title
Gene expression signatures of pediatric myelodysplastic syndromes are associated with risk of evolution into acute myeloid leukemia.
Sample Metadata Fields
Specimen part, Disease
View Samples- Homo sapiens
- 19 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
In this study we analyzed the myeloma cell contact-mediated changes on the transcriptome of skeletal precursor cells. Therefore, human mesenchymal stem cells (MSC) and osteogenic precursor cells (OPC) were co-cultured with the representative myeloma cell line INA-6 for 24 h. Afterwards, MSC and OPC were separated from INA-6 cells by fluorescence activated cell sorting. Total RNA of MSC and OPC fractions was used for whole genome array analysis.
Publication Title
Contact of myeloma cells induces a characteristic transcriptome signature in skeletal precursor cells -Implications for myeloma bone disease.
Sample Metadata Fields
Sex, Age, Specimen part, Disease stage
View Samples- Homo sapiens
- 48 Downloadable Samples
- IlluminaHiSeq2000
Description
Analysis of C4-2 Prostate cancer cell line after 72 hours of knockdown. CHKA is overexpressed in a number of solid tumours, including prostate cancer. Results provide insight into the molecular mechanisms of CHKA in prostate carcinogenesis. Overall design: This experiment was designed to understand the regulation of transcriptome by Choline kinase alpha (CHKA) which is an important enzyme in Kennedy pathway. In order to achieve this, the endogenous protein was knocked down using siRNA pool that targets the CHKA mRNA.
Publication Title
Choline Kinase Alpha as an Androgen Receptor Chaperone and Prostate Cancer Therapeutic Target.
Sample Metadata Fields
No sample metadata fields
View Samples