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E-MEXP-1312
Drosophila melanogaster
13 Downloadable Samples
Affymetrix Drosophila Genome Array (drosgenome1)
Description
Ewg differentially regulated genes in 16-18 h Drosophila embryos. The experiment contains expression measurements from wild type, ewg l1 protein null allele and ewg l1 elavEWG (elavEWG rescue construct expressing a ewg cDNA from the elav promoter) mutants.
Publication Title
Erect wing regulates synaptic growth in Drosophila by integration of multiple signaling pathways.
Sample Metadata Fields
Age
View Samples- Drosophila melanogaster
- 6 Downloadable Samples
Illumina HiSeq 2500
Description
Methylation of mRNA at the N6 position of adenosin is known for a long time, but its function remains poorly understood. Here generated a null mutant in the catalytic subunit of the m6A mRNA methylosome, dIME4, in Drosophila to determine the impact of loss of m6A on gene expression using Illumina sequencing. Overall design: Since dIME4 is preferentially expressed in the nervous system and dIME4 null mutants are viable, we compared gene expression and alternative splicing in wild type (2 samples) and dIME4 mutants (3 samples) with genetic background matched w control females in neuron enriched head/thorax.
Publication Title
m<sup>6</sup>A potentiates Sxl alternative pre-mRNA splicing for robust Drosophila sex determination.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Drosophila melanogaster
- 5 Downloadable Samples
- Illumina HiSeq 2500
Description
Methylation of mRNA at the N6 position of adenosin is known for a long time, but its function remains poorly understood. Here generated a null mutant in the catalytic subunit of the m6A mRNA methylosome, dIME4, in Drosophila to determine the impact of loss of m6A on gene expression using Illumina sequencing. Overall design: Since dIME4 is preferentially expressed in the nervous system and dIME4 null mutants are viable, we compared gene expression and alternative splicing in wild type (2 samples) and dIME4 mutants (3 samples) with genetic background matched w control females in neuron enriched head/thorax.
Publication Title
m<sup>6</sup>A potentiates Sxl alternative pre-mRNA splicing for robust Drosophila sex determination.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 25 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Gene expression profiling of newborn lung tissue revealed few changes in compound FGFR3/FGFR4 deficient mice, consistent with their normal lung morphology at birth, suggesting the sequence of events leading to the phenotype initiates after birth in this model.
Publication Title
Fibroblast growth factor receptors control epithelial-mesenchymal interactions necessary for alveolar elastogenesis.
Sample Metadata Fields
Age, Specimen part
View Samples- Mus musculus
- 293 Downloadable Samples
- Illumina HiSeq 2500
Description
Hematopoietic stem cells (HSCs) balance self-renewal and differentiation to maintain homeostasis. With aging, the frequency of polar HSCs decreases. Cell polarity in HSCs is controlled by the activity of the small RhoGTPase Cdc42. Here we demonstrate, using a comprehensive set of paired daughter cell analyses that include single cell 3D-confocal imaging, single cell transplants, single cell RNA-seq as well as single cell ATAC-seq, that the outcome of HSC divisions is strongly linked to the polarity status before mitosis, which is in turn determined by the level of the activity Cdc42 in stem cells. Aged apolar HSCs undergo preferentially self-renewing symmetric divisions, resulting in daughter stem cells with reduced regenerative capacity and lymphoid potential, while young polar HSCs undergo preferentially asymmetric divisions. Mathematical modeling in combination with experimental data implies a mechanistic role of the asymmetric sorting of Cdc42 in determining the potential of daughter cells via epigenetic mechanisms. Therefore, molecules that control HSC polarity might serve as modulators of the mode of stem cell division regulating the potential of daughter cells. Overall design: Sorted single cells were cultured with and without treatment in the presence of cytokines until first cell division (40-44hrs). The daughter cells were manually separated, washed with PBS and collected for RNA sequencing.
Publication Title
Aging alters the epigenetic asymmetry of HSC division.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Subject
View Samples- Rattus norvegicus
- 6 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
The Akita mutation (C96Y) in the insulin gene results in early onset diabetes in both humans and mice. Expression of the mutant proinsulin (C96Y) causes endoplasmic reticulum (ER) stress in pancreatic -cells and consequently the cell activates the unfolded protein response (UPR). Since the proinsulin is terminally misfolded however, the ER stress is irremediable and chronic activation of the UPR eventually activates apoptosis in the cell population.
Publication Title
IRE1 inhibition perturbs the unfolded protein response in a pancreatic β-cell line expressing mutant proinsulin, but does not sensitize the cells to apoptosis.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Mus musculus
- 2 Downloadable Samples
- Illumina HiSeq 2000
Description
An increasingly common method for predicting gene activity is genome-wide chromatin immunoprecipitation of ‘active’ chromatin modifications followed by massively parallel sequencing (ChIP-seq). Using a novel ChIP-seq quantification method (cRPKM), we tested the power of such ChIP-seq strategies to predict relative protein and RNA levels at the pre-pro-B and pro-B differentiation stages in early B cell lymphopoiesis. Using a multi-omics approach that compares promoter chromatin status (ChIP-seq; published in GSE:21978) with ongoing active transcription (GRO-seq; published in GSE:40173), steady state mRNA (RNA-seq), inferred mRNA stability, and relative proteome abundance measurements (iTRAQ), we demonstrate that active chromatin modifications at promoters are a good indicator of transcription and steady state mRNA levels. Moreover, we found that promoters with active chromatin modifications exclusively in one of these cell states frequently predicted differentially expressed proteins. However, we found that many genes whose promoters have non-differential but active chromatin modifications also displayed changes in expression of their cognate proteins. This large class of developmentally and differentially regulated proteins that was uncoupled from chromatin status used mostly post-transcriptional mechanisms. Interestingly, the most differentially expressed protein in our B-cell development system, 2410004B18Rik, was regulated by a post-transcriptional mechanism, which further analyses indicated was mediated by an identified miRNA. These data provide a striking example of how our integrated multi-omics data set can be useful in uncovering regulatory mechanisms. Overall design: Total RNA from mouse pre-pro-B and pro-B cells, depleted of rRNA and small RNAs, was sequenced using a strand specific, single end sequencing strategy.
Publication Title
Prediction of Gene Activity in Early B Cell Development Based on an Integrative Multi-Omics Analysis.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 20 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
The JAK2V617F mutation has been reported in about 40-60% of Essential Thrombocythemia (ET) patients. However, little is known about specific molecular abnormalities of the hematopoietic stem cell compartment of ET according to JAK2 mutation. Therefore, we compared the gene expression profiles of bone marrow (BM) CD34+ cells from 16 patients with and without the JAK2V617F mutation to identify differentially expressed genes.
Publication Title
Molecular profile of CD34+ stem/progenitor cells according to JAK2V617F mutation status in essential thrombocythemia.
Sample Metadata Fields
No sample metadata fields
View Samples- Glycine max
- 43 Downloadable Samples
- Affymetrix Soybean Genome Array (soybean)
Description
Gene expression profiling in soybean under aluminum stress: genes differentially expressed between Al-tolerant and Al-sensitive genotypes.
Publication Title
Mechanisms of magnesium amelioration of aluminum toxicity in soybean at the gene expression level.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Glycine max
- 24 Downloadable Samples
- Affymetrix Soybean Genome Array (soybean)
Description
Gene expression profiling in soybean under aluminum stress: mechanisms of magnesium amelioration of aluminum toxicity at gene expression level.
Publication Title
Mechanisms of magnesium amelioration of aluminum toxicity in soybean at the gene expression level.
Sample Metadata Fields
Specimen part, Treatment
View Samples