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E-MEXP-623
Drosophila melanogaster
10 Downloadable Samples
Affymetrix Drosophila Genome Array (drosgenome1)
Description
Transcriptome analysis of the targeted overexpression of branchless (UAS-bnl) using a tracheal driver (breathless-GAL4) in comparison to a wildtype reference at two different developmental stages (10-11h AEL and 17-19h AEL), and of a bnl-P1 mutant in comparison to a wildtype reference at 17-19h AEL.
Publication Title
Identification of FGF-dependent genes in the Drosophila tracheal system.
Alternate Accession IDs
None
Sample Metadata Fields
Age, Time
View Samples- Drosophila melanogaster
- 19 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
We profiled the transcriptome of Drosophila melanogaster embryos in ttk2D50 embryos or after over-expression using btl-GAL4; UAS-ttk, respectively. We further isolated cells that express btl-enh-RFPmoe (Cabernard and Affolter 2005) and FACS sorting, and profiled their transcriptomes in the same genetic backgrounds.
Publication Title
Tramtrack is genetically upstream of genes controlling tracheal tube size in Drosophila.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 96 Downloadable Samples
- Illumina human-6 v2.0 expression beadchip
Description
Detailed analysis of androgen regulated gene expression in the LNCaP prostate cancer cell line. Since androgens and the AR are known to be important for prostate cancer cell proliferation and invasion we aimed to identify androgen receptor (AR) regulated genes by combining this detailed Illumina beadarray study of androgen regulated gene expression with AR ChIP-sequencing data.
Publication Title
The androgen receptor fuels prostate cancer by regulating central metabolism and biosynthesis.
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Time
View Samples- Mus musculus
- 15 Downloadable Samples
Illumina HiSeq 2500
Description
Intra-islet crosstalk between islet cells is critical in orchestrating the body’s response to changes in blood glucose levels, but is incompletely understood. In this study, we used transgenic mouse lines that allowed the purification and transcriptomic characterisation of alpha, beta, and delta cells, yielding an RNA-sequencing database that can be searched for regulatory proteins which are differentially expressed between cell types. As an illustrative example, we examined the expression of g-protein coupled receptors, and found that the ghrelin receptor, Ghsr, was highly expressed in delta cells compared to alpha and beta cells. GHSR excitation elicited increases in cytosolic calcium levels in primary delta cells. In the perfused pancreas, the application of ghrelin stimulated somatostatin secretion, correlating with a decrease in insulin and glucagon release, which was sensitive to somatostatin receptor antagonism. These results show that ghrelin acts specifically on delta cells within pancreatic islets to affect blood glucose regulation. Overall design: Examination of transcriptomic profiles obtained from pancreatic alpha, beta and delta cells
Publication Title
Transcriptomic profiling of pancreatic alpha, beta and delta cell populations identifies delta cells as a principal target for ghrelin in mouse islets.
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 2500
Description
Innate lymphoid cells (ILCs) are important regulators in various immune responses. Current paradigm states that all newly-made ILCs originate from common lymphoid progenitors (CLP) in the bone marrow. Id2, an inhibitor of E protein transcription factors, is indispensable for ILC differentiation. Unexpectedly, we found that ectopically expressing Id1 or deleting two E protein genes in the thymus drastically increased ILC2 counts in the thymus and other organs where ILC2 normally reside. Further evidence suggests a thymic origin of these mutant ILC2s. The mutant mice exhibit augmented spontaneous infiltration of eosinophils and heightened responses to papain in the lung and increased ability to expulse the helminth parasite, Nippostrongylus brasiliensis. These results prompt the question whether the thymus naturally has the capacity to produce ILC2s and E proteins restrain such a potential. The abundance of ILC2s in Id1 transgenic mice also offers a unique opportunity for testing the biological functions of ILC2s. Overall design: For RNA-seq analyses, ILC2s (Lin-Thy1+ST2+) were sorted from thymocytes and mesenteric lymph node cells and processed for RNA-seq. In addition, MLN cells were also cultured in the presence of IL-, IL-25 and IL33. Duplicate samples were analyzed.
Publication Title
Downregulation of E Protein Activity Augments an ILC2 Differentiation Program in the Thymus.
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Arabidopsis thaliana
- 14 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Developmental transitions can be described in terms of morphology and individual genes expression patterns, but also in terms of global transcriptional and epigenetic changes. Most of the large-scale studies of such transitions, however, have only been possible in synchronized cell culture systems. Here we generate a cell type specific transcriptome of an adult stem-cell lineage in the Arabidopsis leaf using RNA sequencing and microarrays. RNA profiles of stomatal entry, commitment, and differentiating cells, as well as of mature stomata and the entire aerial epidermis give a comprehensive view of the developmental progression.
Publication Title
Transcriptome dynamics of the stomatal lineage: birth, amplification, and termination of a self-renewing population.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 14 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Developmental transitions can be described in terms of morphology and individual genes expression patterns, but also in terms of global transcriptional and epigenetic changes. Most of the large-scale studies of such transitions, however, have only been possible in synchronized cell culture systems. Here we generate a cell type specific transcriptome of an adult stem-cell lineage in the Arabidopsis leaf using RNA sequencing and microarrays. RNA profiles of stomatal entry, commitment, and differentiating cells, as well as of mature stomata and the entire aerial epidermis give a comprehensive view of the developmental progression.
Publication Title
Transcriptome dynamics of the stomatal lineage: birth, amplification, and termination of a self-renewing population.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 7 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st), Illumina Genome Analyzer IIx
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Hypoxia increases genome-wide bivalent epigenetic marking by specific gain of H3K27me3.
Alternate Accession IDs
Sample Metadata Fields
Cell line, Time
View Samples- Homo sapiens
- 7 Downloadable Samples
- Illumina Genome Analyzer IIx, Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Purpose: Study hypoxia and reoxygenation induced changes in genome-wide gene expression
Publication Title
Quantitative analysis of ChIP-seq data uncovers dynamic and sustained H3K4me3 and H3K27me3 modulation in cancer cells under hypoxia.
Alternate Accession IDs
Sample Metadata Fields
Cell line, Time
View Samples- Homo sapiens
- 129 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Genome-wide identification of expression quantitative trait loci (eQTLs) in human heart.
Alternate Accession IDs
Sample Metadata Fields
Sex, Age, Specimen part
View Samples