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GSE64819
Mus musculus
3 Downloadable Samples
Illumina MouseWG-6 v2.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 2 Downloadable Samples
- Illumina MouseWG-6 v2.0 expression beadchip
Description
How various ATP-dependent chromatin remodellers bind to nucleosomes to regulate transcription is not well defined in mammalian cells. Here, we present genome-wide remodeller-interacting nucleosome profiles for Chd1, Chd2, Chd4, Chd6, Chd8, Chd9, Brg1 and Ep400 in mouse embryonic stem (ES) cells. These remodellers bind to nucleosomes at specific positions, either at one or both nucleosomes that flank each side of nucleosome-free promoter regions (NFRs), at enhancer elements, or within gene bodies. At promoters, bidirectional transcription commonly initiates on either side of remodeller-bound nucleosomes. Transcriptome analysis upon remodeller depletion reveals reciprocal mechanisms of transcriptional regulation by remodellers. At active genes, certain remodellers are positive regulators of transcription, whereas others act as repressors. At bivalent genes, which are bound by repressive Polycomb complexes, the same remodellers act in the opposite way. Together, these findings reveal how remodellers integrate promoter nucleosomal architecture to regulate ES cell transcription programs.
Publication Title
Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 1 Downloadable Sample
- Illumina MouseWG-6 v2.0 expression beadchip
Description
How various ATP-dependent chromatin remodellers bind to nucleosomes to regulate transcription is not well defined in mammalian cells. Here, we present genome-wide remodeller-interacting nucleosome profiles for Chd1, Chd2, Chd4, Chd6, Chd8, Chd9, Brg1 and Ep400 in mouse embryonic stem (ES) cells. These remodellers bind to nucleosomes at specific positions, either at one or both nucleosomes that flank each side of nucleosome-free promoter regions (NFRs), at enhancer elements, or within gene bodies. At promoters, bidirectional transcription commonly initiates on either side of remodeller-bound nucleosomes. Transcriptome analysis upon remodeller depletion reveals reciprocal mechanisms of transcriptional regulation by remodellers. At active genes, certain remodellers are positive regulators of transcription, whereas others act as repressors. At bivalent genes, which are bound by repressive Polycomb complexes, the same remodellers act in the opposite way. Together, these findings reveal how remodellers integrate promoter nucleosomal architecture to regulate ES cell transcription programs.
Publication Title
Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 30 Downloadable Samples
- Affymetrix Human Gene 1.1 ST Array (hugene11st)
Description
We analyzed the transcriptomes of human dendritic cells and macrophages derived from monocytes using MCSF + IL-4 + TNFa, or IL-34 + IL-4 + TNFa, or dendritic cells derived from monocytes using GMCSF + IL-4.
Publication Title
Aryl Hydrocarbon Receptor Controls Monocyte Differentiation into Dendritic Cells versus Macrophages.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Homo sapiens
- 16 Downloadable Samples
Illumina HiSeq 2500
Description
We performed single-cell RNA-seq on CD14+ monocytes isolated from the blood of healthy donors. Using the 10x chromium technology, we analyzed 425 and 431 cells from 2 individual donors. Overall design: Peripheral Blood Mononuclear Cells (PBMC) were prepared by centrifugation on a Ficoll gradient. Blood CD14+ monocytes were isolated from healthy donors' PBMC by positive selection using magnetic beads. Monocytes were 93-95% CD14+CD16- as assessed by flow cytometry. Cellular suspensions (1700 cells) were loaded on a 10X Chromium instrument (10X Genomics) according to manufacturer's protocol.
Publication Title
Aryl Hydrocarbon Receptor Controls Monocyte Differentiation into Dendritic Cells versus Macrophages.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
Myocardial infarction (MI) is one of the most severe manifestations of coronary artery disease (CAD) and the leading cause of death from non-infectious diseases worldwide. It is known, that the central component of CAD pathogenesis is a chronic vascular inflammation. However, the mechanisms underlying the changes that occur in T, B and NK-lymphocytes, monocytes and other immune cells during CAD and MI are still poorly understood. One of those pathogenic mechanisms might be the dysregulation of intracellular signaling pathways in the immune cells.
Publication Title
Collapsing the list of myocardial infarction-related differentially expressed genes into a diagnostic signature.
Sample Metadata Fields
Sex, Specimen part, Disease stage
View Samples- Homo sapiens
- 3 Downloadable Samples
- Illumina HiSeq 2500
Description
We performed single-cell RNA-seq on CD4 T cells isolated from the tonsils of one healthy donor. We used the 10x chromium technology. Overall design: Tonsil CD4 T cells were enriched by negative selection using magnetic beads. Cell populations (CXCR5+PD-1low T cells, CXCR5+PD-1int T cells and CXCR5+PD-1high T cells ) were further isolated by cell sorting. Cellular suspensions (3500 cells) were loaded on a 10X Chromium instrument (10X Genomics) according to manufacturer's protocol.
Publication Title
Human lymphoid organ cDC2 and macrophages play complementary roles in T follicular helper responses.
Sample Metadata Fields
Subject
View Samples- Homo sapiens
- 1 Downloadable Sample
- Illumina HiSeq 2500
Description
We performed single-cell RNA-seq on CD14+ cells isolated from the tonsils of one healthy donor. We used the 10x chromium technology. Overall design: Tonsil phagocytes were prepared by centrifugation on a Ficoll gradient. Dendritic cells and macrophages were enriched by negative selection using magnetic beads. Cell populations were further isolated by cell sorting. Cellular suspensions (3500 cells) were loaded on a 10X Chromium instrument (10X Genomics) according to manufacturer's protocol.
Publication Title
Human lymphoid organ cDC2 and macrophages play complementary roles in T follicular helper responses.
Sample Metadata Fields
Subject
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Extracellular vesicles released from cultured H9 cells were fractionated by differential ultracentrifugation and their total RNA were isolated for microarray analysis.
Publication Title
Human embryonic stem cells extracellular vesicles and their effects on immortalized human retinal Müller cells.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 22 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
There are an estimated 21million diabetics in the United States and 150 million diabetics worldwide. The World Health Organization anticipates that these numbers will double in the next 20 years. Metabolic syndrome is a well recognized set of symptoms that increases a patients risk of developing diabetes. Insulin resistance is a factor in both metabolic syndrome and Type 2 diabetes. It is characterized by decreased insulin stimulated glucose uptake in peripheral tissues, decreased adiponectin levels, increased adipocyte FFA and cytokine production, and increased insulin and hepatic glucose output. Prevention or reversal of insulin resistance should serve as an important strategy in addressing the growing health concerns posed by the Diabetes epidemic. While increased adiposity is associated with insulin resistance, the role of the cell types present within adipose (adipocytes, pre-adipocytes, endothelial cells, macrophages, fibroblasts, leukocytes and smooth muscle cells) in insulin resistance is unclear. In an effort to begin dissection of this question, we examined the transcriptional response of the buoyant and non-buoyant fractions isolated from insulin sensitive or TNF induced insulin resistant hMSC derived adipocytes before and after treatment with insulin.
Publication Title
Genome-wide profiling of H3K56 acetylation and transcription factor binding sites in human adipocytes.
Sample Metadata Fields
Specimen part
View Samples