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SRP162862
Mus musculus
543 Downloadable Samples
Illumina HiSeq 2000
Description
Single cell sequencing of microglia and perivascular macrophages was performed on brain tissue from different brain regions to obtain single cell expression profiles dependent on celltype and regional location. Overall design: 425 cells from mouse (CD-1) brains at different postnatal ages as well as embryonic day E11.5-E18.5.
Publication Title
Spatial and temporal heterogeneity of mouse and human microglia at single-cell resolution.
Sample Metadata Fields
Subject
View Samples- Homo sapiens
- 31 Downloadable Samples
- Illumina HiSeq 3000
Description
Microglia play critical roles in neural development and homeostasis. They are also implicated in neurodegenerative and neuroinflammatory diseases of the central nervous system (CNS). However, little is known about the presence of spatially and temporally restricted subclasses of microglia during CNS development and disease. Here, we combined massively parallel single-cell analysis, single-molecule FISH, advanced immunohistochemistry and computational modelling to comprehensively characterize novel microglia subclasses, which were transcriptionally different from perivascular macrophages, in up to six different CNS regions during development and diseases. Single-cell analysis revealed specific time- and region-dependent microglia subtypes during homeostasis. In contrast, demyelinating and neurodegenerative diseases evoked context-dependent microglia subtypes with distinct molecular hallmarks and diverse cellular kinetics. Finally, diverse microglia subsets were also identified in normal and diseased human brains. Our data provide new insights into the CNS endogenous immune system during development, health and perturbations. Overall design: CD45+ cells isolated from healthy and MS-affected human brains were FACS-sorted in 384-well plates and used for scRNAseq. The patients were aged between 22 and 25 years. Data comprises 5 healthy and 5 MS patients. CEL-Seq2 protocol was used for single cell sequencing (Hashimshony et al. 2016).
Publication Title
Spatial and temporal heterogeneity of mouse and human microglia at single-cell resolution.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 2 Downloadable Samples
Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
AP2 transcription factors play important roles in development and cancer, we tried to clarify the role of the so far uncharacterised TFAP2E in colorectal cancer.
Publication Title
TFAP2E-DKK4 and chemoresistance in colorectal cancer.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Side population (SP) cells isolated from limbal and conjunctival epithelia derive from cells that are slow cycling in vivo, a known feature of tissue stem cells. The purpose of this study was to define the molecular signature of the conjunctival side population cells by global differential gene expression to identify markers and signaling pathways associated with this cell phenotype.
Publication Title
Molecular profiling of conjunctival epithelial side-population stem cells: atypical cell surface markers and sources of a slow-cycling phenotype.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 2 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
Our previous study identified that microRNA-184 as one of the most highly expressed miRNAs in the corneal epithelium. To gain insight into the underlying mechanisms of miR-184 modulation of corneal epithelial cell proliferation and migration, we probed for its gene targets by microarray analysis . HCECs transfected with miR-184 or a NC for 48 h were harvested and a gene microarray evaluated transcriptome expression patterns. Ectopic miR-184 expression resulted in numerous genes undergoing either upregulation or downregulation. Since miRNAs mediate biological functions by impeding expression of their target genes in mammals, a total of 901 differentially downregulated genes (Foldchange ≤ 0.667) were firstly selected.
Publication Title
MicroRNA-184 negatively regulates corneal epithelial wound healing via targeting <i>CDC25A</i>, <i>CARM1</i>, and <i>LASP1</i>.
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 24 Downloadable Samples
- Illumina HiSeq 2500
Description
One of the most common genetic alterations in acute myeloid leukemia is the internal tandem duplication (ITD) in the FLT3 receptor for cytokine FLT3 ligand (FLT3L). The constitutively active FLT3-ITD promotes the expansion of transformed progenitors, but also has pleiotropic effects on normal hematopoiesis. We analyzed the effect of FLT3-ITD on dendritic cells (DCs), which express FLT3 and can be expanded by FLT3L administration. We report that young pre-leukemic mice with the Flt3ITD knock-in allele manifest an expansion of all DCs including classical (cDCs) and plasmacytoid (pDCs). The expansion originated in DC progenitors, occurred in a cell-intrinsic manner and was further enhanced in Flt3ITD/ITD mice. The mutation caused the downregulation of Flt3 on the surface of DCs and reduced their responsiveness to Flt3L. Flt3ITD mice showed enhanced capacity to support T cell proliferation, including a cell-extrinsic expansion of regulatory T cells (Tregs). Accordingly, these mice restricted alloreactive T cell responses during graft-versus-host reaction, but failed to control autoimmunity in the absence of Tregs. Thus, the FLT3-ITD mutation directly affects DC development, thereby indirectly modulating T cell homeostasis and supporting Treg expansion. This effect of FLT3-ITD may subvert immunosurveillance and promote leukemogenesis in a cell-extrinsic manner. Overall design: Sorted splenic dendritic cell subsets from either Flt3+/+ or Flt3ITD/+ mice were sequenced for mRNA profiling. For each subset per genotype contains 2-3 replicates, all from independent experiments.
Publication Title
Leukemia-associated activating mutation of Flt3 expands dendritic cells and alters T cell responses.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 2 Downloadable Samples
- Illumina HumanWG-6_V2_0_R2
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Promoter DNA methylation patterns of differentiated cells are largely programmed at the progenitor stage.
Sample Metadata Fields
Specimen part
View Samples- Drosophila melanogaster
- 6 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Ibf1 and Ibf2 are novel CP190-interacting proteins required for insulator function.
Sample Metadata Fields
Disease, Cell line
View Samples- Homo sapiens
- 12 Downloadable Samples
Illumina HumanHT-12 V4.0 expression beadchip, Illumina HumanWG-6 v3.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Epigenetic priming of inflammatory response genes by high glucose in adipose progenitor cells.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 2 Downloadable Samples
- Illumina HumanWG-6_V2_0_R2
Description
We surveyed DNA methylation profiles of all human RefSeq promoters in relation to gene expression and differentiation in adipose tissue, bone marrow and muscle mesenchymal progenitors, as well as in bone marrow-derived hematopoietic progenitors. We unravel strongly overlapping DNA methylation profiles between adipose stem cells (ASCs), bone marrow mesenchymal stem cells (BMMSCs) and muscle progenitor cells (MPCs), while hematopoietic progenitor cells (HPCs) are more epigenetically distant from MSCs seen as a whole. Differentiation resolves a fraction of methylation patterns common to MSCs, generating epigenetic divergence.
Publication Title
Promoter DNA methylation patterns of differentiated cells are largely programmed at the progenitor stage.
Sample Metadata Fields
Specimen part
View Samples