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GSE116377
Mus musculus
8 Downloadable Samples
Affymetrix Mouse Clariom S Array (clariomsmouse)
Description
Cellular sources of liver endothelial cells remain elusive. Here, we used irradiation-conditioned bone marrow chimeric mice to lineage trace the endothelial cells.
Publication Title
Endothelial cell fitness dictates the source of regenerating liver vasculature.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 48 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Analysis of differences in gene expression between different cell types of the vascular niche. Looking for candidates, that could potentially be up-or downregualted in the different cell types
Publication Title
Pericyte-expressed Tie2 controls angiogenesis and vessel maturation.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 36 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Facioscapulohumeral dystrophy (FSHD) is one of the most common inherited muscular dystrophies. The causative gene remains controversial and the mechanism of pathophysiology unknown. Here we identify genes associated with germline and early stem cell development as targets of the DUX4 transcription factor, a leading candidate gene for FSHD. The genes regulated by DUX4 are reliably detected in FSHD muscle but not in controls, providing direct support for the model that misexpression of DUX4 is a causal factor for FSHD. Additionally, we show that DUX4 binds and activates LTR elements from a class of MaLR endogenous primate retrotransposons and suppresses the innate immune response to viral infection, at least in part through the activation of DEFB103, a human defensin that can inhibit muscle differentiation. These findings suggest specific mechanisms of FSHD pathology and identify candidate biomarkers for disease diagnosis and progression.
Publication Title
DUX4 activates germline genes, retroelements, and immune mediators: implications for facioscapulohumeral dystrophy.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 2 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
We employed GeneChip analysis to investigate the global gene expression profiles of neutrophils from BM
Publication Title
Neutrophil priming occurs in a sequential manner and can be visualized in living animals by monitoring IL-1β promoter activation.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 4 Downloadable Samples
Illumina HiSeq 2000
Description
In order to identify the transcriptome change and heterogeneity in replicative senescent cells and stress-induced senescent cells, =we measured 1600 single cell transcriptomes of young quiescent cells at a population doubling (PD) number of 38, middle age quiescent cells (PD = 48), replicative senescent (PD = 71) cells and 50Gy X-ray induced senescent cells of PD38 control cells by Drop-seq. Overall design: Drop-seq of RS and SIPS cells.
Publication Title
Single senescent cell sequencing reveals heterogeneity in senescent cells induced by telomere erosion.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
The functional role of tumor cell-expressed Angpt2 still remains elusive. Here, we used mouse melanoma cells which have endgeneous Angpt2 expression and invesitgated the functional role of tumor cell-derived Angpt2.
Publication Title
Tumor Cell-Derived Angiopoietin-2 Promotes Metastasis in Melanoma.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 14 Downloadable Samples
- Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
Exercise induces skeletal muscle adaptation, and the p38 mitogen-activated protein kinase signaling pathway is thought to play an important role in the adaptive processes. We have obtained new evidence that the gamma isoform of p38 is required for exercise-induced metabolic adaptation in skeletal muscle; however, the neuromuscular activity-dependent target genes of p38gamma remain to be defined.
Publication Title
p38gamma mitogen-activated protein kinase is a key regulator in skeletal muscle metabolic adaptation in mice.
Sample Metadata Fields
Age, Specimen part
View Samples- Arabidopsis thaliana
- 3 Downloadable Samples
- Illumina HiSeq 4000
Description
DNA methylation on N6-adenine (6mA) has recently been found as a potentially new epigenetic mark in several unicellular and multicellular eukaryotes. However, its distribution patterns and potential functions in land plants, which are primary producers for most ecosystems, remain completely unknown. Here we report global profiling of 6mA sites at single-nucleotide resolution in the genome of Arabidopsis thaliana using single-molecule real-time sequencing. 6mA sites are widely distributed across the Arabidopsis genome and enriched over the pericentromeric heterochromatin regions. Nearly 30% of 6mA sites are present in gene bodies. Further analysis of 6mA methylome and RNA-sequencing data demonstrates that 6mA frequency positively correlates with the gene expression level in Arabidopsis. Consistently, histone variants associated with actively expressed genes interact with 6mA DNA. Our results uncover 6mA as a DNA mark associated with actively expressed genes in Arabidopsis, suggesting that 6mA serves as a novel epigenetic mark in land plants. Overall design: RNA-seq in 3-week-old Arabidopsis thaliana (Col-0) wild-type with three replicates.
Publication Title
DNA N<sup>6</sup>-Adenine Methylation in Arabidopsis thaliana.
Sample Metadata Fields
Subject
View Samples- Arabidopsis thaliana
- 95 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Cell-type specific transcriptional profiles were generated by FACS (Fluorescence Activated Cell Sorting) sorting of roots that express cell-type specific GFP-reporters. Four different GFP-reporter lines were utilized allowing us to obtain transcriptional profiles for cells in major radial zones of the root. FACS cell populations were isolated from roots grown under standard conditions or roots that had been transfered to media supplemented with 140 mM NaCl for 1 hour, 3 hours, 8 hours, 20 hours, 32 hours and 48 hours.
Publication Title
A spatio-temporal understanding of growth regulation during the salt stress response in Arabidopsis.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 5 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The aim of the study was to investigate the activation of human NK cells by IL2 through analyzing the global gene expression at different time points (0, 2, 8 and 24 hours) after culture with the cytokine IL2 at 100 IU/ml. NK cells with the CD56+/CD16+ and CD3- phenotype were negatively selected by immunomagnetic beads and re-examined by flow-cytometry to ensure greater than 90% purity .
Publication Title
Genome wide transcriptional analysis of resting and IL2 activated human natural killer cells: gene expression signatures indicative of novel molecular signaling pathways.
Sample Metadata Fields
No sample metadata fields
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