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GSE49053
Homo sapiens
8 Downloadable Samples
Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Differentiation-defective phenotypes revealed by large-scale analyses of human pluripotent stem cells.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
It remains controversial whether human induced pluripotent stem cells (hiPSCs) are distinct from human embryonic stem cells (hESCs) in their molecular signatures and differentiation properties. We examined the gene expression and DNA methylation of 49 hiPSC and 10 hESC lines and identified no molecular signatures that distinguished hiPSCs from hESCs. Comparisons of the in vitro directed neural differentiation of 40 hiPSC and four hESC lines showed that most hiPSC clones were comparable to hESCs. However, in seven hiPSC clones, significant amount of undifferentiated cells persisted even after neural differentiation and resulted in teratoma formation when transplantated into mouse brains. These differentiation-defective hiPSC clones were marked by higher expression of several genes, including those expressed from long terminal repeats of human endogenous retroviruses. These data demonstrated that many hiPSC clones are indistinguishable from hESCs, while some defective hiPSC clones need to be eliminated prior to their application for regenerative medicine.
Publication Title
Differentiation-defective phenotypes revealed by large-scale analyses of human pluripotent stem cells.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
A functional interaction between peroxisome proliferator-activated receptor alpha (PPARalpha) and components of the circadian clock has been suggested; however, it remains to be clarified whether those transcriptional factors interact with each other to regulate the expression of their target genes.
Publication Title
Bezafibrate induces plasminogen activator inhibitor-1 gene expression in a CLOCK-dependent circadian manner.
Sample Metadata Fields
Sex
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
Human umbilical vein endothelial cells (HUVECs) were incubated for 48 h after transfection of scrambled siRNA or siRNA targeting Jmjd6 .
Publication Title
Jumonji domain-containing protein 6 (Jmjd6) is required for angiogenic sprouting and regulates splicing of VEGF-receptor 1.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
KRAP (Ki-ras-induced actin-interacting protein) is a cytoskeleton-associated protein and a ubiquitous protein among tissues, originally identified as a cancer-related molecule. KRAP-deficient (KRAP-/-) mice show enhanced metabolic rate, decreased adiposity, improved glucose tolerance, hypoinsulinemia and hypoleptinemia. KRAP-/- mice are also protected against high-fat diet-induced obesity and insulin resistance despite of hyperphagia.
Publication Title
Altered energy homeostasis and resistance to diet-induced obesity in KRAP-deficient mice.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Triple-negative breast cancer (TNBC) is defined by the absence of estrogen and progesterone receptors and human epidermal growth factor receptor 2, and is the most lethal and aggressive subtype of breast cancer. However, the genes which relate to promote tumor aggressiveness in TNBC remain unclear.
Publication Title
Molecular hierarchy of heparin-binding EGF-like growth factor-regulated angiogenesis in triple-negative breast cancer.
Sample Metadata Fields
Sex, Specimen part, Disease, Disease stage, Cell line
View Samples- Homo sapiens
- 8 Downloadable Samples
Illumina HiSeq 2000
Description
Through RNA sequencing and gene ontology analyses, we report that immune activation is elicited in the spleen of 4 HIV-1-infected humanized mice when compared to 4 mock-infected humanized mice. Overall design: mRNA expression profiles in the splenic human mononuclear cells of HIV-1-infected humanized mice at 6 weeks post-infection (n=4) and mock-infected humanized mice (n=4) were generated by RNA sequencing. RNA was extracted using QIAamp RNA Blood Mini kit (Qiagen). RNA sequencing was conducted in Medical & Biological Laboratories, co (Nagoya, Japan).
Publication Title
HIV-1 competition experiments in humanized mice show that APOBEC3H imposes selective pressure and promotes virus adaptation.
Sample Metadata Fields
Specimen part, Subject, Time
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
We generated a transgenic mouse line which express EGFP in the retina driven by the Crx promoter using BAC transgenesis. We sorted EGFP-positive photoreceptor precursors at E17.5 using FACS, and subsequently performed microarray analysis of the FACS-sorted cells.
Publication Title
Gene expression analysis of embryonic photoreceptor precursor cells using BAC-Crx-EGFP transgenic mouse.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 4 Downloadable Samples
- Illumina HiSeq 1500
Description
Transcriptomal comparison between group 2 innate lymphoid cells (ILC2s) in the murine small intestine (SI-ILC2s) and those in white adipose tissue (WAT-ILC2s). Overall design: mRNA profiles of group 2 innate lymphoid cells (ILC2s) sort-purified from small intestinal lamina propria and mesenteric white adipose tissue of 9-week-old wild type (WT) mice were generated by sequencing, in duplicate, using Illumina HiSeq1500.
Publication Title
Innate Lymphoid Cells in the Induction of Obesity.
Sample Metadata Fields
Age, Specimen part, Subject
View Samples- Mus musculus
- 2 Downloadable Samples
- Illumina HiSeq 2500
Description
Group 2 innate lymphoid cells (ILC2) are tissue-resident innate lymphocytes that are derived from common lymphoid progenitor (CLP). While specific progenitors and transcription factors essential for ILC2 differentiation have been well studied, external factors that regulate the commitment from CLP to ILC lineage, site that promote ILC2 terminal differentiation, and stromal cells that provide optimal microenvironment for ILC2 specific development are not fully understood. we demonstrated that the three key external factors such as concentration of IL-7 and the strength and duration of Notch signaling conditionally determined the fate of CLP toward T cell, B cell, or ILC lineages, which seems to be an important process from CLP to CHILP differentiation in the fetal liver. Furthermore, we identified ILC progenitors lacking the developmental potential to become T or B cells, and KLRG1- immature ILC2 that require STAT5 for functional maturation in the mesentery. We also identified PDGFRa+gp38+ mesenchymal cells in the mesentery that support ILC2 differentiation from ILC progenitors but not from CLP. Finally, single-cell RNA-sequencing (scRNA-seq) analysis of mesenteric cells demonstrated that PDGFRa+gp38+ cells are heterogeneous populations. Collectively, our result suggested that early differentiation of ILC2 occurs in the primary lymphoid organ with regulation of environmental factors, and final differentiation occurs in the peripheral tissues once after CHILP migrate into the periphery. Overall design: Duplicate samples (mouse 1 and mouse 2) were processed for single cell-based RNA sequencing with Illumina HiSeq 2500 with 50 paired-end reads, using barcorded RNA library.
Publication Title
Peripheral PDGFRα<sup>+</sup>gp38<sup>+</sup> mesenchymal cells support the differentiation of fetal liver-derived ILC2.
Sample Metadata Fields
Sex, Cell line, Subject
View Samples