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GSE46390
Mus musculus
2 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Colony Stimulating Factor 1(CSF1) is known to promote osteoclast progenitor survival but its role in regulating osteoclast differentiation and mature osteoclast function are less well understood.
Publication Title
The transcription factor T-box 3 regulates colony-stimulating factor 1-dependent Jun dimerization protein 2 expression and plays an important role in osteoclastogenesis.
Sample Metadata Fields
Sex, Age, Specimen part, Treatment
View Samples- Mus musculus
- 6 Downloadable Samples
Illumina HiSeq 4000
Description
Induced pluripotent stem cells (iPSCs) can be derived from somatic cells through ectopic expression of transcriptional factors or chemical cocktails. Chemical reprogramming might be safe than transcriptional factors since there is no integration of exogenous genes. However, there is still little direct evidence to prove this hypothesis. In this study, we have performed whole genome profiling of the DNA methylomes of mouse chemical iPSCs (CiPSCs), transcriptional factors induced iPSCs (TF-iPSCs) and embryonic stem cells (ESCs). We find that the methylation levels of high-CpG-density promoters (HCPs) and intermediate- CpG-density promoters (ICPs) have no significant difference among them, but low-CpG-density promoters (LCP) and three retrotransposons (LINEs, LTRs and SINEs) show preference to different methylation levels. Surprisingly, CiPSCs are hypomethylated than TF-iPSCs and the major difference of methylation levels lies in the intergenic regions while two iPSCs lines are generally hypermethylated compared to ESCs. Moveover, we find the methylation states of imprinting control regions (ICRs) and the expression of imprinted genes of CiPSCs are more resemble ESCs than TF-iPSCs. Our data first provide the epigenetic states of chemical induced pluripotent stem cells and compare the difference of mouse CiPSCs, TF-iPSCs and ESCs. These observations might affect ongoing choices of reprogramming methods for disease modeling and give some guides for potential therapeutic applications. Overall design: Comparison of DNA methylation and genes expression patterns in 3 cell types
Publication Title
Genome-wide DNA methylation analysis reveals that mouse chemical iPSCs have closer epigenetic features to mESCs than OSKM-integrated iPSCs.
Sample Metadata Fields
Sex, Specimen part, Subject
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
SND1 protein is a highly conserved protein of eukaryotic cells and is involved in a group of cellular biological processes, such as gene transcription, pre-mRNA splicing, cell cycle, DNA damage repair, proliferation and programmed cell death degradome, adipogenesis and cancerogenesis. SND1 can promote the metastasis and proliferation of breast cancer cells by down-regulating the miR-127 expression.
Publication Title
SND1 acts as an anti-apoptotic factor via regulating the expression of lncRNA UCA1 in hepatocellular carcinoma.
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
RNA-binding proteins (RBPs) are involved in a wide variety of regulatory pathways in mammalian cells. Here, we report that the DEAD-box RBP DDX5 (also known as p68) inhibits induced pluripotency by negatively regulating the expression and function of a non-canonical polycomb complex 1 (PRC1) subunit, RYBP, by modulating microRNA-125b processing. DDX5 loss-of-function, both during reprogramming and the somatic to pluripotent transition, and also in the differentiation of mouse embryonic stem cells, results in the suppression of lineage-specific genes via an RYBP-dependent ubiquitination of histone H2A at K119 (H2AK119ub1). RYBP functions as both transcriptional repressor through PRC1 but also as an activator through its interaction with OCT4 during reprogramming. Diminished DDX5 also potentiates RYBP-mediated recruitment of OCT4 to the promoter of the pluripotency activation gene Kdm2b. These data show that DDX5 down-regulation stimulates silencing of lineage-specific genes by RYBP-PRC1 in the early phase of reprogramming and activation of the pluripotency gene network by RYBP-OCT4 in the later phase of reprogramming. Overall design: RNA-seq profiles of wild type (WT) and knockout DDX5-/- (also known as p68) mouse ESCs were generated by deep sequencing, Samples were sequenced in triplicate.
Publication Title
RNA Helicase DDX5 Inhibits Reprogramming to Pluripotency by miRNA-Based Repression of RYBP and its PRC1-Dependent and -Independent Functions.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 31 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The main goal of our study is to identify the molecular events that determine the gonadal identity in mammals. Although testis and ovary arise from a common embryonic primordium, they represent outcomes of opposing fate determination. This decision to differentiate into a testis or an ovary hinges upon the balance between two antagonizing factors, pro-testis SOX9 and pro-ovary -catenin.
Publication Title
Gonadal Identity in the Absence of Pro-Testis Factor SOX9 and Pro-Ovary Factor Beta-Catenin in Mice.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 21 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The aim of the study was to identify significant alterations in genes and molecular functional pathways in comparison with normal and ACM tissue, and detect the marker genes to differentiate the different stage astrocytomas
Publication Title
Gene expression profiling in human high-grade astrocytomas.
Sample Metadata Fields
Sex, Age, Specimen part, Disease stage
View Samples- Homo sapiens
- 18 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
In this study we performed gene expression profiling of 14 cases of grade II gliomas. The results of these analysis were used in unsupervised analyses to compare correlations between the histological subtype of grade II gliomas and gene expression profiles
Publication Title
Gene expression profiling in human high-grade astrocytomas.
Sample Metadata Fields
Sex, Age, Specimen part, Disease stage
View Samples- Mus musculus
- 19 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The goal of the microarray analysis is to determine the redundant and distinct roles of Dhh and Ihh in ovarian functions
Publication Title
Reproductive, Physiological, and Molecular Outcomes in Female Mice Deficient in Dhh and Ihh.
Sample Metadata Fields
Age, Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This goal of this microarray analysis is to determine whether the mesonephros-derived theca cells exhibt a different gene expression profile from that of the whole theca cell population
Publication Title
Lineage specification of ovarian theca cells requires multicellular interactions via oocyte and granulosa cells.
Sample Metadata Fields
Sex, Age
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
High metastatic nasopharyngeal carcinoma cell line 5-8F expression patterns against low metastatic nasopharyngeal carcinoma cell line 6-10B.
Publication Title
Microarray analysis of differentially expressed genes between nasopharyngeal carcinoma cell lines 5-8F and 6-10B.
Sample Metadata Fields
Cell line
View Samples