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GSE37861
Mus musculus
15 Downloadable Samples
Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
RANKL (receptor acrivator of NFkB ligand) is a member of TNF superfamily cytokines. In the gastrointestinal tract, RANKL is expressed in the stromal cells of Peyer's patches, and involved in the development of the specialized intestinal epithelial cells, called M cells.
Publication Title
The Ets transcription factor Spi-B is essential for the differentiation of intestinal microfold cells.
Sample Metadata Fields
Age, Specimen part, Time
View Samples- Mus musculus
- 6 Downloadable Samples
Illumina HiSeq 4000
Description
RNA-seq is a powerful tool to analyze differential expression of cellular pathways under different conditions. The goal of this study is to analyze the potential pathways involved in cellular defense against high glucose challenge with or without FGF1 intervention. Overall design: MPC cells were starved for 12 hours in serum-free RPMI-1640 medium and pretreated with FGF1 wild type or FGF1 variant (100 ng/mL) for 1 hour. Then, the cells were challenged with high glucose (25 mM) (with D-mannitol as an osmotic control) for 12 hours. After that, cells were harvested for RNA-seq analysis.
Publication Title
FGF1<sup>ΔHBS</sup> ameliorates chronic kidney disease via PI3K/AKT mediated suppression of oxidative stress and inflammation.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Rattus norvegicus
- 13 Downloadable Samples
- Affymetrix Rat Gene 1.0 ST Array (ragene10st)
Description
Skin-derived precursors (SKPs) are multipotent dermal stem cells that reside within a hair follicle niche and that share properties with embryonic neural crest precursors. Here, we have asked whether SKPs and their endogenous dermal precursors originate from the neural crest or whether, like the dermis itself, they originate from multiple developmental origins. To do this, we used two different mouse Cre lines that allow us to perform lineage tracing: Wnt1-cre, which targets cells deriving from the neural crest, and Myf5-cre, which targets cells of a somite origin. By crossing these Cre lines to reporter mice, we show that the endogenous follicle-associated dermal precursors in the face derive from the neural crest, and those in the dorsal trunk derive from the somites, as do the SKPs they generate. In spite of these different developmental origins, SKPs from these two locations are functionally similar, even with regard to their ability to differentiate into Schwann cells, a cell type only thought to be generated from the neural crest. Analysis of global gene expression using microarrays confirmed that facial and dorsal SKPs exhibit a very high degree of similarity, and that they are also very similar to SKPs derived from ventral dermis, which has a lateral plate origin. However, these developmentally-distinct SKPs also retain differential expression of a small number of genes that reflect their developmental origins. Thus, an adult neural crest-like dermal precursor can be generated from a non-neural crest origin, a finding with broad implications for the many neuroendocrine cells in the body.
Publication Title
Convergent genesis of an adult neural crest-like dermal stem cell from distinct developmental origins.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 18 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
In order to study the improtance of HSFA6b in salt and heat stresses of arabidopsis, we generated the HSFA6b-overexpression (HSFA6b-OE) and dominant-negative (HSFA6b-RD) mutant lines.
Publication Title
The Heat Stress Factor HSFA6b Connects ABA Signaling and ABA-Mediated Heat Responses.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 17 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
We here report transcriptome profiles of human embryos at six successive developmental stages (i.e., Carnegie Stages 9 to 14), representing the first comprehensive gene expression database of early human organogenesis.
Publication Title
Transcriptome analysis of early organogenesis in human embryos.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 12 Downloadable Samples
- Illumina Genome Analyzer II, Illumina HiSeq 2000
Description
We report the miRNA profiling in MEF cells, ES cells and three Pluripotent Stem Cells obtained by three different reprogramming approaches from MEF cells based on Solexa sequencing. iPS cells are reprogrammed by four factors (OSKM) from MEF cells. NT-ESCs were established by reprogramming MEF cells into ESCs using nuclear transfer. NT-iPSCs were established to reflect the combination of nuclear transfer and iPS technologies. iPSCs, NT-ESCs, and NT-iPSCs were exactly derived from the same MEF cells. The results indicate NT-ESCs give expression to the unique miRNAs other than both ESCs and iPSCs while pluripotent cells acquire or retain the pluripotent specific miRNAs compared with MEF. Furthermore, the comparison of different reprogramming cells suggests that several miRNAs have key roles in distinctly developmental potential reprogrammine cells. Overall design: Small RNA profiles of MEF, ES, iPS, NT-ES and NT-iPS cells were generated by Solexa sequencing. MEF and ES cells were performed in triplicate. iPS, NT-ES and NT-iPS cells were sequenced in duplicate.
Publication Title
Genome-wide mapping of miRNAs expressed in embryonic stem cells and pluripotent stem cells generated by different reprogramming strategies.
Sample Metadata Fields
No sample metadata fields
View Samples- Danio rerio
- 4 Downloadable Samples
- Affymetrix Zebrafish Genome Array (zebrafish)
Description
Multiciliated cells (MCCs) possess multiple motile cilia on the cell surface and are widely distributed throughout the vertebrate body to perform important physiological functions by regulating fluid movement in the intercellular space. However, neither their function during organ development nor the molecular mechanisms underlying multiciliogenesis are yet well understood. We aim to study the function of miR-34b in multiciliogenesis.
Publication Title
miR-34b regulates multiciliogenesis during organ formation in zebrafish.
Sample Metadata Fields
Specimen part
View Samples- Danio rerio
- 8 Downloadable Samples
- Zebrafish Gene 1.0 ST Array (zebgene10st)
Description
hematopoiesis and myelopoiesis was tightly controled by microRNAs. In the zebrafish adult kidney, specific sets of genes were dysregulated in myelomonocytes or whole kidney marrow after deletion of miR-142-3p.
Publication Title
miR-142-3p acts as an essential modulator of neutrophil development in zebrafish.
Sample Metadata Fields
Age, Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
GDF11 treatment leads to bone loss in mice and strongly stimulates RANKL-induced osteoclastogenesis of bone marrowderived macrophages (BMMs) in vitro.
Publication Title
GDF11 decreases bone mass by stimulating osteoclastogenesis and inhibiting osteoblast differentiation.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Pseudomonas aeruginosa
- 2 Downloadable Samples
- Illumina HiSeq 2000
Description
RNAseq analysis was performed to evaluate gene expression differences between strains 1-9 and PAK-AR2.P. aeruginosa PAK-AR2 and 1-9 cells were grown to OD600 of 0.8 before harvesting. The collected cells were treated with RNAprotect Bacteria Reagent (Qiagen) and subjected to snap freezing in liquid nitrogen and delivered to BGI in dry ice for transcriptome resequencing analysis.The differentially expressed genes (DEGs) were determined between PAK-AR2 and 1-9 with the standards of false discovery rate (FDR ) = 0.001, fold change |log2Ratio|=1.A total of 4,355,305 reads matched to the referenced genome in the sample of PAK-AR2, and 3,544,484 reads in the sample of 1-9.Transcriptome data showed that expression of 361 genes were upregulated while 459 genes were down regulated by at least 2-fold when comparing the srpA mutant strain 1-9 to its parent strain PAK-AR2.These genes were classified into 21 major cellular processes based on the annotation of KEGG_B_class or further grouped into several major metabolic pathways, such as ribosomal proteins, type III secretion system (T3SS), type VI secretion system (T6SS), chemotaxis, cell motility, and cell shape control.More and more small proteins that were ignored from typical genome annotations have now been experimentally demonstrated to play important regulatory roles on various bacterial metabolic. Overall design: Gene expression of PAK-AR2 and 1-9 were generated by deep sequencing, in triplicate, using Illumina HiSeqTM 2000.
Publication Title
Regulatory protein SrpA controls phage infection and core cellular processes in Pseudomonas aeruginosa.
Sample Metadata Fields
Cell line, Subject
View Samples