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.
FGF1<sup>ΔHBS</sup> ameliorates chronic kidney disease via PI3K/AKT mediated suppression of oxidative stress and inflammation.
Specimen part, Treatment, SubjectView Samples
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.
Transcriptome analysis of early organogenesis in human embryos.
Specimen partView Samples
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.
Genome-wide mapping of miRNAs expressed in embryonic stem cells and pluripotent stem cells generated by different reprogramming strategies.
No sample metadata fieldsView Samples
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.
miR-34b regulates multiciliogenesis during organ formation in zebrafish.
Specimen partView Samples
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.
miR-142-3p acts as an essential modulator of neutrophil development in zebrafish.
Age, Specimen partView Samples
GDF11 treatment leads to bone loss in mice and strongly stimulates RANKL-induced osteoclastogenesis of bone marrowderived macrophages (BMMs) in vitro.
GDF11 decreases bone mass by stimulating osteoclastogenesis and inhibiting osteoblast differentiation.
Specimen part, TreatmentView Samples
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.
Regulatory protein SrpA controls phage infection and core cellular processes in Pseudomonas aeruginosa.
Cell line, SubjectView Samples
Abnormal activation of stemness factors is a crucial signature of cancer stem cells (CSCs), a highly tumorigenic subpopulation in malignant tumors. However, it is unclear whether multi-signaling pathways are activated in CSCs, as like normal stem cells. I would like to report that an inhibitor of differentiation 1 (ID1) activates intracellular multi-signaling involved in proliferation, genesis, and maintenance of glioma stem cells (GSCs) by suppression of Cullin3, an E3 ubiquitin ligase that degrades Cyclin E and components of SHH and WNT signaling. ID1 inhibits BMP-dependent differentiation of GSCs by activation of BMPR2-targeting miR17/20a. ID1HIGH-Cullin3LOW signature correlates with a poor prognosis of GBM patients with a significant association to gene signatures enriched in EGF, WNT, SHH, and BMP signaling. Combinational inhibition of GSC intracellular multi-signaling network increases tumor-bearing mice survival. These results provide insights on molecular and cellular basis of GSC biology, and also suggest necessity of multi-signaling inhibition for GSCs therapy.
The ID1-CULLIN3 Axis Regulates Intracellular SHH and WNT Signaling in Glioblastoma Stem Cells.
Specimen part, Cell lineView Samples
Cellular directed migration is critical to invasion-metastasis cascade of cancer cells. We used in vitro transwell model to screen two esophageal cancer cell lines (KYSE30/180) and obtained two pairs of subpopulations with distinct motility ability.
Guanylate-binding protein 1 (GBP1) promotes lymph node metastasis in human esophageal squamous cell carcinoma.
Cell lineView Samples
This SuperSeries is composed of the SubSeries listed below.
PU.1 and C/EBP(alpha) synergistically program distinct response to NF-kappaB activation through establishing monocyte specific enhancers.
Cell line, TreatmentView Samples