Single-cell RNA-seq (10X Genomics Chromium) to profile of cardiac progenitor cells, comparing the transcriptomes of diploid and tetraploid cardiac progenitor cells Overall design: Transcriptional profiling of diploid and tetraploid CPCs by scRNA-Seq approaches using 10X Genomics Chromium
Cardiac interstitial tetraploid cells can escape replicative senescence in rodents but not large mammals.
Sex, Specimen part, Cell line, Subject
View SamplesTranscriptomal 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.
Innate Lymphoid Cells in the Induction of Obesity.
Age, Specimen part, Subject
View SamplesExpression profile of embryonic retinas expressing exogenous c-hairy1, Delta-1, or Wnt2b. These genes inhibits neuronal differentiation, and the results provide insight into the mechanism that keeps retinal progenitor cells undifferentiated.
Hairy1 acts as a node downstream of Wnt signaling to maintain retinal stem cell-like progenitor cells in the chick ciliary marginal zone.
Specimen part
View SamplesUnderstanding the structure and interplay of cellular signalling pathways is one of the great challenges in molecular biology. Boolean Networks can infer signalling networks from observations of protein activation. In situations where it is difficult to assess protein activation directly, Nested Effect Models are an alternative. They derive the network structure indirectly from downstream effects of pathway perturbations. To date, Nested Effect Models cannot resolve signalling details like the formation of signalling complexes or the activation of proteins by multiple alternative input signals. Here we introduce Boolean Nested Effect Models (B-NEM). B-NEMs combine the use of downstream effects with the higher resolution of signalling pathway structures in Boolean Networks. We show that B-NEMs accurately reconstruct signal flows in simulated data. Using B-NEM we then resolve BCR signalling via PI3K and TAK1 kinases in BL2 lymphoma cell lines.
Analyzing synergistic and non-synergistic interactions in signalling pathways using Boolean Nested Effect Models.
Specimen part, Cell line, Treatment
View SamplesIdentification of genes up or down regulated in LPS stimulated samples in comparison to control samples.
Genomic data integration using guided clustering.
Specimen part, Cell line, Treatment
View SamplesWe have generated tumorigenic (S2N) and non-tumorigenic (S2), normal-like to basal-like breast cancer cell lines from primary tumors. At high in vivo inoculation cell numbers of 10^6 cells/mouse both S2N and S2 monolayer as well as sphere culture cells grew at similar rates. However, at low inoculation cell numbers down to 10^3 cells only S2N sphere cells generated xenograft tumors. mRNA profiling revealed a unique cluster pattern of the tumorigenic S2N sphere cells, but a detailed analysis of TIC relevant transcription factors like Oct3, Sox and Nanog family members, Myc, Slug or Twist1 revealed no consistently increased expression in the highly tumorigenic cell lines. Our data indicate that the intrinsic genetic and functional markers investigated are not solely indicative of the in vivo tumorigenicity of putative breast tumor-initiating cells.
Established breast cancer stem cell markers do not correlate with in vivo tumorigenicity of tumor-initiating cells.
Disease, Cell line
View SamplesExpression of insulin in terminally differentiated non-beta pancreatic cell types could be important for treating type-1 diabetes. We observed that the kinase inhibitor GW8510 up-regulated insulin expression in mouse pancreatic alpha cells.
GW8510 increases insulin expression in pancreatic alpha cells through activation of p53 transcriptional activity.
Cell line, Compound
View SamplesArabidopsis MPK4 is involved in the control of antagonism between salicylic acid (SA) and ethylene (ET)/jasmonic acid (JA) pathways in the plant innate immune system as a repressor of the SA pathway, but an activator of the ET/JA pathway. Here we and use comparative microarray analysis of ctr1, ctr1/mpk4, mpk4 and wild type to show that MPK4 is required for only a narrow subset of ET regulated genes.
Arabidopsis systemic immunity uses conserved defense signaling pathways and is mediated by jasmonates.
Age, Specimen part
View SamplesThis SuperSeries is composed of the SubSeries listed below.
A comparative study of RNA-Seq and microarray data analysis on the two examples of rectal-cancer patients and Burkitt Lymphoma cells.
Cell line, Treatment
View SamplesIn hemochorial placentation, trophoblast stem cells differentiate into multiple lineages to aquire specific functions, such as invasive and endocrine phenotype. FOSL1 has been identified as a key regulator for trophoblast differentiation. We used microarray to detail mechanisms underlying FOSL1 signaling pathway in trophoblast differentiation.
Dynamic Regulation of AP-1 Transcriptional Complexes Directs Trophoblast Differentiation.
Specimen part, Cell line
View Samples