Comparison of phosphorylation status of Wnt proteins in control and Fto deficient cells upon Wnt 3a stimulation
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Daniel Osborn
PROVIDER: E-GEOD-52572 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:To gain insight into FTO function, we knocked down and overexpressed FTO in HEK293 cells.Genetrail analyses of expression profiles pointed to the RNA splicing and processing machinery. Intriguingly, using immunocytochemistry and confocal laser scanning microscopy, we observed strong enrichment of FTO in nuclear speckles and - to a lesser extent - in nucleoli, but not in other known nuclear bodies. We also studied RNA samples of Fto knockout and wild type mice with regard to content of methylated and unmethylated nucleosidesand observed that ratios of modified and unmodified uracil and adenine were different depending on the presence of FTO. Taken together, our data suggest that FTO is involved in RNA processing and modification. We used microarrays to investigate global gene expression changes depending on the level of FTO We compared FTO overexpressing and FTO depleted cells to cells with endogeneus level of FTO to determine global gene expression changes.
2012-11-13 | E-GEOD-33870 | biostudies-arrayexpress
Project description:We identified the target genes of FTO ("fat mass and obesity associated") in primary cultures of human skeletal muscle cells using adenoviral vectors expressing FTO or GFP and oligonucleotide microarrays. Human myotubes were prepared from 4 different skeletal muscle biopsies. After differentiation, myotubes were infected for 48 hours with recombinant adenovirus expressing either GFP or FTO. Each FTO-infected myotubes culture was compared to GFP-infected myotubes culture. GFP-infected myotubes were regarded as the control. Four biological replicates were processed.
2011-07-05 | E-GEOD-22857 | biostudies-arrayexpress
Project description:The larval brain of Ciona intestinalis has similar architecture to that of vertebrates, but is only composed of approximately 330 cells. Transgenic embryos that carried Ci-beta-tubulin(promoter)::Kaede exhibited robust Kaede expression in the larval brain. Kaede-expressing cells were isolated, and their transcriptome was compared with that of cells that did not express Kaede using an oligonucleotide-based microarray. Our analysis identified 565 candidate genes that were preferentially expressed in the larval brain, 77 of which have previously been reported to be brain-related. The 565 genes included transcription factors, such as Otx, en, Pax3/7, Prop-A, Lhx1, Six3/6, Unc4-A, FoxC, and DMRT1; and signal transduction molecules, such as FGF4/5/6, Hedgehog1, Hedgehog2, patched, Fringe1, and Dkk3. Nearly 30 of the identified genes coded for receptors for neurotransmitters, neuropeptides or hormone pepetides. In addition, 15 genes encoded neuropeptides and hormone peptides, five of which were novel. Our catalog of genes that are expressed in the Ciona larval brain provides a foundation for future studies exploring the complex gene regulatory networks that mediate chordate brain development and function. Two samples (Brain vs Cells without Brain),Two biological replicates,Dye Swap design
2010-06-21 | E-GEOD-18364 | biostudies-arrayexpress
Project description:In this study, we aimed to examine the changes in gene expression that occur in FTO over expressing mice in order to gain more insight into the underlying mechanisms by which FTO influences body weight and adiposity
2014-06-01 | E-MTAB-2331 | biostudies-arrayexpress
Project description:RNA was purified from liver, skeletal muscle and white adipose tissue of mice with and without a point mutation in exon 6 of the FTO gene.
2009-08-19 | E-MEXP-2201 | biostudies-arrayexpress
Project description:Purpose: The goals of this study are to investigate the mRNAs that bind to the FTO protein in the white fat tissue from mice. Methods: 1. White fat from CAG promoter driven transgenic Flag-tagged FTO mice were extracted with RNA protected. 2. Flag-FTO proteins were immunoprecipitated with control IP using IgG. 3. The immunoprecipitated RNAs were deep sequenced and analyzed. Results: We focused on the mRNAs which have functions related to lipid metabolism and homeostasis. Immunoprecipitated RNAs profiles from Flag-FTO IP and IgG IP were generated by deep sequencing.
2016-01-05 | E-GEOD-74255 | biostudies-arrayexpress
Project description:This analysis revealed ~17.% of all ORFs (292 out of a total 1697 ORFs) differed by at least 1.5 fold (Log2 +0.6) between the mutant and wild-type strains. Of these, ~45% of the ORFs (130 out of 292 ORFs) revealed at least 2-fold (Log2 +1) differences. The complete spectrum of differentially expressed genes in the muatnt strain revealed almost equal number of genes up (143, 49%) or down-regulated (149, 51%). However, at a higher stringency (at least 2-fold), this distribution revealed slightly more leaning towards down-regulated genes (74 out of 130, 57%) indicating the lack of SP-STK results into down regulation of several genes. Amongst the genes belonging to different functional categories, the most notable genes that were affected by the absence of SP-STK were those correspond to Carbohydrate transport and metabolism (57 out of 292, 20% at low stringency and 32 out of 130 ,~25% at high stringency), phage (28, ~10% at low stringency and 24, ~18% at high stringency), and virulence (5-6% irrespective of stringency level). Almost 20-25% of differentially expressed genes revealed at two stringencies were found to be either with unknown or undefined functions. Keywords: knockout mutant This analysis is based on a total of three independent prearations of total RNA from the wild-type S. pyogenes M1SF370 and the isogenic knockout mutant lacking SP-STK (SPy1625). First two preparations included dyeswap experiment and hence repeated twice (exp1-4). The third preparation done only one (Exp#5). Thus, the present analysis is based on five separate experiments
2013-02-28 | E-GEOD-10914 | biostudies-arrayexpress
Project description:Myxomas, the most common primary tumor of the heart, usually develop in the atria and consist of a myxoid matrix composed of an acid-mucopolysaccharide-rich stroma with polygonal stromal cells scattered throughout the matrix. These benign tumors, despite their rarity, are a research focus because of their clinical presentation and uncertain histogenesis. The objective of this study was to assess whether adult cardiac stem/progenitor cells (CSCs) give rise to myxoma stromal cells and secrete the typical myxoid matrix. 23 collected tumors showed the typical histological features of cardiac atrial myxoma with polygonal cells positive for the myxoma tumor-cell marker, calretinin, dispersed in an abundant myxoid matrix. We detected myxoma cells positive for c-kit (c-kitpos) but very rare Isl-1 positive cells. Most of these c-kitpos cells were lineage-committed CD45pos/CD31pos cells. However, c-kitpos /CD45neg/CD31neg cardiac myxoma cells expressed stemness and cardiac progenitor cell transcription factors. Some (<10%) of these c-kitpos/ CD45neg/CD31neg/ myxoma cells expressed also calretinin, representing myxoma stromal precursor cells. c-kitpos/CD45neg/CD31neg cardiac myxoma cells secrete in vitro chondroitin-6-sulfate and hyaluronic acid, composing the gelatinous matrix of cardiac myxoma in vivo. In vitro, c-kitpos/CD45neg/CD31neg myxoma cells have stem cell properties being clonogenic, self-renewing and sphere forming. On the other hand, they exhibited an abortive cardiac differentiation potential with significant changes in their mRNA and microRNA transcriptome compared to normal c-kitpos/CD45neg /CD31neg CSCs. Importantly, myxoma-derived CSCs seed human atrial myxoma in xenograft’s experiments in NOD/SCID mice. Thus, un-committed c-kitpos/CD45neg /CD31neg cells fulfill the criteria of myxoma stem cells in atrial myxoma. Myxomas appear to be the first CSC-related human cardiac disease.
2020-04-01 | E-MTAB-8701 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2013-04-01 | E-GEOD-42184 | biostudies-arrayexpress
Project description:Purpose: There is evidence that therapeutic cancer vaccines can lengthen survival for some cancer patients, but responses vary widely from one person to another. Methods to predict clinical outcomes will advance the field and provide new insights into critical determinants of in vivo efficacy. This study uses a high-throughput glycan microarray to assess correlations between a subject's overall survival after receiving PROSTVAC-VF and his baseline serum anti-glycan antibody levels. Results: Pre-vaccination antibody levels to blood group A trisaccharide (BG-Atri) were found to have a statistically significant correlation with survival. Long-term survival was approximately doubled in subjects with abundant anti-BG-Atri IgM relative to subjects with little or no pre-existing IgM for BG-Atri. This survival correlation was specific to vaccine treatment, as no correlation was observed in control patients immunized with wild-type poxviruses lacking the key tumor antigen, prostate specific antigen (PSA). Moreover, anti-BG-Atri IgM levels were not correlated with general measures of disease severity, such as PSA levels, Gleason score, or Halabi predicted survival. Conclusion: In addition to reporting a new potentially predictive biomarker for PROSTVAC-VF, this study highlights the potential of glycan microarray technology for personalized medicine. The overall study was a retrospective analysis of 141 subjects from phase II trials of PROSTVAC-VF, a poxvirus based cancer vaccine currently in phase III clinical trials for advanced prostate cancer. The subjects were divided into a training set (n=28) and a validation set (n=113). A glycan microarray was used to profile pre-vaccination anti-glycan antibody populations in sera as potential biomarkers for PROSTVAC-VF. For both the training set and validation set, the anti-glycan profiles were measured using four variations of serum dilution and isotype specific secondary antibody (IgM at 1:50, IgG at 1:50, total Ig at 1:50, and total Ig at 1:200). IgG levels for the training set measured at serum dilution of 1:50 are detailed here. The screen for predictive biomarkers identified anti-glycan antibodies that consistently stratified subjects into groups with different Kaplan Meier survival estimates. Due to the potential for overfitting, a permutation test was used to estimate the false discovery rate. Raw data on superSeries GSE42184 record.
2013-04-01 | E-GEOD-42019 | biostudies-arrayexpress