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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Comparison of Flk-1+/PDGFRa+(Flk-1PRa+(DP)) population from Etv2Het vs Etv2KO ES cells

ABSTRACT: Screening for genes regulated by Etv2 within Flk-1+/PDGFRa+ ES derived mesoderm.Microarray analysis performed to screen for the candidate genes regulated by Etv2. TT2 ES cells differentiated on OP9 feeder cells were sorted using Flk-1 and PDGFRa antibodies.Gene expressions from these two populations were compared. Extract RNA from sorted Flk-1+/PDGFRa+ populations from Etv2Het vs KO cells. To obtain primitive mesoderm cells TT2 ES cells of corresponding genotypes were differentiated on OP9 cells for 4 days. Flk-1+/PDGFRa+ populations were sorted from Etv2 Het vs. KO cells for RNA extraction.

ORGANISM(S): Mus musculus

SUBMITTER: Hiroshi Kataoka

PROVIDER: E-GEOD-31744 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Comparison of Flk-1+/Etv2- vs Flk-1+/Etv2+ populations

Project description:Screening for genes up in Etv2+ cells within Flk-1+ ES derived mesoderm Microarray analysis performed to screen for the candidate genes regulated by Etv2. Differentiated Flk-1+ mesoderm can be devided into Etv2+ or-. Etv2+ cells are assumed to be committed to hemato/endothelial cells. Comparison of two populations can reveal genes relevant in this commitment. Extract RNA from sorted Flk-1+/Etv2- vs Flk-1+/Etv2+ populations.Etv2-Venus KI ES cells were differentiated on OP9 for 4-5 days and Flk-1+ population was separated into Etv2-Venus+ or- cells. Total RNA was purified from each population for analysis.

2011-08-30 | E-GEOD-31743 | biostudies-arrayexpress

Comparison of Flk-1+/PDGFRa+(Flk-1PRa+(DP)) population from Etv2Het vs Etv2KO ES cells

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Comparison of Flk-1+/Etv2- vs Flk-1+/Etv2+ populations

2011-08-31 | GSE31743 | GEO

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Mus musculus

Project description:Comparison of Flk-1+/Etv2- vs Flk-1+/Etv2+ populations

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Genome-wide analysis of gene expression of Flk1Cre;ETV2 CKO mouse yolk sacs.

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2014-11-17 | E-GEOD-51407 | biostudies-arrayexpress

Constitutive activation of oncogenic PDGFR-mutants found in GIST patients induces receptor mislocalisation and alters PDGFR-A signalling characteristics

Project description:Gastrointestinal stomal tumors (GIST) are mainly characterised by the presence of activating mutations in either of the two receptor tyrosine kinases c-KIT and Platelet-derived growth factor receptor-a (PDGFRa). Most mechanistic studies dealing with GIST mutations have focused on c-KIT and far less is known about the signalling characteristics of the mutated PDGFRa proteins. Comparative studies of the signal transduction capacities of different mutant proteins cannot be performed in patient cells due to the patient specific background which may influence the signalling behaviour of the investigated mutants. In addition, the lack of a real wild-type signalling control (PDGFRa-WT) hampers comparisons of the signalling of wild-type and mutant proteins. Therefore, we stably and inducibly expressed different PDGFRa mutants as well as wild-type PDGFRa on an isogenic background in 293T cells in order to study the signalling capacities and corresponding transcriptional responses of the different proteins. We found that the constitutive signalling via the oncogenic PDGFRa mutants favours a mislocalisation of the receptors and that this modifies the signalling characteristics of the mutated receptors. We show that signalling via the oncogenic PDGFRa mutants is not solely characterised by a constitutive activation of the conventional PDGFRa signalling pathways.

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Gene expression signatures for fractions of E7.5 whole embryos based on Endoglin and Flk-1 markers

Project description:Much remains unknown about the signals that induce early mesoderm to initiate hematopoietic differentiation. Here we show that endoglin (Eng), a receptor for the TGFÎ² superfamily, identifies all cells with hematopoietic fate in the early embryo. These arise in an Eng+Flk1+ mesodermal precursor population at E7.5, a cell fraction also endowed with endothelial potential. In Eng knockout embryos, hematopoietic colony activity and numbers of CD71+Ter119+ erythroid progenitors were severely reduced. This coincided with severely reduced expression of embryonic globin and key BMP target genes including the hematopoietic regulators Scl, Gata1, Gata2 and Msx-1. To interrogate molecular pathways active in the earliest hematopoietic progenitors, we applied transcriptional profiling to sorted cells from E7.5 embryos. Eng+Flk-1+ progenitors co-expressed TGFÎ² and BMP receptors and target genes. Furthermore, Eng+Flk-1+ cells presented high levels of phospho-SMAD1/5, indicating active TGFÎ² and/or BMP signaling. Remarkably, under hematopoietic serum-free culture conditions, hematopoietic outgrowth of endoglin-expressing cells was dependent on TGFÎ² superfamily ligands: BMP4, BMP2, or TGF-Î²1. These data demonstrate that the E+F+ fraction at E7.5 represents mesodermal cells competent to respond to TGFb1, BMP4, or BMP2, shaping their hematopoietic development, and that endoglin is a critical regulator in this process by modulating TGF/BMP signaling. E7.5 pooled embryos (25 litters; 300 embryos approximately) were dissected and 3,000 cells were sorted in triplicate for Eng-Flk1-, Eng-Flk1+, Eng+Flk1+, and Eng+Flk1- fractions. Microarray results were analyzed with GeneSpring GX software.

2012-04-22 | E-GEOD-37515 | biostudies-arrayexpress

Next Generation Sequencing to Study FLK-affected genes

Project description:Purpose: The goals of this study are to compare RNA-seq profiles of Col-0, acd6-1, flk-1, flk-5, acd6-1flk-1, and acd6-1flk-5 to identify genes affected by FLK. Methods: Total RNA was extracted from 25-d old plants. A total amount of 1 μg RNA per sample was used to generate cDNA libraries, using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Deep sequencing was performed using Illumina NovaSeq 6000 (Novogene Corporation Inc.). Triplicate biological samples were used for all genotypes except acd6-1flk-5, which had duplicate samples because one sample failed to pass quality control. The samples were multiplexed and sequenced with the standard paired-end sequencing that has a read length of 150bp per end and 20M reads per end per sample. Results: We found that over 8000 genes are differentially affected by FLK based on the RNAseq analysis. GO analysis revealed that FLK-affected genes are enchriched for genes involved in primary metabolism and in response to abiotic and biotic stimuli. Conclusions: The RNAseq analysis support a role of FLK in regulation of plant development and defense.

2023-04-12 | GSE164424 | GEO

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