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In vivo RNA-seq for for Hh Dependent genes in E7.5 mesoderm

ABSTRACT: Mesp1-Cre+ cells from E7.5 mouse embryos (from the cross Mesp1-Cre/+ x Rosa26-Gli3R-IRES-YFP/tdTomato) were sorted by FACS where wild type (tdTomato-expressing) and mutant (Gli3R + YFP co-expressing) cells were collected separately from single litters.

ORGANISM(S): Mus musculus

PROVIDER: GSE147868 | GEO | 2020/05/28

REPOSITORIES: GEO

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Genome wide mapping of histone 3 lysine 79 mono, di and trimethylation and histone 3 lysine 27 trimethylation in LSKs, GMPs and retroviral MLL-AF9 driven murine leukemias

Project description:We report the genome wide distribution of the three states of H3K79 methylation (H3K79me1/me2/me3) and H3K27me3 in mouse lineage negative Sca-1 positive Kit positive cells (LSKs), granulocyte macrophage progenitors (GMPs) and LSK derived MLL-AF9 leukemias in the presence or absence of the Af10 OM-LZ domain. Legend- MIT:MSCV-IRES-tdTomato (Empty vector control) and CRE (MIT vector with the Cre recombinase). We examined the H3K79 me1,me2,me3 and H3K27me3 profiles by ChIP-seq in lineage negative Sca-1 positive, Kit positive (LSK) cells, granulocyte macrophage progenitors (GMPs) and bone marrow cells from sacrificed terminally ill secondary MLL-AF9 positive leukemic mice. In case of the MLL-AF9 leukemias, the ChIP-seq experiments were performed in 2 conditions in the presence or absence of the Dot1l interacing octapeptide-motif leucine zipper (OM-LZ) domain of Af10. For the leukemia experiments, leukemias derived from the Af10 OM-LZ homozygous floxed background were transduced with MSCV-IRES-tdTomato control vector (MIT) or its Cre-recombinase expressing counterparts (CRE). Subsequently, we sorted tdTomato positive cells and injected them into sub-lethally irradiated syngenic secondary recipient mice. Seconday leukemias obtained from these MIT or CRE expressing cells were used for ChIP -seq studies.

2014-09-08 | E-GEOD-55038 | biostudies-arrayexpress

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

Expression profile of conditional knock out of beta-catenin by K19-CRE at E7.5

Project description:expression profile of conditional knock out of beta-catenin by K19-CRE at E7.5. Tested a wild type with two alleles of beta-catenin, a heterzyote with one deleted allele and the conditional null in the domain on cytokeratin 19 driven CRE expression Keywords: other

2005-04-13 | GSE2519 | GEO

Transcription profiling of mouse conditional knock out of beta-catenin by K19-CRE at E7.5

2008-06-12 | E-GEOD-2519 | biostudies-arrayexpress

Transcriptome analysis of FOXF1 expressing cells at E7.5 of embryonic development

Project description:Comparison of the transcriptional profile of cells expressing FOXF1::VENUS and/or FLK1 in E7.5 mouse embryos carrying a foxf1::venus knock-in allele

2015-10-10 | GSE66574 | GEO

Distinct mesenchymal lineages and niches promote epithelial self-renewal and myofibrogenesis in the lung

Project description:Using flourescence activated cell sorting, we gated on cells negative for CD45, CD326 and CD31, from single cell suspension generated from Adult mice. We then isolated subsets of YFP-, GFP- or TdTomato expressing cells from the indicated reporter mice. tdTomato indicates Wnt-responsive cells, GFP reports Pdgfr-alpha expression and YFP- was used to isolate lineaged Wnt2-positive cells. Additionally we included cells that were negative for the aforementioned reporters. We performed RNAseq on biological duplicates for each subset.

2017-09-11 | GSE92699 | GEO

Maternal Influenza A Virus Infection Restricts Fetal and Placental Growth and Adversely Affects the Fetal Thymic Transcriptome

Project description:Maternal influenza A viral infections in humans are associated with low birth weight, increased risk of pre-term birth, stillbirth and congenital defects. To examine the effect of maternal influenza virus infection on placental and fetal growth, pregnant C57BL/6 mice were inoculated intranasally with influenza A virus A/CA/07/2009 pandemic H1N1 or PBS at E3.5, E7.5 or E12.5, and the placentae and fetuses collecgted and weighed at E18.5. Fetal thymuses were pooled from each litter. Placentae were examined histologically, stained by IHC for CD34 and vascular channels quantified. RNA from E7.5 and E12.5 placentae and E7.5 fetal thymuses was subjected to RNA sequencing and pathway analysis. Placental weights were decreased in litters inoculated with influenza at E3.5 and E7.5. Placentae from E7.5 and E12.5 inoculated litters exhibited decreased labyrinth development and transmembrane protein 150A gene was upregulated in E7.5 placentae. Fetal weights were decreased in litters inoculated at E7.5 and E12.5 compared to controls. RNA sequencing of E7.5 thymuses indicated that 957 genes were downregulated 2-fold including Mal, which is associated with Toll-like receptor signaling and T cell differentiation. There were 28 upregulated genes. It is concluded that maternal influenza A virus infection impairs fetal thymic gene expression as well as restricting placental and fetal growth.

2020-09-11 | GSE157132 | GEO

Genome wide mapping of histone 3 lysine 79 mono, di and trimethylation and histone 3 lysine 27 trimethylation in LSKs, GMPs and retroviral MLL-AF9 driven murine leukemias

2014-09-08 | GSE55038 | GEO

Transcription profiling by high throughput sequencing of primordial germ cells from e6.5, e7.5, e8.5 embryos and e7.5 somatic neighbours and Blimp1-KO mice

Project description:Primordial germ cell mRNA profiles from cells microdissected from e6.5, e7.5 and e8.5 embryos, e7.5 somatic neighbours and Blimp1-KO mice were generated by single cell library construction and sequencing in duplicate using Applied Biosystems SOLiD sequencer. Single cell library construction is described in: Tang f. et. al, Nature Protocols (2010), Vol. 5, p.516.

2013-07-01 | E-MTAB-1178 | biostudies-arrayexpress

Single cell RNA sequencing of aortic CX3CR1-derived monocyte/macrophage from atherosclerotic aorta during progression and regression

Project description:In atherosclerosis progression and regression, monocytes or monocyte-derived macrophages are the major immune cells in the plaque. It is important to understand the fate and characteristics of monocyte/macrophage during the plaque progression and regression. To characterize the fate of monocytes/macrophages, we performed single cell RNA sequencing of fate-mapped aortic CX3CR1-derived monocytes/macrophages from Cx3cr1CreERT2-IRES-YFP/+Rosa26floxed-tdTomato/+ mice with AAV-PCSK9 injection and fed a Western Diet. The single cell RNA-seq analyses revealed the heterogeneity of aortic macrophages and identified a stem-like cell cluster in atherosclerotic aorta.

2019-02-21 | GSE123587 | GEO

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