Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and cardiac-specific Bmi1 deletion [mouse]

ABSTRACT: To explore the primary cause of Dilated Cardiomyopathy in Bmi1-null mice, we set out to identify differentially expressed genes by massively parallel sequencing of heart samples from Bmi1f/f;?MHCTM-Cretg/+ mice versus ?MHCTM-Cretg/+ control mice (17 weeks postinduction). Methods: Heart mRNA profiles of 17-weeks post-induction Bmi1f/f; MHCTM-Cretg/+ mice and MHCTM-Cretg/+ control mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. Sequence reads were pre-processed with Cutadapt 1.2.1, to remove TruSeq adapters and mapped on the mouse transcriptome (Ensembl gene-build GRCm38.v70) using RSEM v1.2.3. The Bioconductor package EdgeR was used to normalize data with TMM and to test for differential expression of genes using GLM.

ORGANISM(S): Mus musculus

SUBMITTER: Manuel Gomez

PROVIDER: E-GEOD-64391 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Similar Datasets

Project description:Ventricular chambers are essential for the rhythmic contraction and relaxation that occurs in every hearbeat throughout life. Congenital abnormalities in ventricular chamber formation cause severe human heart defects. How the early trabecular meshwork of myocardial fibres forms and subsequently develops into mature chambers is still poorly understood. Here we show that Notch signalling first connects chamber endocardium and myocardium to sustain trabeculation and later coordinates ventricular patterning and compaction with coronary vessel development to give rise to the mature chamber via a temporal sequence of ligand signalling determined by the glycosyltransferase Manic Fringe (Mfng). The early endocardial expression of Mfng favours Dll4-Notch1 signalling, Which induces trabeculation in the developing ventricle.Ventricular maturation and compaction in turn require Mfng and Dll4 downregulation in the endocardium, Which allows myocardial Jag1- And Jag2- Signalling to Notch1 in this tissue.Timely and spatial perturbation of this signalling equilibrium severely disrupts heart chamber formation. Our results open a new research avenue into the pathogenesis of cardiomyopathies. Dll4 and Notch1 conditional KOs using Nfact1 and/or Tie2 driven Cre expression: RNA was isolated from pooled whole hearts of 8 (Nfact1) or 9 (Tie2) E9.5 embryos per replicate. Dll4flox;Nfatc1-Cre and WT siblings (4 KO and 4 WT replicates), Notch1flox;Nfatc1-Cre and WT siblings (3 KO and 2 WT replicates), Dll4flox;Tie2-Cre and WT siblings (3 KO and 3 WT replicates). Jag1, Jag2 and Jag1Jag2 conditional KOs using cTnT driven Cre expression: RNA was isolated from pooled heart ventricles of 4 E15.5 embryos per replicate. Jag1flox;cTnT-Cre and WT siblings (3 KO and 3 WT replicates), Jag2flox;cTnT-Cre and WT siblings (3 KO and 2 WT replicates). Jag1flox;jag2flox;cTnT-Cre and WT siblings (3 KO and 2 WT replicates). MFng Gain Of Function using Tie2 driven Cre expression: RNA was isolated from pooled heart ventricles of 4 E15.5 embryos per replicate. MFng;Tie2-Cre and WT siblings (4 GOF and 4 WT replicates). For Dll4, Noth1 and Jag1 KOs, libraries were prepared using the standard Illumina TrueSeq RNASeq library preparation kit and sequenced in a GAIIx Illumina sequencer using a 75bp single end elongation protocol. For Jag2 and Jag1Jag2 KOs and MFng GOF libraries were prepared prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina and sequenced in a HiSeq2500 Illumina sequencer using a 61bp single end elongation protocol

Project description:We have previously generated ABIN1[D485N] knock-in mice that appear relatively normal for 2 months after birth, but develop large spleen at 3 months, which is followed by the appearance of high levels of antibodies against self DNA and self-nuclear antigens and severe inflammation of the kidney and other tissues after 4-5 months, hall marks of lupus like autoimmunity. Autoimmunity in ABIN1[D485N] mice appears to be caused by hyper activation of pathogen sensing Toll-like Receptor (TLR) pathway, because the phenotype of the ABIN1[D485N] mice is completely suppressed by crossing them to mice that are either lacking or expressing functionally defective proteins, which play key role in TLR signalling. MyD88 KO, IRAK4 or IRAK1 kinase-inactive knock-in mice. However, cell type(s) required to drive lupus, and how this contributes to the development of the pathology, is unknown. Recently, we have identified atypical myeloid (CD11b+ve) populations in the blood, lungs liver, kidney and spleen of ABIN1[D485N] mice. Importantly, these cells are detectable at four weeks, at least two months before auto-antibodies are detected in the serum. More detailed flow cytometry analysis of these cells revealed that, in the blood, the majority were CD115+ve and these cells could be further subdivided into Ly6C+ve and Ly6C-ve, which are characteristics of the inflammatory and patrolling monocytes, respectively. While in the lungs and spleen of WT mice the Ly6C-ve CD115+ve (patrolling monocytes) are almost absent, in the ABIN1[D485N] mice this population is more than 20-fold increased. There is also increase in the number of neutrophil population (CD11b+ GR-1hi) in the spleen of the ABIN1[D485N] mice. Although we have shown that the formation of these atypical myeloid cells proceeds the development of auto-antibodies and organ inflammation in the ABIN1[D485] mice, the signalling pathway leading to formation of these cells and their role in autoimmunity is unknown. We therefore undertook RNAseq analysis to characterise these cells in more detail. The atypical CD11b+ve cells present in spleen of ABIN1[D485N] mice are heterogeneous with three major populations, neutrophils (CD11b+ GR-1hi), Ly6C+veCD115+ve cells and Ly6C-veCD115+ve. How these cell populations in ABIN1[D485N] mice relate to one another, and whether they share a common precursor is unknown. In order to profile the cells, the neutrophils, Ly6C+veCD115+ve cells and Ly6C-veCD115+ve populations were purified by cell sorting and RNAseq analysis carried out. The RNA seq analysis was carried out with at least four replicate samples from each cell populations from ABIN1[D485N] and WT controls.

Dataset Information

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and cardiac-specific Bmi1 deletion [mouse]

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets