Project description:Using Chromatin-immunoprecipitation and NGS, we profiled the genome-wdie H3K9Me3, H3K27Me and Brg1 distribution between Wild Type (Wt) and Actb-/- (KNO) Mouse Embryonic Fibroblast
Project description:Using Chromatin-immunoprecipitation and NGS, we investigated the binding of TFAM protein at mitochondrial genome between Actb+/+ Wild Type (WT) and Actb-/- (KO) Mouse Embryonic Fibroblast
Project description:Purpose: The goals of this study are to use NGS to perform transcriptome profiling (RNA-seq) to find the difference of the gene expression programs among Wild Type (Wt), Actb+/- (Hetero) and Actb-/- (KNO) Mouse Embryonic Fibroblasts Methods: Total RNA was extracted from 70% confluent cells using TRI Reagent according to the manufacturer protocol (Sigma-Aldrich). Quality of total RNA was evaluated at SciLIfe lab (Stockholm, Sweden) using Qubit and Bioanalyzer respectively, samples which pass the QC were used for library construction according to the SciLife lab guideline using TruSeq Stranded mRNA Library Prep Kit (Illumina). Deep sequencing was performed at Science for Life Laboratory, the National Genomics Infrastructure, NGI, Karolinska Institute, Stockholm. Data was processed through the standard RNAseq analysis pipeline at NYUAD. Read aligmnet was performed using tophat2 v2.1.0 against Mus musculus GRCm38.p4 genome version. Cufflinks v2.2.1 was used to derive expression (FPKM) values. Cuffdiff was used to identify differential gene expression. Results: Using an optimized data analysis workflow, we identified genes differentially expressed between Wild Type and Actb+/-, WT and Actb-/-, Actb+/- and Actb-/- Mouse Embryonic Fibroblasts. Selected differentially expressed genes were confirmed by qRT-PCR. Gene ontology analysis further identified biological processes, cellular components and molecular functions that were overrepresented in the differentially expressed genes. Conclusions: Our study shows that there are gene programs differentially regulated among Wild Type, Actb+/- and Actb-/- Mouse Embryonic Fibroblasts
Project description:RNA sequencing of Wild Type (WT) and Actb-/- (KO) Mouse Embryonic Fibroblasts. Total RNA was sequenced to analyse noncoding transcripts and repeats
Project description:We investigate the role of Brg1 and Olig2 during oligodendrocyte differentiation by combining gene conditional knockout and next generation sequencing technology. We generate genome-wide maps of RNA polymerase II (RPolII), Brg1 (Smarca4), Olig2 and histone modifications in primary rat oligodendrocyte precursor cells (iOLs), differentiating oligodendrocytes and mature oligodendrocytes.We found that Brg1 is intensely regulated by RPolII at the initiation of oligodedrocyte differentiation. The genomic distribution of Brg1 in differentiating oligodendrocytes is pre-directed by Olig2 in iOLs. The dynamic interaction of Brg1 and chromatin is correlate with the distinct stages of gene expression during maturation. Finally, we show that Brg1 and Olig2 localization predict critical genes controling CNS myeliantion. Our study represents the first detailed analysis of genomic landscape during the oligodendrocyte development and provides a framework for further understanding of molecular mechanisms underlying oligodendrocyte lineage progression. Genomic distribution of Brg1, Olig2, RPolII and three different histone modifications in three oligodendrocyte developemtal stages were examined using primary cells by ChIP-sequencing. Spinal cord mRNA profiles of 14-day old control and Brg1c/c;Olig1-Cre mice were generated by RNA-sequencing.
Project description:The chromatin remodeler BRG1 is altered in the Letmd1 KO mice. We performed chromatin IP for BRG1 from BAT of wild-type (WT) versus Letmd1 KO mice.
