GSE81556_Primary_BAT_Lsd1_treat_afterfiting_all.wig. GSE81556_Primary_BAT_Lsd1_control_afterfiting_ Lysine-specific demethylase 1 target genes in brown adipocytes 2015ĭuteil D, Willmann D, Arrigoni L, Schüle R Cells were fixed for 5 min at room temperature according to Arrigoni et al. Lsd1 binding profile in brown adipocytes Primary brown adipocytes were differentiated for 10 days in adipogenic medium. Therefore, it is reasonable to use annotatePeakInBatch or annoPeaks to annotate the peaks to the promoter regions of Hg19 genes. ChIP-seq analysis revealed that Lsd1 was located at the promoter of 11735 genes. As shown from the distribution of aggregated peak numbers around TSS and the distribution of peaks in different of chromosome regions, most of the peaks locate around TSS. Genes annotated by HOMER were further used for a pathway analysis in WebGestalt (Heinz et al., 2010 Wang et al., 2013). The genomic features (promoter, exon, intron, 3’ UTR, and intergenic regions) were defined and calculated using Refseq and HOMER. Results: HOMER (Heinz et al., 2010) was used to annotate peaks, to calculate overlaps between different peak files, and for motif searches. The uniquely mapped reads were used to generate the genome-wide intensity profiles, which were visualized using the IGV genome browser (Thorvaldsdottir et al., 2012). All peaks with FDR greater than 0.3 % were excluded from further analysis. Data were further analysed using the peak finding algorithm MACS 1.41 (Zhang et al., 2008) using input as control. ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the mm10 reference genome using bowtie 2 (Langmead et al., 2009). Methods: Libraries were prepared from Lsd1-immunoprecipitated DNA according to standard methods. Purpose: The aim of this study is to identify the Lsd1 genome binding profile in brown adipocytes. The aim of this study is to identify the Lsd1 genome binding profile in brown adipocytes. Genome binding/occupancy profiling by high throughput sequencing Lysine-specific demethylase 1 targets in brown adipocytes "/group/card2/Evangelyn_Sim/Collaboration_Kev_UoM/Sequencing_ATAC_RNA/20190530_ATAC_run1/R/2.pks/4.pkstats//edgeR_atac_cov2_. help: Mouse over screen elements for information. Plot Homer peak annotation results files = list.files(path = "/group/card2/Evangelyn_Sim/Collaboration_Kev_UoM/Sequencing_ATAC_RNA/20190530_ATAC_run1/R/2.pks/4.pkstats/", pattern = ".stats.txt", full.names = T)įiles "/group/card2/Evangelyn_Sim/Collaboration_Kev_UoM/Sequencing_ATAC_RNA/20190530_ATAC_run1/R/2.pks/4.pkstats//edgeR_atac_cov2_." Res]= mutate(res], FDRdn= nrow(mxFDR_Dn)) Res]= mutate(res], FDRup= nrow(mxFDR_Up)) Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes. Untracked: output/mrna_fulllen_pe_strrev.mx.fix_filt Untracked: output/mouseATAC_peaks_.mx.fix_filt Untracked: output/logCPM_mrna_fulllen_pe_strrev.mx.fix_filt.csv Untracked: output/edgeR_rna_LacZvsYap.xls Untracked: output/edgeR_atac_cov2_LacZvsYap.xls Untracked: output/YAP_shRNA_D28_Proteomics_results.xls Untracked: Mus_musculus.GRCm38.96.fulllength.saf Below is the status of the Git repository when the results were generated: workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). See the Past versions tab to see a history of the changes made to the R Markdown and HTML files. The results in this page were generated with repository version 704a4cf. Tracking code development and connecting the code version to the results is critical for reproducibility. Great! You are using Git for version control.
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