Gene body coverage for transcripts longer than 5000 nt.Benjamín, SigurgeirssonOlof, EmanuelssonJoakim, Lundeberg
Before doing gene body coverage analysis, there is a need to split BAM files by cells. Since 10x Genomics output one BAM file, split step is needed. If BAM files are split by cells already, you can skip this step. If you don't mind using "input" as directory name, you can omit $...
Library and mapping quality was assessed by analysis of cumulative gene assignment diversity and gene-body coverage (Supplementary Figure 14e–h) using the QoRTs package54. In total, 89 nuclei passed these quality controls and were included for further analysis. Next, to improve statistical ...
2b, c). Using DESeq2 analysis, we identified 386 TSS regions and 1979 gene body regions with significant changes in HIF1A−/− cells in normoxia (Supplementary Fig. 2f, g, Supplementary Data 1). These observations led us to test if basal levels of HIF1A contribute to the expression ...
Coverage profiles suggested that ASH1 and FSH normally bind close to the TSS of active genes, but are absent from promoter distal parts of the gene body. Deviating from this canonical observation, we found signals within gene bodies at a subset of active genes: predominantly, these genes fall...
The term “housekeeping gene” refers to a gene used in the ordinary, day-to-day, metabolism of a typical or generic cell in the body, and that maintains constant expression, even when drugs are administered (160 From:Clinical Trials (Second Edition),2016 ...
2018), which may promote increased expression of ACE2 receptors and viral receptors in smokers, thus increasing the opportunity for SARS-CoV-2 to invade the body (Berlin et al. 2020). However, the role of nicotine in COVID-19 requires further investigation. The regulatory role of calcium ...
The information stored within our chromosomes can be likened to an instruction manual for all cells in our body. Every cell contains the same chromosomes, so every cell contains exactly the same set of genes and exactly the same set of instructions. Yet, different cell types, such as muscle ...
with a methylation difference of at least 0.2 and a significance level of 0.01. DMRs separated by not more than one window were joined together in a larger DMR. DmCs and DMRs were also categorized based on the characteristics of their genomic locations including gene body (from transcriptional ...
Males (top) are smaller than females (bottom) and have complex color patterns on the body. The encircled region (white outline) indicates the tissues that were used for preparing the barcoded libraries, 1) brain and eyes; 2) Male testis and female ovary; and 3) tail. Full size image Th...