ABSTRACT
Nowadays, huge volumes of chromatin immunoprecipitation-sequencing (ChIP-Seq) data are generated to increase the knowledge on DNA-protein interactions in the cell, and accordingly, many tools have been developed for ChIP-Seq analysis. Here, we provide an example of a streamlined workflow for ChIP-Seq data analysis composed of only four packages in Bioconductor: dada2, QuasR, mosaics, and ChIPseeker. ‘dada2’ performs trimming of the high-throughput sequencing data. ‘QuasR’ and ‘mosaics’ perform quality control and mapping of the input reads to the reference genome and peak calling, respectively. Finally, ‘ChIPseeker’ performs annotation and visualization of the called peaks. This workflow runs well independently of operating systems (e.g., Windows, Mac, or Linux) and processes the input fastq files into various results in one run. R code is available at github: https://github.com/ddhb/Workflow_of_Chipseq.git.
Subject(s)
Chromatin , Chromatin Immunoprecipitation , Genome , Quality Control , Statistics as TopicABSTRACT
The wound healing effect of topical application of the recombinant human epidermal growth factor(rhEGF) on full-thickness dermal injury was investigated. Two full-thickness excisions were made on the back of the experimental animals. The rhEGF was applied twice a day and the rate of wound closure was measured every day for 14 days. On the seventh postoperative day, the histological findings of epithelization and granulation were examined by Massons tichrome stain, and immunohistochemical staining for proliferating cell nuclear antigen (PCNA) and alpha-smooth muscle actin(alpha-SMA). The wound size was a significant reduction in the rhEGF treated groups as compared with the control group (p<0.05). However, there was no statistical difference in the wound size among the concentrations of the rhEGF treated group. Histological examination revealed that epithelization and granulation was increased significantly in the rhEGF group compared to control group (p < 0.01, 0.05). PCNA and alpha-SMA immunoreactive cells were observed at the margin of wound and the rhEGF treatments significantly increased the number of PCNA and alpha-SMA immunoreactive cells as compared to those of control group (p < 0.01, 0.05). Taken together, these findings suggest that rhEGF enhance the epithelial wound healing by the stimulate of cell proliferation. The wound contraction might be also affected by rhEGF application.
Subject(s)
Animals , Humans , Rats , Cell Proliferation , Epidermal Growth Factor , Proliferating Cell Nuclear Antigen , Skin , Wound Healing , Wounds and InjuriesABSTRACT
This study was designed to investigate the optimal poloxamer concentration in the mixed solution of recombinant human epidermal growth factor and poloxamer which can be effective in the wound healing process. Two full-thickness excisions were made on the back of the experimental animals. Recombinant human epidermal growth factors(RhEGF) containing different poloxamer concentrations were applied twice a day and the rates of wound closure were measured every day for 14 days. On the 7th and 14th postoperative day, the histological analysis for epithelization and granulation were performed using computerized imaging analysis system after Masson's trichrome stains. The healing times 50% were significantly reduced in the RhEGF containing 0, 3 and 6% poloxamer treated groups as compared with both the non treated control and vehicle control group(p < 0.05). However, there were no statistical differences in the healing times 50% in the RhEGF containing 10, 15 and 20% poloxamer treated groups as compared with both the non treated control and vehicle control group. Histological examinations revealed that epithelization and granulation were increased significantly in the RhEGF containing 0, 3 and 6% poloxamer treated groups as compared with control group and vehicle control group at the 7th day after operation(p < 0.05). In conclusion, these findings suggest that RhEGF may enhance the epithelial wound healing process through stimulating cell proliferation. The concentration of 0, 3 and 6% of poloxamers can be applied to stabilize and enhance the wound healing effect of RhEGF for clinical application.