Sequencing FASTQ reads were aligned to the hg19 human reference genome with Bowtie2 (52) with the following restrictions “--very-sensitive --score-min L,-0.6,-0.15” for mapping sensitivity and accuracy. Only uniquely mapped reads, and in the case of paired-end sequenced data, only uniquely mapped sequence pairs that were aligned concordantly, were used for subsequent analyses. In S100A8 or S100A9 ChIP-seq data, confident peaks were defined as fulfilling all the following restrictions: (i) MACS2 peak-calling q value ≤1 × 10−7 against sample-corresponding chromatin input background; (ii) peaks called by MACS2 were identified in at least two biological replicates; (iii) at least five raw reads were aligned at the peak region. Depending on the comparisons indicated, peak regions from different datasets were merged if overlapping at least 1 bp. Confident Pol II ChIP-seq peaks were defined as MACS2 paired-end peak-calling P value ≤1 × 10−8 against genomic background of 1-Mb genomic region around. In ChIP-seq data of histone modifications and DNase-seq data, confident sites were defined as previously described (21). Meta-gene and heatmap analyses were carried out with deepTools (53).

Note: The content above has been extracted from a research article, so it may not display correctly.



Q&A
Please log in to submit your questions online.
Your question will be posted on the Bio-101 website. We will send your questions to the authors of this protocol and Bio-protocol community members who are experienced with this method. you will be informed using the email address associated with your Bio-protocol account.



We use cookies on this site to enhance your user experience. By using our website, you are agreeing to allow the storage of cookies on your computer.