bisulfite_sequencing_of_homo_sapien:breast_cancer_cell_line
5 g of genomic DNA isolated from treated MDA-MB-231 cells were used as input for library preparation. 260/280 ratio for each sample was calculated, and samples with ratio 1.82.0 were considered. Covaris shearing was used to generate dsDNA fragments with 3 or 5 overhangs of 250 bp (peak size). Bisulfite treatment is given to convert any unmethylated Cytosine to Thymidine. To create blunt ends, end repairing is done using T4 DNA polymerase and Klenow enzyme. 3' ends are then adenylated to prevent them from ligating to one another during the adapter ligation reaction. After methyl-adapter ligation, Enrichment of DNA fragments was done using PCR[20]. After constructing the libraries, their concentrations and insert sizes were detected using Qubit and Agilent Tapestation, respectively. High throughput sequencing was performed using Illumina HiSeq2500 to obtain 100-bp paired-end reads.