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Whole genome sequencing

OK Ohman Kwon
HL Hana Lee
JJ Jaeeun Jung
YS Ye Seul Son
SJ Sojeong Jeon
WY Won Dong Yoo
NS Naeun Son
KJ Kwang Bo Jung
EC Eunho Choi
IL In-Chul Lee
HK Hyung-Jun Kwon
CK Chuna Kim
ML Mi-Ok Lee
HC Hyun-Soo Cho
DK Dae Soo Kim
MS Mi-Young Son
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For whole genome sequecing of ISC3D-hIO (passage 8, 27, and 54), 100 ng of genomic DNA was used to construct DNA library with TruSeq Nano DNA (Illumina, USA) following the manufacturer’s instruction. Multiple libraries were sequenced on an Illumina NovaSeq 6000 using paired-end 150, 6 G reads. Reads were aligned to the reference genome Trimmomatic was used to remove low quality reads to reduce bias. Map the reads to the reference genome (hg38 from UCSC) of choice Burrows-Wheeler Aligner (BWA)41. Properly mapped reads were extracted from BAM files after duplicated reads were removed. ngCGH (version 0.4.4) was used to compare two matched BAM data with a window size of 10 kb for copy number estimate. Then, the copy number altered regions were defined by segmentation of the genome using DNAcopy (version 1.74.1)42.

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