title: WES of homo sapien colorectal tumor tissue: Sample CR692T
design: RNA-free genomic DNA was extracted from fresh frozen tumor specimens and from organoids using the Macherey-Nagel NucleoSpin Tissue mini kit according to manufacturer instructions. DNA from patient CR1107 tissues was extracted from formalin fixed paraffin embedded (FFPE) sections of tissue at Novogene Co., Ltd in Beijing, China. Whole exome capture and sequencing (WES) was performed at Novogene Co.at sequencing depth of 100X, Ltd. Briefly, genomic DNA was randomly sheared into short fragments of 180-280 bp. The fragments were end repaired, A-tailed, and further ligated with Illumina adapters. The fragments with adapters were PCR amplified, size selected, and purified. The prepared libraries were hybridized in buffer with biotin-labeled probes, and magnetic beads with streptavidin captured the exons of genes. Agilent SureSelect Human All Exome V6 (58 M) was used for exome capture. Subsequently, non-hybridized fragments were washed out and probes were digested. The captured libraries were enriched by PCR amplification. Library quality was assessed using Qubit instrument and real-time PCR for quantification, and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina Novaseq 6000 platform with PE150. Burrows-Wheeler Aligner (BWA) mapped the paired-end clean reads to the reference genome (GRCh38). SAMtools sorted and indexed the original BAM file followed by Picard to mark duplicate reads.