NODEGenomicsYe YaoWXShttps://www.biosino.org/node/experiment/detail/OEX00002020Illumina HiSeq 1500PairedRANDOM50['hematocyte', 'rectum']['Homo sapiens']DNA degradation and contamination were monitored on 1% agarose gels and DNA concentration was measured by Qubit DNA Assay Kit in Qubit 2.0 Flurometer (Invitrogen, USA). A total amount of 0.6 μg genomic DNA per sample were used as input material for DNA sample preparation. Sequencing libraries were generated using Agilent SureSelect Human All Exon kit (Agilent Technologies, CA, USA) following manufacture’s recommendations and index codes were added to each sample. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using Hiseq PE Cluster Kit (Illumina) according to the manufacturer’s instructions. After cluster generation, the DNA libraries were sequenced on Illumina Hiseq platform and 150bp paired-end reads were generated. Sequence reads were mapped against human reference genome GRCh37 using Burrows-Wheeler Alignment with maximal exact matches (BWA-MEM) v0.7.8-r455(Li and Durbin, 2009), then bam files were processed in terms of marked duplicates, realignment of indels and base recalibration using Genome Analysis Toolkit (GATK) v3.8.0(McKenna et al., 2010) according to best practices guidelines(Van der Auwera et al., 2013). Somatic mutations were identified by providing the reference and tumors or organoids sequencing data to the MuTect2 (involved in GATK v3.8.0) with default parameters. Effect predictions and annotations were added using annovar(Wang et al., 2010). To detect high quality somatic CNAs, BAM files were analyzed for read-depth variations by Control-FREEC v11.4(Boeva et al., 2012) with comparing tumors or organoids to reference plasma. Mutational signatures were analyzed using the Mutational Patterns R package, release 3.4(Blokzijl et al., 2018) to determine genomic context for all somatic SNVs and determine the contribution of ‘‘signatures of mutational processes in human cancer’’ in tumor tissues and organoid samples.NODEfalseorganoids_zhang-hua-1To study whether organoids derived from rectal cancer biopsy tissues can recapitulate the genomic profiles of corresponding tumors, including DNA mutation and DNA copy number variations (CNVs).2019-10-142019-10-14OEX00002020OEP00000599