title: whole genome sequencing for donor 5828; library 1
design: Genomic DNA was isolated using the Qiagen DNA Mini kit (Qiagen 51304) according to manufacturer's protocol for tissues. Approximately 25mg of fresh frozen tissue was minced on ice into small still-frozen pieces. Tissue was transferred to a dry-ice chilled sterile 1.5ml microcentrifuge tubes with 180ul of Buffer ATL. Then, 20ul of Proteinase K (20mg/ml) was added prior to 4 hours of agitation at 56 degrees centigrade on a thermomixer (1400 RPM). DNA isolation proceeded as written in the protocol with the inclusion of the optional RNase A treatment step.  A small sample was sent for Fragment Analyzing and gDNA quality assessment. Libraries were prepared following the KAPA HyperPlus Library Preparation protocol. The KAPA fragmentation step was included in the bulk processed gDNA samples. Bulk gDNA sample libraries were sent to Genuity Sciences (Dublin, Ireland) and sequenced on the Illumina NovaSeq 6000 platform (150 bp × 2) at minimum 30× coverage and used as a reference genome against the case-match single cell genomes. Bulk DNA for cases 1278, 4638, 4643, 5657, and 5817 was previously isolated and sequenced for Lodato et al. (2018) on an Illumina Hi-Seq X Ten platform by Macrogen Genomics or the New York Genome Center (New York, NY).
identifiers.namespace: NIA-phs003445
identifiers.id: 5828_220923_PFC.bulkDNAseq