Table 1.
Summary of the assays applied to tissues of the neurotypical somatic mosaicism reference brain in C2458.
| Assay No. | Type | Tissues | DNA Extraction Kit | Library Prep Kit | Sequencing Platform | Coverage |
|---|---|---|---|---|---|---|
| 1 | WES | uDLPFC, Fibroblasts | MagAttract HMW DNA Kit | SeqCap EZ Exome Probes v3.0 | Illumina HiSeqX | 350 - 435X |
| 2 | uDLPFC, Fibroblasts | Qiagen Maxiprep Kit | Agilent SureSelect X7 Human All Exon v5 Kit | Illumina HiSeqX 2500 | ||
| 3 | WGS | cDLPFC | DNeasy Blood and Tissue Kit | NEBNext Ultra II DNA Library Prep Kit | Illumina HiSeq. 4000 | 85 - 245X |
| 4 | uDLPFC, Fibroblasts, cerebellum, dura mater, NeuN+, NeuN− | DNeasy Blood and Tissue Kit | TruSeq DNA PCR-Free Library Prep Kit | Illumina HiSeqX | ||
| 5 | uDLPFC | QIAamp DNA Mini Kit with phenol chloroform and isopropanol workup | TruSeq DNA PCR-Free Library Prep Kit | Illumina HiSeqX Ten | ||
| 6 | uDLPFC, Fibroblasts, uDLPFC NeuN+, uDLPFC NeuN− | DNeasy Blood and Tissue Kit | TruSeq DNA PCR-Free Library Prep Kit | Illumina HiSeq. 2000 | ||
| 7 | LR | uDLPFC, Fibroblasts | MagAttract HMW DNA Kit | Submission to HudsonAlpha Discovery | 10X Genomics | ~70X |
| 8 | sc | uDLPFC NeuN+ | (1) REPLI-g Single Cell Kit & DNeasy Blood and Tissue Kit | (1) TruSeq DNA PCR-Free Library Prep Kit | Illumina HiSeqX | ~30X |
| uDLPFC NeuN+ | (2) REPLI-g Single Cell Kit | (2) S1 Maker 10 kb High Pass Protocol on BluePippin | 10X Genomics & Illumina HiSeqX |
Four assays were applied to various tissues and cells (WES = whole exome sequencing, WGS = whole genome sequencing, LR = linked read, sc = single cell sequencing). Tissues included uniformly pulverized dorsolateral prefrontal cortex (uDLPFC), frozen chunk of dorsolateral prefrontal cortex (cDLPFC), fibroblasts cultured from the dura mater, NeuN+ neurons, NeuN− cell fraction, the cerebellum, and the dura mater.