| المؤلفون: |
Olsen TR; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032., Talla P; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032., Furnari J; Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY 10032., Bruce JN; Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY 10032., Canoll P; Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032., Zha S; Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032.; Institute for Cancer Genetics, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, 10032., Sims PA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032.; Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY, 10032.; Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032. |
| مستخلص: |
The ideal technology for directly investigating the relationship between genotype and phenotype would analyze both RNA and DNA genome-wide and with single-cell resolution. However, existing tools lack the throughput required for comprehensive analysis of complex tumors and tissues. We introduce a highly scalable method for jointly profiling DNA and expression following nucleosome depletion (DEFND-seq). In DEFND-seq, nuclei are nucleosome-depleted, tagmented, and separated into individual droplets for mRNA and genomic DNA barcoding. Once nuclei have been depleted of nucleosomes, subsequent steps can be performed using the widely available 10x Genomics droplet microfluidic technology and commercial kits without experimental modification. We demonstrate the production of high-complexity mRNA and gDNA sequencing libraries from thousands of individual nuclei from both cell lines and archived surgical specimens for associating gene expression phenotypes with both copy number and single nucleotide variants.
Competing Interests: Competing Interests P.A.S. receives patent royalties from Guardant Health. |
