TY  - JOUR
A1  - Han, Kyung Yeon
A1  - Kim, Kyu-Tae
A1  - Joung, Je-Gun
A1  - Son, Dae-Soon
A1  - Kim, Yeon Jeong
A1  - Jo, Areum
A1  - Jeon, Hyo-Jeong
A1  - Moon, Hui-Sung
A1  - Yoo, Chang Eun
A1  - Chung, Woosung
A1  - Eum, Hye Hyeon
A1  - Kim, Sangmin
A1  - Kim, Hong Kwan
A1  - Lee, Jeong Eon
A1  - Ahn, Myung-Ju
A1  - Lee, Hae-Ock
A1  - Park, Donghyun
A1  - Park, Woong-Yang
T1  - SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells
Y1  - 2018/01/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 75 
EP  - 87 
DO  - 10.1101/gr.223263.117 
VL  - 28 
IS  - 1 
UR  - http://genome.cshlp.org/content/28/1/75.abstract 
N2  - Simultaneous sequencing of the genome and transcriptome at the single-cell level is a powerful tool for characterizing genomic and transcriptomic variation and revealing correlative relationships. However, it remains technically challenging to analyze both the genome and transcriptome in the same cell. Here, we report a novel method for simultaneous isolation of genomic DNA and total RNA (SIDR) from single cells, achieving high recovery rates with minimal cross-contamination, as is crucial for accurate description and integration of the single-cell genome and transcriptome. For reliable and efficient separation of genomic DNA and total RNA from single cells, the method uses hypotonic lysis to preserve nuclear lamina integrity and subsequently captures the cell lysate using antibody-conjugated magnetic microbeads. Evaluating the performance of this method using real-time PCR demonstrated that it efficiently recovered genomic DNA and total RNA. Thorough data quality assessments showed that DNA and RNA simultaneously fractionated by the SIDR method were suitable for genome and transcriptome sequencing analysis at the single-cell level. The integration of single-cell genome and transcriptome sequencing by SIDR (SIDR-seq) showed that genetic alterations, such as copy-number and single-nucleotide variations, were more accurately captured by single-cell SIDR-seq compared with conventional single-cell RNA-seq, although copy-number variations positively correlated with the corresponding gene expression levels. These results suggest that SIDR-seq is potentially a powerful tool to reveal genetic heterogeneity and phenotypic information inferred from gene expression patterns at the single-cell level. 
ER  -