Single-cell sequencing data using DOP-PCR, MDA and MALBAC whole genome amplification methods.

Dataset type: Genomic
Data released on July 02, 2015

Hou Y; Wu K; Shi X; Li F; Song L; Wu H; Dean M; Li G; Tsang S; Jiang R; Zhang X; Li B; Liu G; Bedekar N; Lu N; Xie G; Liang H; Wang T; Chen J; Li Y; Zhang X; Yang H; Xu X; Wang L; Wang J (2015): Single-cell sequencing data using DOP-PCR, MDA and MALBAC whole genome amplification methods. GigaScience Database. http://dx.doi.org/10.5524/100115

DOI10.5524/100115

Single-cell sequencing (SCS) provides many biomedical advances but currently relies on whole-genome amplification (WGA). Three methods are commonly used for WGA: multiple displacement amplification (MDA), degenerate oligonucleotide-primed PCR (DOP-PCR) and multiple annealing and looping-based amplification cycles (MALBAC). Here we systematically compare the advantages and disadvantages and performance of each method. To systematically evaluate the SCS performance of commonly used WGA methods, we performed single cell WGA using six commercial kits based on DOP-PCR and MDA and then performed whole genome sequencing (WGS) of the successfully amplified DNA. A total of 36 single cells were collected in our study, 19 from a lymphoblastoid cell-line (YH cell-line), the rest from a widely-known gastric cancer cell-line, BGC823. Corresponding pooled DNA was extracted as a non-amplified control. BGC823 cell-line was provided by Professor Youyong Lv at Beijing Cancer Hospital. All samples and experimental protocols were approved by the Institutional Review Board of BGI-Shenzhen.

Additional details

Read the peer-reviewed publication(s):

Hou, Y., Wu, K., Shi, X., Li, F., Song, L., Wu, H., … Wang, J. (2015). Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing. GigaScience, 4(1). doi:10.1186/s13742-015-0068-3

Accessions (data generated as part of this study):

SRA: SRP050588

Accessions (data referenced by this study):

SRA: SRP017032





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
DOP-1_979606HumanhumanHomo sapiens
MDA-2_469606HumanhumanHomo sapiens
MDA-2_479606HumanhumanHomo sapiens
MDA-2_669606HumanhumanHomo sapiens
MDA-2_M169606HumanhumanHomo sapiens
MDA-2_M69606HumanhumanHomo sapiens
MDA-3_459606HumanhumanHomo sapiens
SW480-19606HumanhumanHomo sapiens
SW480-29606HumanhumanHomo sapiens
SW480-39606HumanhumanHomo sapiens
Displaying 1-10 of 15 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
MDA-3_45AlignmentsBAM6.3 GB2014-12-09
DOP-1_97Sequence variantsVCF1.4 MB2014-12-09
DOP-1_97Sequence variantsVCF9.2 GB2014-12-09
MDA-2_46AlignmentsBAM86.05 GB2014-12-09
MDA-2_46Sequence variantsVCF17.57 MB2014-12-09
MDA-2_46Sequence variantsVCF15.08 GB2014-12-09
MDA-2_47AlignmentsBAM60.93 GB2014-12-09
MDA-2_47Sequence variantsVCF23.13 MB2014-12-09
MDA-2_47Sequence variantsVCF15.01 GB2014-12-09
MDA-2_66AlignmentsBAM85.4 GB2014-12-09
Displaying 1-10 of 46 File(s).
Date Action
July 2, 2015 Dataset publish
August 10, 2015 Manuscript Link added : 10.1186/s13742-015-0068-3
November 4, 2015 File MDA-2_M6.dedup.bam updated
November 4, 2015 File YH-mix.dedup.bam updated
November 5, 2015 File MDA-2_M16.dedup.bam updated
November 5, 2015 File YH-mix.dedup.bam updated