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. https://doi.org/10.5524/100115
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., Dean, M., Li, G., Tsang, S., Jiang, R., Zhang, X., Li, B., Liu, G., Bedekar, N., Lu, N., Xie, G., Liang, H., Chang, L., Wang, T., … Wang, J. (2015). Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing. GigaScience, 4(1). https://doi.org/10.1186/s13742-015-0068-3 (PubMed:26251698)
Accessions (data included in GigaDB):
SRA: SRP050588
Accessions (data not in GigaDB):
SRA: SRP017032
Click on a table column to sort the results.
Table SettingsSample ID | Common Name | Scientific Name | Sample Attributes | Taxonomic ID | Genbank Name |
---|---|---|---|---|---|
SW480-1 | Human | Homo sapiens | 9606 | human | |
SW480-2 | Human | Homo sapiens | 9606 | human | |
SW480-3 | Human | Homo sapiens | 9606 | human | |
SW480-4 | Human | Homo sapiens | 9606 | human | |
SW480-5 | Human | Homo sapiens | 9606 | human | |
SW480-HEC | Human | Homo sapiens | 9606 | human | |
SW480-SCD | Human | Homo sapiens | 9606 | human | |
MDA-3_45 | Human | Homo sapiens | 9606 | human | |
MDA-2_46 | Human | Homo sapiens | 9606 | human | |
MDA-2_47 | Human | Homo sapiens | 9606 | human |
Click on a table column to sort the results.
Table SettingsFile Name | Description | Sample ID | Data Type | File Format | Size | Release Date | File Attributes | Download |
---|---|---|---|---|---|---|---|---|
Summary of manuscript and data | Readme | TEXT | 914 B | 2014-12-09 | MD5 checksum: 560f57266ff15a53b0ab56025aa56375 |
|||
Alignments | BAM | 62.52 GB | 2014-12-09 | MD5 checksum: 12162edcd9c21cb1475ccc0c449de8ae |
||||
Alignments | BAM | 66.53 GB | 2014-12-09 | MD5 checksum: e1d9fd81519e2fe815b5294971b484c0 |
||||
Alignments | BAM | 69.42 GB | 2014-12-09 | MD5 checksum: b4041bda094f6ec3f69f597bc8cf18f3 |
||||
Alignments | BAM | 86.00 GB | 2014-12-09 | MD5 checksum: 473f18aff8f796e81529be387434834b |
||||
Alignments | BAM | 45.29 GB | 2014-12-09 | MD5 checksum: 1d54a74f4d89ea004c059db9992ca56f |
||||
Alignments | BAM | 92.05 GB | 2014-12-09 | MD5 checksum: 34969b5a23e5db75e212e9aecacf352c |
||||
Alignments | BAM | 93.36 GB | 2014-12-09 | MD5 checksum: 8e47557ad2cc395cd5b6eee12906d242 |
||||
Alignments | BAM | 6.77 GB | 2014-12-09 | MD5 checksum: 32fb77c372b9a449e1cc7a4c03d210c6 |
||||
Alignments | BAM | 92.39 GB | 2014-12-09 | MD5 checksum: c86797427f1e89efea6b2cbff33d98d3 |
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 |
June 21, 2021 | Manuscript Link updated : 10.1186/s13742-015-0068-3 |