Study
Scalable whole-genome single-cell library preparation without pre-amplification
Study ID | Alternative Stable ID | Type |
---|---|---|
EGAS00001002170 | Other |
Study Description
Single-cell genomics is critical for understanding cellular heterogeneity in cancer, but existing library preparation methods are expensive, require sample preamplification and introduce coverage bias. Here we describe direct library preparation (DLP), a robust, scalable, and high-fidelity method that uses nanoliter-volume transposition reactions for single-cell whole-genome library preparation without preamplification. We examined 782 cells from cell lines and triple-negative breast xenograft tumors. Low-depth sequencing, compared with existing methods, revealed greater coverage uniformity and more reliable detection of copy-number alterations. Using phylogenetic analysis, we found minor xenograft subpopulations that were undetectable by bulk sequencing, as well as dynamic clonal expansion and diversification between passages. Merging single-cell genomes in silico, we generated "bulk-equivalent" genomes with high depth and uniform coverage. Thus, low-depth sequencing of DLP libraries may provide an attractive replacement for conventional bulk sequencing methods, permitting analysis ... (Show More)
Study Datasets 5 datasets.
Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data
Dataset ID | Description | Technology | Samples |
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EGAD00001003148 |
Microfluidic direct library preparation (DLP) single-cell whole-genome BAM files for near-diploid immortalized lymphoblastoid cell line GM18507.
|
NextSeq 500 | 192 |
EGAD00001003149 |
Microfluidic direct library preparation (DLP) single-cell whole-genome BAM files for third-passage patient-derived primary triple-negative breast cancer xenograft SA501X3F.
|
Illumina HiSeq 2500 | 384 |
EGAD00001003150 |
Microfluidic direct library preparation (DLP) single-cell whole-genome BAM files for fourth-passage patient-derived primary triple-negative breast cancer xenograft SA501X4F.
|
Illumina HiSeq 2500 | 384 |
EGAD00001003151 |
Bulk whole-genome BAM files for 184-hTERT-L2, SA501X3F, and SA501X4F.
|
Illumina HiSeq 2500 | 3 |
EGAD00001003152 |
Microfluidic direct library preparation (DLP) single-cell whole-genome BAM files for near-diploid immortalized breast epithelial cell line 184-hTERT-L2.
|
Illumina HiSeq 2500 | 192 |
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