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| Status |
Public on Aug 08, 2022 |
| Title |
Direct transposition of native DNA for sensitive multimodal single-molecule sequencing I |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
Concurrent readout of sequence and base modifications from long unamplified DNA templates by PacBio single-molecule sequencing requires large amounts of input material. Here we adapt Tn5 transposition to introduce hairpin oligonucleotides and fragment (tagment) limiting quantities of DNA for generating PacBio-compatible circular molecules. We developed two methods that implement tagmentation and use 90–99% less input than current protocols: (1) single-molecule real-time sequencing by tagmentation (SMRT-Tag), which allows detection of genetic variation and CpG methylation; and (2) single-molecule adenine-methylated oligonucleosome sequencing assay by tagmentation (SAMOSA-Tag), which uses exogenous adenine methylation to add a third channel for probing chromatin accessibility. SMRT-Tag of 40 ng or more human DNA (approximately 7,000 cell equivalents) yielded data comparable to gold standard whole-genome and bisulfite sequencing. SAMOSA-Tag of 30,000–50,000 nuclei resolved single-fiber chromatin structure, CTCF binding and DNA methylation in patient-derived prostate cancer xenografts and uncovered metastasis-associated global epigenome disorganization. Tagmentation thus promises to enable sensitive, scalable and multimodal single-molecule genomics for diverse basic and clinical applications.
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| Overall design |
Chromatin profiling with m6dA methyltransferase footprinting of the OS152 osteosarcoma cell line, followed by transposase-mediated PCR-free library construction in situ (SAMOSA-Tag) and single molecule sequencing.
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| Contributor(s) |
Nanda AS, Wu K, Kasinathan S, Ostrowski MS, Satpathy AT, Sweet-Cordero EA, Goodarzi H, Ramani V |
| Citation(s) |
38724748 |
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| Submission date |
Jul 31, 2022 |
| Last update date |
Jun 28, 2024 |
| Contact name |
Arjun S Nanda |
| Organization name |
Gladstone Institutes / UCSF
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| Department |
Gladstone Institute for Data Science & Biotechnology
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| Lab |
Ramani Lab
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| Street address |
1700 Owens St
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| City |
San Francisco |
| State/province |
California |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platforms (1) |
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| Samples (11)
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| GSM6422266 |
OS152, nuclei, m6dA methylated, rep4 |
| GSM6422267 |
OS152, nuclei, m6dA methylated, rep5 |
| GSM6422268 |
OS152, nuclei, m6dA methylated, rep6 |
| GSM6422269 |
OS152, nuclei, m6dA methylated, rep7 |
| GSM6422270 |
OS152, nuclei, m6dA methylated, rep8 |
| GSM6422271 |
OS152, nuclei, unmethylated, rep1 |
| GSM6422272 |
OS152, nuclei, unmethylated, rep2 |
| GSM6422273 |
OS152, nuclei, unmethylated, rep3 |
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| This SubSeries is part of SuperSeries: |
| GSE225314 |
Direct transposition of native DNA for sensitive multimodal single-molecule sequencing |
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| Relations |
| BioProject |
PRJNA864052 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE210136_RAW.tar |
84.9 Gb |
(http)(custom) |
TAR (of PICKLE) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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