The Strand-seq Core at the BC Cancer Research Institute offers production of Strand-seq data on a fee-for-service basis using state of the art instrumentation and innovative protocols. Experienced Core staff support the needs of researchers with tailored Strand-seq workflows including culturing primary cells or cell lines, constructing single-cell libraries using the cellenONE nanolitre liquid handler and cell isolation system, and next-generation short read DNA sequencing with the AVITI. Inquiries about available Strand-seq services, custom technical Strand-seq needs, and pricing are welcome.

The single cell Strand-seq technology was developed in the Lansdorp lab (1) and has proven to be a key technology to advance a wide variety of studies. Strand-seq has been used for de novo genome assembly and mapping genomic structural variants for genome instability and mutation studies in Nature (2,3), Cell (4) and Science (5). It was recently shown that the unique chromosome-length haplotype information produced by Strand-seq (6) can be leveraged using long-read methylation data at imprint locations to assign any allele on any chromosome in a person to its parent of origin without analysis of parental DNA (7).

Strand-seq library production has been improved by constructing libraries in nanoliter volumes in open nanoliter arrays (8). This advance has resulted in a major increase in the quality of Strand-seq libraries and throughput of library construction.

References

  1. Falconer, E., Hills, M., Naumann, U., Poon, S.S., Chavez, E.A., Sanders, A.D., Zhao, Y., Hirst, M. and Lansdorp, P.M. (2012) DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution. Nat Methods, 9, 1107-1112.
  2. Liao, W.W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J.K., Monlong, J., Abel, H.J. et al. (2023) A draft human pangenome reference. Nature, 617, 312-324.
  3. Logsdon, G.A., Rozanski, A.N., Ryabov, F., Potapova, T., Shepelev, V.A., Catacchio, C.R., Porubsky, D., Mao, Y., Yoo, D., Rautiainen, M. et al. (2024) The variation and evolution of complete human centromeres. Nature, 629, 136-145.
  4. Porubsky, D., Hops, W., Ashraf, H., Hsieh, P., Rodriguez-Martin, B., Yilmaz, F., Ebler, J., Hallast, P., Maria Maggiolini, F.A., Harvey, W.T. et al. (2022) Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders. Cell, 185, 1986-2005 e1926.
  5. Ebert, P., Audano, P.A., Zhu, Q., Rodriguez-Martin, B., Porubsky, D., Bonder, M.J., Sulovari, A., Ebler, J., Zhou, W., Serra Mari, R. et al. (2021) Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science, 372.
  6. Porubsky, D., Ebert, P., Audano, P.A., Vollger, M.R., Harvey, W.T., Marijon, P., Ebler, J., Munson, K.M., Sorensen, M., Sulovari, A. et al. (2021) Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads. Nat Biotechnol, 39, 302-308.
  7. Akbari, V., Hanlon, V.C.T., O’Neill, K., Lefebvre, L., Schrader, K.A., Lansdorp, P.M. and Jones, S.J.M. (2022) Parent-of-origin detection and chromosome-scale haplotyping using long-read DNA methylation sequencing and Strand-seq. Cell Genomics, 100233.
  8. Hanlon, V.C.T., Chan, D.D., Hamadeh, Z., Wang, Y., Mattsson, C.A., Spierings, D.C.J., Coope, R.J.N. and Lansdorp, P.M. (2022) Construction of Strand-seq libraries in open nanoliter arrays. Cell Rep Methods, 2, 100150.

Services

On a fee-for-service basis, our SSCORE offers the following services: 

Cell Culture

Strand-seq requires culture of live cells to incorporate BrdU in nascent DNA strands after one complete cycle of cell division. For human samples, typically immortalized lymophoblastoid cell lines or fresh blood samples in heparin tubes for primary T-cell culture may be used. Strand-seq work has been done with other non-human samples, including other mammals, yeast, and plants, but may require more optimizing work. Fixed nuclei with incorporated BrdU may be submitted instead if appropriate.

Single Cell Deposition and Library Preparation

Fluorescence-activated cell sorting (FACS) for enriching cells/nuclei with BrdU is done at the Terry Fox Laboratory Flow Cytometry Core Facility. Trained Strand-seq Core staff operate the cellenONE instrument for nanoliter single cell and reagent spotting for library preparation.

Library Quality Control

Completed pooled libraries are purified and size selected for Next-generation sequencing. Quality control and quantification of libraries are done using the Agilent Bioanalyzer High Sensitivity DNA assay and Qubit dsDNA HS assay.

Next-generation Sequencing

Libraries are sequenced using the AVITI instrument with 2x75 bp sequencing kits. Sequencing depth will vary, but typically at least 20M unique reads from good-quality Strand-seq libraries can be provided per sample, with an aggregate coverage of about 0.5X for human genomes from phased SNV reads.

Bioinformatics

Demultiplexed FastQ files for each single cell Strand-seq library are provided. Basic sequencing metrics and Strand-seq plots (eg. breakpointR plots) can be provided if requested. Instructions for use of Strand-seq bioinformatics tools for custom downstream

Workflow

External Collaboration

For collaborators outside UBC and BC Cancer, service/material transfer agreements need to be set up before samples can be received and processed. Please contact Dr. Peter Lansdorp, using the contact form below, and provide relevant details for collaboration requests.

Workflow

  1. Send a message through the online form on this page for any Strand-seq inquiries. The Core can help determine the best suited cell culture, library preparation, and sequencing strategy depending on the single cell Strand-seq application.
  2. Complete any statements of work (SOW) or material transfer agreements (MTA) as applicable.
  3. When ready to submit samples, detailed sample shipping instructions will be provided. The following sample formats are acceptable:
    1. Sample information for cell line from Coriell to be ordered and shipped by the Core directly
    2. Shipped viable cells in culture flasks at room temperature or frozen in cryovials on dry ice
    3. Shipped fresh blood sample in heparin tubes at room temperature
    4. Shipped fixed nuclei with BrdU (>5 million) (with ice packs)
  4. Demultiplexed FastQ files will be provided after sequencing is complete.
  5. Invoices will be sent for billing via wire transfer.

Selected Bioinformatics Tools for Strand-Seq

breakpointR

ASHLEYS QC

StrandPhaseR

InvertyperR

Core Director

Core Team

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