Educating Ressources for Next Generation Sequencing based applications

NGS Technology

Reviews

NGS technology reviews to get an idea how NGS started and conceptional principles of the different platforms

Platforms

Illumina

Pacific Biosciences

Oxford Nanopore

Single cell resolved large scale genomics using NGS

Reviews

Methods papers

  • Cel-Seq - linear RNA amplification with high sensitivity for scTranscriptomics from teh lab of Itai Yanai (Hashimshony et al. 2012)
  • Drop-Seq method paper from Evan Macosko (Macosko et al. 2015)
  • Early 10X Genomics publication of their microfluidic device assisted scRNA-Seq technology (Zheng et al. 2017)

Spatially resolved large scale genomics using NGS

Reviews

  • Spatially resolved Trancriptomics was selected as the method of the year 2020 by Nature Methods (Marx 2021)
  • Review of spatial trancriptomics methods and available analysis tools (Rao et al. 2021)

Methods papers

  • Academic publication of the HybISS technology, the foundation of the 10X Genomics Xenium workflows (Gyllborg et al. 2020)

Bulk large scale genomics using NGS

Shotgun DNA Library Preparation

References

Baysoy, Alev, Zhiliang Bai, Rahul Satija, and Rong Fan. 2023. “The Technological Landscape and Applications of Single-Cell Multi-Omics.” Nature Reviews Molecular Cell Biology. Nature Publishing Group. https://doi.org/10.1038/s41580-023-00615-w.
Bruinsma, Stephen, Joshua Burgess, Daniel Schlingman, Agata Czyz, Natalie Morrell, Catherine Ballenger, Heather Meinholz, et al. 2018. “Bead-Linked Transposomes Enable a Normalization-Free Workflow for NGS Library Preparation.” BMC Genomics 19 (1). https://doi.org/10.1186/S12864-018-5096-9.
Eberwine, James, Jai Yoon Sul, Tamas Bartfai, and Junhyong Kim. 2014. “The Promise of Single-Cell Sequencing.” Nature Methods. https://doi.org/10.1038/nmeth.2769.
Gunasekera, Samantha, Sam Abraham, Marc Stegger, Stanley Pang, Penghao Wang, Shafi Sahibzada, and Mark O’Dea. 2021. “Evaluating Coverage Bias in Next-Generation Sequencing of Escherichia Coli.” PloS One 16 (6). https://doi.org/10.1371/JOURNAL.PONE.0253440.
Gyllborg, Daniel, Christoffer Mattsson Langseth, Xiaoyan Qian, Eunkyoung Choi, Sergio Marco Salas, Markus M. Hilscher, Ed S. Lein, and Mats Nilsson. 2020. “Hybridization-Based in Situ Sequencing (HybISS) for Spatially Resolved Transcriptomics in Human and Mouse Brain Tissue.” Nucleic Acids Research 48 (19): E112. https://doi.org/10.1093/nar/gkaa792.
Hashimshony, Tamar, Florian Wagner, Noa Sher, and Itai Yanai. 2012. “CEL-seq: Single-cell RNA-seq by Multiplexed Linear Amplification.” Cell Reports. https://doi.org/10.1016/j.celrep.2012.08.003.
Kumar, Kishore R., Mark J. Cowley, and Ryan L. Davis. 2019. “Next-Generation Sequencing and Emerging Technologies.” Seminars in Thrombosis and Hemostasis 45 (7): 661–73. https://doi.org/10.1055/S-0039-1688446.
Macosko, Evan Z, Anindita Basu, Rahul Satija, James Nemesh, Karthik Shekhar, Melissa Goldman, Itay Tirosh, et al. 2015. “Highly Parallel Genome-Wide Expression Profiling of Individual Cells Using Nanoliter Droplets.” Cell 161 (5): 1202–14. https://doi.org/10.1016/j.cell.2015.05.002.
Mardis, Elaine R. 2013. “Next-Generation Sequencing Platforms.” Annu. Rev. Anal. Chem. (Palo Alto Calif.) 6 (June): 287–303. https://doi.org/10.1146/annurev-anchem-062012-092628.
Marx, Vivien. 2021. “Method of the Year: Spatially Resolved Transcriptomics.” Nature Methods 2021 18:1 18 (1): 9–14. https://doi.org/10.1038/s41592-020-01033-y.
McCombie, W. Richard, John D. McPherson, and Elaine R. Mardis. 2019. “Next-Generation Sequencing Technologies.” Cold Spring Harbor Perspectives in Medicine 9 (11). https://doi.org/10.1101/CSHPERSPECT.A036798.
Rao, Anjali, Dalia Barkley, Gustavo S. França, and Itai Yanai. 2021. “Exploring Tissue Architecture Using Spatial Transcriptomics.” Nature 2021 596:7871 596 (7871): 211–20. https://doi.org/10.1038/s41586-021-03634-9.
Ribarska, Teodora, Pål Marius Bjørnstad, Arvind Y. M. Sundaram, and Gregor D. Gilfillan. 2022. “Optimization of Enzymatic Fragmentation Is Crucial to Maximize Genome Coverage: A Comparison of Library Preparation Methods for Illumina Sequencing.” BMC Genomics 23 (1). https://doi.org/10.1186/S12864-022-08316-Y.
Shen, Wei, Heidi L. Sellers, Lauren A. Choate, Mariam I. Stein, Pratyush P. Tandale, Jiayu Tan, Rohit Setlem, et al. 2023. “Clinical Validation of Tagmentation-Based Genome Sequencing for Germline Disorders.” The Journal of Molecular Diagnostics : JMD 25 (7): 524–31. https://doi.org/10.1016/J.JMOLDX.2023.04.001.
Zheng, Grace X. Y., Jessica M. Terry, Phillip Belgrader, Paul Ryvkin, Zachary W. Bent, Ryan Wilson, Solongo B. Ziraldo, et al. 2017. “Massively Parallel Digital Transcriptional Profiling of Single Cells.” Nature Communications 8 (January): 14049. https://doi.org/10.1038/ncomms14049.