The DOI matches its Crossref record; 14 of the 14 references it cites were found in a registry or an index.
Preparation of Single‐Cell RNA‐Seq Libraries for Next Generation Sequencing
Open accessAbstract
For the past several decades, due to technical limitations, the field of transcriptomics has focused on population‐level measurements that can mask significant differences between individual cells. With the advent of single‐cell RNA‐Seq, it is now possible to profile the responses of individual cells at unprecedented depth and thereby uncover, transcriptome‐wide, the heterogeneity that exists within these populations. This unit describes a method that merges several important technologies to produce, in high‐throughput, single‐cell RNA‐Seq libraries. Complementary DNA (cDNA) is made from full‐length mRNA transcripts using a reverse transcriptase that has terminal transferase activity. This, when combined with a second “template‐switch” primer, allows for cDNAs to be constructed that have two universal priming sequences. Following preamplification from these common sequences, Nextera XT is used to prepare a pool of 96 uniquely indexed samples ready for Illumina sequencing. Curr. Protoc. Mol. Biol . 107:4.22.1‐4.22.17. © 2014 by John Wiley & Sons, Inc.
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Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
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TopHat: discovering splice junctions with RNA-Seq
Trapnell, C., Pachter, L., & Salzberg, S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp120 · Cited by 11,617
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
Thorvaldsdottir, H., Robinson, J. T., & Mesirov, J. P. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbs017 · Cited by 9,049
mRNA-Seq whole-transcriptome analysis of a single cell
Tang, F., Barbacioru, C., Wang, Y., Nordman, E., Lee, C., Xu, N., Wang, X., Bodeau, J., Tuch, B. B., Siddiqui, A., et al. (2009) · Nature Methods · doi:10.1038/nmeth.1315 · Cited by 3,969
Smart-seq2 for sensitive full-length transcriptome profiling in single cells
Picelli, S., Björklund, Å. K., Faridani, O. R., Sagasser, S., Winberg, G., & Sandberg, R. (2013) · Nature Methods · doi:10.1038/nmeth.2639 · Cited by 2,358 · cited 3×
“SMART-Seq2 published by Picelli et al. (2013) modified the traditional SMARTer protocol to address this by improving transcript detection, coverage, accuracy, yield, and cost.”
BackgroundMethodCEL-seq: single-cell RNA-seq by multiplexed linear amplification
Hashimshony, T., Wagner, F., Sher, N., & Yanai, I. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.08.003 · Cited by 1,231
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
Shalek, A. K., Satija, R., Adiconis, X., Gertner, R. S., Gaublomme, J. T., Raychowdhury, R., Schwartz, S., Yosef, N., Malboeuf, C., Lu, D., et al. (2013) · Nature · doi:10.1038/nature12172 · Cited by 1,190
Self-citationSingle-cell sequencing-based technologies will revolutionize whole-organism science
Shapiro, E., Biezuner, T., & Linnarsson, S. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3542 · Cited by 1,177
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Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq
Tirosh, I., Izar, B., Prakadan, S. M., Wadsworth, M. H., Treacy, D., Trombetta, J. J., Rotem, A., Rodman, C., Lian, C., Murphy, G., et al. (2016) · Science · doi:10.1126/science.aad0501 · Cited by 4,944
Self-citationSingle-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors
Villani, A.-C., Satija, R., Reynolds, G., Sarkizova, S., Shekhar, K., Fletcher, J., Griesbeck, M., Butler, A., Zheng, S., Lazo, S., et al. (2017) · Science · doi:10.1126/science.aah4573 · Cited by 2,413
Self-citationSingle-cell reconstruction of the early maternal–fetal interface in humans
Vento-Tormo, R., Efremova, M., Botting, R. A., Turco, M. Y., Vento-Tormo, M., Meyer, K. B., Park, J.-E., Stephenson, E., Polański, K., Goncalves, A., et al. (2018) · Nature · doi:10.1038/s41586-018-0698-6 · Cited by 2,358
Ziegler, C. G. K., Allon, S. J., Nyquist, S. K., Mbano, I. M., Miao, V. N., Tzouanas, C. N., Cao, Y., Yousif, A. S., Bals, J., Hauser, B. M., et al. (2020) · Cell · doi:10.1016/j.cell.2020.04.035 · Cited by 2,284
Self-citationNeoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial
Keskin, D. B., Anandappa, A. J., Sun, J., Tirosh, I., Mathewson, N. D., Li, S., Oliveira, G., Giobbie-Hurder, A., Felt, K., Gjini, E., et al. (2019) · Nature · doi:10.1038/s41586-018-0792-9 · Cited by 1,432
Self-citation
Metadata
- Authors
- Trombetta, J. J., Gennert, D., Lu, D., Satija, R., Shalek, A. K., & Regev, A.
- Venue
- Current Protocols in Molecular Biology
- Publisher
- Wiley
- Published
- 2014-07
- Volume
- 107
- Issue
- 1
- Pages
- 4.22.1-4.22.17
- ISSN
- 1934-3639 (ISSN-L)
- 1934-3647
- OpenAlex
- W1526404082
- Cited by
- 290
- References
- 14
- FWCI
- 5.96
- Type
- journal article
- Language
- en
- Open access
- green
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