Biology:List of single cell omics methods
From HandWiki
A list of more than 100 different single cell sequencing (omics) methods have been published.[1] The large majority of methods are paired with short-read sequencing technologies, although some of them are compatible with long read sequencing.
List
Method | Reference | Sequencing Mode | Early Estimate | Late Estimate |
---|---|---|---|---|
Tang method | [2] | Short Reads | 2008 | 2009 |
CyTOF | [3] | Short Reads | 2011 | 2012 |
STRT-seq / C1 | [4] | Short Reads | 2011 | 2012 |
SMART-seq | [5] | Short Reads | 2012 | 2013 |
CEL-seq | [6] | Short Reads | 2012 | 2013 |
Quartz-Seq | [7] | Short Reads | 2012 | 2013 |
PMA / SMA | [8] | Short Reads | 2012 | 2013 |
scBS-seq | [9] | Short Reads | 2013 | 2014 |
AbPair | [10] | Short Reads | 2014 | 2014 |
MARS-seq | [11] | Short Reads | 2014 | 2015 |
DR-seq | [12] | Short Reads | 2014 | 2015 |
G&T-Seq | [13] | Short Reads | 2014 | 2015 |
SCTG | [14] | Short Reads | 2014 | 2015 |
SIDR-seq | [15] | Short Reads | 2014 | 2015 |
sci-ATAC-seq | [16] | Short Reads | 2014 | 2015 |
Hi-SCL | [17] | Short Reads | 2015 | 2015 |
SUPeR-seq | [18] | Short Reads | 2015 | 2015 |
Drop-Chip | [19] | Short Reads | 2015 | 2015 |
CytoSeq | [20] | Short Reads | 2015 | 2016 |
inDrop | [21] | Short Reads | 2015 | 2016 |
sc-GEM | [22] | Short Reads | 2015 | 2016 |
scTrio-seq | [23] | Short Reads | 2015 | 2016 |
scM&T-seq | Short Reads | 2015 | 2016 | |
PLAYR | [24] | Short Reads | 2015 | 2016 |
Genshaft-et-al-2016 | [25] | Short Reads | 2015 | 2016 |
Darmanis-et-al-2016 | [26] | Short Reads | 2015 | 2016 |
CRISP-seq | [27] | Short Reads | 2015 | 2016 |
scGESTALT | [28] | Short Reads | 2015 | 2016 |
CEL-Seq2 / C1 | [29] | Short Reads | 2015 | 2016 |
STRT-seq-2i | [30] | Short Reads | 2016 | 2017 |
RNAseq @10xgenomics | [31] | Short Reads | 2016 | 2017 |
RNAseq / Gene Expression @nanostringtech | [32] | Short Reads | 2016 | 2017 |
sc Targeted Gene Expression @fluidigm | [33] | Short Reads | 2016 | 2017 |
scTCR Wafergen | [34] | Short Reads | 2016 | 2017 |
CROP-seq | [35] | Short Reads | 2016 | 2017 |
SiC-seq | [36] | Short Reads | 2016 | 2017 |
mcSCRB-seq | [37] | Short Reads | 2016 | 2017 |
Patch-seq | [38] | Short Reads | 2016 | 2017 |
Geo-seq | [39] | Short Reads | 2016 | 2017 |
scNOMe-seq | [40] | Short Reads | 2016 | 2017 |
scCOOL-seq | [41] | Short Reads | 2016 | 2017 |
CUT&Run | [42] | Short Reads | 2016 | 2017 |
MATQ-seq | [43] | Short Reads | 2016 | 2017 |
Quartz-Seq2 | [44] | Short Reads | 2017 | 2018 |
Seq-Well | [45] | Short Reads | 2017 | 2018 |
DroNC-Seq | [46] | Short Reads | 2017 | 2018 |
sci-RNA-seq | [47] | Short Reads | 2017 | 2018 |
scATAC @10xgenomics | [48] | Short Reads | 2017 | 2018 |
scVDJ @10xgenomics | [49] | Short Reads | 2017 | 2018 |
scNMT triple omics | [50] | Short Reads | 2017 | 2018 |
SPLIT-seq Parse Biosciences | [51] | Short Reads | 2017 | 2018 |
CITE-Seq | [52] | Short Reads | 2017 | 2018 |
scMNase-seq | [53] | Short Reads | 2017 | 2018 |
Chaligne-et-al-2018 | [54] | Short Reads | 2017 | 2018 |
LINNAEUS | [55] | Short Reads | 2017 | 2018 |
TracerSeq | [56] | Short Reads | 2017 | 2018 |
CellTag | [57] | Short Reads | 2017 | 2018 |
ScarTrace | [58] | Short Reads | 2017 | 2018 |
scRNA-Seq Dolomite Bio | [59] | Short Reads | 2017 | 2018 |
Trac-looping | [60] | Short Reads | 2017 | 2018 |
Perturb-ATAC | [61] | Short Reads | 2018 | 2019 |
scMethylation | [62] | Short Reads | 2018 | 2019 |
scHiC | [63] | Short Reads | 2018 | 2019 |
Multiplex Droplet scRNAseq | [64] | Short Reads | 2018 | 2019 |
sci-CAR | [65] | Short Reads | 2018 | 2019 |
C1 CAGE single cell | [66] | Short Reads | 2018 | 2019 |
sc paired microRNA-mRNA | [67] | Short Reads | 2018 | 2019 |
scCAT-seq | [68] | Short Reads | 2018 | 2019 |
REAP-seq @fluidigm | [69] | Short Reads | 2018 | 2019 |
scCC | [70] | Short Reads | 2018 | 2019 |
yscRNA-SEQ | [71] | Short Reads | 2018 | 2019 |
TARGET-seq | [72] | Short Reads | 2018 | 2019 |
MULTI-seq | [73] | Short Reads | 2018 | 2019 |
snRNA-seq | [74] | Short Reads | 2018 | 2019 |
sci-RNA-seq3 | [75] | Short Reads | 2018 | 2019 |
BRIF-seq | [76] | Short Reads | 2018 | 2019 |
Drop-seq Dolomite Bio | [59] | Short Reads | 2018 | 2019 |
Slide-seq | [77] | Short Reads | 2018 | 2019 |
CUT&Tag | [78] | Short Reads | 2018 | 2019 |
CellTagging | [79] | Short Reads | 2018 | 2019 |
DART-Seq | [80] | Short Reads | 2018 | 2019 |
scDamID&T | [81] | Short Reads | 2018 | 2019 |
ACT-seq | [82] | Short Reads | 2018 | 2019 |
Sci-Hi-C | [83] | Short Reads | 2018 | 2019 |
Slide-seq | [84] | Short Reads | 2018 | 2019 |
Simplified-Drop-seq | [85] | Short Reads | 2018 | 2019 |
scChIC-seq | [86] | Short Reads | 2018 | 2019 |
Dip-C | [87] | Short Reads | 2018 | 2019 |
CoBATCH | [88] | Short Reads | 2018 | 2019 |
Convert-seq | [89] | Short Reads | 2018 | 2019 |
Droplet-based scATAC-seq | [90] | Short Reads | 2018 | 2019 |
ECCITE-seq | [91] | Short Reads | 2018 | 2019 |
dsciATAC-seq | [90] | Short Reads | 2018 | 2019 |
CLEVER-seq | [92] | Short Reads | 2018 | 2019 |
scISOr-Seq | [93] | Short Reads | 2018 | 2019 |
MARS-seq2.0 | [94] | Short Reads | 2018 | 2019 |
nano-NOMe | [95] | Long Reads | 2018 | 2019 |
MeSMLR-seq | [96] | Long Reads | 2018 | 2019 |
SMAC-seq | [97] | Long Reads | 2018 | 2019 |
MoonTag/SunTag | [98] | Short Reads | 2018 | 2019 |
SCoPE2 | [99] | Short Reads | 2018 | 2019 |
sci-fate | [100] | Short Reads | 2018 | 2019 |
µDamID | [101] | Short Reads | 2018 | 2019 |
Methyl-HiC | [102] | Short Reads | 2018 | 2019 |
RAGE-seq | [103] | Long Reads | 2018 | 2019 |
Paired-Seq | [104] | Short Reads | 2018 | 2019 |
Tn5Prime | [105] | Short Reads | 2018 | 2019 |
NanoPARE | [106] | Short Reads | 2018 | 2019 |
BART-Seq | [107] | Short Reads | 2018 | 2019 |
scDam&T-seq | [108] | Short Reads | 2018 | 2019 |
itChIP-seq | [109] | Short Reads | 2018 | 2019 |
SNARE-seq | [110] | Short Reads | 2018 | 2019 |
ASTAR-seq | [111] | Short Reads | 2018 | 2019 |
sci-Plex | [112] | Short Reads | 2018 | 2019 |
MIX-Seq | [113] | Short Reads | 2018 | 2019 |
microSPLiT | [114] | Short Reads | 2018 | 2019 |
PAIso-seq | [115] | Short Reads | 2018 | 2019 |
FIN-Seq | [116] | Short Reads | 2018 | 2019 |
LIBRA-seq | [117] | Short Reads | 2018 | 2019 |
scifi-RNA-seq | [118] | Short Reads | 2018 | 2019 |
plexDIA | [119] | Short Reads | 2021 | 2021 |
MPX | [120] | Short Reads | 2023 | 2023 |
References
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- ↑ Luginbühl, Joachim; Kouno, Tsukasa; Nakano, Rei; Chater, Thomas E.; Sivaraman, Divya M.; Kishima, Mami et al. (April 5, 2019). "Decoding neuronal diversity by single-cell Convert-seq". bioRxiv: 600239. doi:10.1101/600239. https://www.biorxiv.org/content/10.1101/600239v1.
- ↑ 90.0 90.1 "Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility". Nature Biotechnology 37 (8): 916–924. August 2019. doi:10.1038/s41587-019-0147-6. PMID 31235917.
- ↑ "Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells". Nature Methods 16 (5): 409–412. May 2019. doi:10.1038/s41592-019-0392-0. PMID 31011186.
- ↑ "Single-Cell 5fC Sequencing". Single Cell Methods. Methods in Molecular Biology. 1979. Clifton, N.J.. January 1, 2019. pp. 251–267. doi:10.1007/978-1-4939-9240-9_16. ISBN 978-1-4939-9239-3.
- ↑ "Single-Cell Virus Sequencing of Influenza Infections That Trigger Innate Immunity". Journal of Virology 93 (14). July 2019. doi:10.1128/JVI.00500-19. PMID 31068418.
- ↑ "MARS-seq2.0: an experimental and analytical pipeline for indexed sorting combined with single-cell RNA sequencing". Nature Protocols 14 (6): 1841–1862. June 2019. doi:10.1038/s41596-019-0164-4. PMID 31101904.
- ↑ Lee, Isac; Razaghi, Roham; Gilpatrick, Timothy; Molnar, Michael; Sadowski, Norah; Simpson, Jared T. et al. (February 2, 2019). "Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing". bioRxiv: 504993. doi:10.1101/504993. https://www.biorxiv.org/content/10.1101/504993v2.
- ↑ "Single-molecule long-read sequencing reveals the chromatin basis of gene expression". Genome Research 29 (8): 1329–1342. August 2019. doi:10.1101/gr.251116.119. PMID 31201211.
- ↑ Shipony, Zohar; Marinov, Georgi K.; Swaffer, Matthew P.; Sinott-Armstrong, Nasa A.; Skotheim, Jan M.; Kundaje, Anshul et al. (December 22, 2018). "Long-range single-molecule mapping of chromatin accessibility in eukaryotes". bioRxiv 17 (3): 319–327. doi:10.1101/504662. PMID 32042188.
- ↑ "Multi-Color Single-Molecule Imaging Uncovers Extensive Heterogeneity in mRNA Decoding". Cell 178 (2): 458–472.e19. July 2019. doi:10.1016/j.cell.2019.05.001. PMID 31178119.
- ↑ Specht, Harrison; Emmott, Edward; Koller, Toni; Slavov, Nikolai (June 9, 2019). "High-throughput single-cell proteomics quantifies the emergence of macrophage heterogeneity". bioRxiv: 665307. doi:10.1101/665307. https://www.biorxiv.org/content/10.1101/665307v1.
- ↑ Cao, Junyue; Zhou, Wei; Steemers, Frank; Trapnell, Cole; Shendure, Jay (June 11, 2019). "Characterizing the temporal dynamics of gene expression in single cells with sci-fate". bioRxiv: 666081. doi:10.1101/666081. https://www.biorxiv.org/content/10.1101/666081v1.
- ↑ Altemose, Nicolas; Maslan, Annie; Lai, Andre; White, Jonathan A.; Streets, Aaron M. (July 18, 2019). "μDamID: a microfluidic approach for imaging and sequencing protein-DNA interactions in single cells". bioRxiv: 706903. doi:10.1101/706903. https://www.biorxiv.org/content/10.1101/706903v1.
- ↑ "Joint profiling of DNA methylation and chromatin architecture in single cells". Nature Methods 16 (10): 991–993. October 2019. doi:10.1038/s41592-019-0502-z. PMID 31384045.
- ↑ "High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes". Nature Communications 10 (1): 3120. July 2019. doi:10.1038/s41467-019-11049-4. PMID 31311926. Bibcode: 2019NatCo..10.3120S.
- ↑ "An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome". Nature Structural & Molecular Biology 26 (11): 1063–1070. November 2019. doi:10.1038/s41594-019-0323-x. PMID 31695190.
- ↑ "Tn5Prime, a Tn5 based 5' capture method for single cell RNA-seq". Nucleic Acids Research 46 (10): e62. June 2018. doi:10.1093/nar/gky182. PMID 29548006.
- ↑ "NanoPARE: parallel analysis of RNA 5' ends from low-input RNA". Genome Research 28 (12): 1931–1942. December 2018. doi:10.1101/gr.239202.118. PMID 30355603.
- ↑ "BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single-cell analysis". Genome Biology 20 (1): 155. August 2019. doi:10.1186/s13059-019-1748-6. PMID 31387612.
- ↑ "Simultaneous quantification of protein-DNA contacts and transcriptomes in single cells". Nature Biotechnology 37 (7): 766–772. July 2019. doi:10.1038/s41587-019-0150-y. PMID 31209373.
- ↑ "Profiling chromatin states using single-cell itChIP-seq". Nature Cell Biology 21 (9): 1164–1172. September 2019. doi:10.1038/s41556-019-0383-5. PMID 31481796.
- ↑ "High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell". Nature Biotechnology 37 (12): 1452–1457. December 2019. doi:10.1038/s41587-019-0290-0. PMID 31611697.
- ↑ Xing, Qiao Rui; Farran, Chadi EL; Yi, Yao; Warrier, Tushar; Gautam, Pradeep; Collins, James J. et al. (November 4, 2019). "Parallel Bimodal Single-cell Sequencing of Transcriptome and Chromatin Accessibility". bioRxiv 30 (7): 1027–1039. doi:10.1101/829960. PMID 32699019.
- ↑ "Massively multiplex chemical transcriptomics at single cell resolution". Science 367 (6473): 45–51. December 2019. doi:10.1126/science.aax6234. PMID 31806696.
- ↑ McFarland, James M.; Paolella, Brenton R.; Warren, Allison; Geiger-Schuller, Kathryn; Shibue, Tsukasa; Rothberg, Michael et al. (December 8, 2019). "Multiplexed single-cell profiling of post-perturbation transcriptional responses to define cancer vulnerabilities and therapeutic mechanism of action". bioRxiv: 868752. doi:10.1101/868752. https://www.biorxiv.org/content/10.1101/868752v1.
- ↑ Kuchina, Anna; Brettner, Leandra M.; Paleologu, Luana; Roco, Charles M.; Rosenberg, Alexander B.; Carignano, Alberto et al. (December 11, 2019). "Microbial single-cell RNA sequencing by split-pool barcoding". bioRxiv: 869248. doi:10.1101/869248. https://www.biorxiv.org/content/10.1101/869248v2.
- ↑ "Poly(A) inclusive RNA isoform sequencing (PAIso-seq) reveals wide-spread non-adenosine residues within RNA poly(A) tails". Nature Communications 10 (1): 5292. November 2019. doi:10.1038/s41467-019-13228-9. PMID 31757970. Bibcode: 2019NatCo..10.5292L.
- ↑ "FIN-Seq: transcriptional profiling of specific cell types from frozen archived tissue of the human central nervous system". Nucleic Acids Research 48 (1): e4. November 2019. doi:10.1093/nar/gkz968. PMID 31728515.
- ↑ "High-Throughput Mapping of B Cell Receptor Sequences to Antigen Specificity". Cell 179 (7): 1636–1646.e15. December 2019. doi:10.1016/j.cell.2019.11.003. PMID 31787378.
- ↑ Datlinger, Paul; Rendeiro, André F.; Boenke, Thorina; Krausgruber, Thomas; Barreca, Daniele; Bock, Christoph (December 18, 2019). "Ultra-high throughput single-cell RNA sequencing by combinatorial fluidic indexing". bioRxiv: 2019.12.17.879304. doi:10.1101/2019.12.17.879304. https://www.biorxiv.org/content/10.1101/2019.12.17.879304v1.
- ↑ Derks, Jason; Leduc, Andrew; Wallmann, Georg; Huffman, R. Gray; Willetts, Matthew; Khan, Saad; Specht, Harrison; Ralser, Markus et al. (2022-07-14). "Increasing the throughput of sensitive proteomics by plexDIA" (in en). Nature Biotechnology 41 (1): 50–59. doi:10.1038/s41587-022-01389-w. ISSN 1546-1696. PMID 35835881.
- ↑ Karlsson, Filip; Kallas, Tomasz; Thiagarajan, Divya; Karlsson, Max; Schweitzer, Maud; Fernandez Navarro, Jose; Leijonancker, Louise; Geny, Sylvain et al. (2023-06-08). "Molecular Pixelation: Single cell spatial proteomics by sequencing" (in en). bioRxiv. doi:10.1101/2023.06.05.543770.
![]() | Original source: https://en.wikipedia.org/wiki/List of single cell omics methods.
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