List of single cell omics methods

Last updated

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

MethodReferenceSequencing ModeEarly EstimateLate Estimate
Tang method [2] Short Reads20082009
CyTOF [3] Short Reads20112012
STRT-seq / C1 [4] Short Reads20112012
SMART-seq [5] Short Reads20122013
CEL-seq [6] Short Reads20122013
Quartz-Seq [7] Short Reads20122013
PMA / SMA [8] Short Reads20122013
scBS-seq [9] Short Reads20132014
AbPair [10] Short Reads20142014
MARS-seq [11] Short Reads20142015
DR-seq [12] Short Reads20142015
G&T-Seq [13] Short Reads20142015
SCTG [14] Short Reads20142015
SIDR-seq [15] Short Reads20142015
sci-ATAC-seq [16] Short Reads20142015
Hi-SCL [17] Short Reads20152015
SUPeR-seq [18] Short Reads20152015
Drop-Chip [19] Short Reads20152015
CytoSeq [20] Short Reads20152016
inDrop [21] Short Reads20152016
sc-GEM [22] Short Reads20152016
scTrio-seq [23] Short Reads20152016
scM&T-seq [24] Short Reads20152016
PLAYR [25] Short Reads20152016
Genshaft-et-al-2016 [26] Short Reads20152016
Darmanis-et-al-2016 [27] Short Reads20152016
CRISP-seq [28] Short Reads20152016
scGESTALT [29] Short Reads20152016
CEL-Seq2 / C1 [30] Short Reads20152016
STRT-seq-2i [31] Short Reads20162017
RNAseq @10xgenomics [32] Short Reads20162017
RNAseq / Gene Expression @nanostringtech [33] Short Reads20162017
sc Targeted Gene Expression @fluidigm [34] Short Reads20162017
scTCR Wafergen [35] Short Reads20162017
CROP-seq [36] Short Reads20162017
SiC-seq [37] Short Reads20162017
mcSCRB-seq [38] Short Reads20162017
Patch-seq [39] Short Reads20162017
Geo-seq [40] Short Reads20162017
scNOMe-seq [41] Short Reads20162017
scCOOL-seq [42] Short Reads20162017
CUT&Run [43] Short Reads20162017
MATQ-seq [44] Short Reads20162017
Quartz-Seq2 [45] Short Reads20172018
Seq-Well [46] Short Reads20172018
DroNC-Seq [47] Short Reads20172018
sci-RNA-seq [48] Short Reads20172018
scATAC @10xgenomics [49] Short Reads20172018
scVDJ @10xgenomics [50] Short Reads20172018
scNMT triple omics [51] Short Reads20172018
SPLIT-seq Parse Biosciences [52] Short Reads20172018
CITE-Seq [53] Short Reads20172018
scMNase-seq [54] Short Reads20172018
Chaligne-et-al-2018 [55] Short Reads20172018
LINNAEUS [56] Short Reads20172018
TracerSeq [57] Short Reads20172018
CellTag [58] Short Reads20172018
ScarTrace [59] Short Reads20172018
scRNA-Seq Dolomite Bio [60] Short Reads20172018
Trac-looping [61] Short Reads20172018
Perturb-ATAC [62] Short Reads20182019
scMethylation [63] Short Reads20182019
scHiC [64] Short Reads20182019
Multiplex Droplet scRNAseq [65] Short Reads20182019
sci-CAR [66] Short Reads20182019
C1 CAGE single cell [67] Short Reads20182019
sc paired microRNA-mRNA [68] Short Reads20182019
scCAT-seq [69] Short Reads20182019
REAP-seq @fluidigm [70] Short Reads20182019
scCC [71] Short Reads20182019
yscRNA-SEQ [72] Short Reads20182019
TARGET-seq [73] Short Reads20182019
MULTI-seq [74] Short Reads20182019
snRNA-seq [75] Short Reads20182019
sci-RNA-seq3 [76] Short Reads20182019
BRIF-seq [77] Short Reads20182019
Drop-seq Dolomite Bio [60] Short Reads20182019
Slide-seq [78] Short Reads20182019
CUT&Tag [79] Short Reads20182019
CellTagging [80] Short Reads20182019
DART-Seq [81] Short Reads20182019
scDamID&T [82] Short Reads20182019
ACT-seq [83] Short Reads20182019
Sci-Hi-C [84] Short Reads20182019
Slide-seq [85] Short Reads20182019
Simplified-Drop-seq [86] Short Reads20182019
scChIC-seq [87] Short Reads20182019
Dip-C [88] Short Reads20182019
CoBATCH [89] Short Reads20182019
Convert-seq [90] Short Reads20182019
Droplet-based scATAC-seq [91] Short Reads20182019
ECCITE-seq [92] Short Reads20182019
dsciATAC-seq [91] Short Reads20182019
CLEVER-seq [93] Short Reads20182019
scISOr-Seq [94] Short Reads20182019
MARS-seq2.0 [95] Short Reads20182019
nano-NOMe [96] Long Reads20182019
MeSMLR-seq [97] Long Reads20182019
SMAC-seq [98] Long Reads20182019
MoonTag/SunTag [99] Short Reads20182019
SCoPE2 [100] Short Reads20182019
sci-fate [101] Short Reads20182019
μDamID [102] Short Reads20182019
Methyl-HiC [103] Short Reads20182019
RAGE-seq [104] Long Reads20182019
Paired-Seq [105] Short Reads20182019
Tn5Prime [106] Short Reads20182019
NanoPARE [107] Short Reads20182019
BART-Seq [108] Short Reads20182019
scDam&T-seq [109] Short Reads20182019
itChIP-seq [110] Short Reads20182019
SNARE-seq [111] Short Reads20182019
ASTAR-seq [112] Short Reads20182019
sci-Plex [113] Short Reads20182019
MIX-Seq [114] Short Reads20182019
microSPLiT [115] Short Reads20182019
PAIso-seq [116] Short Reads20182019
FIN-Seq [117] Short Reads20182019
LIBRA-seq [118] Short Reads20182019
scifi-RNA-seq [119] Short Reads20182019
plexDIA [120] Short Reads20212021
MPX [121] Short Reads20232023

References

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