List of single cell omics methods

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	[24]	Short Reads	2015	2016
PLAYR	[25]	Short Reads	2015	2016
Genshaft-et-al-2016	[26]	Short Reads	2015	2016
Darmanis-et-al-2016	[27]	Short Reads	2015	2016
CRISP-seq	[28]	Short Reads	2015	2016
scGESTALT	[29]	Short Reads	2015	2016
CEL-Seq2 / C1	[30]	Short Reads	2015	2016
STRT-seq-2i	[31]	Short Reads	2016	2017
RNAseq @10xgenomics	[32]	Short Reads	2016	2017
RNAseq / Gene Expression @nanostringtech	[33]	Short Reads	2016	2017
sc Targeted Gene Expression @fluidigm	[34]	Short Reads	2016	2017
scTCR Wafergen	[35]	Short Reads	2016	2017
CROP-seq	[36]	Short Reads	2016	2017
SiC-seq	[37]	Short Reads	2016	2017
mcSCRB-seq	[38]	Short Reads	2016	2017
Patch-seq	[39]	Short Reads	2016	2017
Geo-seq	[40]	Short Reads	2016	2017
scNOMe-seq	[41]	Short Reads	2016	2017
scCOOL-seq	[42]	Short Reads	2016	2017
CUT&Run	[43]	Short Reads	2016	2017
MATQ-seq	[44]	Short Reads	2016	2017
Quartz-Seq2	[45]	Short Reads	2017	2018
Seq-Well	[46]	Short Reads	2017	2018
DroNC-Seq	[47]	Short Reads	2017	2018
sci-RNA-seq	[48]	Short Reads	2017	2018
scATAC @10xgenomics	[49]	Short Reads	2017	2018
scVDJ @10xgenomics	[50]	Short Reads	2017	2018
scNMT triple omics	[51]	Short Reads	2017	2018
SPLIT-seq Parse Biosciences	[52]	Short Reads	2017	2018
CITE-Seq	[53]	Short Reads	2017	2018
scMNase-seq	[54]	Short Reads	2017	2018
Chaligne-et-al-2018	[55]	Short Reads	2017	2018
LINNAEUS	[56]	Short Reads	2017	2018
TracerSeq	[57]	Short Reads	2017	2018
CellTag	[58]	Short Reads	2017	2018
ScarTrace	[59]	Short Reads	2017	2018
scRNA-Seq Dolomite Bio	[60]	Short Reads	2017	2018
Trac-looping	[61]	Short Reads	2017	2018
Perturb-ATAC	[62]	Short Reads	2018	2019
scMethylation	[63]	Short Reads	2018	2019
scHiC	[64]	Short Reads	2018	2019
Multiplex Droplet scRNAseq	[65]	Short Reads	2018	2019
sci-CAR	[66]	Short Reads	2018	2019
C1 CAGE single cell	[67]	Short Reads	2018	2019
sc paired microRNA-mRNA	[68]	Short Reads	2018	2019
scCAT-seq	[69]	Short Reads	2018	2019
REAP-seq @fluidigm	[70]	Short Reads	2018	2019
scCC	[71]	Short Reads	2018	2019
yscRNA-SEQ	[72]	Short Reads	2018	2019
TARGET-seq	[73]	Short Reads	2018	2019
MULTI-seq	[74]	Short Reads	2018	2019
snRNA-seq	[75]	Short Reads	2018	2019
sci-RNA-seq3	[76]	Short Reads	2018	2019
BRIF-seq	[77]	Short Reads	2018	2019
Drop-seq Dolomite Bio	[60]	Short Reads	2018	2019
Slide-seq	[78]	Short Reads	2018	2019
CUT&Tag	[79]	Short Reads	2018	2019
CellTagging	[80]	Short Reads	2018	2019
DART-Seq	[81]	Short Reads	2018	2019
scDamID&T	[82]	Short Reads	2018	2019
ACT-seq	[83]	Short Reads	2018	2019
Sci-Hi-C	[84]	Short Reads	2018	2019
Slide-seq	[85]	Short Reads	2018	2019
Simplified-Drop-seq	[86]	Short Reads	2018	2019
scChIC-seq	[87]	Short Reads	2018	2019
Dip-C	[88]	Short Reads	2018	2019
CoBATCH	[89]	Short Reads	2018	2019
Convert-seq	[90]	Short Reads	2018	2019
Droplet-based scATAC-seq	[91]	Short Reads	2018	2019
ECCITE-seq	[92]	Short Reads	2018	2019
dsciATAC-seq	[91]	Short Reads	2018	2019
CLEVER-seq	[93]	Short Reads	2018	2019
scISOr-Seq	[94]	Short Reads	2018	2019
MARS-seq2.0	[95]	Short Reads	2018	2019
nano-NOMe	[96]	Long Reads	2018	2019
MeSMLR-seq	[97]	Long Reads	2018	2019
SMAC-seq	[98]	Long Reads	2018	2019
MoonTag/SunTag	[99]	Short Reads	2018	2019
SCoPE2	[100]	Short Reads	2018	2019
sci-fate	[101]	Short Reads	2018	2019
μDamID	[102]	Short Reads	2018	2019
Methyl-HiC	[103]	Short Reads	2018	2019
RAGE-seq	[104]	Long Reads	2018	2019
Paired-Seq	[105]	Short Reads	2018	2019
Tn5Prime	[106]	Short Reads	2018	2019
NanoPARE	[107]	Short Reads	2018	2019
BART-Seq	[108]	Short Reads	2018	2019
scDam&T-seq	[109]	Short Reads	2018	2019
itChIP-seq	[110]	Short Reads	2018	2019
SNARE-seq	[111]	Short Reads	2018	2019
ASTAR-seq	[112]	Short Reads	2018	2019
sci-Plex	[113]	Short Reads	2018	2019
MIX-Seq	[114]	Short Reads	2018	2019
microSPLiT	[115]	Short Reads	2018	2019
PAIso-seq	[116]	Short Reads	2018	2019
FIN-Seq	[117]	Short Reads	2018	2019
LIBRA-seq	[118]	Short Reads	2018	2019
scifi-RNA-seq	[119]	Short Reads	2018	2019
plexDIA	[120]	Short Reads	2021	2021
MPX	[121]	Short Reads	2023	2023