| class="wikitable" |
| Method
! Reference
! Sequencing Mode
! Early Estimate
! Late Estimate |
|---|
| Tang method
|[{{cite journal | vauthors = Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, Wang X, Bodeau J, Tuch BB, Siddiqui A, Lao K, Surani MA | display-authors = 6 | title = mRNA-Seq whole-transcriptome analysis of a single cell | journal = Nature Methods | volume = 6 | issue = 5 | pages = 377–82 | date = May 2009 | pmid = 19349980 | doi = 10.1038/nmeth.1315 | s2cid = 16570747 }}]
|Short Reads
|2008
|2009 |
| CyTOF
|[{{cite web|url=https://www.fluidigm.com/applications/single-cell-advances|title=Fluidigm | Single-Cell Advances|website=www.fluidigm.com}}]
|Short Reads
|2011
|2012 |
| STRT-seq / C1
|[{{cite journal | vauthors = Hashimshony T, Wagner F, Sher N, Yanai I | title = CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification | journal = Cell Reports | volume = 2 | issue = 3 | pages = 666–73 | date = September 2012 | pmid = 22939981 | doi = 10.1016/j.celrep.2012.08.003 | doi-access = free }}]
|Short Reads
|2011
|2012 |
| SMART-seq
|[{{cite journal | vauthors = Islam S, Zeisel A, Joost S, La Manno G, Zajac P, Kasper M, Lönnerberg P, Linnarsson S | display-authors = 6 | title = Quantitative single-cell RNA-seq with unique molecular identifiers | journal = Nature Methods | volume = 11 | issue = 2 | pages = 163–6 | date = February 2014 | pmid = 24363023 | doi = 10.1038/nmeth.2772 | s2cid = 6765530 }}]
|Short Reads
|2012
|2013 |
| CEL-seq
|[{{cite journal | vauthors = Jaitin DA, Kenigsberg E, Keren-Shaul H, Elefant N, Paul F, Zaretsky I, Mildner A, Cohen N, Jung S, Tanay A, Amit I | display-authors = 6 | title = Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types | journal = Science | volume = 343 | issue = 6172 | pages = 776–9 | date = February 2014 | pmid = 24531970 | pmc = 4412462 | doi = 10.1126/science.1247651 | bibcode = 2014Sci...343..776J }}]
|Short Reads
|2012
|2013 |
| Quartz-Seq
|[{{cite journal | vauthors = Sasagawa Y, Nikaido I, Hayashi T, Danno H, Uno KD, Imai T, Ueda HR | title = Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity | journal = Genome Biology | volume = 14 | issue = 4 | pages = R31 | date = April 2013 | pmid = 23594475 | pmc = 4054835 | doi = 10.1186/gb-2013-14-4-r31 | doi-access = free }}]
|Short Reads
|2012
|2013 |
| PMA / SMA
|[{{cite journal | vauthors = Pan X, Durrett RE, Zhu H, Tanaka Y, Li Y, Zi X, Marjani SL, Euskirchen G, Ma C, Lamotte RH, Park IH, Snyder MP, Mason CE, Weissman SM | display-authors = 6 | title = Two methods for full-length RNA sequencing for low quantities of cells and single cells | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 110 | issue = 2 | pages = 594–9 | date = January 2013 | pmid = 23267071 | pmc = 3545756 | doi = 10.1073/pnas.1217322109 | bibcode = 2013PNAS..110..594P | doi-access = free }}]
|Short Reads
|2012
|2013 |
| scBS-seq
|[{{cite journal | vauthors = Smallwood SA, Lee HJ, Angermueller C, Krueger F, Saadeh H, Peat J, Andrews SR, Stegle O, Reik W, Kelsey G | display-authors = 6 | title = Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity | journal = Nature Methods | volume = 11 | issue = 8 | pages = 817–820 | date = August 2014 | pmid = 25042786 | pmc = 4117646 | doi = 10.1038/nmeth.3035 }}]
|Short Reads
|2013
|2014 |
| AbPair
|[{{cite journal|url=https://www.biorxiv.org/content/10.1101/134841v1|title=Tumor-infiltrating immune repertoires captured by single-cell barcoding in emulsion|first1=Adrian W.|last1=Briggs|first2=Stephen J.|last2=Goldfless|first3=Sonia|last3=Timberlake|first4=Brian J.|last4=Belmont|first5=Christopher R.|last5=Clouser|first6=David|last6=Koppstein|first7=Devin|last7=Sok|first8=Jason Vander A.|last8=Heiden|first9=Manu V.|last9=Tamminen|first10=Steven H.|last10=Kleinstein|first11=Dennis R.|last11=Burton|first12=George M.|last12=Church|first13=Francois|last13=Vigneault | name-list-style = vanc | display-authors = 6 |date=May 5, 2017|journal=bioRxiv|pages=134841 | doi=10.1101/134841|doi-access=free}}]
|Short Reads
|2014
|2014 |
| MARS-seq
|[{{cite journal | vauthors = Picelli S, Björklund ÅK, Faridani OR, Sagasser S, Winberg G, Sandberg R | title = Smart-seq2 for sensitive full-length transcriptome profiling in single cells | journal = Nature Methods | volume = 10 | issue = 11 | pages = 1096–8 | date = November 2013 | pmid = 24056875 | doi = 10.1038/nmeth.2639 | s2cid = 6356570 }}]
|Short Reads
|2014
|2015 |
| DR-seq
|[{{cite journal | vauthors = Dey SS, Kester L, Spanjaard B, Bienko M, van Oudenaarden A | title = Integrated genome and transcriptome sequencing of the same cell | journal = Nature Biotechnology | volume = 33 | issue = 3 | pages = 285–289 | date = March 2015 | pmid = 25599178 | pmc = 4374170 | doi = 10.1038/nbt.3129 }}]
|Short Reads
|2014
|2015 |
| G&T-Seq
|[{{cite journal | vauthors = Macaulay IC, Haerty W, Kumar P, Li YI, Hu TX, Teng MJ, Goolam M, Saurat N, Coupland P, Shirley LM, Smith M, Van der Aa N, Banerjee R, Ellis PD, Quail MA, Swerdlow HP, Zernicka-Goetz M, Livesey FJ, Ponting CP, Voet T | display-authors = 6 | title = G&T-seq: parallel sequencing of single-cell genomes and transcriptomes | journal = Nature Methods | volume = 12 | issue = 6 | pages = 519–22 | date = June 2015 | pmid = 25915121 | doi = 10.1038/nmeth.3370 | s2cid = 969246 | url = https://zenodo.org/record/895966 }}]
|Short Reads
|2014
|2015 |
| SCTG
|[{{cite journal | vauthors = Li W, Calder RB, Mar JC, Vijg J | title = Single-cell transcriptogenomics reveals transcriptional exclusion of ENU-mutated alleles | journal = Mutation Research | volume = 772 | pages = 55–62 | date = February 2015 | pmid = 25733965 | pmc = 4342853 | doi = 10.1016/j.mrfmmm.2015.01.002 }}]
|Short Reads
|2014
|2015 |
| SIDR-seq
|[{{cite journal | vauthors = Han KY, Kim KT, Joung JG, Son DS, Kim YJ, Jo A, Jeon HJ, Moon HS, Yoo CE, Chung W, Eum HH, Kim S, Kim HK, Lee JE, Ahn MJ, Lee HO, Park D, Park WY | display-authors = 6 | title = SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells | journal = Genome Research | volume = 28 | issue = 1 | pages = 75–87 | date = January 2018 | pmid = 29208629 | pmc = 5749184 | doi = 10.1101/gr.223263.117 }}]
|Short Reads
|2014
|2015 |
| sci-ATAC-seq
|[{{cite journal | vauthors = Cusanovich DA, Daza R, Adey A, Pliner HA, Christiansen L, Gunderson KL, Steemers FJ, Trapnell C, Shendure J | display-authors = 6 | title = Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing | journal = Science | volume = 348 | issue = 6237 | pages = 910–4 | date = May 2015 | pmid = 25953818 | pmc = 4836442 | doi = 10.1126/science.aab1601 | bibcode = 2015Sci...348..910C }}]
|Short Reads
|2014
|2015 |
| Hi-SCL
|[{{cite journal | vauthors = Rotem A, Ram O, Shoresh N, Sperling RA, Schnall-Levin M, Zhang H, Basu A, Bernstein BE, Weitz DA | display-authors = 6 | title = High-Throughput Single-Cell Labeling (Hi-SCL) for RNA-Seq Using Drop-Based Microfluidics | journal = PLOS ONE | volume = 10 | issue = 5 | pages = e0116328 | date = January 1, 2015 | pmid = 26000628 | pmc = 4441486 | doi = 10.1371/journal.pone.0116328 | bibcode = 2015PLoSO..1016328R | doi-access = free }}]
|Short Reads
|2015
|2015 |
| SUPeR-seq
|[{{cite journal | vauthors = Fan X, Zhang X, Wu X, Guo H, Hu Y, Tang F, Huang Y | title = Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos | journal = Genome Biology | volume = 16 | issue = 1 | pages = 148 | date = July 2015 | pmid = 26201400 | pmc = 4511241 | doi = 10.1186/s13059-015-0706-1 | doi-access = free }}]
|Short Reads
|2015
|2015 |
| Drop-Chip
|[{{cite web|url=https://pubs.broadinstitute.org/drop-chip/index.php|title=Drop-Chip|website=pubs.broadinstitute.org}}]
|Short Reads
|2015
|2015 |
| CytoSeq
|[{{cite journal | vauthors = Fan HC, Fu GK, Fodor SP | title = Expression profiling. Combinatorial labeling of single cells for gene expression cytometry | journal = Science | volume = 347 | issue = 6222 | pages = 1258367 | date = February 2015 | pmid = 25657253 | doi = 10.1126/science.1258367 | s2cid = 5493175 }}]
|Short Reads
|2015
|2016 |
| inDrop
|[{{cite journal | vauthors = Klein AM, Mazutis L, Akartuna I, Tallapragada N, Veres A, Li V, Peshkin L, Weitz DA, Kirschner MW | display-authors = 6 | title = Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells | journal = Cell | volume = 161 | issue = 5 | pages = 1187–1201 | date = May 2015 | pmid = 26000487 | pmc = 4441768 | doi = 10.1016/j.cell.2015.04.044 }}]
|Short Reads
|2015
|2016 |
| sc-GEM
|[{{cite journal | vauthors = Cheow LF, Courtois ET, Tan Y, Viswanathan R, Xing Q, Tan RZ, Tan DS, Robson P, Loh YH, Quake SR, Burkholder WF | display-authors = 6 | title = Single-cell multimodal profiling reveals cellular epigenetic heterogeneity | journal = Nature Methods | volume = 13 | issue = 10 | pages = 833–6 | date = October 2016 | pmid = 27525975 | doi = 10.1038/nmeth.3961 | s2cid = 3531201 }}]
|Short Reads
|2015
|2016 |
| scTrio-seq
|[{{cite journal | vauthors = Hou Y, Guo H, Cao C, Li X, Hu B, Zhu P, Wu X, Wen L, Tang F, Huang Y, Peng J | display-authors = 6 | title = Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas | journal = Cell Research | volume = 26 | issue = 3 | pages = 304–19 | date = March 2016 | pmid = 26902283 | pmc = 4783472 | doi = 10.1038/cr.2016.23 }}]
|Short Reads
|2015
|2016 |
| scM&T-seq
|[{{cite journal | vauthors = Angermueller C, Clark SJ, Lee HJ, Macaulay IC, Teng MJ, Hu TX, Krueger F, Smallwood S, Ponting CP, Voet T, Kelsey G, Stegle O, Reik W | display-authors = 6 | title = Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity | journal = Nature Methods | volume = 13 | issue = 3 | pages = 229–232 | date = March 2016 | pmid = 26752769 | pmc = 4770512 | doi = 10.1038/nmeth.3728 }}]
|Short Reads
|2015
|2016 |
| PLAYR
|[{{cite journal | vauthors = Frei AP, Bava FA, Zunder ER, Hsieh EW, Chen SY, Nolan GP, Gherardini PF | title = Highly multiplexed simultaneous detection of RNAs and proteins in single cells | journal = Nature Methods | volume = 13 | issue = 3 | pages = 269–75 | date = March 2016 | pmid = 26808670 | pmc = 4767631 | doi = 10.1038/nmeth.3742 }}]
|Short Reads
|2015
|2016 |
| Genshaft-et-al-2016
|[{{cite journal | vauthors = Genshaft AS, Li S, Gallant CJ, Darmanis S, Prakadan SM, Ziegler CG, Lundberg M, Fredriksson S, Hong J, Regev A, Livak KJ, Landegren U, Shalek AK | display-authors = 6 | title = Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction | journal = Genome Biology | volume = 17 | issue = 1 | pages = 188 | date = September 2016 | pmid = 27640647 | pmc = 5027636 | doi = 10.1186/s13059-016-1045-6 | doi-access = free }}]
|Short Reads
|2015
|2016 |
| Darmanis-et-al-2016
|[{{cite journal | vauthors = Darmanis S, Sloan SA, Croote D, Mignardi M, Chernikova S, Samghababi P, Zhang Y, Neff N, Kowarsky M, Caneda C, Li G, Chang SD, Connolly ID, Li Y, Barres BA, Gephart MH, Quake SR | display-authors = 6 | title = Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma | journal = Cell Reports | volume = 21 | issue = 5 | pages = 1399–1410 | date = October 2017 | pmid = 29091775 | pmc = 5810554 | doi = 10.1016/j.celrep.2017.10.030 }}]
|Short Reads
|2015
|2016 |
| CRISP-seq
|[{{cite journal | vauthors = Jaitin DA, Weiner A, Yofe I, Lara-Astiaso D, Keren-Shaul H, David E, Salame TM, Tanay A, van Oudenaarden A, Amit I | display-authors = 6 | title = Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq | journal = Cell | volume = 167 | issue = 7 | pages = 1883–1896.e15 | date = December 2016 | pmid = 27984734 | doi = 10.1016/j.cell.2016.11.039 | doi-access = free }}]
|Short Reads
|2015
|2016 |
| scGESTALT
|[{{cite journal | vauthors = Raj B, Wagner DE, McKenna A, Pandey S, Klein AM, Shendure J, Gagnon JA, Schier AF | display-authors = 6 | title = Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain | journal = Nature Biotechnology | volume = 36 | issue = 5 | pages = 442–450 | date = June 2018 | pmid = 29608178 | pmc = 5938111 | doi = 10.1038/nbt.4103 }}]
|Short Reads
|2015
|2016 |
| CEL-Seq2 / C1
|[{{cite journal | vauthors = Hashimshony T, Senderovich N, Avital G, Klochendler A, de Leeuw Y, Anavy L, Gennert D, Li S, Livak KJ, Rozenblatt-Rosen O, Dor Y, Regev A, Yanai I | display-authors = 6 | title = CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq | journal = Genome Biology | volume = 17 | issue = 1 | pages = 77 | date = April 2016 | pmid = 27121950 | pmc = 4848782 | doi = 10.1186/s13059-016-0938-8 | doi-access = free }}]
|Short Reads
|2015
|2016 |
| STRT-seq-2i
|[{{cite journal | vauthors = Hochgerner H, Lönnerberg P, Hodge R, Mikes J, Heskol A, Hubschle H, Lin P, Picelli S, La Manno G, Ratz M, Dunne J, Husain S, Lein E, Srinivasan M, Zeisel A, Linnarsson S | display-authors = 6 | title = STRT-seq-2i: dual-index 5' single cell and nucleus RNA-seq on an addressable microwell array | journal = Scientific Reports | volume = 7 | issue = 1 | pages = 16327 | date = November 2017 | pmid = 29180631 | pmc = 5703850 | doi = 10.1038/s41598-017-16546-4 | bibcode = 2017NatSR...716327H }}]
|Short Reads
|2016
|2017 |
| RNAseq @10xgenomics
|[{{cite web | title = Single Cell RNA-Seq | url = https://www.10xgenomics.com/single-cell-technology/ | publisher = 10x Genomic }}]
|Short Reads
|2016
|2017 |
| RNAseq / Gene Expression @nanostringtech
|[{{cite web |url= https://www.nanostring.com/scientific-content/technology-overview/ncounter-technology|title=nCounter® Technology | publisher = NanoString Technologies }}]
|Short Reads
|2016
|2017 |
| sc Targeted Gene Expression @fluidigm
|[{{cite web|url=https://www.fluidigm.com/reagents/single-cell-targeted-gene-expression|title=Fluidigm | Consumables | Single-Cell Targeted Gene Expression|website=www.fluidigm.com}}]
|Short Reads
|2016
|2017 |
| scTCR Wafergen
|[{{cite web|url=https://www.prnewswire.com/news-releases/wafergen-presents-single-cell-t-cell-receptor-sequencing-results-using-the-icell8-single-cell-system-at-the-2016-single-cell-genomics-meeting-300327741.html|title=WaferGen Presents Single-Cell T-Cell Receptor Sequencing Results Using the ICELL8™ Single-Cell System at the 2016 Single Cell Genomics Meeting|first=WaferGen Bio-systems|last=Inc|website=www.prnewswire.com}}]
|Short Reads
|2016
|2017 |
| CROP-seq
|[{{cite journal | vauthors = Datlinger P, Rendeiro AF, Schmidl C, Krausgruber T, Traxler P, Klughammer J, Schuster LC, Kuchler A, Alpar D, Bock C | display-authors = 6 | title = Pooled CRISPR screening with single-cell transcriptome readout | journal = Nature Methods | volume = 14 | issue = 3 | pages = 297–301 | date = March 2017 | pmid = 28099430 | pmc = 5334791 | doi = 10.1038/nmeth.4177 }}]
|Short Reads
|2016
|2017 |
| SiC-seq
|[{{cite journal | vauthors = Lan F, Demaree B, Ahmed N, Abate AR | title = Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding | journal = Nature Biotechnology | volume = 35 | issue = 7 | pages = 640–646 | date = July 2017 | pmid = 28553940 | pmc = 5531050 | doi = 10.1038/nbt.3880 }}]
|Short Reads
|2016
|2017 |
| mcSCRB-seq
|[{{cite journal|url=https://www.biorxiv.org/content/10.1101/188367v1|title=mcSCRB-seq: sensitive and powerful single-cell RNA sequencing|first1=Johannes W.|last1=Bagnoli|first2=Christoph|last2=Ziegenhain|first3=Aleksandar|last3=Janjic|first4=Lucas E.|last4=Wange|first5=Beate|last5=Vieth|first6=Swati|last6=Parekh|first7=Johanna|last7=Geuder|first8=Ines|last8=Hellmann|first9=Wolfgang|last9=Enard| name-list-style = vanc | display-authors = 6 |date=October 18, 2017|journal=bioRxiv|pages=188367 | doi=10.1101/188367|doi-access=free}}]
|Short Reads
|2016
|2017 |
| Patch-seq
|[{{cite journal | vauthors = Cadwell CR, Sandberg R, Jiang X, Tolias AS | title = Q&A: using Patch-seq to profile single cells | journal = BMC Biology | volume = 15 | issue = 1 | pages = 58 | date = July 2017 | pmid = 28679385 | pmc = 5499043 | doi = 10.1186/s12915-017-0396-0 | doi-access = free }}]
|Short Reads
|2016
|2017 |
| Geo-seq
|[{{cite journal | vauthors = Chen J, Suo S, Tam PP, Han JJ, Peng G, Jing N | title = Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq | journal = Nature Protocols | volume = 12 | issue = 3 | pages = 566–580 | date = March 2017 | pmid = 28207000 | doi = 10.1038/nprot.2017.003 | s2cid = 3879096 }}]
|Short Reads
|2016
|2017 |
| scNOMe-seq
|[{{cite journal | vauthors = Pott S | title = Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells | journal = eLife | volume = 6 | pages = e23203 | date = June 2017 | pmid = 28653622 | pmc = 5487215 | doi = 10.7554/eLife.23203 | editor-first = Bing | editor-last = Ren | doi-access = free }}]
|Short Reads
|2016
|2017 |
| scCOOL-seq
|[{{cite journal | vauthors = Guo F, Li L, Li J, Wu X, Hu B, Zhu P, Wen L, Tang F | display-authors = 6 | title = Single-cell multi-omics sequencing of mouse early embryos and embryonic stem cells | journal = Cell Research | volume = 27 | issue = 8 | pages = 967–988 | date = August 2017 | pmid = 28621329 | pmc = 5539349 | doi = 10.1038/cr.2017.82 }}]
|Short Reads
|2016
|2017 |
| CUT&Run
|[{{cite journal | vauthors = Skene PJ, Henikoff S | title = An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites | journal = eLife | volume = 6 | pages = e21856 | date = January 2017 | pmid = 28079019 | pmc = 5310842 | doi = 10.7554/eLife.21856 | editor-first = Danny | editor-last = Reinberg | doi-access = free }}]
|Short Reads
|2016
|2017 |
| MATQ-seq
|[{{cite journal | vauthors = Sheng K, Cao W, Niu Y, Deng Q, Zong C | title = Effective detection of variation in single-cell transcriptomes using MATQ-seq | journal = Nature Methods | volume = 14 | issue = 3 | pages = 267–270 | date = March 2017 | pmid = 28092691 | doi = 10.1038/nmeth.4145 | s2cid = 582788 }}]
|Short Reads
|2016
|2017 |
| Quartz-Seq2
|[{{cite journal | vauthors = Sasagawa Y, Danno H, Takada H, Ebisawa M, Tanaka K, Hayashi T, Kurisaki A, Nikaido I | display-authors = 6 | title = Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads | journal = Genome Biology | volume = 19 | issue = 1 | pages = 29 | date = March 2018 | pmid = 29523163 | pmc = 5845169 | doi = 10.1186/s13059-018-1407-3 | doi-access = free }}]
|Short Reads
|2017
|2018 |
| Seq-Well
|[{{cite journal | vauthors = Gierahn TM, Wadsworth MH, Hughes TK, Bryson BD, Butler A, Satija R, Fortune S, Love JC, Shalek AK | display-authors = 6 | title = Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput | journal = Nature Methods | volume = 14 | issue = 4 | pages = 395–398 | date = April 2017 | pmid = 28192419 | pmc = 5376227 | doi = 10.1038/nmeth.4179 | hdl = 1721.1/113430 }}]
|Short Reads
|2017
|2018 |
| DroNC-Seq
|[{{cite journal | vauthors = Habib N, Avraham-Davidi I, Basu A, Burks T, Shekhar K, Hofree M, Choudhury SR, Aguet F, Gelfand E, Ardlie K, Weitz DA, Rozenblatt-Rosen O, Zhang F, Regev A | display-authors = 6 | title = Massively parallel single-nucleus RNA-seq with DroNc-seq | journal = Nature Methods | volume = 14 | issue = 10 | pages = 955–958 | date = October 2017 | pmid = 28846088 | pmc = 5623139 | doi = 10.1038/nmeth.4407 }}]
|Short Reads
|2017
|2018 |
| sci-RNA-seq
|[{{cite journal | vauthors = Cao J, Packer JS, Ramani V, Cusanovich DA, Huynh C, Daza R, Qiu X, Lee C, Furlan SN, Steemers FJ, Adey A, Waterston RH, Trapnell C, Shendure J | display-authors = 6 | title = Comprehensive single-cell transcriptional profiling of a multicellular organism | journal = Science | volume = 357 | issue = 6352 | pages = 661–667 | date = August 2017 | pmid = 28818938 | pmc = 5894354 | doi = 10.1126/science.aam8940 | bibcode = 2017Sci...357..661C }}]
|Short Reads
|2017
|2018 |
| scATAC @10xgenomics
|[{{cite web| url = https://www.10xgenomics.com/solutions/single-cell-atac/| title = Single Cell ATAC - 10x Genomics}} ]
|Short Reads
|2017
|2018 |
| scVDJ @10xgenomics
|[{{cite web| url = https://www.10xgenomics.com/solutions/vdj/| title = Single Cell Immune Profiling - 10x Genomics}} ]
|Short Reads
|2017
|2018 |
| scNMT triple omics
|[{{cite journal|url=https://www.biorxiv.org/content/10.1101/519207v1|title=Single cell multi-omics profiling reveals a hierarchical epigenetic landscape during mammalian germ layer specification|first1=Ricard|last1=Argelaguet|first2=Hisham|last2=Mohammed|first3=Stephen J.|last3=Clark|first4=L. Carine|last4=Stapel|first5=Christel|last5=Krueger|first6=Chantriolnt-Andreas|last6=Kapourani|first7=Yunlong|last7=Xiang|first8=Courtney|last8=Hanna|first9=Sebastien|last9=Smallwood|first10=Ximena|last10=Ibarra-Soria|first11=Florian|last11=Buettner|first12=Guido|last12=Sanguinetti|first13=Felix|last13=Krueger|first14=Wei|last14=Xie|first15=Peter|last15=Rugg-Gunn|first16=Gavin|last16=Kelsey|first17=Wendy|last17=Dean|first18=Jennifer|last18=Nichols|first19=Oliver|last19=Stegle|first20=John C.|last20=Marioni|first21=Wolf|last21=Reik| name-list-style = vanc | display-authors = 6 |date=January 13, 2019|journal=bioRxiv|pages=519207 | doi=10.1101/519207|doi-access=free}}]
|Short Reads
|2017
|2018 |
| SPLIT-seq Parse Biosciences
|[{{cite journal | vauthors = Rosenberg AB, Roco CM, Muscat RA, Kuchina A, Sample P, Yao Z, Graybuck LT, Peeler DJ, Mukherjee S, Chen W, Pun SH, Sellers DL, Tasic B, Seelig G | display-authors = 6 | title = Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding | journal = Science | volume = 360 | issue = 6385 | pages = 176–182 | date = April 2018 | pmid = 29545511 | doi = 10.1126/science.aam8999 | pmc = 7643870 | bibcode = 2018Sci...360..176R | doi-access = free }}]
|Short Reads
|2017
|2018 |
| CITE-Seq
|[{{cite journal | vauthors = Stoeckius M, Hafemeister C, Stephenson W, Houck-Loomis B, Chattopadhyay PK, Swerdlow H, Satija R, Smibert P | display-authors = 6 | title = Simultaneous epitope and transcriptome measurement in single cells | journal = Nature Methods | volume = 14 | issue = 9 | pages = 865–868 | date = September 2017 | pmid = 28759029 | pmc = 5669064 | doi = 10.1038/nmeth.4380 }}]
|Short Reads
|2017
|2018 |
| scMNase-seq
|[{{cite journal | vauthors = Lai B, Gao W, Cui K, Xie W, Tang Q, Jin W, Hu G, Ni B, Zhao K | display-authors = 6 | title = Principles of nucleosome organization revealed by single-cell micrococcal nuclease sequencing | journal = Nature | volume = 562 | issue = 7726 | pages = 281–285 | date = October 2018 | pmid = 30258225 | doi = 10.1038/s41586-018-0567-3 | bibcode = 2018Natur.562..281L | s2cid = 52841785 | pmc = 8353605 }}]
|Short Reads
|2017
|2018 |
| Chaligne-et-al-2018
|[{{cite journal|url=https://www.biorxiv.org/content/10.1101/444687v1|title=High throughput droplet single-cell Genotyping of Transcriptomes (GoT) reveals the cell identity dependency of the impact of somatic mutations|first1=Anna S.|last1=Nam|first2=Kyu-Tae|last2=Kim|first3=Ronan|last3=Chaligne|first4=Franco|last4=Izzo|first5=Chelston|last5=Ang|first6=Ghaith|last6=Abu-Zeinah|first7=Nathaniel D.|last7=Omans|first8=Justin|last8=Taylor|first9=Alessandro|last9=Pastore|first10=Alicia|last10=Alonso|first11=Marisa|last11=Mariani|first12=Juan R.|last12=Cubillos-Ruiz|first13=Wayne|last13=Tam|first14=Ronald|last14=Hoffman|first15=Joseph M.|last15=Scandura|first16=Raul|last16=Rabadan|first17=Omar|last17=Abdel-Wahab|first18=Peter|last18=Smibert|first19=Dan A.|last19=Landau| name-list-style = vanc | display-authors = 6 |date=October 16, 2018|journal=bioRxiv|pages=444687 | doi=10.1101/444687|doi-access=free}}]
|Short Reads
|2017
|2018 |
| LINNAEUS
|[{{cite journal | vauthors = Spanjaard B, Hu B, Mitic N, Olivares-Chauvet P, Janjuha S, Ninov N, Junker JP | title = Simultaneous lineage tracing and cell-type identification using CRISPR-Cas9-induced genetic scars | journal = Nature Biotechnology | volume = 36 | issue = 5 | pages = 469–473 | date = June 2018 | pmid = 29644996 | pmc = 5942543 | doi = 10.1038/nbt.4124 }}]
|Short Reads
|2017
|2018 |
| TracerSeq
|[{{cite journal | vauthors = Wagner DE, Weinreb C, Collins ZM, Briggs JA, Megason SG, Klein AM | title = Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo | journal = Science | volume = 360 | issue = 6392 | pages = 981–987 | date = June 2018 | pmid = 29700229 | pmc = 6083445 | doi = 10.1126/science.aar4362 | bibcode = 2018Sci...360..981W }}]
|Short Reads
|2017
|2018 |
| CellTag
|[{{cite journal | vauthors = Guo C, Kong W, Kamimoto K, Rivera-Gonzalez GC, Yang X, Kirita Y, Morris SA | title = CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics | journal = Genome Biology | volume = 20 | issue = 1 | pages = 90 | date = May 2019 | pmid = 31072405 | pmc = 6509836 | doi = 10.1186/s13059-019-1699-y | doi-access = free }}]
|Short Reads
|2017
|2018 |
| ScarTrace
|[{{cite journal | vauthors = Alemany A, Florescu M, Baron CS, Peterson-Maduro J, van Oudenaarden A | title = Whole-organism clone tracing using single-cell sequencing | journal = Nature | volume = 556 | issue = 7699 | pages = 108–112 | date = April 2018 | pmid = 29590089 | doi = 10.1038/nature25969 | bibcode = 2018Natur.556..108A | s2cid = 4633026 }}]
|Short Reads
|2017
|2018 |
| scRNA-Seq Dolomite Bio
|[{{cite web|url=https://www.dolomite-bio.com/product/nadia-instrument/|title=Nadia Instrument |website=Dolomite Bio}}]
|Short Reads
|2017
|2018 |
| Trac-looping
|[{{cite journal | vauthors = Lai B, Tang Q, Jin W, Hu G, Wangsa D, Cui K, Stanton BZ, Ren G, Ding Y, Zhao M, Liu S, Song J, Ried T, Zhao K | display-authors = 6 | title = Trac-looping measures genome structure and chromatin accessibility | journal = Nature Methods | volume = 15 | issue = 9 | pages = 741–747 | date = September 2018 | pmid = 30150754 | doi = 10.1038/s41592-018-0107-y | pmc = 7212307 }}]
|Short Reads
|2017
|2018 |
| Perturb-ATAC
|[{{cite journal | vauthors = Rubin AJ, Parker KR, Satpathy AT, Qi Y, Wu B, Ong AJ, Mumbach MR, Ji AL, Kim DS, Cho SW, Zarnegar BJ, Greenleaf WJ, Chang HY, Khavari PA | display-authors = 6 | title = Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks | journal = Cell | volume = 176 | issue = 1–2 | pages = 361–376.e17 | date = January 2019 | pmid = 30580963 | pmc = 6329648 | doi = 10.1016/j.cell.2018.11.022 }}]
|Short Reads
|2018
|2019 |
| scMethylation
|[{{cite journal | vauthors = Karemaker ID, Vermeulen M | title = Single-Cell DNA Methylation Profiling: Technologies and Biological Applications | journal = Trends in Biotechnology | volume = 36 | issue = 9 | pages = 952–965 | date = September 2018 | pmid = 29724495 | doi = 10.1016/j.tibtech.2018.04.002 | hdl = 2066/200393 | s2cid = 19248693 | hdl-access = free }}]
|Short Reads
|2018
|2019 |
| scHiC
|[{{cite journal | vauthors = de Wit E | title = Capturing heterogeneity: single-cell structures of the 3D genome | journal = Nature Structural & Molecular Biology | volume = 24 | issue = 5 | pages = 437–438 | date = May 2017 | pmid = 28471429 | doi = 10.1038/nsmb.3404 | s2cid = 5132000 }}]
|Short Reads
|2018
|2019 |
| Multiplex Droplet scRNAseq
|[{{cite journal | vauthors = Kang HM, Subramaniam M, Targ S, Nguyen M, Maliskova L, McCarthy E, Wan E, Wong S, Byrnes L, Lanata CM, Gate RE, Mostafavi S, Marson A, Zaitlen N, Criswell LA, Ye CJ | display-authors = 6 | title = Multiplexed droplet single-cell RNA-sequencing using natural genetic variation | journal = Nature Biotechnology | volume = 36 | issue = 1 | pages = 89–94 | date = January 2018 | pmid = 29227470 | pmc = 5784859 | doi = 10.1038/nbt.4042 }}]
|Short Reads
|2018
|2019 |
| sci-CAR
|[{{cite journal | vauthors = Cao J, Cusanovich DA, Ramani V, Aghamirzaie D, Pliner HA, Hill AJ, Daza RM, McFaline-Figueroa JL, Packer JS, Christiansen L, Steemers FJ, Adey AC, Trapnell C, Shendure J | display-authors = 6 | title = Joint profiling of chromatin accessibility and gene expression in thousands of single cells | journal = Science | volume = 361 | issue = 6409 | pages = 1380–1385 | date = September 2018 | pmid = 30166440 | pmc = 6571013 | doi = 10.1126/science.aau0730 | bibcode = 2018Sci...361.1380C }}]
|Short Reads
|2018
|2019 |
| C1 CAGE single cell
|[{{cite journal | vauthors = Kouno T, Moody J, Kwon AT, Shibayama Y, Kato S, Huang Y, Böttcher M, Motakis E, Mendez M, Severin J, Luginbühl J, Abugessaisa I, Hasegawa A, Takizawa S, Arakawa T, Furuno M, Ramalingam N, West J, Suzuki H, Kasukawa T, Lassmann T, Hon CC, Arner E, Carninci P, Plessy C, Shin JW | display-authors = 6 | title = C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution | journal = Nature Communications | volume = 10 | issue = 1 | pages = 360 | date = January 2019 | pmid = 30664627 | pmc = 6341120 | doi = 10.1038/s41467-018-08126-5 | bibcode = 2019NatCo..10..360K }}]
|Short Reads
|2018
|2019 |
| sc paired microRNA-mRNA
|[{{cite journal | vauthors = Wang N, Zheng J, Chen Z, Liu Y, Dura B, Kwak M, Xavier-Ferrucio J, Lu YC, Zhang M, Roden C, Cheng J, Krause DS, Ding Y, Fan R, Lu J | display-authors = 6 | title = Single-cell microRNA-mRNA co-sequencing reveals non-genetic heterogeneity and mechanisms of microRNA regulation | journal = Nature Communications | volume = 10 | issue = 1 | pages = 95 | date = January 2019 | pmid = 30626865 | pmc = 6327095 | doi = 10.1038/s41467-018-07981-6 | bibcode = 2019NatCo..10...95W }}]
|Short Reads
|2018
|2019 |
| scCAT-seq
|[{{cite journal | vauthors = Liu L, Liu C, Quintero A, Wu L, Yuan Y, Wang M, Cheng M, Leng L, Xu L, Dong G, Li R, Liu Y, Wei X, Xu J, Chen X, Lu H, Chen D, Wang Q, Zhou Q, Lin X, Li G, Liu S, Wang Q, Wang H, Fink JL, Gao Z, Liu X, Hou Y, Zhu S, Yang H, Ye Y, Lin G, Chen F, Herrmann C, Eils R, Shang Z, Xu X | display-authors = 6 | title = Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity | journal = Nature Communications | volume = 10 | issue = 1 | pages = 470 | date = January 2019 | pmid = 30692544 | pmc = 6349937 | doi = 10.1038/s41467-018-08205-7 | bibcode = 2019NatCo..10..470L }}]
|Short Reads
|2018
|2019 |
| REAP-seq @fluidigm
|[{{cite press release|url=http://www.globenewswire.com/news-release/2019/01/31/1708388/0/en/Fluidigm-Introduces-REAP-Seq-for-Multi-Omic-Single-Cell-Analysis-on-the-C1.html|title=Fluidigm Introduces REAP-Seq for Multi-Omic Single-Cell Analysis on the C1|first=Fluidigm|last=Corporation|date=January 31, 2019|website=GlobeNewswire News Room}}]
|Short Reads
|2018
|2019 |
| scCC
|[{{cite journal|url=https://www.biorxiv.org/content/10.1101/538553v1|title=Self-reporting transposons enable simultaneous readout of gene expression and transcription factor binding in single cells|first1=Arnav|last1=Moudgil|first2=Michael N.|last2=Wilkinson|first3=Xuhua|last3=Chen|first4=June|last4=He|first5=Alex J.|last5=Cammack|first6=Michael J.|last6=Vasek|first7=Tomas|last7=Lagunas|first8=Zongtai|last8=Qi|first9=Samantha A.|last9=Morris|first10=Joseph D.|last10=Dougherty|first11=Robi D.|last11=Mitra| name-list-style = vanc | display-authors = 6 |date=February 1, 2019|journal=bioRxiv|volume=182|issue=4|pages=992–1008.e21 | doi=10.1101/538553|pmid=32710817|pmc=7510185|doi-access=free}}]
|Short Reads
|2018
|2019 |
| yscRNA-SEQ
|[{{cite journal | vauthors = Nadal-Ribelles M, Islam S, Wei W, Latorre P, Nguyen M, de Nadal E, Posas F, Steinmetz LM | display-authors = 6 | title = Sensitive high-throughput single-cell RNA-seq reveals within-clonal transcript correlations in yeast populations | journal = Nature Microbiology | volume = 4 | issue = 4 | pages = 683–692 | date = April 2019 | pmid = 30718850 | pmc = 6433287 | doi = 10.1038/s41564-018-0346-9 }}]
|Short Reads
|2018
|2019 |
| TARGET-seq
|[{{cite journal | vauthors = Rodriguez-Meira A, Buck G, Clark SA, Povinelli BJ, Alcolea V, Louka E, McGowan S, Hamblin A, Sousos N, Barkas N, Giustacchini A, Psaila B, Jacobsen SE, Thongjuea S, Mead AJ | display-authors = 6 | title = Unravelling Intratumoral Heterogeneity through High-Sensitivity Single-Cell Mutational Analysis and Parallel RNA Sequencing | journal = Molecular Cell | volume = 73 | issue = 6 | pages = 1292–1305.e8 | date = March 2019 | pmid = 30765193 | pmc = 6436961 | doi = 10.1016/j.molcel.2019.01.009 }}]
|Short Reads
|2018
|2019 |
| MULTI-seq
|[{{cite journal | vauthors = McGinnis CS, Patterson DM, Winkler J, Conrad DN, Hein MY, Srivastava V, Hu JL, Murrow LM, Weissman JS, Werb Z, Chow ED, Gartner ZJ | display-authors = 6 | title = MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices | journal = Nature Methods | volume = 16 | issue = 7 | pages = 619–626 | date = July 2019 | pmid = 31209384 | pmc = 6837808 | doi = 10.1038/s41592-019-0433-8 }}]
|Short Reads
|2018
|2019 |
| snRNA-seq
|[{{cite journal | vauthors = Gaublomme JT, Li B, McCabe C, Knecht A, Yang Y, Drokhlyansky E, Van Wittenberghe N, Waldman J, Dionne D, Nguyen L, De Jager PL, Yeung B, Zhao X, Habib N, Rozenblatt-Rosen O, Regev A | display-authors = 6 | title = Nuclei multiplexing with barcoded antibodies for single-nucleus genomics | journal = Nature Communications | volume = 10 | issue = 1 | pages = 2907 | date = July 2019 | pmid = 31266958 | pmc = 6606589 | doi = 10.1038/s41467-019-10756-2 | bibcode = 2019NatCo..10.2907G }}]
|Short Reads
|2018
|2019 |
| sci-RNA-seq3
|[{{cite web|url=https://oncoscape.v3.sttrcancer.org/atlas.gs.washington.edu.mouse.rna/sciRnaSeq3|title=Mouse RNA Atlas|website=oncoscape.v3.sttrcancer.org}}]
|Short Reads
|2018
|2019 |
| BRIF-seq
|[{{cite journal | vauthors = Li X, Chen L, Zhang Q, Sun Y, Li Q, Yan J | title = BRIF-Seq: Bisulfite-Converted Randomly Integrated Fragments Sequencing at the Single-Cell Level | journal = Molecular Plant | volume = 12 | issue = 3 | pages = 438–446 | date = March 2019 | pmid = 30639749 | doi = 10.1016/j.molp.2019.01.004 | doi-access = free }}]
|Short Reads
|2018
|2019 |
| Drop-seq Dolomite Bio
|
|Short Reads
|2018
|2019 |
| Slide-seq
|[{{cite journal | vauthors = Rodriques SG, Stickels RR, Goeva A, Martin CA, Murray E, Vanderburg CR, Welch J, Chen LM, Chen F, Macosko EZ | display-authors = 6 | title = Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution | journal = Science | volume = 363 | issue = 6434 | pages = 1463–1467 | date = March 2019 | pmid = 30923225 | pmc = 6927209 | doi = 10.1126/science.aaw1219 | bibcode = 2019Sci...363.1463R }}]
|Short Reads
|2018
|2019 |
| CUT&Tag
|[{{cite journal | vauthors = Kaya-Okur HS, Wu SJ, Codomo CA, Pledger ES, Bryson TD, Henikoff JG, Ahmad K, Henikoff S | display-authors = 6 | title = CUT&Tag for efficient epigenomic profiling of small samples and single cells | journal = Nature Communications | volume = 10 | issue = 1 | pages = 1930 | date = April 2019 | pmid = 31036827 | pmc = 6488672 | doi = 10.1038/s41467-019-09982-5 | bibcode = 2019NatCo..10.1930K }}]
|Short Reads
|2018
|2019 |
| CellTagging
|[{{cite journal|url=https://www.protocols.io/view/single-cell-mapping-of-lineage-and-identity-via-ce-yxifxke|title=Single-cell mapping of lineage and identity via CellTagging|first=Brent A.|last=Biddy|date=March 7, 2019|website=Protocols.io|doi=10.17504/protocols.io.yxifxke|doi-access=free}}]
|Short Reads
|2018
|2019 |
| DART-Seq
|[{{cite journal | vauthors = Saikia M, Burnham P, Keshavjee SH, Wang MF, Heyang M, Moral-Lopez P, Hinchman MM, Danko CG, Parker JS, De Vlaminck I | display-authors = 6 | title = Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells | journal = Nature Methods | volume = 16 | issue = 1 | pages = 59–62 | date = January 2019 | pmid = 30559431 | pmc = 6378878 | doi = 10.1038/s41592-018-0259-9 }}]
|Short Reads
|2018
|2019 |
| scDamID&T
|[{{cite journal | vauthors = Rooijers K, Markodimitraki CM, Rang FJ, de Vries SS, Chialastri A, de Luca KL, Mooijman D, Dey SS, Kind J | display-authors = 6 | title = Simultaneous quantification of protein-DNA contacts and transcriptomes in single cells | journal = Nature Biotechnology | volume = 37 | issue = 7 | pages = 766–772 | date = July 2019 | pmid = 31209373 | pmc = 6609448 | doi = 10.1038/s41587-019-0150-y }}]
|Short Reads
|2018
|2019 |
| ACT-seq
|[{{cite journal | vauthors = Carter B, Ku WL, Kang JY, Hu G, Perrie J, Tang Q, Zhao K | title = Mapping histone modifications in low cell number and single cells using antibody-guided chromatin tagmentation (ACT-seq) | journal = Nature Communications | volume = 10 | issue = 1 | pages = 3747 | date = August 2019 | pmid = 31431618 | pmc = 6702168 | doi = 10.1038/s41467-019-11559-1 | bibcode = 2019NatCo..10.3747C }}]
|Short Reads
|2018
|2019 |
| Sci-Hi-C
|[{{cite journal | vauthors = Ramani V, Deng X, Qiu R, Lee C, Disteche CM, Noble WS, Shendure J, Duan Z | display-authors = 6 | title = Sci-Hi-C: A single-cell Hi-C method for mapping 3D genome organization in large number of single cells | journal = Methods | volume = 170| pages = 61–68 | date = September 2019 | pmid = 31536770 | pmc = 6949367 | doi = 10.1016/j.ymeth.2019.09.012 }}]
|Short Reads
|2018
|2019 |
| Slide-seq
|[{{cite journal | vauthors = Rodriques SG, Stickels RR, Goeva A, Martin CA, Murray E, Vanderburg CR, Welch J, Chen LM, Chen F, Macosko EZ | display-authors = 6 | title = Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution | journal = Science | volume = 363 | issue = 6434 | pages = 1463–1467 | date = March 2019 | pmid = 30923225 | pmc = 6927209 | doi = 10.1126/science.aaw1219 | bibcode = 2019Sci...363.1463R }}]
|Short Reads
|2018
|2019 |
| Simplified-Drop-seq
|[{{cite journal | vauthors = Biočanin M, Bues J, Dainese R, Amstad E, Deplancke B | title = Simplified Drop-seq workflow with minimized bead loss using a bead capture and processing microfluidic chip | journal = Lab on a Chip | volume = 19 | issue = 9 | pages = 1610–1620 | date = April 2019 | pmid = 30920557 | doi = 10.1039/C9LC00014C | doi-access = free }}]
|Short Reads
|2018
|2019 |
| scChIC-seq
|[{{cite journal | vauthors = Ku WL, Nakamura K, Gao W, Cui K, Hu G, Tang Q, Ni B, Zhao K | display-authors = 6 | title = Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification | journal = Nature Methods | volume = 16 | issue = 4 | pages = 323–325 | date = April 2019 | pmid = 30923384 | doi = 10.1038/s41592-019-0361-7 | pmc = 7187538 }}]
|Short Reads
|2018
|2019 |
| Dip-C
|[{{cite journal | vauthors = Tan L, Xing D, Daley N, Xie XS | title = Three-dimensional genome structures of single sensory neurons in mouse visual and olfactory systems | journal = Nature Structural & Molecular Biology | volume = 26 | issue = 4 | pages = 297–307 | date = April 2019 | pmid = 30936528 | doi = 10.1038/s41594-019-0205-2 | s2cid = 89616808 }}]
|Short Reads
|2018
|2019 |
| CoBATCH
|[{{cite journal | vauthors = Wang Q, Xiong H, Ai S, Yu X, Liu Y, Zhang J, He A | title = CoBATCH for High-Throughput Single-Cell Epigenomic Profiling | journal = Molecular Cell | volume = 76 | issue = 1 | pages = 206–216.e7 | date = October 2019 | pmid = 31471188 | doi = 10.1016/j.molcel.2019.07.015 | doi-access = free }}]
|Short Reads
|2018
|2019 |
| Convert-seq
|[{{cite journal|url=https://www.biorxiv.org/content/10.1101/600239v1|title=Decoding neuronal diversity by single-cell Convert-seq|first1=Joachim|last1=Luginbühl|first2=Tsukasa|last2=Kouno|first3=Rei|last3=Nakano|first4=Thomas E.|last4=Chater|first5=Divya M.|last5=Sivaraman|first6=Mami|last6=Kishima|first7=Filip|last7=Roudnicky|first8=Piero|last8=Carninci|first9=Charles|last9=Plessy|first10=Jay W.|last10=Shin| name-list-style = vanc | display-authors = 6 |date=April 5, 2019|journal=bioRxiv|pages=600239 | doi=10.1101/600239|doi-access=free}}]
|Short Reads
|2018
|2019 |
| Droplet-based scATAC-seq
|[{{cite journal | vauthors = Lareau CA, Duarte FM, Chew JG, Kartha VK, Burkett ZD, Kohlway AS, Pokholok D, Aryee MJ, Steemers FJ, Lebofsky R, Buenrostro JD | display-authors = 6 | title = Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility | journal = Nature Biotechnology | volume = 37 | issue = 8 | pages = 916–924 | date = August 2019 | pmid = 31235917 | doi = 10.1038/s41587-019-0147-6 | s2cid = 195329871 | pmc = 10299900 }}]
|Short Reads
|2018
|2019 |
| ECCITE-seq
|[{{cite journal | vauthors = Mimitou EP, Cheng A, Montalbano A, Hao S, Stoeckius M, Legut M, Roush T, Herrera A, Papalexi E, Ouyang Z, Satija R, Sanjana NE, Koralov SB, Smibert P | display-authors = 6 | title = Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells | journal = Nature Methods | volume = 16 | issue = 5 | pages = 409–412 | date = May 2019 | pmid = 31011186 | pmc = 6557128 | doi = 10.1038/s41592-019-0392-0 }}]
|Short Reads
|2018
|2019 |
| dsciATAC-seq
|
|Short Reads
|2018
|2019 |
| CLEVER-seq
|[{{cite book | vauthors = Zhu C, Gao Y, Peng J, Tang F, Yi C | title = Single Cell Methods | chapter = Single-Cell 5fC Sequencing | volume = 1979 | pages = 251–267 | date = January 1, 2019 | pmid = 31028643 | doi = 10.1007/978-1-4939-9240-9_16 | isbn = 978-1-4939-9239-3 | series = Methods in Molecular Biology | location = Clifton, N.J. | s2cid = 135447312 }}]
|Short Reads
|2018
|2019 |
| scISOr-Seq
|[{{cite journal | vauthors = Russell AB, Elshina E, Kowalsky JR, Te Velthuis AJ, Bloom JD | title = Single-Cell Virus Sequencing of Influenza Infections That Trigger Innate Immunity | journal = Journal of Virology | volume = 93 | issue = 14 | date = July 2019 | pmid = 31068418 | pmc = 6600203 | doi = 10.1128/JVI.00500-19 }}]
|Short Reads
|2018
|2019 |
| MARS-seq2.0
|[{{cite journal | vauthors = Keren-Shaul H, Kenigsberg E, Jaitin DA, David E, Paul F, Tanay A, Amit I | title = MARS-seq2.0: an experimental and analytical pipeline for indexed sorting combined with single-cell RNA sequencing | journal = Nature Protocols | volume = 14 | issue = 6 | pages = 1841–1862 | date = June 2019 | pmid = 31101904 | doi = 10.1038/s41596-019-0164-4 | s2cid = 156055842 }}]
|Short Reads
|2018
|2019 |
| nano-NOMe
|[{{cite journal|url=https://www.biorxiv.org/content/10.1101/504993v2|title=Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing|first1=Isac|last1=Lee|first2=Roham|last2=Razaghi|first3=Timothy|last3=Gilpatrick|first4=Michael|last4=Molnar|first5=Norah|last5=Sadowski|first6=Jared T.|last6=Simpson|first7=Fritz J.|last7=Sedlazeck|first8=Winston|last8=Timp| name-list-style = vanc | display-authors = 6 |date=February 2, 2019|journal=bioRxiv|pages=504993 | doi=10.1101/504993|doi-access=free}}]
|Long Reads
|2018
|2019 |
| MeSMLR-seq
|[{{cite journal | vauthors = Wang Y, Wang A, Liu Z, Thurman AL, Powers LS, Zou M, Zhao Y, Hefel A, Li Y, Zabner J, Au KF | display-authors = 6 | title = Single-molecule long-read sequencing reveals the chromatin basis of gene expression | journal = Genome Research | volume = 29 | issue = 8 | pages = 1329–1342 | date = August 2019 | pmid = 31201211 | pmc = 6673713 | doi = 10.1101/gr.251116.119 }}]
|Long Reads
|2018
|2019 |
| SMAC-seq
|[{{cite journal|title=Long-range single-molecule mapping of chromatin accessibility in eukaryotes|first1=Zohar|last1=Shipony|first2=Georgi K.|last2=Marinov|first3=Matthew P.|last3=Swaffer|first4=Nasa A.|last4=Sinott-Armstrong|first5=Jan M.|last5=Skotheim|first6=Anshul|last6=Kundaje|first7=William J.|last7=Greenleaf| name-list-style = vanc | display-authors = 6 |date=December 22, 2018|journal=bioRxiv|volume=17|issue=3|pages=319–327 | doi=10.1101/504662|pmid=32042188|pmc=7968351|doi-access=free}}]
|Long Reads
|2018
|2019 |
| MoonTag/SunTag
|[{{cite journal | vauthors = Boersma S, Khuperkar D, Verhagen BM, Sonneveld S, Grimm JB, Lavis LD, Tanenbaum ME | title = Multi-Color Single-Molecule Imaging Uncovers Extensive Heterogeneity in mRNA Decoding | journal = Cell | volume = 178 | issue = 2 | pages = 458–472.e19 | date = July 2019 | pmid = 31178119 | pmc = 6630898 | doi = 10.1016/j.cell.2019.05.001 }}]
|Short Reads
|2018
|2019 |
| SCoPE2
|[{{cite journal|url=https://www.biorxiv.org/content/10.1101/665307v1|title=High-throughput single-cell proteomics quantifies the emergence of macrophage heterogeneity|first1=Harrison|last1=Specht|first2=Edward|last2=Emmott|first3=Toni|last3=Koller|first4=Nikolai|last4=Slavov| name-list-style = vanc |date=June 9, 2019|journal=bioRxiv|pages=665307 | doi=10.1101/665307|doi-access=free}}]
|Short Reads
|2018
|2019 |
| sci-fate
|[{{cite journal|url=https://www.biorxiv.org/content/10.1101/666081v1|title=Characterizing the temporal dynamics of gene expression in single cells with sci-fate|first1=Junyue|last1=Cao|first2=Wei|last2=Zhou|first3=Frank|last3=Steemers|first4=Cole|last4=Trapnell|first5=Jay|last5=Shendure| name-list-style = vanc |date=June 11, 2019|journal=bioRxiv|pages=666081 | doi=10.1101/666081|doi-access=free}}]
|Short Reads
|2018
|2019 |
| μDamID
|[{{cite journal|url=https://www.biorxiv.org/content/10.1101/706903v1|title=μDamID: a microfluidic approach for imaging and sequencing protein-DNA interactions in single cells|first1=Nicolas|last1=Altemose|first2=Annie|last2=Maslan|first3=Andre|last3=Lai|first4=Jonathan A.|last4=White|first5=Aaron M.|last5=Streets| name-list-style = vanc |date=July 18, 2019|journal=bioRxiv|pages=706903 | doi=10.1101/706903|doi-access=free}}]
|Short Reads
|2018
|2019 |
| Methyl-HiC
|[{{cite journal | vauthors = Li G, Liu Y, Zhang Y, Kubo N, Yu M, Fang R, Kellis M, Ren B | display-authors = 6 | title = Joint profiling of DNA methylation and chromatin architecture in single cells | journal = Nature Methods | volume = 16 | issue = 10 | pages = 991–993 | date = October 2019 | pmid = 31384045 | pmc = 6765429 | doi = 10.1038/s41592-019-0502-z }}]
|Short Reads
|2018
|2019 |
| RAGE-seq
|[{{cite journal | vauthors = Singh M, Al-Eryani G, Carswell S, Ferguson JM, Blackburn J, Barton K, Roden D, Luciani F, Giang Phan T, Junankar S, Jackson K, Goodnow CC, Smith MA, Swarbrick A | display-authors = 6 | title = High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes | journal = Nature Communications | volume = 10 | issue = 1 | pages = 3120 | date = July 2019 | pmid = 31311926 | pmc = 6635368 | doi = 10.1038/s41467-019-11049-4 | bibcode = 2019NatCo..10.3120S }}]
|Long Reads
|2018
|2019 |
| Paired-Seq
|[{{cite journal | vauthors = Zhu C, Yu M, Huang H, Juric I, Abnousi A, Hu R, Lucero J, Behrens MM, Hu M, Ren B | display-authors = 6 | title = An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome | journal = Nature Structural & Molecular Biology | volume = 26 | issue = 11 | pages = 1063–1070 | date = November 2019 | pmid = 31695190 | doi = 10.1038/s41594-019-0323-x | pmc = 7231560 }}]
|Short Reads
|2018
|2019 |
| Tn5Prime
|[{{cite journal | vauthors = Cole C, Byrne A, Beaudin AE, Forsberg EC, Vollmers C | title = Tn5Prime, a Tn5 based 5' capture method for single cell RNA-seq | journal = Nucleic Acids Research | volume = 46 | issue = 10 | pages = e62 | date = June 2018 | pmid = 29548006 | pmc = 6007450 | doi = 10.1093/nar/gky182 }}]
|Short Reads
|2018
|2019 |
| NanoPARE
|[{{cite journal | vauthors = Schon MA, Kellner MJ, Plotnikova A, Hofmann F, Nodine MD | title = NanoPARE: parallel analysis of RNA 5' ends from low-input RNA | journal = Genome Research | volume = 28 | issue = 12 | pages = 1931–1942 | date = December 2018 | pmid = 30355603 | pmc = 6280765 | doi = 10.1101/gr.239202.118 }}]
|Short Reads
|2018
|2019 |
| BART-Seq
|[{{cite journal | vauthors = Uzbas F, Opperer F, Sönmezer C, Shaposhnikov D, Sass S, Krendl C, Angerer P, Theis FJ, Mueller NS, Drukker M | display-authors = 6 | title = BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single-cell analysis | journal = Genome Biology | volume = 20 | issue = 1 | pages = 155 | date = August 2019 | pmid = 31387612 | pmc = 6683345 | doi = 10.1186/s13059-019-1748-6 | doi-access = free }}]
|Short Reads
|2018
|2019 |
| scDam&T-seq
|[{{cite journal | vauthors = Rooijers K, Markodimitraki CM, Rang FJ, de Vries SS, Chialastri A, de Luca KL, Mooijman D, Dey SS, Kind J | display-authors = 6 | title = Simultaneous quantification of protein-DNA contacts and transcriptomes in single cells | journal = Nature Biotechnology | volume = 37 | issue = 7 | pages = 766–772 | date = July 2019 | pmid = 31209373 | pmc = 6609448 | doi = 10.1038/s41587-019-0150-y }}]
|Short Reads
|2018
|2019 |
| itChIP-seq
|[{{cite journal | vauthors = Ai S, Xiong H, Li CC, Luo Y, Shi Q, Liu Y, Yu X, Li C, He A | display-authors = 6 | title = Profiling chromatin states using single-cell itChIP-seq | journal = Nature Cell Biology | volume = 21 | issue = 9 | pages = 1164–1172 | date = September 2019 | pmid = 31481796 | doi = 10.1038/s41556-019-0383-5 | s2cid = 201815293 }}]
|Short Reads
|2018
|2019 |
| SNARE-seq
|[{{cite journal | vauthors = Chen S, Lake BB, Zhang K | title = High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell | journal = Nature Biotechnology | volume = 37 | issue = 12 | pages = 1452–1457 | date = December 2019 | pmid = 31611697 | pmc = 6893138 | doi = 10.1038/s41587-019-0290-0 }}]
|Short Reads
|2018
|2019 |
| ASTAR-seq
|[{{cite journal|title=Parallel Bimodal Single-cell Sequencing of Transcriptome and Chromatin Accessibility|first1=Qiao Rui|last1=Xing|first2=Chadi EL|last2=Farran|first3=Yao|last3=Yi|first4=Tushar|last4=Warrier|first5=Pradeep|last5=Gautam|first6=James J.|last6=Collins|first7=Jian|last7=Xu|first8=Hu|last8=Li|first9=Li-Feng|last9=Zhang|first10=Yuin-Han|last10=Loh| name-list-style = vanc | display-authors = 6 |date=November 4, 2019|journal=bioRxiv|volume=30|issue=7|pages=1027–1039 | doi=10.1101/829960|pmid=32699019|pmc=7397874|doi-access=free}}]
|Short Reads
|2018
|2019 |
| sci-Plex
|[{{cite journal | vauthors = Srivatsan SR, McFaline-Figueroa JL, Ramani V, Saunders L, Cao J, Packer J, Pliner HA, Jackson DL, Daza RM, Christiansen L, Zhang F, Steemers F, Shendure J, Trapnell C | display-authors = 6 | title = Massively multiplex chemical transcriptomics at single cell resolution | journal = Science | volume = 367 | issue = 6473 | pages = 45–51 | date = December 2019 | pmid = 31806696 | doi = 10.1126/science.aax6234 | pmc = 7289078 }}]
|Short Reads
|2018
|2019 |
| MIX-Seq
|[{{cite journal|url=https://www.biorxiv.org/content/10.1101/868752v1|title=Multiplexed single-cell profiling of post-perturbation transcriptional responses to define cancer vulnerabilities and therapeutic mechanism of action|first1=James M.|last1=McFarland|first2=Brenton R.|last2=Paolella|first3=Allison|last3=Warren|first4=Kathryn|last4=Geiger-Schuller|first5=Tsukasa|last5=Shibue|first6=Michael|last6=Rothberg|first7=Olena|last7=Kuksenko|first8=Andrew|last8=Jones|first9=Emily|last9=Chambers|first10=Danielle|last10=Dionne|first11=Samantha|last11=Bender|first12=Brian M.|last12=Wolpin|first13=Mahmoud|last13=Ghandi|first14=Itay|last14=Tirosh|first15=Orit|last15=Rozenblatt-Rosen|first16=Jennifer A.|last16=Roth|first17=Todd R.|last17=Golub|first18=Aviv|last18=Regev|first19=Andrew J.|last19=Aguirre|first20=Francisca|last20=Vazquez|first21=Aviad|last21=Tsherniak| name-list-style = vanc | display-authors = 6 |date=December 8, 2019|journal=bioRxiv|pages=868752 | doi=10.1101/868752|doi-access=free}}]
|Short Reads
|2018
|2019 |
| microSPLiT
|[{{cite journal|url=https://www.biorxiv.org/content/10.1101/869248v2|title=Microbial single-cell RNA sequencing by split-pool barcoding|first1=Anna|last1=Kuchina|first2=Leandra M.|last2=Brettner|first3=Luana|last3=Paleologu|first4=Charles M.|last4=Roco|first5=Alexander B.|last5=Rosenberg|first6=Alberto|last6=Carignano|first7=Ryan|last7=Kibler|first8=Matthew|last8=Hirano|first9=R. William|last9=DePaolo|first10=Georg|last10=Seelig| name-list-style = vanc | display-authors = 6 |date=December 11, 2019|journal=bioRxiv|pages=869248 | doi=10.1101/869248|doi-access=free}}]
|Short Reads
|2018
|2019 |
| PAIso-seq
|[{{cite journal | vauthors = Liu Y, Nie H, Liu H, Lu F | title = Poly(A) inclusive RNA isoform sequencing (PAIso-seq) reveals wide-spread non-adenosine residues within RNA poly(A) tails | journal = Nature Communications | volume = 10 | issue = 1 | pages = 5292 | date = November 2019 | pmid = 31757970 | pmc = 6876564 | doi = 10.1038/s41467-019-13228-9 | bibcode = 2019NatCo..10.5292L }}]
|Short Reads
|2018
|2019 |
| FIN-Seq
|[{{cite journal | vauthors = Amamoto R, Zuccaro E, Curry NC, Khurana S, Chen HH, Cepko CL, Arlotta P | title = FIN-Seq: transcriptional profiling of specific cell types from frozen archived tissue of the human central nervous system | journal = Nucleic Acids Research | volume = 48 | issue = 1 | pages = e4 | date = November 2019 | pmid = 31728515 | doi = 10.1093/nar/gkz968 | pmc = 7145626 | doi-access = free }}]
|Short Reads
|2018
|2019 |
| LIBRA-seq
|[{{cite journal | vauthors = Setliff I, Shiakolas AR, Pilewski KA, Murji AA, Mapengo RE, Janowska K, Richardson S, Oosthuysen C, Raju N, Ronsard L, Kanekiyo M, Qin JS, Kramer KJ, Greenplate AR, McDonnell WJ, Graham BS, Connors M, Lingwood D, Acharya P, Morris L, Georgiev IS | display-authors = 6 | title = High-Throughput Mapping of B Cell Receptor Sequences to Antigen Specificity | journal = Cell | volume = 179 | issue = 7 | pages = 1636–1646.e15 | date = December 2019 | pmid = 31787378 | doi = 10.1016/j.cell.2019.11.003 | pmc = 7158953 }}]
|Short Reads
|2018
|2019 |
| scifi-RNA-seq
|[{{cite journal|url=https://www.biorxiv.org/content/10.1101/2019.12.17.879304v1|title=Ultra-high throughput single-cell RNA sequencing by combinatorial fluidic indexing|first1=Paul|last1=Datlinger|first2=André F.|last2=Rendeiro|first3=Thorina|last3=Boenke|first4=Thomas|last4=Krausgruber|first5=Daniele|last5=Barreca|first6=Christoph|last6=Bock| name-list-style = vanc |date=December 18, 2019|journal=bioRxiv|pages=2019.12.17.879304 | doi=10.1101/2019.12.17.879304|doi-access=free}}]
|Short Reads
|2018
|2019 |
| plexDIA
|[{{Cite journal |last1=Derks |first1=Jason |last2=Leduc |first2=Andrew |last3=Wallmann |first3=Georg |last4=Huffman |first4=R. Gray |last5=Willetts |first5=Matthew |last6=Khan |first6=Saad |last7=Specht |first7=Harrison |last8=Ralser |first8=Markus |last9=Demichev |first9=Vadim |last10=Slavov |first10=Nikolai |date=2022-07-14 |title=Increasing the throughput of sensitive proteomics by plexDIA |journal=Nature Biotechnology |volume=41 |issue=1 |language=en |pages=50–59 |doi=10.1038/s41587-022-01389-w |pmid=35835881 |pmc=9839897 |issn=1546-1696}}]
|Short Reads
|2021
|2021 |
| MPX
|[{{Cite journal |last1=Karlsson|first1=Filip |last2=Kallas|first2=Tomasz |last3=Thiagarajan |first3=Divya |last4=Karlsson|first4=Max |last5=Schweitzer |first5=Maud |last6=Fernandez Navarro|first6=Jose |last7=Leijonancker|first7=Louise |last8=Geny|first8=Sylvain |last9=Pettersson|first9=Erik |last10=Rhomberg-Kauert|first10=Jan |last11=Gonzalez Granillo|first11=Marcela |last12=Bunz|first12=Jessica |last13=Dahlberg|first13=Johan |last14=Simonetti|first14=Michele |last15=Sathe|first15=Prajakta |last16=Brodin|first16=Petter |last17=Martinez Barrio|first17=Alvaro |last18=Fredriksson|first18=Simon |date=2023-06-08 |title=Molecular Pixelation: Single cell spatial proteomics by sequencing |journal=bioRxiv |language=en |doi=10.1101/2023.06.05.543770 |s2cid=259127075 }}]
|Short Reads
|2023
|2023 |