Single cell studies database

	A	B	C	D	E	F	G	H	I	J	K	L	M	N	O	P	Q	R	S	T	U	V	W	X	Y	Z	AA	AB
1	Shorthand	DOI	Authors	Journal	Title	Date	bioRxiv DOI	Reported cells total	Organism	Tissue	Technique	Data location	Panel size	Measurement	Cell source	Disease	Contrasts	Developmental stage	Number of reported cell types or clusters	Cell clustering	Pseudotime	RNA Velocity	PCA	tSNE	H5AD location	Isolation	BC --> Cell ID _OR_ BC --> Cluster ID	Number individuals

2	Cauli et al PNAS	10.1073/pnas.97.11.6144	B. Cauli, J. T. Porter, K. Tsuzuki, B. Lambolez, J. Rossier, B. Quenet, E. Audinat	Proceedings of the National Academy of Sciences	Classification of fusiform neocortical interneurons based on unsupervised clustering	20020726	-	85	Rat	Brain	sc-RT-mPCR		30	qPCR	Cerebral cortex			21-27 days	3	Yes	No	No	Yes	No		Patch-clamp
3	Malnic et al Cell	10.1016/S0092-8674(00)80581-4	Bettina Malnic, Junzo Hirono, Takaaki Sato, Linda B Buck	Cell	Combinatorial Receptor Codes for Odors	20040410	-	18	Mouse	Brain	PCR			qPCR	Olfactory neurons
4	Tietjen et al Neuron	10.1016/S0896-6273(03)00229-0	Ian Tietjen, Jason M. Rihel, Yanxiang Cao, Georgy Koentges, Lisa Zakhary, Catherine Dulac	Neuron	Single-Cell Transcriptional Analysis of Neuronal Progenitors	20040415	-	37	Human, Mouse	Brain	PCR		13,000	Microarray	OSNs, OPCs				6							Manual, LCM		2
5	Gallopin et al CCortex	10.1093/cercor/bhj081	Thierry Gallopin, Hélène Geoffroy, Jean Rossier, Bertrand Lambolez	Cerebral Cortex	Cortical Sources of CRF, NKB, and CCK and Their Effects on Pyramidal Cells in the Neocortex	20051208	-	157	Rat	Brain	sc-RT-mPCR		50	qPCR	Cerebral cortex			21-27 days	4	Yes	No	No	Yes	No		Patch-clamp
6	Kurimoto et al NAR	10.1093/nar/gkl050	K. Kurimoto	Nucleic Acids Research	An improved single-cell cDNA amplification method for efficient high-density oligonucleotide microarray analysis	20060330	-	20	Mouse	ICM	aRNA amplification	GSE4309		Microarray	E3.5 ICM			E3.5	2
7	Ferezou et al CCortex	10.1093/cercor/bhl104	I. Ferezou, E. L. Hill, B. Cauli, N. Gibelin, T. Kaneko, J. Rossier, B. Lambolez	Cerebral Cortex	Extensive Overlap of Mu-Opioid and Nicotinic Sensitivity in Cortical Interneurons	20061027	-	360	Rat	Brain	sc-RT-mPCR		30	qPCR	Cerebral cortex			21-27 days	4	No	No	No	No	No		Patch-clamp
8	Esumi et al NResearch	10.1016/j.neures.2007.12.011	Shigeyuki Esumi, Sheng-Xi Wu, Yuchio Yanagawa, Kunihiko Obata, Yukihiko Sugimoto, Nobuaki Tamamaki	Neuroscience Research	Method for single-cell microarray analysis and application to gene-expression profiling of GABAergic neuron progenitors	20080107	-	8	Mouse	Brain	Super SMART			Microarray	GABAergic NPCs				1					No
9	Subkhankulova et al BMCGenomics	10.1186/1471-2164-9-268	Tatiana Subkhankulova, Michael J Gilchrist, Frederick J Livesey	BMC Genomics	Modelling and measuring single cell RNA expression levels find considerable transcriptional differences among phenotypically identical cells	20080613	-	12	Mouse	Brain	PCR		23,232	Microarray	E11.5 NPCs			E11.5
10	Karagiannis et al JNeuroscience	10.1523/JNEUROSCI.0058-09.2009	A. Karagiannis, T. Gallopin, C. David, D. Battaglia, H. Geoffroy, J. Rossier, E. M. C. Hillman, J. F. Staiger, B. Cauli	Journal of Neuroscience	Classification of NPY-Expressing Neocortical Interneurons	20090318	-	200	Rat	Brain	sc-RT-mPCR		30	qPCR	Cerebral cortex			21-27 days	4	Yes	No	No	Yes	No		Patch-clamp
11	Tang et al NMeth	10.1038/NMETH.1315	Fuchou Tang, Catalin Barbacioru, Yangzhou Wang, Ellen Nordman, Clarence Lee, Nanlan Xu, Xiaohui Wang, John Bodeau, Brian B Tuch, Asim Siddiqui, Kaiqin Lao, M Azim Surani	Nat Methods	mRNA-Seq whole-transcriptome analysis of a single cell	20090406	-	5	Mouse	Oocyte	Tang	GSE14605		RNA-seq	Oocyte			E0		No	No	No	No	No		Pipetting (Manual picking)
12	Sul et al PNAS	10.1073/pnas.0902161106	J.-Y. Sul, C.-w. K. Wu, F. Zeng, J. Jochems, M. T. Lee, T. K. Kim, T. Peritz, P. Buckley, D. J. Cappelleri, M. Maronski, M. Kim, V. Kumar, D. Meaney, J. Kim, J. Eberwine	Proceedings of the National Academy of Sciences	Transcriptome transfer produces a predictable cellular phenotype	20090421	-	48	Rat	Brain	aRNA amplification			Microarray	Brain				6	Yes
13	Guo et al DCell	10.1016/j.devcel.2010.02.012	Guoji Guo, Mikael Huss, Guo Qing Tong, Chaoyang Wang, Li Li Sun, Neil D. Clarke, Paul Robson	Developmental Cell	Resolution of Cell Fate Decisions Revealed by Single-Cell Gene Expression Analysis from Zygote to Blastocyst	20100420	-	387	Mouse	Embryo	BioMark		48	qPCR	Preimplantation embryos			8-cell, 16-cell, 32-cell, 64-cell		Yes
14	Tang et al CSC	10.1016/j.stem.2010.03.015	Fuchou Tang, Catalin Barbacioru, Siqin Bao, Caroline Lee, Ellen Nordman, Xiaohui Wang, Kaiqin Lao, M. Azim Surani	Cell Stem Cell	Tracing the Derivation of Embryonic Stem Cells from the Inner Cell Mass by Single-Cell RNA-Seq Analysis	20100507	-	34	Mouse	Embryo	Tang	GSE20187		RNA-seq	ICM, ESC, Epiblast			E3, E5				No	Yes
15	Islam et al GR	10.1101/gr.110882.110	S. Islam, U. Kjallquist, A. Moliner, P. Zajac, J.-B. Fan, P. Lonnerberg, S. Linnarsson	Genome Research	Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq	20110505	-	85	Mouse	Culture	STRT-seq	GSE29087		RNA-seq	mESCs, MEFs				2	Yes	No		Yes	No		Pipetting (Manual picking)
16	Tang et al POne	10.1371/journal.pone.0021208	Fuchou Tang, Catalin Barbacioru, Ellen Nordman, Siqin Bao, Caroline Lee, Xiaohui Wang, Brian B. Tuch, Edith Heard, Kaiqin Lao, M. Azim Surani	PLoS ONE	Deterministic and Stochastic Allele Specific Gene Expression in Single Mouse Blastomeres	20110623	-	24	Mouse	Embryo	Tang	GSE22182		RNA-seq	Blastomeres				7	No			Yes
17	Ramsköld et al NBT	10.1038/nbt.2282	Daniel Ramsköld, Shujun Luo, Yu-Chieh Wang, Robin Li, Qiaolin Deng, Omid R Faridani, Gregory A Daniels, Irina Khrebtukova, Jeanne F Loring, Louise C Laurent, Gary P Schroth, Rickard Sandberg	Nat Biotechnol	Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells	20120722	-	12	Human, Mouse	Embryo, Culture, Tumor	SMART-seq	GSE38495		RNA-seq	Oocyte, hESC, CTC, Melanocyte											Sorting (FACS)		3
18	Brouilette et al DevDyn	10.1002/dvdy.23850	Scott Brouilette, Scott Kuersten, Charles Mein, Monika Bozek, Anna Terry, Kerith-Rae Dias, Leena Bhaw-Rosun, Yasunori Shintani, Steven Coppen, Chiho Ikebe, Vinit Sawhney, Niall Campbell, Masahiro Kaneko, Nobuko Tano, Hidekazu Ishida, Ken Suzuki, Kenta Yashiro	Dev. Dyn.	A simple and novel method for RNA-seq library preparation of single cell cDNA analysis by hyperactive Tn5 transposase	20120821	-	6	Mouse	Culture	Brouilette	GSE38198		RNA-seq	mESCs
19	Hashimshony et al CR	10.1016/j.celrep.2012.08.003	Tamar Hashimshony, Florian Wagner, Noa Sher, Itai Yanai	Cell Reports	CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification	20120830	-	96	C elegans	Embryo	CEL-seq	SRP014672		RNA-seq	Blastomeres				3	No	No		No	No		Pipetting (Manual picking)
20	Buganim et al Cell	10.1016/j.cell.2012.08.023	Yosef Buganim, Dina A. Faddah, Albert W. Cheng, Elena Itskovich, Styliani Markoulaki, Kibibi Ganz, Sandy L. Klemm, Alexander van Oudenaarden, Rudolf Jaenisch	Cell	Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase	20120913	-	1,864	Mouse	Culture	BioMark		48	qPCR	MEF to iPSC reprogramming
21	Moignard et al NCB	10.1038/ncb2709	Victoria Moignard, Iain C. Macaulay, Gemma Swiers, Florian Buettner, Judith Schütte, Fernando J. Calero-Nieto, Sarah Kinston, Anagha Joshi, Rebecca Hannah, Fabian J. Theis, Sten Eirik Jacobsen, Marella F. de Bruijn, Berthold Göttgens	Nat Cell Biol	Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis	20130322	-	597	Mouse	Bone marrow	BioMark		18	qPCR				9-12-week-old	5		No	No	Yes	No		IFC Capture
22	Sasagawa et al GB	10.1186/gb-2013-14-4-r31	Yohei Sasagawa, Itoshi Nikaido, Tetsutaro Hayashi, Hiroki Danno, Kenichiro D Uno, Takeshi Imai, Hiroki R Ueda	Genome Biol	Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity	20130417	-	77	Mouse	Culture	Quartz-seq	GSE42268		RNA-seq	mESCs, PrE				2	Yes	No	No	Yes	No		Sorting (FACS)
23	Shalek et al Nature	10.1038/nature12172	Alex K. Shalek, Rahul Satija, Xian Adiconis, Rona S. Gertner, Jellert T. Gaublomme, Raktima Raychowdhury, Schraga Schwartz, Nir Yosef, Christine Malboeuf, Diana Lu, John J. Trombetta, Dave Gennert, Andreas Gnirke, Alon Goren, Nir Hacohen, Joshua Z. Levin, Hongkun Park, Aviv Regev	Nature	Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells	20130517	-	18	Mouse	Culture	SMARTer	GSE41265		RNA-seq	BMDCs				2	Yes	No	No	Yes	No		Sorting (FACS)
24	Magnusdottir et al NCB	10.1038/ncb2798	Erna Magnúsdóttir, Sabine Dietmann, Kazuhiro Murakami, Ufuk Günesdogan, Fuchou Tang, Siqin Bao, Evangelia Diamanti, Kaiqin Lao, Berthold Gottgens, M. Azim Surani	Nat Cell Biol	A tripartite transcription factor network regulates primordial germ cell specification in mice	20130714	-	10	Mouse	Embryo	Tang	E-MTAB-1178		RNA-seq	Embryos
25	Xue et al Nature	10.1038/nature12364	Zhigang Xue, Kevin Huang, Chaochao Cai, Lingbo Cai, Chun-yan Jiang, Yun Feng, Zhenshan Liu, Qiao Zeng, Liming Cheng, Yi E. Sun, Jia-yin Liu, Steve Horvath, Guoping Fan	Nature	Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing	20130726	-	47	Human, Mouse	Embryo	Tang	GSE44183		RNA-seq	Embryos				14									18
26	Yan et al NSMB	10.1038/nsmb.2660	Liying Yan, Mingyu Yang, Hongshan Guo, Lu Yang, Jun Wu, Rong Li, Ping Liu, Ying Lian, Xiaoying Zheng, Jie Yan, Jin Huang, Ming Li, Xinglong Wu, Lu Wen, Kaiqin Lao, Ruiqiang Li, Jie Qiao, Fuchou Tang	Nat Struct Mol Biol	Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells	20130809	-	124	Human	Culture	Tang	GSE36552		RNA-seq	hESCs				7	Yes	No		Yes	No
27	Brennecke et al NMeth	10.1038/nmeth.2645	Philip Brennecke, Simon Anders, Jong Kyoung Kim, Aleksandra A Kołodziejczyk, Xiuwei Zhang, Valentina Proserpio, Bianka Baying, Vladimir Benes, Sarah A Teichmann, John C Marioni, Marcus G Heisler	Nat Methods	Accounting for technical noise in single-cell RNA-seq experiments	20130922	-	100	Arabidopsis, Mouse	Root, Spleen	SMARTer (C1)	E-MTAB-1499		RNA-seq	QC and GL2 cells				3	No	No		Yes	No		IFC Capture
28	Picelli et al NMeth	10.1038/nmeth.2639	Simone Picelli, Åsa K Björklund, Omid R Faridani, Sven Sagasser, Gösta Winberg, Rickard Sandberg	Nat Methods	Smart-seq2 for sensitive full-length transcriptome profiling in single cells	20130922	-	68	Human, Mouse	Culture	Smart-seq2	GSE49321		RNA-seq	HEK, MEF											Sorting (FACS)
29	Wu et al NMeth	10.1038/nmeth.2694	Angela R Wu, Norma F Neff, Tomer Kalisky, Piero Dalerba, Barbara Treutlein, Michael E Rothenberg, Francis M Mburu, Gary L Mantalas, Sopheak Sim, Michael F Clarke, Stephen R Quake	Nat Methods	Quantitative assessment of single-cell RNA-sequencing methods	20131020	-	100	Human	Culture	SMARTer (C1)	GSE51254		RNA-seq	HCT116											IFC Capture
30	Grindberg et al PNAS	10.1073/pnas.1319700110	R. V. Grindberg, J. L. Yee-Greenbaum, M. J. McConnell, M. Novotny, A. L. O'Shaughnessy, G. M. Lambert, M. J. Arauzo-Bravo, J. Lee, M. Fishman, G. E. Robbins, X. Lin, P. Venepally, J. H. Badger, D. W. Galbraith, F. H. Gage, R. S. Lasken	Proceedings of the National Academy of Sciences	RNA-sequencing from single nuclei	20131119	-	18	Mouse	Culture	Tang (nuclei)	SRP020097		RNA-seq	NPCs											Sorting (FACS)
31	Marinov et al GR	10.1101/gr.161034.113	G. K. Marinov, B. A. Williams, K. McCue, G. P. Schroth, J. Gertz, R. M. Myers, B. J. Wold	Genome Research	From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing	20131204	-	15	Human	Culture	SMARTer	GSE44618		RNA-seq	GM12878 cell line											Pipetting (Manual picking)
32	Islam et al NMeth	10.1038/nmeth.2772	Saiful Islam, Amit Zeisel, Simon Joost, Gioele La Manno, Pawel Zajac, Maria Kasper, Peter Lönnerberg, Sten Linnarsson	Nat Methods	Quantitative single-cell RNA-seq with unique molecular identifiers	20131222	-	192	Mouse	Culture	STRT-seq (C1)	GSE46980		RNA-seq	mESCs				1	No	No		No	No		IFC Capture
33	Deng et al Science	10.1126/science.1245316	Q. Deng, D. Ramskold, B. Reinius, R. Sandberg	Science	Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells	20140109	-	269	Mouse	Embryo	Smart-seq2	GSE45719		RNA-seq	preimplantation embryos				11	No	No	No	Yes	No
34	Jaitin et al Science	10.1126/science.1247651	D. A. Jaitin, E. Kenigsberg, H. Keren-Shaul, N. Elefant, F. Paul, I. Zaretsky, A. Mildner, N. Cohen, S. Jung, A. Tanay, I. Amit	Science	Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types	20140214	-	4,468	Mouse	Spleen	MARS-seq	GSE54006		RNA-seq	CD11c+ enriched splenocytes				9	Yes	No		No	No		Sorting (FACS)
35	Soumillon et al bioRxiv	10.1101/003236	Magali Soumillon, Davide Cacchiarelli, Stefan Semrau, Alexander van Oudenaarden, Tarjei S Mikkelsen	bioRxiv	Characterization of directed differentiation by high-throughput single-cell RNA-Seq	20140310	10.1101/003236	12,832	Human	Culture	SCRB-seq	GSE53638		RNA-seq	adipose derived stem/stromal cells
36	Trapnell et al NBT	10.1038/nbt.2859	Cole Trapnell, Davide Cacchiarelli, Jonna Grimsby, Prapti Pokharel, Shuqiang Li, Michael Morse, Niall J Lennon, Kenneth J Livak, Tarjei S Mikkelsen, John L Rinn	Nat Biotechnol	The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells	20140323	-	270	Human	Muscle	SMARTer (C1)	GSE52529		RNA-seq	Human Skeletal Muscle Myoblasts				3	Yes	Yes	No				IFC Capture		1
37	Treutlein et al Nature	10.1038/nature13173	Barbara Treutlein, Doug G. Brownfield, Angela R. Wu, Norma F. Neff, Gary L. Mantalas, F. Hernan Espinoza, Tushar J. Desai, Mark A. Krasnow, Stephen R. Quake	Nature	Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq	20140411	-	400	Mouse	Lung	SMARTer (C1)	GSE52583		RNA-seq	Lung epithelial cells				6	Yes	No		Yes	No		IFC Capture
38	Durruthy-Durruthy et al Cell	10.1016/j.cell.2014.03.036	Robert Durruthy-Durruthy, Assaf Gottlieb, Byron H. Hartman, Jörg Waldhaus, Roman D. Laske, Russ Altman, Stefan Heller	Cell	Reconstruction of the Mouse Otocyst and Early Neuroblast Lineage at Single-Cell Resolution	20140424		382	Mouse	Ear	BioMark		96	qPCR	Otocyst and early neuroblast			E10.5
39	Streets et al PNAS	10.1073/pnas.1402030111	A. M. Streets, X. Zhang, C. Cao, Y. Pang, X. Wu, L. Xiong, L. Yang, Y. Fu, L. Zhao, F. Tang, Y. Huang	Proceedings of the National Academy of Sciences	Microfluidic single-cell whole-transcriptome sequencing	20140430	-	102	Mouse	Culture	Tang	GSE47835		RNA-seq	mESCs, MEFs
40	Mahata et al CReports	10.1016/j.celrep.2014.04.011	Bidesh Mahata, Xiuwei Zhang, Aleksandra A. Kolodziejczyk, Valentina Proserpio, Liora Haim-Vilmovsky, Angela E. Taylor, Daniel Hebenstreit, Felix A. Dingler, Victoria Moignard, Berthold Göttgens, Wiebke Arlt, Andrew N.J. McKenzie, Sarah A. Teichmann	Cell Reports	Single-Cell RNA Sequencing Reveals T Helper Cells Synthesizing Steroids De Novo to Contribute to Immune Homeostasis	20140510	-	91	Mouse	Spleen	SMARTer (C1)	E-MTAB-2512		RNA-seq	Th2 cells					No	No	No	No	No		IFC Capture
41	Shalek et al Nature	10.1038/nature13437	Alex K. Shalek, Rahul Satija, Joe Shuga, John J. Trombetta, Dave Gennert, Diana Lu, Peilin Chen, Rona S. Gertner, Jellert T. Gaublomme, Nir Yosef, Schraga Schwartz, Brian Fowler, Suzanne Weaver, Jing Wang, Xiaohui Wang, Ruihua Ding, Raktima Raychowdhury, Nir Friedman, Nir Hacohen, Hongkun Park, Andrew P. May, Aviv Regev	Nature	Single-cell RNA-seq reveals dynamic paracrine control of cellular variation	20140611	-	1,775	Mouse	Culture	SMARTer (C1)	GSE48968		RNA-seq	Bone marror derived dendritic cells				1	No	No		No	No		IFC Capture
42	Patel et al Science	10.1126/science.1254257	A. P. Patel, I. Tirosh, J. J. Trombetta, A. K. Shalek, S. M. Gillespie, H. Wakimoto, D. P. Cahill, B. V. Nahed, W. T. Curry, R. L. Martuza, D. N. Louis, O. Rozenblatt-Rosen, M. L. Suva, A. Regev, B. E. Bernstein	Science	Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma	20140613	-	672	Human	Brain	SMARTer	GSE57872		RNA-seq	Glioblastoma				7	Yes	No		No	No		Sorting (FACS)		5
43	Brunskill et al Development	10.1242/dev.110601	E. W. Brunskill, J.-S. Park, E. Chung, F. Chen, B. Magella, S. S. Potter	Development	Single cell dissection of early kidney development: multilineage priming	20140722		235	Mouse	Kidney	SMARTer (C1)			RNA-seq				E11.5, E12.5, P4
44	Pollen et al NBT	10.1038/nbt.2967	Alex A Pollen, Tomasz J Nowakowski, Joe Shuga, Xiaohui Wang, Anne A Leyrat, Jan H Lui, Nianzhen Li, Lukasz Szpankowski, Brian Fowler, Peilin Chen, Naveen Ramalingam, Gang Sun, Myo Thu, Michael Norris, Ronald Lebofsky, Dominique Toppani, Darnell W Kemp, Michael Wong, Barry Clerkson, Brittnee N Jones, Shiquan Wu, Lawrence Knutsson, Beatriz Alvarado, Jing Wang, Lesley S Weaver, Andrew P May, Robert C Jones, Marc A Unger, Arnold R Kriegstein, Jay A A West	Nat Biotechnol	Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex	20140803		301	Human	Brain	SMARTer (C1)	SRP041736		RNA-seq	Neocortex, primary cortex			GW16, GW21										11
45	Sansom et al GResearch	10.1101/gr.171645.113	Stephen N. Sansom, Noriko Shikama-Dorn, Saule Zhanybekova, Gretel Nusspaumer, Iain C. Macaulay, Mary E. Deadman, Andreas Heger, Chris P. Ponting, Georg A. Holländer	Genome Res.	Population and single-cell genomics reveal theAiredependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia	20140916	-	174	Mouse	Thymus	SMARTer (C1)	GSE60297		RNA-seq	mTECs											IFC Capture
46	Ting et al CReports	10.1016/j.celrep.2014.08.029	David T. Ting, Ben S. Wittner, Matteo Ligorio, Nicole Vincent Jordan, Ajay M. Shah, David T. Miyamoto, Nicola Aceto, Francesca Bersani, Brian W. Brannigan, Kristina Xega, Jordan C. Ciciliano, Huili Zhu, Olivia C. MacKenzie, Julie Trautwein, Kshitij S. Arora, Mohammad Shahid, Haley L. Ellis, Na Qu, Nabeel Bardeesy, Miguel N. Rivera, Vikram Deshpande, Cristina R. Ferrone, Ravi Kapur, Sridhar Ramaswamy, Toshi Shioda, Mehmet Toner, Shyamala Maheswaran, Daniel A. Haber	Cell Reports	Single-Cell RNA Sequencing Identifies Extracellular Matrix Gene Expression by Pancreatic Circulating Tumor Cells	20140918	-	153	Mouse	Tumor, Culture, Blood	Tang	GSE51372		RNA-seq	CTCs, pancreatic tumor, MEF, white blood cells				7	Yes	No	No	Yes	No		IFC Capture
47	Usoskin et al NNeuroscience	10.1038/nn.3881	Dmitry Usoskin, Alessandro Furlan, Saiful Islam, Hind Abdo, Peter Lönnerberg, Daohua Lou, Jens Hjerling-Leffler, Jesper Haeggström, Olga Kharchenko, Peter V Kharchenko, Sten Linnarsson, Patrik Ernfors	Nat Neurosci	Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing	20141124	-	799	Mouse	Brain	STRT-seq	GSE59739		RNA-seq	Dorsal root ganglia			6-8 week old	5	Yes			Yes	No
48	Romanov et al EMBOJounral	10.15252/embj.201488977	R. A. Romanov, A. Alpar, M.-D. Zhang, A. Zeisel, A. Calas, M. Landry, M. Fuszard, S. L. Shirran, R. Schnell, A. Dobolyi, M. Olah, L. Spence, J. Mulder, H. Martens, M. Palkovits, M. Uhlen, H. H. Sitte, C. H. Botting, L. Wagner, S. Linnarsson, T. Hokfelt, T. Harkany	The EMBO Journal	A secretagogin locus of the mammalian hypothalamus controls stress hormone release	20141128	-	151	Mouse	Brain	STRT-seq (C1)	GSE63093		RNA-seq	hypothalamic paraventricular nucleus				7	Yes	No		No	No		IFC Capture
49	Kumar et al Nature	10.1038/nature13920	Roshan M. Kumar, Patrick Cahan, Alex K. Shalek, Rahul Satija, A. Jay DaleyKeyser, Hu Li, Jin Zhang, Keith Pardee, David Gennert, John J. Trombetta, Thomas C. Ferrante, Aviv Regev, George Q. Daley, James J. Collins	Nature	Deconstructing transcriptional heterogeneity in pluripotent stem cells	20141202	-	415	Mouse	Culture	SMARTer (C1)	GSE60749		RNA-seq	mESCs				18	No	No		Yes	No		IFC Capture
50	Rossier et al MPsychiatry	10.1038/mp.2014.162	J Rossier, A Bernard, J-H Cabungcal, Q Perrenoud, A Savoye, T Gallopin, M Hawrylycz, M Cuénod, K Do, A Urban, Ed S Lein	Mol Psychiatry	Cortical fast-spiking parvalbumin interneurons enwrapped in the perineuronal net express the metallopeptidases Adamts8, Adamts15 and Neprilysin	20141216		218	Mouse	Brain	sc-RT-mPCR		50	qPCR	Cerebral cortex			21-27 days	6	Yes	No	No	Yes	No		Patch-clamp
51	Kim et al CSC	10.1016/j.stem.2014.11.005	Daniel H. Kim, Georgi K. Marinov, Shirley Pepke, Zakary S. Singer, Peng He, Brian Williams, Gary P. Schroth, Michael B. Elowitz, Barbara J. Wold	Cell Stem Cell	Single-Cell Transcriptome Analysis Reveals Dynamic Changes in lncRNA Expression during Reprogramming	20150108	-	95	Mouse	Culture	SMARTer	GSE55291		RNA-seq	iPSCs
52	Buettner et al NBT	10.1038/nbt.3102	Florian Buettner, Kedar N Natarajan, F Paolo Casale, Valentina Proserpio, Antonio Scialdone, Fabian J Theis, Sarah A Teichmann, John C Marioni, Oliver Stegle	Nat Biotechnol	Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells	20150119	-	288	Mouse	Culture	SMARTer (C1)	E-MTAB-2805		RNA-seq	mESCs		Cell cycle stages									IFC Capture
53	Dey et al NBT	10.1038/nbt.3129	Siddharth S Dey, Lennart Kester, Bastiaan Spanjaard, Magda Bienko, Alexander van Oudenaarden	Nat Biotechnol	Integrated genome and transcriptome sequencing of the same cell	20150119	-	34	Mouse, Human	Culture	DR-Seq	GSE62952		RNA-seq	E14 and SK-BR-3 cells			E14	2	No	No	No	No	No
54	Efroni et al GBiology	10.1186/s13059-015-0580-x	Idan Efroni, Pui-Leng Ip, Tal Nawy, Alison Mello, Kenneth D Birnbaum	Genome Biol	Quantification of cell identity from single-cell gene expression profiles	20150121	-	71	Arabidopsis thaliana	Root	CEL-seq	GSE46226		RNA-seq	Root				3
55	Fan et al Science	10.1126/science.1258367	H. Christina Fan, Glenn K. Fu, Stephen P. A. Fodor	Science	Combinatorial labeling of single cells for gene expression cytometry	20150205	-	15,000	Human	Blood, Culture	CytoSeq		111	RNA-seq	PBMCs, K563, Ramos				9	Yes	No		Yes	No		Picowell deposition		2
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57	Zeisel et al Science	10.1126/science.aaa1934	A. Zeisel, A. B. Munoz-Manchado, S. Codeluppi, P. Lonnerberg, G. La Manno, A. Jureus, S. Marques, H. Munguba, L. He, C. Betsholtz, C. Rolny, G. Castelo-Branco, J. Hjerling-Leffler, S. Linnarsson	Science	Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq	20150221	-	3,005	Mouse	Brain	STRT-seq (C1)	GSE60361		RNA-seq	Somatosensory cortex, hippocampus CA1			Adult	47	Yes	No		Yes	Yes		IFC Capture
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64	Klein et al Cell	10.1016/j.cell.2015.04.044	Allon M. Klein, Linas Mazutis, Ilke Akartuna, Naren Tallapragada, Adrian Veres, Victor Li, Leonid Peshkin, David A. Weitz, Marc W. Kirschner	Cell	Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells	20150521	-	9,000	Human, Mouse	Culture	InDrops	GSE65525		RNA-seq	mESCs, K562 cells											Nanodroplet dilution
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100	Paul et al Cell	10.1016/j.cell.2015.11.013	Franziska Paul, Ya’ara Arkin, Amir Giladi, Diego Adhemar Jaitin, Ephraim Kenigsberg, Hadas Keren-Shaul, Deborah Winter, David Lara-Astiaso, Meital Gury, Assaf Weiner, Eyal David, Nadav Cohen, Felicia Kathrine Bratt Lauridsen, Simon Haas, Andreas Schlitzer, Alexander Mildner, Florent Ginhoux, Steffen Jung, Andreas Trumpp, Bo Torben Porse, Amos Tanay, Ido Amit	Cell	Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors	20151125	-	10,260	Mouse	Bone marrow	MARS-seq	GSE72857		RNA-seq	Bone marrow				19	Yes	No	No	No	No		Sorting (FACS)