Non Immune Related Datasets
Dataset ID Dataset Description Paper Title Citation Organism Conditions (#) Cell (#)
GSE109774 Transcriptomic characterization of 20 organs and tissues Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris Schaum ... Wyss-Coray,Nature 2018 Mus musculus 18 99840
E-MTAB-3929 Embryonic cells taken from days 3 - 7 Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Homo sapiens Preimplantation Embryos Petropoulos ... Lanner,Cell 2016 Homo sapiens 7 1529
GSE75688 Breast cancer cells Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer Chung ... Park,Nature Communications 2017 Homo sapiens 13 549
GSE75659 Mouse fibroblasts. Human T-cells from this experiment can be found in the immune part. Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA-seq Reinius ... Sandberg,Nature Genetics 2016 Mus musculus 6 421
GSE67310 Direct reprogramming from Mouse embryonic fibroblasts (MEFs) to induced neuronal (iN) cells. Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq Treutlein ... Quake,Nature 2016 Mus musculus 7 405
GSE57872 Glioblastoma (GBM) Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma Patel ... Bernstein,Science 2014 Homo sapiens 7 430
GSE51372 Mice pancreatic cancer cells and human CTCs Single-cell RNA sequencing identifies extracellular matrix gene expression by pancreatic circulating tumor cells Ting ... Haber,Cell Reports 2014 Mus musculus 6 153
GSE67980 Single cell RNA-sequencing profiles of 77 intact CTCs isolated from 13 patients RNA-Seq of single prostate CTCs implicates noncanonical Wnt signaling in antiandrogen resistance Miyamoto ... Haber,Science 2015 Homo sapiens 5 157
E-MTAB-2600 Mouse embryonic stem cells cultured in serum/leukaemia inhibitory factor (LIF) or 2i/LIF Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression Kim ... Marioni,Nature Communications 2016 Mus musculus   869
E-MTAB-2805 Mouse embryonic stem cells in G1, S and G2M stages of cell cycle Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells Buettner ... Stegle,Nature Biotechnology 2015 Mus musculus   288
E-MTAB-2865 Cells from dissociated P. dumerilii larval brains High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin Achim ... Marioni,Nature Biotechnology 2015 Platynereis dumerilii   213
E-MTAB-3321 Blastomeres of embryos at the 2, 4 d 8-cell stages, and for individual cells taken from 16 and 32 cell stage embryos Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in Four-Cell Mus musculus Embryos Goolam ... Zernicka-Goetz,Cell 2016 Mus musculus   124
E-MTAB-3707 Liver of a 14-week old B6CastF1 (C57Bl/6J mother x CAST/Ei father) female Mouse Computational assignment of cell-cycle stage from single-cell transcriptome data Scialdone ... Buettner,Methods 2015 Mus musculus   96
ERP016000 Single Cell RNAseq at various stages of HiPSCs differentiating toward definitive endoderm and endoderm derived lineages   Homo sapiens   4799
GSE29087 embryonic stem cells and embryonic fibroblasts (MEFs) Characterization of the single-cell (ES and MEF) transcriptional landscape by highly multiplex RNA-Seq Islam ... Linnarsson,Genome Research 2011 Mus musculus   96
GSE36552 Human embryonic stem cells Single-cell RNA-Seq profiling of Homo sapiens preimplantation embryos and embryonic stem cells Yan ... Tang,Nat Struct Mol Biol 2013 Homo sapiens   124
GSE38495 Human putative circulating tumor cells (CTCs), Mouse oocytes and human lymphocytes Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells Ramskold ... Sandberg,Nature Biotechnology 2012 Homo sapiens; Mus musculus   121
GSE45719 Cells from F1 embryos (CAST/EiJ ?€” C57BL/6J and liver cells Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells Deng ... Sandberg,Science 2014 Mus musculus   317
GSE46980 Mouse embryonic stem cells Quantitative single-cell RNA-seq with unique molecular identifiers Islam ... Linnarsson,Nature Methods 2014 Mus musculus   192
GSE47835 Mouse embryonic stem cells Microfluidic single-cell whole-transcriptome sequencing Streets ... Huang,PNAS 2014 Mus musculus   102
GSE51254 HCT116 (human colon cancer cells) Quantitative assessment of single-cell RNA-sequencing methods Wu ... Quake,Nature Methods 2014 Homo sapiens   113
GSE52529 human skeletal muscle myoblasts The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells Trapnell ... Rinn,Nature Biotechnology 2014 Homo sapiens   384
GSE52583 Mouse lung epithelial cells Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq Treutlein ... Quake,Nature 2014 Mus musculus   198
GSE53386 3 Single Mouse ES cells, 7 single HEK293T cells, 8 diluted Mouse ES total RNA samples and 19 Mouse embryo samples Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in Mus musculus preimplantation embryos Fan ... Huang,Genome Biology 2015 Homo sapiens; Mus musculus   118
GSE55291 iPS cells Single-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming Kim ... Wold,Cell Stem Cell 2015 Mus musculus   95  
GSE56638 Embryonic day 18 (E18) hippocampal and cortical neurons from Mouse and Rattus norvegicus Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation Dueck ... Kim,Genome Biology 2015 Rattus norvegicus; Mus musculus   143
GSE59739 Dorsal root ganglion cells Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing Usoskin ... Emfors,Nature Neuroscience 2015 Mus musculus   622
GSE60361 Mice S1 cortex and CA1 hippocampus cells Brain structure. Cell types in the Mus musculus cortex and hippocampus revealed by single-cell RNA-seq Zeisel ... Linnarsson,Science 2015 Mus musculus   3005
GSE60749 Mouse embryonic stem cells (mESCs) and induced pluripotent stem cells (iPSCs) Deconstructing transcriptional heterogeneity in pluripotent stem cells Kumar ... Collins,Nature 2014 Mus musculus   441
GSE60768 Mouse embryonic stem cells Single-cell polyadenylation site mapping reveals 3' isoform choice variability Velten ... Steinmetz,Molecular Systems Biology 2015 Mus musculus   195
GSE63266 Mouse embryonic stem cells SC3-seq: a method for highly parallel and quantitative measurement of single-cell gene expression Nakamura ... Saitou,Nucleic Acids Research 2014 Homo sapiens; Mus musculus   98
GSE63576 Dorsal root ganglion cells Somatosensory Neuron Types Identified by High-Coverage Single-Cell RNA-Sequencing and Functional Heterogeneity Li ... Zhang,Cell Research 2016 Mus musculus   197
GSE63818 Human primordial germ cells taken from 4-19 week old fetuses The Transcriptome and DNA Methylome Landscapes of Homo sapiens Primordial Germ Cells Guo ... Qiao,Cell 2015 Homo sapiens   364
GSE64016 Undifferentiated H1 human embryonic stem cells (hESCs) Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments Leng ... Kendziorski,Nature Methods 2015 Homo sapiens   460
GSE64960 Juvenile and adult granulosa cells Sexual cell-fate reprogramming in the ovary by DMRT1 Linderman ... Zarkower,Current Biology 2015 Mus musculus   68
GSE65364 Human hepatocellular carcinoma cells, Mouse embryonic stem cells Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas Hou ... Peng,Cell Research 2016 Homo sapiens; Mus musculus   95
GSE65924 Mice epiblast cells Spatial Transcriptome for the Molecular Annotation of Lineage Fates and Cell Identity in Mid-gastrula Mus musculus Embryo Peng ... Jing,Developmental Cell 2016 Mus musculus   70
GSE66053 Primary human foreskin fibroblast cells and A549 cells (human lung carcinoma, A549, ATCC CCL-185) Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms Padovan-Merhar ... Raj,Molecular Cell 2015 Homo sapiens   98
GSE66202 Nephron progenitor cells Intrinsic Age-Dependent Changes and Cell-Cell Contacts Regulate Nephron Progenitor Lifespan Chen ... Kopan,Developmental Cell 2015 Mus musculus   91
GSE66357 Single cell analysis of different cell lines Scalable Microfluidics for Single Cell RNA Printing and Sequencing Bose ... Sims,Genome Biology 2015 Homo sapiens   643
GSE66688 Danio rerio embryonic cells Spatial reconstruction of single-cell gene expression data Satija ... Regev,Nature Biotechnology 2015 Danio rerio   1152
GSE67833 Neural stem cells Single-Cell Transcriptomics Reveals a Population of Dormant Neural Stem Cells that Become Activated upon Brain Injury Llorens-Bobadilla ... Martin-Villalba,Cell Stem Cell 2015 Mus musculus   272
GSE67835 Neuronal, glial, and vascular brain cells A survey of Homo sapiens brain transcriptome diversity at the single cell level Darmanis ... Quake,PNAS 2015 Homo sapiens   466
GSE68596 Chronic myelogenous leukemia cells (KBM-7 line) Genome-wide maps of nuclear lamina interactions in single Homo sapiens cells Kind ... Steensel,Cell 2015 Homo sapiens   96
GSE68625 Pancreatic -cells Inhibition of DYRK1A and GSK3B induces Homo sapiens -cell proliferation Shen ... Laffitte,Nature Communications 2015 Rattus norvegicus   170
GSE69405 Lung adenocarcinoma tumor cells Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells Kim ... Park,Genome Biology 2015 Homo sapiens   208
GSE69761 Fetal mice E16.5 lung cells 'LungGENS': a web-based tool for mapping single-cell gene expression in the developing lung Du ... Xu,Thorax 2015 Mus musculus   148
GSE70605 Nuclear transfer embryonic stem cells Identification of key factors conquering developmental arrest of somatic cell cloned embryos by combining embryo biopsy and single-cell sequencing Liu ... Gao,Cell Discovery 2016 Mus musculus   145
GSE71315 Neocortex cells Single cell analysis of long non-coding RNAs in the developing Homo sapiens neocortex Liu ... Lim,Genome Biology 2016 Homo sapiens   242
GSE71485 Neural Precursor Cells Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis Shin ... Song,Cell Stem Cell 2015 Mus musculus   173
GSE71585 Primary visual cortex cells Adult Mus musculus cortical cell taxonomy revealed by single cell transcriptomics Tasic ... Zeng,Nature Neuroscience 2016 Mus musculus   1809
GSE71982 Utricular and cochlear sensory epithelia cells Single-cell RNA-Seq resolves cellular complexity in sensory organs from the neonatal inner ear Burns ... Kelley,Nature Communications 2015 Mus musculus   301
GSE73121 Metastatic renal cell carcinoma Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma Kim ... Park,Genome Biology 2016 Homo sapiens   121
GSE74360 Muscle cells Two FGFRL-Wnt circuits organize the planarian anteroposterior axis Scimone ... Reddien,eLife 2016 Schmidtea mediterranea   115
GSE74488 Stele tissue cells (after separation from the root) Root Regeneration Triggers an Embryo-like Sequence Guided by Hormonal Interactions Efroni ... Birnbaum,Cell 2017 Arabidopsis thaliana   215
GSE74533 Fused Mouse-Rattus norvegicus allodiploid embryonic stem cells Generation and Application of Mus musculus-Rattus norvegicus Allodiploid Embryonic Stem Cells Li ... Zhou,Cell 2016 Rattus norvegicus; Mus musculus   95
GSE74534 E14 ES cells Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity Angermueller ... Reik,Nature Methods 2016 Mus musculus   96
GSE75140 human fetal brain tissue and cerebral organoid cells Homo sapiens cerebral organoids recapitulate gene expression programs of fetal neocortex development Camp ... Treutlein,PNAS 2015 Homo sapiens   734
GSE75413 Epithelial neurons Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis Hanchate ... Buck,Science 2015 Mus musculus   93
GSE75804 Embryonic stem cells Serum-Based Culture Conditions Provoke Gene Expression Variability in Mus musculus Embryonic Stem Cells as Revealed by Single-Cell Analysis Guo ... Orkin,Cell Reports 2016 Mus musculus   96
GSE76157 Growth plate cells Systematic Reconstruction of Molecular Cascades Regulating GP Development Using Single-Cell RNA-Seq Li ... Wu,Cell Reports 2016 Mus musculus   217
GSE76284 Pronuclear transfer zygotes Towards clinical application of pronuclear transfer to prevent mitochondrial DNA disease Hyslop ... Herbert,Nature 2016 Homo sapiens   94
GSE76483 Dorsal root ganglion cells Simultaneous profiling of transcriptome and DNA methylome from a single cell Hu ... Fan,Genome Biology 2016 Mus musculus   192
GSE77067 Dentate granule cells Nuclear RNA-seq of single neurons reveals molecular signatures of activation Lacar ... Gage,Nature Communications 2016 Mus musculus   201
GSE77308 Breast cancer cells Loss of CSL Unlocks a Hypoxic Response and Enhanced Tumor Growth Potential in Breast Cancer Cells Braune ... Lendahl,Stem Cell Reports 2016 Homo sapiens   404
GSE77847 Bone marrow, splenocytes, spleen, liver and sternum blood cells DNMT3A Haploinsufficiency Transforms FLT3ITD Myeloproliferative Disease into a Rapid, Spontaneous, and Fully Penetrant Acute Myeloid Leukemia Meyer ... Grimes,Cancer Discovery 2016 Mus musculus   96
GSE77980 C57BL/6 pancreatic islet cells Use of the Fluidigm C1 platform for RNA sequencing of single Mus musculus pancreatic islet cells Xin ... Gromada,PNAS 2016 Mus musculus   622
GSE78779 Mouse dendritic and fibroblast cells CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq Hashimshony ... Yanai,Genome Biology 2016 Caenorhabditis elegans; Mus musculus   228
GSE79866 Stem and progeny cells taken from the head In silico lineage tracing through single cell transcriptomics identifies a neural stem cell population in planarians Molinaro ... Pearson,Genome Biology 2016 Schmidtea mediterranea   168
GSE79920 KD3 myoblasts, myotubes and mononucleated cells Single-nucleus RNA-seq of differentiating Homo sapiens myoblasts reveals the extent of fate heterogeneity Zeng ... Mortazavi,Nucleic Acids Research 2016 Homo sapiens   254
GSE83146 Pancreatic islet beta cells Single-Cell RNAseq Reveals That Pancreatic -Cells From Very Old Male Mice Have a Young Gene Signature Xin ... Gromada,Endocrinology 2016 Mus musculus   207
GSE83533 Acute Myeloid Leukemia cells Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia Li ... Mason,Nature Medicine 2016 Homo sapiens   138
PRJNA236018 Fetal cortical tissue Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex Pollem ... West,Nature Biotechnology 2014 Homo sapiens   347
GSE78845 Sympathetic neuronal cells from the Mouse thoracic ganglion Visceral motor neuron diversity delineates a cellular basis for nipple- and pilo-erection muscle control Furian ... Emfors,Nature Neuroscience 2016 Mus musculus   298
GSE75330 Various central nervous system cells (spinal cord, substantia nigra-ventral tegmental area, striatum, amygdala, hypothalamic nuclei, zona incerta, hippocampus, somatosensory cortex) Oligodendrocyte heterogeneity in the Mus musculus juvenile and adult central nervous system Marques ... Castelo-Branco,Science 2016 Mus musculus   5069
GSE70844 Cortical neurons Integration of electrophysiological recordings with single-cell RNA-seq data identifies neuronal subtypes Fuzik ... Harkany,Nature Biotechnology 2016 Mus musculus   83
GSE63093 Parvocellular neurons A secretagogin locus of the mammalian hypothalamus controls stress hormone release Romanov ... Harkany,The EMBO journal 2015 Mus musculus   151
GSE84371 Adult mice new spinal chord neurons (close to neurogenesis) Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons Habib ... Regev,Science 2016 Mus musculus   924
GSE65525 Embryonic stem cells Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells Klein ... Kirschner,Cell 2015 Homo sapiens; Mus musculus   8
ERP010108 Sequencing of single cell genomes and transcriptomes from Mus musculus 8 cell stage embryos Power analysis of single-cell RNA-sequencing experiments Svensson ... Teichmann,Nature Methods 2017 Mus musculus   224
EGAD00001001332 human breast cancer cells, lymphoblastoid cells. Mice ESCs G&T-seq: parallel sequencing of single-cell genomes and transcriptomes Macaulay ... Voet,Nature Methods 2015 Homo sapiens; Mus musculus   700
E-MTAB-3707 Liver of a 14-week old B6CastF1 (C57Bl/6J mother x CAST/Ei father) female Mouse Computational assignment of cell-cycle stage from single-cell transcriptome data Scialdone ... Buettner,Methods 2015 Mus musculus   96
GSE54695 J1 Mouse embryonic stem cells Validation of noise models for single-cell transcriptomics Grun ... Van Oudenaarden,Nature Methods 2014 Mus musculus   320
GSE62270 Intestinal gland cells Single-cell messenger RNA sequencing reveals rare intestinal cell types Gr?¼n ... Van Oudenaarden,Nature 2015 Mus musculus   96
GSE63473 Retinal cells Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets Macosko ... McCarroll,Cell 2015 Homo sapiens; Mus musculus   203
GSE63525 Lymphoblastoid cells Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes Sanborn ... Aiden,PNAS 2015 Homo sapiens; Mus musculus   200
SRP073767 Peripheral blood mononuclear cells, bone marrow mononuclear cells Massively parallel digital transcriptional profiling of single cells Zeng ... Bielas,Nature Communications 2017 Homo sapiens; Mus musculus   31
GSE82187 Striatal cells Cellular Taxonomy of the Mus musculus Striatum as Revealed by Single-Cell RNA-Seq Gocke ... Quake,Cell Reports 2016 Mus musculus   1208
GSE70630 Oligodendroglioma tumor cells Single-cell RNA-seq supports a developmental hierarchy in Homo sapiens oligodendroglioma Tirosh ... Suv,Nature 2016 Homo sapiens   4825
GSE75748 Embronic stem and progenitor cells Single-cell RNA-seq reveals novel regulators of Homo sapiens embryonic stem cell differentiation to definitive endoderm Chu ... Thomson,Genome Biology 2016 Homo sapiens   1810
GSE85183 Pancreatic cancer cells Selective single cell isolation for genomics using microraft arrays Welch ... Jones,Nucleic Acids Research 2016 Homo sapiens   120
GSE71453 Dorsal root ganglion cells Single-cell RNA-seq reveals distinct injury responses in different types of DRG sensory neurons Hu ... Fan,Scientific Reports 2016 Mus musculus   123
GSE81475 Neural epithelial stem cells Zika Virus Disrupts Phospho-TBK1 Localization and Mitosis in Homo sapiens Neuroepithelial Stem Cells and Radial Glia Onorati ... Sestan,Cell Reports 2016 Homo sapiens   1608
SRP078083 Squamous cell carcinoma cells from urinary bladder Single-cell analyses of transcriptional heterogeneity in squamous cell carcinoma of urinary bladder Zhang ... Wu,Oncotarget 2016 Homo sapiens   1000
GSE85241 Langerhans pancreatic cells A Single-Cell Transcriptomic Map of the Homo sapiens and Mus musculus Pancreas Reveals Inter- and Intra-cell Population Structure Muraro ... Van Oudenaarden,Cell Systems 2016 Homo sapiens   0
GSE85783 Pluripotent stem cells Laminin-guided highly efficient endothelial commitment from Homo sapiens pluripotent stem cells Ohta ... Saito,Scientific Reports 2016 Homo sapiens   92
GSE88850 Universal human reference RNA and Universal brain reference Assessing characteristics of RNA amplification methods for single cell RNA sequencing Dueck ... Kim,BMC genomics 2016 Homo sapiens   138
GSE81383 Melanomas Mapping heterogeneity in patient-derived melanoma cultures by single-cell RNA-seq Gerber ... Kunz,Oncotarget 2017 Homo sapiens   307
GSE90063 BMDC, BMDC stimulated at 3hr; K562 at 7 and 13 days post trasnduction, and 13 days at a higher MOI of perturbations Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens Dixit ... Regev,Cell 2016 Homo sapiens; Mus musculus   200000
GSE85066 Embryonic stem cells and mesoderm progenitors An atlas of transcriptional, chromatin accessibility, and surface marker changes in Homo sapiens mesoderm development Koh ... Loh,Scientific Data 2016 Homo sapiens   0
GSE81608 human non-diabetic and type 2 diabetic pancreatic islet cells RNA Sequencing of Single Homo sapiens Islet Cells Reveals Type 2 Diabetes Genes Xin ... Gromada,Cell Metabolism 2016 Homo sapiens   1600
GSE81905 Single cell RNA-sequencing of retinal bipolar cells (GSE80232, GSE819903) Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics Shekhar ... Sanes,Cell 2016 Mus musculus   291
GSE74767 Cynomolgus monkey: embryo E6-17; Mouse: embryo E4.5 - E6.5; Both: ESCs A developmental coordinate of the spectrum of pluripotency among mice, monkeys, and Homo sapienss Nakamura ... Saitou,Nature 2016 Macaca fascicularis; Mus musculus   492
GSE75386 CA1 cholecystokinin, parvalbumin, pyramidal and subiculum neurons Single cell RNAseq of electrophysiologically characterized neurons of the hippocampus Foldy ... Sudhof,PNAS 2016 Mus musculus   108
GSE77944 C. elegans 1 to 16 cell stage embryo cells A Transcriptional Lineage of the Early C. elegans Embryo Tinton ... Goldstein,Developmental Cell 2016 Caenorhabditis elegans   219
GSE74155 Embryonic stem cells Single-cell analyses of X Chromosome inactivation dynamics and pluripotency during differentiation Chen ... Deng,Genome Research 2016 Mus musculus   617
GSE79818 Microglia Microglia development follows a stepwise program to regulate brain homeostasis Matcovitch-Natan ... Amit,Science 2016 Mus musculus   0
GSE77288 Induced pluripotent stem cell Batch effects and the effective design of single-cell gene expression studies Tung ... Gilad,Scientific Reports 2017 Homo sapiens   873
GSE83139 Pancreatic endocrine cells Single-Cell Transcriptomics of the Homo sapiens Endocrine Pancreas Wang ... Kaestner,Diabetes 2016 Homo sapiens   635
E-MTAB-4026 Postimplantation embryo cells Resolving early mesoderm diversification through single-cell expression profiling Scialdone ... Gottgens,Nature 2016 Mus musculus   768
E-MTAB-4079 Embryonic blood cells Resolving early mesoderm diversification through single-cell expression profiling Scialdone ... Gottgens,Nature 2016 Mus musculus   1205
E-MTAB-5061 Transcriptional profiles of endocrine and exocrine cell types of the human pancre Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes Segerstolpe ... Smith,Cell Metab 2016 Homo sapiens   3514
GSE74672 Neurons from gap between paraventricular and arcuate hypothalamic nuclei as well as the Ventromedial and dorsomedial hypothalamic nuclei Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes Romanov ... Harkany,Nature Neuroscience 2017 Mus musculus   1983
GSE76184 Single cell transcriptome dynamics and subpopulation heterogeneity in radiation treated recurrent glioma     Homo sapiens   288
GSE76381 Embryo ventral midbrain in human and mouse. stem cell-derived dopaminergic neurons Molecular Diversity of Midbrain Development in Mus musculus, Homo sapiens, and Stem Cells La Manno ... Linnarsson,Cell 2016 Homo sapiens; Mus musculus   6179
GSE78045 Airway epithelial progenitor cells p53 Regulates Progenitor Cell Quiescence and Differentiation in the Airway McConnell ... Stripp,Cell Reports 2016 Mus musculus   150
GSE78968 Human embryonic kidney cells Effective detection of variation in single-cell transcriptomes using MATQ-seq Sheng ... Zong,Nature Methods 2017 Homo sapiens   91
GSE79136 single cell RNA sequencing of human nasal epithelial cells grown (GSE89236, GSE89237) A cost effective 5' selective single cell transcriptome profiling approach with improved UMI design Arguel ... Waldmann,Nucleic Acids Research 2017 Homo sapiens   192
GSE80032 Pancreas Acinar cells Single-Cell Analysis Uncovers Clonal Acinar Cell Heterogeneity in the Adult Pancreas Wollny ... Martin-Villalba,Developmental Cell 2016 Mus musculus   108
GSE80810 Pre-implantation embryo cells (research targets sex chromosomes) Xist-dependent imprinted X inactivation and the early developmental consequences of its failure Borensztein ... Heard,Nat Struct Mol Biol 2017 Mus musculus   182
GSE81275 ESCs during programming into motor neurons A Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem Cells Velasco ... Mazzoni,Cell Stem Cell 2017 Mus musculus   768
GSE81287 Human ESCs and HEK293FT cells Single-cell sequencing of the small-RNA transcriptome Faridani ... Sandberg,Nature Biotechnology 2016 Homo sapiens   539
GSE81673 EZH2-deficient ESC Deletion of the Polycomb-Group Protein EZH2 Leads to Compromised Self-Renewal and Differentiation Defects in Homo sapiens Embryonic Stem Cells Collinson ... Rugg-Gunn0,Cell Reports 2016 Homo sapiens   221
GSE82174 Testicular cells The Homeobox Transcription Factor RHOX10 Drives Mus musculus Spermatogonial Stem Cell Establishment Song ... Wilkinson,Cell Reports 2016 Mus musculus   193
GSE83948 Neural progenitor cells Neurogenic Radial Glia-like Cells in Meninges Migrate and Differentiate into Functionally Integrated Neurons in the Neonatal Cortex Bifari ... Carmeliet,Cell Stem Cell 2017 Mus musculus   179
GSE86207 Cerebral organoid cells Differences and similarities between Homo sapiens and chimpanzee neural progenitors during cerebral cortex development. Mora-Berm?·dez ... Huttner,eLife 2016 Pan troglodytes; Homo sapiens   396
GSE86469 Pancreatic islet/other single cells Single cell transcriptomes identify Homo sapiens islet cell signatures and reveal cell-type-specific expression changes in type 2 diabetes Lawlor ... Stitzel,Genome Research 2017 Homo sapiens   638
GSE86618 Epithelial lung cells (IPF and control) Single-cell RNA sequencing identifies diverse roles of epithelial cells in idiopathic pulmonary fibrosis Xu ... Whitsett,JCI insight 2016 Homo sapiens   540
GSE86894 Single-cell RNA-seq from human embryonic stem cells (GSE86977, GSE86982) A Single-Cell Roadmap of Lineage Bifurcation in Human ESC Models of Embryonic Brain Development. Yao ... Ramanathan,Cell Stem Cell 2016 Homo sapiens   4530
GSE87069 Developing ventral midbrain cells Single-Cell Analysis Reveals a Close Relationship between Differentiating Dopamine and Subthalamic Nucleus Neuronal Lineages Kee ... Perlmann,Cell Stem Cell 2017 Mus musculus   574
GSE87237 Human ESCs Homo sapiens Naive Pluripotent Stem Cells Model X Chromosome Dampening and X Inactivation Sahakyan ... Plath,Cell Stem Cell 2017 Homo sapiens   288
GSE76118 Embryonic cardiac cells Transcriptomic Profiling Maps Anatomically Patterned Subpopulations among Single Embryonic Cardiac Cells Li ... Wu,Developmental Cell 2016 Mus musculus   3241
ERP015781 Trophoblast stem cells     Mus musculus   96
SRP072988 Acinar cells Single-Cell Analysis Uncovers Clonal Acinar Cell Heterogeneity in the Adult Pancreas Wollny ... Martin-Villalba,Developmental Cell 2016 Mus musculus   108
SRP093546 Etv2-EYFP transgenic embryo cells Dpath software reveals hierarchical haemato-endothelial lineages of Etv2 progenitors based on single-cell transcriptome analysis Gong ... Garry,Nature Communications 2017 Mus musculus   562
GSE67602 Dorsal telogen skin cells Single-Cell Transcriptomics Reveals that Differentiation and Spatial Signatures Shape Epidermal and Hair Follicle Heterogeneity Joost ... Kasper,Cell Systems 2016 Mus musculus   1422
ERP016754 Single cell RNA-seq and bisulfite-seq at various states of HiPSCs differentiating toward definitive endoderm derived lineages     Homo sapiens   384
GSE90848 Mouse bulge hair follicle stem cell, hair germ, basal transient amplifying cells (TACs) and dermal papilla at the indicated hair cycle were FACS-purified for single cell RNA-seq. Epithelial-Mesenchymal Micro-niches Govern Stem Cell Lineage Choices Yang ... Fuchs,Cell 2017 Mus musculus   1119
GSE95601 The lineage of the horizontal basal cells (HBC) stem cells and other Sox2eGFP-positive cells from the olfactory epithelium were profiled by single-cell RNA-Seq to identify differentiated cells types, intermediate stages, transition states, and to infer the lineage trajectories Deconstructing Olfactory Stem Cell Trajectories at Single-Cell Resolution Fletcher ... Ngai,Cell Stem Cell 2017 Mus musculus   849
GSE85917 Single cell RNA-seq data of human hESCs to evaluate SCnorm: robust normalization of single-cell rna-seq data SCnorm: robust normalization of single-cell RNA-seq data Bacher ... Kendziorski, Nat Methods 2017 Homo sapiens   183
GSE89567 Single cell RNA-seq analysis of IDH-mutant astrocytoma Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq Venteicher ... Suva, Science 2017 Homo sapiens   6341
GSE70713 Examination of 108 EPI cells, 8 VE cells and 8 EXE cells from 3 pregastrulation embryos (E5.5 and early-stage E6.5), and 112 cells from 3 early gastrulation embryos (late-stage E6.5). Single-cell analysis reveals lineage segregation in early post-implantation mouse embryos. Wen ... Jin,J Biol Chem 2017 Mus musculus   236
GSE81861 Two single cell dataset are included: (1) 1,591 single cells from 11 colorectal cancer patients. (2) 630 single cells from 7 cell lines. Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors. Li ... Prabhakar,Nat Genet 2017 Homo sapiens   1220
GSE79137 single cell RNA-seq on mouse embryonic kidneys. Repression of Interstitial Identity in Nephron Progenitor Cells by Pax2 Establishes the Nephron-Interstitium Boundary during Kidney Development. Naiman ... Kobayashi,Dev Cell 2017 Mus musculus   237
GSE94641 Single-cell RNA-Seq from medial ganglionic eminence at E11.5, E13.5, E15.5 or E17.5. Single-cell RNA sequencing identifies distinct mouse medial ganglionic eminence cell types. Chen ... Modrusan,Sci Rep. 2017 Mus musculus   225
GSE79457 Single-cell RNA-seq of in-vivo conversion of pancreatic -cells into -cells Enge ... Chakravarthy, 2017 Mus musculus   182
GSE79102 Examination of three different patients with myeloproloferative disease SC3: consensus clustering of single-cell RNA-seq data Kiselev ... Hemberg,Nat Methods 2017 Homo sapiens   192
GSE94883 In vitro differentiation of mESCs into motor neurons Rizvi ... Rabadan, 2017 Mus musculus   2744
GSE81252 Single-cell transcriptomes from multiple time points during hepatocyte-like lineage progression Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development. Mora-Bermdez ... Huttner,Elife 2016 Homo sapiens   770
GSE92872 Human HEK293T and mouse 3T3 cells Pooled CRISPR screening with single-cell transcriptome readout. Datlinger ... Bock,Nat Methods 2017 Homo sapiens; Mus musculus   100
GSE93421 Single-cell RNA-seq of 1.3 million brain cells from E18 mice Massively parallel digital transcriptional profiling of single cells. Zheng ... Bielas,Nat Commun 2017 Mus musculus   1E+06
GSE94579 J14 ES cells differentiated into MGE-like cells Friedman ... Modrusan, 2017 Mus musculus   140
GSE95837 Single cell gene expression in Dlxi1/2b::eGFP+ cells before and after migration, 4 weeks Islam ... Wei, 2017 Homo sapiens   181
GSE96066 Probing Plasmodium falciparum sexual differentiation at the single cell level Brancucci ... Marti, 2017 Plasmodium falciparum NF54   1155
GSE97564 Single cell RNAseq of hPSC derived V2a interneuron cultures McDevit ... Butts, 2017 Homo sapiens   4492
GSE93593 Single cell RNAseq characterization of cell types produced over time in an in vitro model of human inhibitory interneuron differentiation. Single-Cell Profiling of an In Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation Close ... Lein,Neuron 2017 Homo sapiens   1733
GSE87544 single-cell RNA-seq of mouse hypothalamus Single-Cell RNA-Seq Reveals Hypothalamic Cell Diversity. Chen ... Zhang,Cell Rep 2017 Mus musculus   10000
GSE81884 (GSE81747, GSE81748, GSE81749, GSE81750, GSE81848, GSE96827) RNA sequencing in bulk and in single K562 cells Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells. Xie ... Hon,Mol Cell 2017 Homo sapiens; Mus musculus   96
E-MTAB-5485 scRNA-seq on a homogenous population of mouse embryonic stem cells Power analysis of single-cell RNA-sequencing experiments Svensson ... Teichmann,NATURE METHODS 2017 Mus musculus   96
E-MTAB-5484 scRNA-seq on a homogenous population of mouse embryonic stem cells Power analysis of single-cell RNA-sequencing experiments Svensson ... Teichmann,NATURE METHODS 2017 Mus musculus   61
E-MTAB-5483 scRNA-seq on a homogenous population of mouse embryonic stem cells Power analysis of single-cell RNA-sequencing experiments Svensson ... Teichmann,NATURE METHODS 2017 Mus musculus   96
E-MTAB-5481 scRNA-seq on a homogenous population of mouse embryonic stem cells Power analysis of single-cell RNA-sequencing experiments Svensson ... Teichmann,NATURE METHODS 2017 Mus musculus   56
E-MTAB-5208 single celltranscriptomics to define the molecular signature of in vivo and in vitro NMPs Briscoe ... Gouti, 2017 Mus musculus   539
PRJNA360884 Time course profiling of scRNA-seq of non-directed differentiation of human NPC generated from hESC ... , 2017 Homo sapiens   958
PRJEB4461 Single cell transcriptomics in olfactory sensory neurons Variation in olfactory neuron repertoires is genetically controlled and environmentally modulated Ibarra-Soria ... Logan,Elife 2017 Mus musculus   528
PRJNA324289 Single cell RNA-Sequencing of adult NSCs and related populations from the sub-ventricular zone Single-Cell Transcriptomic Analysis Defines Heterogeneity and Transcriptional Dynamics in the Adult Neural Stem Cell Lineage. Dulken ... Brunet,Cell Rep. 2017 Mus musculus   452
PRJNA350294 Etv2 single cell transcriptome Dpath software reveals hierarchical haemato-endothelial lineages of Etv2 progenitors based on single-cell transcriptome analysis. ... Gong,Garry 2017 Mus musculus   562
SRP052546 full transcriptome data on single cells and nuclei from three areas (visual, temporal, prefrontal) of the human cortex ... , 2017 Homo sapiens   3916
SRP052738 variability in the expressed transcriptome of human excitable cells. ... , 2017 Homo sapiens   990
SRP051388 The technical and biological noise in measured RNA levels in single cells in a number of human tissue types ... , 2017 Homo sapiens   2328
SRP098798 Single-cell profiling of an in vitro model of human interneuron development ... , 2017 Homo sapiens   104
SRP104455 the transcriptomes of thousands of individual cells from the tissue explants and organoids ... , 2017 Mus musculus   1000
GSE95025 Single cell transcriptomics of the early Drosophila embryo The Drosophila embryo at single-cell transcriptome resolution Karaiskos ... Zinzen,Science 2017 Drosophila   96
DRA001287 Lung epithelial tumor cells Single-cell analysis of lung adenocarcinoma cell lines reveals diverse expression patterns of individual cells invoked by a molecular target drug treatment Suzuki ... Suzuki,Genome Biology 2015 Homo sapiens   336
DRA002399 Cervical cancer cells Single-cell transcriptomes of fluorescent, ubiquitination-based cell cycle indicator cells Bttcher ... Plessy, Homo sapiens   96
DRA002730 Lung epithelial tumor cells Single-cell analysis of lung adenocarcinoma cell lines reveals diverse expression patterns of individual cells invoked by a molecular target drug treatment Suzuki ... Suzuki,Genome Biology 2015 Homo sapiens   336
E-MTAB-2600 Embryonic stem cells Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation Kolodziejczyk ... Teichmann,Cell Stem Cell 2015 Mus musculus   96
E-MTAB-5060 Pancreatic islet cells (healthy and type 2 diabetes) Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes Segerstolpe ... Sandberg,Cell Metabolism 2016 Homo sapiens   2209
E-MTAB-5061 Pancreatic islet cells (healthy and type 2 diabetes) Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes Segerstolpe ... Sandberg,Cell Metabolism 2016 Homo sapiens   2209
PRJEB8994 Oocyte, zygote and blastomere cells Novel PRD-like homeodomain transcription factors and retrotransposon elements in early human development Thnen ... Kere,Nature Communications 2015 Homo sapiens   348
ERP021229 Variability across individual Plasmodium parasites Single-cell transcriptomics of malaria parasites Reid ... Lawniczak,bioRxiv 2017 Plasmodium berghei   521