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A repository of standardized single cell RNA-Seq datasets for analysis and visualization at the single cell level


Non-immune Datasets (182 Entries)

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BAMBAI
E-MTAB-3929Embryonic cells taken from days 3 - 7Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Homo sapiens Preimplantation EmbryosPetropoulos ... Lanner,Cell 2016Homo sapiens (hg38)71529466.9Download BAM
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1. day38121.4Download BAMDownload BAI
2. day414242.9Download BAMDownload BAI
3. day4late4813.8Download BAMDownload BAI
4. day5353112.7Download BAMDownload BAI
5. day5early246.7Download BAMDownload BAI
6. day6415108.8Download BAMDownload BAI
7. day7466160.6Download BAMDownload BAI
GSE75688Breast cancer cellsSingle-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancerChung ... Park,Nature Communications 2017Homo sapiens (hg38)13549372Download BAM
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1. BC012616.8Download BAMDownload BAI
2. BC025631.4Download BAMDownload BAI
3. BC03LN3743.1Download BAMDownload BAI
4. BC035530.6Download BAMDownload BAI
5. BC045939.2Download BAMDownload BAI
6. BC057739.1Download BAMDownload BAI
7. BC062516.3Download BAMDownload BAI
8. BC07LN5142.1Download BAMDownload BAI
9. BC075345.7Download BAMDownload BAI
10. BC082311.1Download BAMDownload BAI
11. BC096039.9Download BAMDownload BAI
12. BC101610.8Download BAMDownload BAI
13. BC11116.3Download BAMDownload BAI
GSE75659Mouse 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-seqReinius ... Sandberg,Nature Genetics 2016Mus musculus (mm10)6421180Download BAM
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1. brain_E1542.6Download BAMDownload BAI
2. fibroblast_adult_female17777.4Download BAMDownload BAI
3. fibroblast_adult_male8332.1Download BAMDownload BAI
4. fibroblast_E15_male3813.4Download BAMDownload BAI
5. fibroblast_female8838.7Download BAMDownload BAI
6. liver_E153115Download BAMDownload BAI
GSE67310Direct reprogramming from Mouse embryonic fibroblasts (MEFs) to induced neuronal (iN) cells.Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seqTreutlein ... Quake,Nature 2016Mus musculus (mm10)7405150.8Download BAM
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1. day_07334.1Download BAMDownload BAI
2. day_28131.9Download BAMDownload BAI
3. day_2_uniform4712.9Download BAMDownload BAI
4. day_203310.7Download BAMDownload BAI
5. day_22_Ascl1_Brn2_Myt1l4318.2Download BAMDownload BAI
6. day_22_viral7323.6Download BAMDownload BAI
7. day_55519.4Download BAMDownload BAI
GSE67980Single cell RNA-sequencing profiles of 77 intact CTCs isolated from 13 patientsRNA-Seq of single prostate CTCs implicates noncanonical Wnt signaling in antiandrogen resistanceMiyamoto ... Haber,Science 2015Homo sapiens (hg19)515774.8Download BAM
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1. WBC20.7Download BAMDownload BAI
2. WBC_healthy31.9Download BAMDownload BAI
3. candidate_PCa_CTC4520Download BAMDownload BAI
4. Pca_cell_line3015.3Download BAMDownload BAI
5. confirmed_Pca_CTC7736.8Download BAMDownload BAI
E-MTAB-2600Mouse embryonic stem cells cultured in serum/leukaemia inhibitory factor (LIF) or 2i/LIFCharacterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expressionKim ... Marioni,Nature Communications 2016Mus musculusOn Demand8690Download BAM
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E-MTAB-2805Mouse embryonic stem cells in G1, S and G2M stages of cell cycleComputational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cellsBuettner ... Stegle,Nature Biotechnology 2015Mus musculusOn Demand2880Download BAM
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E-MTAB-2865Cells from dissociated P. dumerilii larval brainsHigh-throughput spatial mapping of single-cell RNA-seq data to tissue of originAchim ... Marioni,Nature Biotechnology 2015Platynereis dumeriliiOn Demand2130Download BAM
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E-MTAB-3321Blastomeres of embryos at the 2, 4 d 8-cell stages, and for individual cells taken from 16 and 32 cell stage embryosHeterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in Four-Cell Mus musculus EmbryosGoolam ... Zernicka-Goetz,Cell 2016Mus musculusOn Demand1240Download BAM
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E-MTAB-3707Liver of a 14-week old B6CastF1 (C57Bl/6J mother x CAST/Ei father) female MouseComputational assignment of cell-cycle stage from single-cell transcriptome dataScialdone ... Buettner,Methods 2015Mus musculusOn Demand960Download BAM
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ERP016000Single Cell RNAseq at various stages of HiPSCs differentiating toward definitive endoderm and endoderm derived lineages ... , 2016Homo sapiensOn Demand47990Download BAM
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GSE29087embryonic stem cells and embryonic fibroblasts (MEFs)Characterization of the single-cell (ES and MEF) transcriptional landscape by highly multiplex RNA-SeqIslam ... Linnarsson,Genome Research 2011Mus musculusOn Demand960Download BAM
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GSE36552Human embryonic stem cellsSingle-cell RNA-Seq profiling of Homo sapiens preimplantation embryos and embryonic stem cellsYan ... Tang,Nat Struct Mol Biol 2013Homo sapiensOn Demand1240Download BAM
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GSE38495Human putative circulating tumor cells (CTCs), Mouse oocytes and human lymphocytesFull-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cellsRamskold ... Sandberg,Nature Biotechnology 2012Homo sapiens; Mus musculusOn Demand1210Download BAM
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GSE45719Cells from F1 embryos (CAST/EiJ ?€” C57BL/6J and liver cellsSingle-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cellsDeng ... Sandberg,Science 2014Mus musculusOn Demand3170Download BAM
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GSE46980Mouse embryonic stem cellsQuantitative single-cell RNA-seq with unique molecular identifiersIslam ... Linnarsson,Nature Methods 2014Mus musculusOn Demand1920Download BAM
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GSE47835Mouse embryonic stem cellsMicrofluidic single-cell whole-transcriptome sequencingStreets ... Huang,PNAS 2014Mus musculusOn Demand1020Download BAM
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GSE51254HCT116 (human colon cancer cells)Quantitative assessment of single-cell RNA-sequencing methodsWu ... Quake,Nature Methods 2014Homo sapiensOn Demand1130Download BAM
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GSE51372Mice pancreatic cancer cells and human CTCsSingle-cell RNA sequencing identifies extracellular matrix gene expression by pancreatic circulating tumor cellsTing ... Haber,Cell Reports 2014Homo sapiens; Mus musculusOn Demand1870Download BAM
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GSE52529human skeletal muscle myoblastsThe dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cellsTrapnell ... Rinn,Nature Biotechnology 2014Homo sapiensOn Demand3840Download BAM
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GSE52583Mouse lung epithelial cellsReconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seqTreutlein ... Quake,Nature 2014Mus musculusOn Demand1980Download BAM
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GSE533863 Single Mouse ES cells, 7 single HEK293T cells, 8 diluted Mouse ES total RNA samples and 19 Mouse embryo samplesSingle-cell RNA-seq transcriptome analysis of linear and circular RNAs in Mus musculus preimplantation embryosFan ... Huang,Genome Biology 2015Homo sapiens; Mus musculusOn Demand1180Download BAM
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GSE55291iPS cellsSingle-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogrammingKim ... Wold,Cell Stem Cell 2015Mus musculusOn Demand950Download BAM
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GSE56638Embryonic day 18 (E18) hippocampal and cortical neurons from Mouse and Rattus norvegicusDeep sequencing reveals cell-type-specific patterns of single-cell transcriptome variationDueck ... Kim,Genome Biology 2015Rattus norvegicus; Mus musculusOn Demand1430Download BAM
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GSE57872Glioblastoma (GBM)Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastomaPatel ... Bernstein,Science 2014Homo sapiensOn Demand4300Download BAM
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GSE59739Dorsal root ganglion cellsUnbiased classification of sensory neuron types by large-scale single-cell RNA sequencingUsoskin ... Emfors,Nature Neuroscience 2015Mus musculusOn Demand6220Download BAM
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GSE60361Mice S1 cortex and CA1 hippocampus cellsBrain structure. Cell types in the Mus musculus cortex and hippocampus revealed by single-cell RNA-seqZeisel ... Linnarsson,Science 2015Mus musculusOn Demand30050Download BAM
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GSE60749Mouse embryonic stem cells (mESCs) and induced pluripotent stem cells (iPSCs)Deconstructing transcriptional heterogeneity in pluripotent stem cellsKumar ... Collins,Nature 2014Mus musculusOn Demand4410Download BAM
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GSE60768Mouse embryonic stem cellsSingle-cell polyadenylation site mapping reveals 3' isoform choice variabilityVelten ... Steinmetz,Molecular Systems Biology 2015Mus musculusOn Demand1950Download BAM
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GSE63266Mouse embryonic stem cellsSC3-seq: a method for highly parallel and quantitative measurement of single-cell gene expressionNakamura ... Saitou,Nucleic Acids Research 2014Homo sapiens; Mus musculusOn Demand980Download BAM
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GSE63576Dorsal root ganglion cellsSomatosensory Neuron Types Identified by High-Coverage Single-Cell RNA-Sequencing and Functional HeterogeneityLi ... Zhang,Cell Research 2016Mus musculusOn Demand1970Download BAM
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GSE63818Human primordial germ cells taken from 4-19 week old fetusesThe? Transcriptome? and DNA Methylome Landscapes of Homo sapiens Primordial Germ CellsGuo ... Qiao,Cell 2015Homo sapiensOn Demand3640Download BAM
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GSE64016Undifferentiated H1 human embryonic stem cells (hESCs)Oscope identifies oscillatory genes in unsynchronized? single-cell? RNA-seq? experimentsLeng ... Kendziorski,Nature Methods 2015Homo sapiensOn Demand4600Download BAM
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GSE64960Juvenile and adult granulosa cellsSexual cell-fate reprogramming in the ovary by DMRT1Linderman ... Zarkower,Current Biology 2015Mus musculusOn Demand680Download BAM
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GSE65364Human hepatocellular carcinoma cells, Mouse embryonic stem cellsSingle-cell? triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomasHou ... Peng,Cell Research 2016Homo sapiens; Mus musculusOn Demand950Download BAM
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GSE65924Mice epiblast cellsSpatial Transcriptome for the Molecular Annotation of Lineage Fates and Cell Identity in Mid-gastrula Mus musculus EmbryoPeng ... Jing,Developmental Cell 2016Mus musculusOn Demand700Download BAM
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GSE66053Primary 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 mechanismsPadovan-Merhar ... Raj,Molecular Cell 2015Homo sapiensOn Demand980Download BAM
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GSE66202Nephron progenitor cellsIntrinsic Age-Dependent Changes and Cell-Cell Contacts Regulate Nephron Progenitor LifespanChen ... Kopan,Developmental Cell 2015Mus musculusOn Demand910Download BAM
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GSE66357Single cell analysis of different cell linesScalable Microfluidics for Single Cell RNA Printing and SequencingBose ... Sims,Genome Biology 2015Homo sapiensOn Demand6430Download BAM
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GSE66688Danio rerio embryonic cellsSpatial reconstruction of single-cell gene expression dataSatija ... Regev,Nature Biotechnology 2015Danio rerioOn Demand11520Download BAM
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GSE67833Neural stem cellsSingle-Cell Transcriptomics Reveals a Population of Dormant Neural Stem Cells that Become Activated upon Brain InjuryLlorens-Bobadilla ... Martin-Villalba,Cell Stem Cell 2015Mus musculusOn Demand2720Download BAM
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GSE67835Neuronal, glial, and vascular brain cellsA survey of Homo sapiens brain transcriptome diversity at the single cell levelDarmanis ... Quake,PNAS 2015Homo sapiensOn Demand4660Download BAM
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GSE68596Chronic myelogenous leukemia cells (KBM-7 line)Genome-wide maps of nuclear lamina interactions in single Homo sapiens cellsKind ... Steensel,Cell 2015Homo sapiensOn Demand960Download BAM
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GSE68625Pancreatic -cellsInhibition of DYRK1A and GSK3B induces Homo sapiens -cell proliferationShen ... Laffitte,Nature Communications 2015Rattus norvegicusOn Demand1700Download BAM
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GSE69405Lung adenocarcinoma tumor cellsSingle-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cellsKim ... Park,Genome Biology 2015Homo sapiensOn Demand2080Download BAM
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GSE69761Fetal mice E16.5 lung cells'LungGENS': a web-based tool for mapping single-cell gene expression in the developing lungDu ... Xu,Thorax 2015Mus musculusOn Demand1480Download BAM
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GSE70605Nuclear transfer embryonic stem cellsIdentification of key factors conquering developmental arrest of somatic cell cloned embryos by combining embryo biopsy and single-cell sequencingLiu ... Gao,Cell Discovery 2016Mus musculusOn Demand1450Download BAM
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GSE71315Neocortex cellsSingle cell analysis of long non-coding RNAs in the developing Homo sapiens neocortexLiu ... Lim,Genome Biology 2016Homo sapiensOn Demand2420Download BAM
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GSE71485Neural Precursor CellsSingle-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult NeurogenesisShin ... Song,Cell Stem Cell 2015Mus musculusOn Demand1730Download BAM
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GSE71585Primary visual cortex cellsAdult Mus musculus cortical cell taxonomy revealed by single cell transcriptomicsTasic ... Zeng,Nature Neuroscience 2016Mus musculusOn Demand18090Download BAM
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GSE71982Utricular and cochlear sensory epithelia cellsSingle-cell RNA-Seq resolves cellular complexity in sensory organs from the neonatal inner earBurns ... Kelley,Nature Communications 2015Mus musculusOn Demand3010Download BAM
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GSE72056Malignant, immune and stromal cells from melanoma tumorsDissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seqTirosh ... Garraway,Science 2016Homo sapiensOn Demand46450Download BAM
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GSE73121Metastatic renal cell carcinomaApplication of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinomaKim ... Park,Genome Biology 2016Homo sapiensOn Demand1210Download BAM
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GSE74360Muscle cellsTwo FGFRL-Wnt circuits organize the planarian anteroposterior axisScimone ... Reddien,eLife 2016Schmidtea mediterraneaOn Demand1150Download BAM
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GSE74488Stele tissue cells (after separation from the root)Root Regeneration Triggers an Embryo-like Sequence Guided by Hormonal InteractionsEfroni ... Birnbaum,Cell 2017Arabidopsis thalianaOn Demand2150Download BAM
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GSE74533Fused Mouse-Rattus norvegicus allodiploid embryonic stem cellsGeneration and Application of Mus musculus-Rattus norvegicus Allodiploid Embryonic Stem CellsLi ... Zhou,Cell 2016Rattus norvegicus; Mus musculusOn Demand950Download BAM
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GSE74534E14 ES cellsParallel single-cell sequencing links transcriptional and epigenetic heterogeneityAngermueller ... Reik,Nature Methods 2016Mus musculusOn Demand960Download BAM
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GSE75140human fetal brain tissue and cerebral organoid cellsHomo sapiens cerebral organoids recapitulate gene expression programs of fetal neocortex developmentCamp ... Treutlein,PNAS 2015Homo sapiensOn Demand7340Download BAM
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GSE75413Epithelial neuronsSingle-cell transcriptomics reveals receptor transformations during olfactory neurogenesisHanchate ... Buck,Science 2015Mus musculusOn Demand930Download BAM
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GSE75804Embryonic stem cellsSerum-Based Culture Conditions Provoke Gene Expression Variability in Mus musculus Embryonic Stem Cells as Revealed by Single-Cell AnalysisGuo ... Orkin,Cell Reports 2016Mus musculusOn Demand960Download BAM
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GSE76157Growth plate cellsSystematic Reconstruction of Molecular Cascades Regulating GP Development Using Single-Cell RNA-SeqLi ... Wu,Cell Reports 2016Mus musculusOn Demand2170Download BAM
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GSE76284Pronuclear transfer zygotesTowards clinical application of pronuclear transfer to prevent mitochondrial DNA diseaseHyslop ... Herbert,Nature 2016Homo sapiensOn Demand940Download BAM
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GSE76483Dorsal root ganglion cellsSimultaneous profiling of transcriptome and DNA methylome from a single cellHu ... Fan,Genome Biology 2016Mus musculusOn Demand1920Download BAM
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GSE77067Dentate granule cellsNuclear RNA-seq of single neurons reveals molecular signatures of activationLacar ... Gage,Nature Communications 2016Mus musculusOn Demand2010Download BAM
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GSE77308Breast cancer cellsLoss of CSL Unlocks a Hypoxic Response and Enhanced Tumor Growth Potential in Breast Cancer CellsBraune ... Lendahl,Stem Cell Reports 2016Homo sapiensOn Demand4040Download BAM
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GSE77847Bone marrow, splenocytes, spleen, liver and sternum blood cellsDNMT3A Haploinsufficiency Transforms FLT3ITD Myeloproliferative Disease into a Rapid, Spontaneous, and Fully Penetrant Acute Myeloid LeukemiaMeyer ... Grimes,Cancer Discovery 2016Mus musculusOn Demand960Download BAM
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GSE77980C57BL/6 pancreatic islet cellsUse of the Fluidigm C1 platform for RNA sequencing of single Mus musculus pancreatic islet cellsXin ... Gromada,PNAS 2016Mus musculusOn Demand6220Download BAM
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GSE78779Mouse dendritic and fibroblast cellsCEL-Seq2: sensitive highly-multiplexed single-cell RNA-SeqHashimshony ... Yanai,Genome Biology 2016Caenorhabditis elegans; Mus musculusOn Demand2280Download BAM
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GSE79866Stem and progeny cells taken from the headIn silico lineage tracing through single cell transcriptomics identifies a neural stem cell population in planariansMolinaro ... Pearson,Genome Biology 2016Schmidtea mediterraneaOn Demand1680Download BAM
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GSE79920KD3 myoblasts, myotubes and mononucleated cellsSingle-nucleus RNA-seq of differentiating Homo sapiens myoblasts reveals the extent of fate heterogeneityZeng ... Mortazavi,Nucleic Acids Research 2016Homo sapiensOn Demand2540Download BAM
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GSE83146Pancreatic islet beta cellsSingle-Cell RNAseq Reveals That Pancreatic -Cells From Very Old Male Mice Have a Young Gene SignatureXin ... Gromada,Endocrinology 2016Mus musculusOn Demand2070Download BAM
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GSE83533Acute Myeloid Leukemia cellsDistinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemiaLi ... Mason,Nature Medicine 2016Homo sapiensOn Demand1380Download BAM
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PRJNA236018Fetal cortical tissueLow-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortexPollem ... West,Nature Biotechnology 2014Homo sapiensOn Demand3470Download BAM
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GSE78845Sympathetic neuronal cells from the Mouse thoracic ganglionVisceral motor neuron diversity delineates a cellular basis for nipple- and pilo-erection muscle controlFurian ... Emfors,Nature Neuroscience 2016Mus musculusOn Demand2980Download BAM
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GSE75330Various 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 systemMarques ... Castelo-Branco,Science 2016Mus musculusOn Demand50690Download BAM
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GSE70844Cortical neuronsIntegration of electrophysiological recordings with single-cell RNA-seq data identifies neuronal subtypesFuzik ... Harkany,Nature Biotechnology 2016Mus musculusOn Demand830Download BAM
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GSE63093Parvocellular neuronsA secretagogin locus of the mammalian hypothalamus controls stress hormone releaseRomanov ... Harkany,The EMBO journal 2015Mus musculusOn Demand1510Download BAM
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GSE84371Adult mice new spinal chord neurons (close to neurogenesis)Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neuronsHabib ... Regev,Science 2016Mus musculusOn Demand9240Download BAM
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GSE65525Embryonic stem cellsDroplet barcoding for single-cell transcriptomics applied to embryonic stem cellsKlein ... Kirschner,Cell 2015Homo sapiens; Mus musculusOn Demand80Download BAM
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ERP010108Sequencing of single cell genomes and transcriptomes from Mus musculus 8 cell stage embryosPower analysis of single-cell RNA-sequencing experimentsSvensson ... Teichmann,Nature Methods 2017Mus musculusOn Demand2240Download BAM
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EGAD00001001332human breast cancer cells, lymphoblastoid cells. Mice ESCsG&T-seq: parallel sequencing of single-cell genomes and transcriptomesMacaulay ... Voet,Nature Methods 2015Homo sapiens; Mus musculusOn Demand7000Download BAM
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E-MTAB-3707Liver of a 14-week old B6CastF1 (C57Bl/6J mother x CAST/Ei father) female MouseComputational assignment of cell-cycle stage from single-cell transcriptome dataScialdone ... Buettner,Methods 2015Mus musculusOn Demand960Download BAM
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GSE54695J1 Mouse embryonic stem cellsValidation of noise models for single-cell transcriptomicsGr?¼n ... Van Oudenaarden,Nature Methods 2014Mus musculusOn Demand3200Download BAM
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GSE62270Intestinal gland cellsSingle-cell messenger RNA sequencing reveals rare intestinal cell typesGr?¼n ... Van Oudenaarden,Nature 2015Mus musculusOn Demand960Download BAM
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GSE63473Retinal cellsHighly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter DropletsMacosko ... McCarroll,Cell 2015Homo sapiens; Mus musculusOn Demand2030Download BAM
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GSE63525Lymphoblastoid cellsChromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomesSanborn ... Aiden,PNAS 2015Homo sapiens; Mus musculusOn Demand2000Download BAM
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SRP073767Peripheral blood mononuclear cells, bone marrow mononuclear cellsMassively parallel digital transcriptional profiling of single cellsZeng ... Bielas,Nature Communications 2017Homo sapiens; Mus musculusOn Demand310Download BAM
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GSE82187Striatal cellsCellular Taxonomy of the Mus musculus Striatum as Revealed by Single-Cell RNA-SeqGocke ... Quake,Cell Reports 2016Mus musculusOn Demand12080Download BAM
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GSE70630Oligodendroglioma tumor cellsSingle-cell RNA-seq supports a developmental hierarchy in Homo sapiens oligodendrogliomaTirosh ... Suv,Nature 2016Homo sapiensOn Demand48250Download BAM
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GSE75748Embronic stem and progenitor cellsSingle-cell RNA-seq reveals novel regulators of Homo sapiens embryonic stem cell differentiation to definitive endodermChu ... Thomson,Genome Biology 2016Homo sapiensOn Demand18100Download BAM
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GSE85183Pancreatic cancer cellsSelective single cell isolation for genomics using microraft arraysWelch ... Jones,Nucleic Acids Research 2016Homo sapiensOn Demand1200Download BAM
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GSE71453Dorsal root ganglion cellsSingle-cell RNA-seq reveals distinct injury responses in different types of DRG sensory neuronsHu ... Fan,Scientific Reports 2016Mus musculusOn Demand1230Download BAM
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GSE81475Neural epithelial stem cellsZika Virus Disrupts Phospho-TBK1 Localization and Mitosis in Homo sapiens Neuroepithelial Stem Cells and Radial GliaOnorati ... Sestan,Cell Reports 2016Homo sapiensOn Demand16080Download BAM
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SRP078083Squamous cell carcinoma cells from urinary bladderSingle-cell analyses of transcriptional heterogeneity in squamous cell carcinoma of urinary bladderZhang ... Wu,Oncotarget 2016Homo sapiensOn Demand10000Download BAM
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GSE85241Langerhans pancreatic cellsA Single-Cell Transcriptomic Map of the Homo sapiens and Mus musculus Pancreas Reveals Inter- and Intra-cell Population StructureMuraro ... Van Oudenaarden,Cell Systems 2016Homo sapiensOn Demand00Download BAM
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GSE85783Pluripotent stem cellsLaminin-guided highly efficient endothelial commitment from Homo sapiens pluripotent stem cellsOhta ... Saito,Scientific Reports 2016Homo sapiensOn Demand920Download BAM
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GSE88850Universal human reference RNA and Universal brain referenceAssessing characteristics of RNA amplification methods for single cell RNA sequencingDueck ... Kim,BMC genomics 2016Homo sapiensOn Demand1380Download BAM
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GSE81383MelanomasMapping heterogeneity in patient-derived melanoma cultures by single-cell RNA-seqGerber ... Kunz,Oncotarget 2017Homo sapiensOn Demand3070Download BAM
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GSE90063BMDC, BMDC stimulated at 3hr; K562 at 7 and 13 days post trasnduction, and 13 days at a higher MOI of perturbationsPerturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic ScreensDixit ... Regev,Cell 2016Homo sapiens; Mus musculusOn Demand2000000Download BAM
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GSE85066Embryonic stem cells and mesoderm progenitorsAn atlas of transcriptional, chromatin accessibility, and surface marker changes in Homo sapiens mesoderm developmentKoh ... Loh,Scientific Data 2016Homo sapiensOn Demand00Download BAM
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GSE81608human pancreatic a-, -, d- and PP cellsRNA Sequencing of Single Homo sapiens Islet Cells Reveals Type 2 Diabetes GenesXin ... Gromada,Cell Metabolism 2016Homo sapiensOn Demand16000Download BAM
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GSE81905Single cell RNA-sequencing of retinal bipolar cells (GSE80232, GSE819903)Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell TranscriptomicsShekhar ... Sanes,Cell 2016Mus musculusOn Demand2910Download BAM
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GSE74767Cynomolgus monkey: embryo E6-17; Mouse: embryo E4.5 - E6.5; Both: ESCsA developmental coordinate of the spectrum of pluripotency among mice, monkeys, and Homo sapienssNakamura ... Saitou,Nature 2016Macaca fascicularis; Mus musculusOn Demand4920Download BAM
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GSE75386CA1 cholecystokinin, parvalbumin, pyramidal and subiculum? neuronsSingle cell RNAseq of electrophysiologically characterized neurons of the hippocampusF?¶ldy ... S?¼dhof,PNAS 2016Mus musculusOn Demand1080Download BAM
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GSE77944C. elegans 1 to 16 cell stage embryo cellsA Transcriptional Lineage of the Early? C.? elegans? EmbryoTinton ... Goldstein,Developmental Cell 2016Caenorhabditis elegansOn Demand2190Download BAM
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GSE74155Embryonic stem cellsSingle-cell analyses of X Chromosome inactivation dynamics and pluripotency during differentiationChen ... Deng,Genome Research 2016Mus musculusOn Demand6170Download BAM
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GSE79818MicrogliaMicroglia development follows a stepwise program to regulate brain homeostasisMatcovitch-Natan ... Amit,Science 2016Mus musculusOn Demand00Download BAM
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GSE77288Induced pluripotent stem cellBatch effects and the effective design of single-cell gene expression studiesTung ... Gilad,Scientific Reports 2017Homo sapiensOn Demand8730Download BAM
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GSE83139Pancreatic endocrine cellsSingle-Cell Transcriptomics of the Homo sapiens Endocrine PancreasWang ... Kaestner,Diabetes 2016Homo sapiensOn Demand6350Download BAM
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E-MTAB-4026Postimplantation embryo cellsResolving early mesoderm diversification through single-cell expression profilingScialdone ... Gottgens,Nature 2016Mus musculusOn Demand7680Download BAM
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E-MTAB-4079Embryonic blood cellsResolving early mesoderm diversification through single-cell expression profilingScialdone ... Gottgens,Nature 2016Mus musculusOn Demand12050Download BAM
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E-MTAB-5061Transcriptional profiles of endocrine and exocrine cell types of the human pancreSingle-Cell? Transcriptome? Profiling? of? Human? Pancreatic? Islets? in? Health? and? Type? 2? DiabetesSegerstolpe ... Smith,Cell Metab 2016Homo sapiensOn Demand35140Download BAM
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GSE74672Neurons from gap between paraventricular and arcuate hypothalamic nuclei as well as the Ventromedial and dorsomedial hypothalamic nucleiMolecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypesRomanov ... Harkany,Nature Neuroscience 2017Mus musculusOn Demand19830Download BAM
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GSE76184Single cell transcriptome dynamics and subpopulation heterogeneity in radiation treated recurrent glioma Li ... Greenfield, Homo sapiensOn Demand2880Download BAM
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GSE76381Embryo ventral midbrain in human and mouse. stem cell-derived dopaminergic neuronsMolecular Diversity of Midbrain Development in Mus musculus, Homo sapiens, and Stem CellsLa Manno ... Linnarsson,Cell 2016Homo sapiens; Mus musculusOn Demand61790Download BAM
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GSE78045Airway epithelial progenitor cellsp53 Regulates Progenitor Cell Quiescence and Differentiation in the AirwayMcConnell ... Stripp,Cell Reports 2016Mus musculusOn Demand1500Download BAM
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GSE78968Human embryonic kidney cellsEffective detection of variation in single-cell transcriptomes using MATQ-seqSheng ... Zong,Nature Methods 2017Homo sapiensOn Demand910Download BAM
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GSE79136single cell RNA sequencing of human nasal epithelial cells grown (GSE89236, GSE89237)A cost effective 5' selective single cell transcriptome profiling approach with improved UMI designArguel ... Waldmann,Nucleic Acids Research 2017Homo sapiensOn Demand1920Download BAM
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GSE80032Pancreas Acinar cellsSingle-Cell Analysis Uncovers Clonal Acinar Cell Heterogeneity in the Adult PancreasWollny ... Martin-Villalba,Developmental Cell 2016Mus musculusOn Demand1080Download BAM
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GSE80810Pre-implantation embryo cells (research targets sex chromosomes)Xist-dependent imprinted X inactivation and the early developmental consequences of its failureBorensztein ... Heard,Nat Struct Mol Biol 2017Mus musculusOn Demand1820Download BAM
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GSE81275ESCs during programming into motor neuronsA Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem CellsVelasco ... Mazzoni,Cell Stem Cell 2017Mus musculusOn Demand7680Download BAM
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GSE81287Human ESCs and HEK293FT cellsSingle-cell sequencing of the small-RNA transcriptomeFaridani ... Sandberg,Nature Biotechnology 2016Homo sapiensOn Demand5390Download BAM
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GSE81673EZH2-deficient ESCDeletion of the Polycomb-Group Protein EZH2 Leads to Compromised Self-Renewal and Differentiation Defects in Homo sapiens Embryonic Stem CellsCollinson ... Rugg-Gunn0,Cell Reports 2016Homo sapiensOn Demand2210Download BAM
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GSE82174Testicular cellsThe Homeobox Transcription Factor RHOX10 Drives Mus musculus Spermatogonial Stem Cell EstablishmentSong ... Wilkinson,Cell Reports 2016Mus musculusOn Demand1930Download BAM
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GSE83948Neural progenitor cellsNeurogenic Radial Glia-like Cells in Meninges Migrate and Differentiate into Functionally Integrated Neurons in the Neonatal CortexBifari ... Carmeliet,Cell Stem Cell 2017Mus musculusOn Demand1790Download BAM
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GSE86207Cerebral organoid cellsDifferences and similarities between Homo sapiens and chimpanzee neural progenitors during cerebral cortex development.Mora-Berm?·dez ... Huttner,eLife 2016Pan troglodytes; Homo sapiensOn Demand3960Download BAM
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GSE86469Pancreatic islet/other single cellsSingle cell transcriptomes identify Homo sapiens islet cell signatures and reveal cell-type-specific expression changes in type 2 diabetesLawlor ... Stitzel,Genome Research 2017Homo sapiensOn Demand6380Download BAM
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GSE86618Epithelial lung cells (IPF and control)Single-cell RNA sequencing identifies diverse roles of epithelial cells in idiopathic pulmonary fibrosisXu ... Whitsett,JCI insight 2016Homo sapiensOn Demand5400Download BAM
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GSE86894Single-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 2016Homo sapiensOn Demand45300Download BAM
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GSE87069Developing ventral midbrain cellsSingle-Cell Analysis Reveals a Close Relationship between Differentiating Dopamine and Subthalamic Nucleus Neuronal LineagesKee ... Perlmann,Cell Stem Cell 2017Mus musculusOn Demand5740Download BAM
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GSE87237Human ESCsHomo sapiens Naive Pluripotent Stem Cells Model X Chromosome Dampening and X InactivationSahakyan ... Plath,Cell Stem Cell 2017Homo sapiensOn Demand2880Download BAM
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GSE76118Embryonic cardiac cellsTranscriptomic Profiling Maps Anatomically Patterned Subpopulations among Single Embryonic Cardiac CellsLi ... Wu,Developmental Cell 2016Mus musculusOn Demand32410Download BAM
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ERP015781Trophoblast stem cells ... , Mus musculusOn Demand960Download BAM
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SRP072988Acinar cellsSingle-Cell Analysis Uncovers Clonal Acinar Cell Heterogeneity in the Adult PancreasWollny ... Martin-Villalba,Developmental Cell 2016Mus musculusOn Demand1080Download BAM
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SRP087797Single-cell RNA-Seq of homo sapien fetal cortex (brain)Region-Specific Neural Stem Cell Lineages Revealed By Single-Cell RNA-Seq From Homo sapiens Embryonic Stem CellsYao ... Levi, Homo sapiensOn Demand4720Download BAM
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SRP093546Etv2-EYFP? transgenic embryo cellsDpath software reveals hierarchical haemato-endothelial lineages of Etv2 progenitors based on single-cell transcriptome analysisGong ... Garry,Nature Communications 2017Mus musculusOn Demand5620Download BAM
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GSE67602Dorsal telogen skin cellsSingle-Cell Transcriptomics Reveals that Differentiation and Spatial Signatures Shape Epidermal and Hair Follicle HeterogeneityJoost ... Kasper,Cell Systems 2016Mus musculusOn Demand14220Download BAM
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ERP016754Single cell RNA-seq and bisulfite-seq at various states of HiPSCs differentiating toward definitive endoderm derived lineages ... , Homo sapiensOn Demand3840Download BAM
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GSE90848Mouse 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 ChoicesYang ... Fuchs,Cell 2017Mus musculusOn Demand11190Download BAM
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GSE95601The 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 trajectoriesFletcher ... Ngai, 2017Mus musculusOn Demand8490Download BAM
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GSE85917Single cell RNA-seq data of human hESCs to evaluate SCnorm: robust normalization of single-cell rna-seq dataBacher ... Swanson, 2017Homo sapiensOn Demand1830Download BAM
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GSE89567Single cell RNA-seq analysis of IDH-mutant astrocytomaTirosh ... Regev, 2017Homo sapiensOn Demand63410Download BAM
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GSE70713Examination 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 2017Mus musculusOn Demand2360Download BAM
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GSE81861Two 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 2017Homo sapiensOn Demand12200Download BAM
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GSE79137single cell RNA-seq on mouse embryonic kidneys.Naiman ... Kobayashi, 2017Mus musculusOn Demand2370Download BAM
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GSE94641Single-cell RNA-Seq from medial ganglionic eminence at E11.5, E13.5, E15.5 or E17.5.Friedman ... Modrusan, 2017Mus musculusOn Demand2250Download BAM
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GSE79457Single-cell RNA-seq of in-vivo conversion of pancreatic -cells into -cellsEnge ... Chakravarthy, 2017Mus musculusOn Demand1820Download BAM
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GSE79102Examination of three different patients with myeloproloferative diseaseSC3: consensus clustering of single-cell RNA-seq dataKiselev ... Hemberg,Nat Methods 2017Homo sapiensOn Demand1920Download BAM
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GSE94883In vitro differentiation of mESCs into motor neuronsRizvi ... Rabadan, 2017Mus musculusOn Demand27440Download BAM
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GSE81252Single-cell transcriptomes from multiple time points during hepatocyte-like lineage progressionDifferences and similarities between human and chimpanzee neural progenitors during cerebral cortex development.Mora-Bermdez ... Huttner,Elife 2016Homo sapiensOn Demand7700Download BAM
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GSE92872Human HEK293T and mouse 3T3 cellsPooled CRISPR screening with single-cell transcriptome readout.Datlinger ... Bock,Nat Methods 2017Homo sapiens;? Mus musculusOn Demand1000Download BAM
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GSE93421Single-cell RNA-seq of 1.3 million brain cells from E18 miceMassively parallel digital transcriptional profiling of single cells.Zheng ... Bielas,Nat Commun 2017Mus musculusOn Demand13000000Download BAM
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GSE94579J14 ES cells differentiated into MGE-like cellsFriedman ... Modrusan, 2017Mus musculusOn Demand1400Download BAM
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GSE95837Single cell gene expression in Dlxi1/2b::eGFP+ cells before and after migration, 4 weeksIslam ... Wei, 2017Homo sapiensOn Demand1810Download BAM
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GSE96066Probing Plasmodium falciparum sexual differentiation at the single cell levelBrancucci ... Marti, 2017Plasmodium falciparum NF54On Demand11550Download BAM
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GSE97564Single cell RNAseq of hPSC derived V2a interneuron culturesMcDevit ... Butts, 2017Homo sapiensOn Demand44920Download BAM
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GSE93593Single 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 MaturationClose ... Lein,Neuron 2017Homo sapiensOn Demand17330Download BAM
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GSE87544single-cell RNA-seq of mouse hypothalamusSingle-Cell RNA-Seq Reveals Hypothalamic Cell Diversity.Chen ... Zhang,Cell Rep 2017Mus musculusOn Demand100000Download BAM
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GSE81884 (GSE81747, GSE81748, GSE81749, GSE81750, GSE81848, GSE96827)RNA sequencing in bulk and in single K562 cellsMultiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells.Xie ... Hon,Mol Cell 2017Homo sapiens;? Mus musculusOn Demand960Download BAM
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E-MTAB-5485scRNA-seq on a homogenous population of mouse embryonic stem cellsPower analysis of single-cell RNA-sequencing experimentsSvensson ... Teichmann,NATURE METHODS 2017Mus musculusOn Demand960Download BAM
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E-MTAB-5484scRNA-seq on a homogenous population of mouse embryonic stem cellsPower analysis of single-cell RNA-sequencing experimentsSvensson ... Teichmann,NATURE METHODS 2017Mus musculusOn Demand610Download BAM
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E-MTAB-5483scRNA-seq on a homogenous population of mouse embryonic stem cellsPower analysis of single-cell RNA-sequencing experimentsSvensson ... Teichmann,NATURE METHODS 2017Mus musculusOn Demand960Download BAM
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E-MTAB-5481scRNA-seq on a homogenous population of mouse embryonic stem cellsPower analysis of single-cell RNA-sequencing experimentsSvensson ... Teichmann,NATURE METHODS 2017Mus musculusOn Demand560Download BAM
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E-MTAB-5208single? celltranscriptomics to define the molecular signature of in vivo and in vitro NMPsBriscoe ... Gouti, 2017Mus musculusOn Demand5390Download BAM
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PRJNA360884Time course profiling of scRNA-seq of non-directed differentiation of human NPC generated from hESC ... , 2017Homo sapiensOn Demand9580Download BAM
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PRJEB4461Single cell transcriptomics in olfactory sensory neuronsVariation in olfactory neuron repertoires is genetically controlled and environmentally modulatedIbarra-Soria ... Logan,Elife 2017Mus musculusOn Demand5280Download BAM
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PRJNA324289Single cell RNA-Sequencing of adult NSCs and related populations from the sub-ventricular zoneSingle-Cell Transcriptomic Analysis Defines Heterogeneity and Transcriptional Dynamics in the Adult Neural Stem Cell Lineage.Dulken ... Brunet,Cell Rep. 2017Mus musculusOn Demand4520Download BAM
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PRJNA350294Etv2 single cell transcriptomeDpath software reveals hierarchical haemato-endothelial lineages of Etv2 progenitors based on single-cell transcriptome analysis. ... Gong,Garry 2017Mus musculusOn Demand5620Download BAM
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SRP052546full transcriptome data on single cells and nuclei from three areas (visual, temporal, prefrontal) of the human cortex ... , 2017Homo sapiensOn Demand39160Download BAM
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SRP052738variability in the expressed transcriptome of human excitable cells. ... , 2017Homo sapiensOn Demand9900Download BAM
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SRP051388The technical and biological noise in measured RNA levels in single cells in a number of human tissue types ... , 2017Homo sapiensOn Demand23280Download BAM
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SRP098798Single-cell profiling of an in vitro model of human interneuron development ... , 2017Homo sapiensOn Demand1040Download BAM
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SRP104455the transcriptomes of thousands of individual cells from the tissue explants and organoids ... , 2017Mus musculusOn Demand10000Download BAM
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GSE95025Single cell transcriptomics of the early Drosophila embryoThe? Drosophila? embryo at single-cell transcriptome resolutionKaraiskos ... Zinzen,Science 2017DrosophilaOn Demand960Download BAM
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DRA001287Lung epithelial tumor cellsSingle-cell analysis of lung adenocarcinoma cell lines reveals diverse expression patterns of individual cells invoked by a molecular target drug treatmentSuzuki ... Suzuki,Genome Biology 2015Homo sapiensOn Demand3360Download BAM
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DRA002399Cervical cancer cellsSingle-cell transcriptomes of fluorescent, ubiquitination-based cell cycle indicator cellsBttcher ... Plessy, Homo sapiensOn Demand960Download BAM
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DRA002730Lung epithelial tumor cellsSingle-cell analysis of lung adenocarcinoma cell lines reveals diverse expression patterns of individual cells invoked by a molecular target drug treatmentSuzuki ... Suzuki,Genome Biology 2015Homo sapiensOn Demand3360Download BAM
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E-MTAB-2600Embryonic stem cellsSingle Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional VariationKolodziejczyk ... Teichmann,Cell Stem Cell 2015Mus musculusOn Demand960Download BAM
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E-MTAB-5060Pancreatic islet cells (healthy and type 2 diabetes)Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 DiabetesSegerstolpe ... Sandberg,Cell Metabolism 2016Homo sapiensOn Demand22090Download BAM
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E-MTAB-5061Pancreatic islet cells (healthy and type 2 diabetes)Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 DiabetesSegerstolpe ... Sandberg,Cell Metabolism 2016Homo sapiensOn Demand22090Download BAM
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PRJEB8994Oocyte, zygote and blastomere cellsNovel PRD-like homeodomain transcription factors and retrotransposon elements in early human developmentThnen ... Kere,Nature Communications 2015Homo sapiensOn Demand3480Download BAM
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ERP021229Variability across individual Plasmodium parasitesSingle-cell transcriptomics of malaria parasitesReid ... Lawniczak,bioRxiv 2017Plasmodium bergheiOn Demand5210Download BAM
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