DRscDB Coverage



Rows:47
pubmed id pubmed date paper title dataset ids subset names species species id tissue type ontology stage genotype cell/nuclei number cell or nuleus reads cell genes cell total gene platforms clustering pseudotime batch correction no of clusters data in supp table web link available URL landing page linkout URL data accession number web link
27365425 2016 Aug 25 A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation 100 all Mouse 10090 Blood Blood Adult C57BL/6 1656 Cells >200,000 6558 Not reported Illumina HiSeq R Ocone et al. ComBat from SVA package 4 N Y http://blood.stemcells.cam.ac.uk/single_cell_atlas.html GSE81682 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81682
28428369 2017 Apr 21 Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes and progenitors 52 all Human 9606 Blood Blood - 1081 Cells ~1-2 million 5426 21581 Smart-Seq2 Seurat None Not reported 10 Y N N/A GSE94820 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE94820
28860209 2017 Oct 13 The Drosophila embryo at single-cell transcriptome resolution 96 all Drosophila 7227 Embryo Embryo Embryo y1 w1118; P{st.2::Gal4}; P{vnd::dsRED} 7975 Cells 84755 1159 Not reported Drop-seq Seurat None Not reported 9 Y Y www.dvex.org GSE95025 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE95025
28878000 2017 Oct 2 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing 99 all Zebrafish 7955 Kidney Kidney Adult Casper 3782 Cells Not reported 811 Not reported inDrop Seurat Monocle, ARIADNE Not reported 17 Y N GSE100910 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100910
29144463 2017 Nov 16 A single-cell survey of the small intestinal epithelium 111 all Mouse 10090 Intestine 12
29545511 2018 Apr 13 Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding 69 all Mouse 10090 Brain Brain C57BL/6 x DBA/2 156049 Nuclei 15063 677 Not reported SPLiT-seq Jaccard-Louvain t-SNE Not reported 73 Y N GSE110823 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110823
29576475 2018 Apr 2 Comprehensive Identification and Spatial Mapping of Habenular Neuronal Types Using Single-Cell RNA-Seq 53 all Zebrafish 7955 Habenula Brain Tg(gng8-nfsB-CAAX-GFP) 7782 Cells 96000 709 Not reported 10x Genomics Seurat Not reported Not reported 17 Y Y stackjoint.com, Search for Tags: "Pandey2017_WholeBrain," "Pandey2017_habenula" GSE105115 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE105115
29608178 2018 Jun Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain 42 all Zebrafish 7955 Brain Brain 23-25 days post-fertlization (juvenile) Danio rerio TL/AB strain 58492 Cells 22500 1300 3100 inDrop Seurat Monocle 2 Not reported 63 Y Y http://krishna.gs.washington.edu/content/members/aaron/fate_map/harvard_temp_trees/. GSE105010 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE105010
29622724 2018 May 18 Single-cell transcriptomics of the mouse kidney reveals potential cellular targets of kidney disease 68 all Mouse 10090 Kidney Kidney C57BL/6 43745 Cells Not reported Not reported 16383 10x Genomics Seurat Monocle 2 edgeR 16 Y N GSE107585 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE107585
29695820 2018 Apr 25 Characterization of germ cell differentiation in the male mouse through single-cell RNA sequencing 118 all Mouse 10090 Testis Testis 9
29794128 2018 Aug A Single-Cell Transcriptome Atlas of the Mouse Glomerulus 92 all Mouse 10090 Glomerulus Renal glomerulus Adult CD1 12954 Cells 9400 630 Not reported Drop-seq Seurat None Not reported 5 Y Y https://shiny.mdc-berlin.de/mgsca/ GSE111107 https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/geo/query/acc.cgi?acc=GSE111107
29870722 2018 Jun 4 Progressive Recruitment of Mesenchymal Progenitors Reveals a Time-Dependent Process of Cell Fate Acquisition in Mouse and Human Nephrogenesis 102 all Human 9606 Kidney Kidney Fetal - 8000 Cells Not reported Not reported Not reported 10x Genomics Seurat, Gaussian Mixture Model Monocle 2 Not reported 22 Y N Â GSE112570 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE112570
29909982 2018 Aug 9 A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain. 59,60,61,62,63,64,65,66 age_0,age_1,age_3,age_6,age_9,age_15,age_30,age_50 Drosophila 7227 Brain Brain DGRP, w1118 56902 Cells 53553 1308 12436 10x Genomics Seurat Not reported Not reported 87 Y Y https://aertslab.org/#scenic GSE107451 https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/geo/query/acc.cgi?acc=GSE107451
29980650 2018 Aug Single-Cell Transcriptomics of a Human Kidney Allograft Biopsy Specimen Defines a Diverse Inflammatory Response 36,37,38,39,40 Combined-Epithelia,Combined-Epithelia healthy,Combined-Epithelia allograft,healthy,allograft Human 9606 Kidney epithelium Kidney epithelium Adult WT 4259 Nuclei 50000 Not reported Not reported inDrop Seurat Monocle Not reported 6 N N GSE114156 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE114156
30315278 2018 Dec The adult human testis transcriptional cell atlas 47 all Human 9606 Testis Testis - 6490 Cells 250000 2500 Not reported 10x Genomics Seurat Slingshot Not reported 13 Y N GSE120508 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE120508
30479347 2018 Nov 27 Single cell RNA-sequencing identifies a metabolic aspect of apoptosis in Rbf mutant 54,55,56,57 combined,combined_rbf,combined_WT,WT Drosophila 7227 eye disc eye disc Rbf120a/FM7, GFP 5203 Cells Not reported Not reported Not reported Drop-seq Seurat Not reported Not reported 15 Y Y GSE115476, E-MTAB-7195 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE115476, https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-7195/
30526881 2018 Dec 6 Human Intestinal Organoids Maintain Self-Renewal Capacity and Cellular Diversity in Niche-Inspired Culture Condition 113 all Human 9606 Intestine Intestine 9
30726734 2019 Feb 5 The Neonatal and Adult Human Testis Defined at the Single-Cell Level 48,49,50,51 LowRes Adult,LowRes Neonate,HighRes Adult,HighRes Neonate Human 9606 Testis Testis - 14862 Cells Not reported Not reported Not reported 10x Genomics Seurat, PAGODA2 Monocle Seurat 5 Y N GSE124263 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE124263
30789893 2019 Feb Single-cell transcriptomics reveals gene expression dynamics of human fetal kidney development 70,71,72,73,74,75 combined,wk09,wk11,wk13,wk16,wk18 Human 9606 Kidney Kidney Fetal - 8503 Cells Not reported 1789 Not reported 10x Genomics scran Monocle 2 Mutual nearest neighbors 22 Y Y Â http://www.semraulab.com/kidney GSE114530 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE114530
30840884 2019 Mar 5 Single-Cell RNA-Seq Reveals Cellular Heterogeneity of Pluripotency Transition and X Chromosome Dynamics during Early Mouse Development 109 all Mouse 10090 Embryo Embryo Embryo C57BL/6J CAST/EiJ hybrid 1724 Cells Not reported 8577 12137 SMART-Seq2 DESeq2 DESeq2 Not reported 3 Y N GSE109071 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE109071
31018142 2019 Apr 23 Single-Cell Transcriptomics Analyses of Neural Stem Cell Heterogeneity and Contextual Plasticity in a Zebrafish Brain Model of Amyloid Toxicity 32,33,34,35 merged,AB42,IL4,PBS Zebrafish 7955 Brain Brain Tg(her4.1:GFP) 450 Cells See comment See comment Not reported 10x Genomics Seurat Monocle Not reported 20 Y Y http://www.kizillab.org/singlecell GSE118577 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE118577
31042697 2019 Jun Single-cell transcriptomic analysis of Alzheimer's disease 104 all Human 9606 Prefrontal cortex Brain Adult - 80660 Nuclei Not reported Not reported 17926 10x Genomics Fishers exact test None Not reported 40 Y Y Â https://www.radc.rush.edu/docs/omics.htm https://www.synapse.org/#!Synapse:syn18485175
31118232 2019 Jun 12 Single cell analysis of the developing mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk 105 all Mouse 10090 Kidney Kidney Fetal C57BL/6 5639 Cells Not reported 2896 13116 10x Genomics Seurat, edgeR Monocle 2 Not reported 16 Y N GSE108291 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE108291
31237565 2019 Jun 25 Unified single-cell analysis of testis gene regulation and pathology in five mouse strains 94 all Mouse 10090 Testis Testis Adult - 57600 Cells 1689 1292 Not reported Drop-seq SDA SDA SDA 32 Y N GSE113293 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE113293
31303374 2019 Sep 4 A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation 30,31 cluster,subcluster Human 9606 Neocortex Brain - 40000 Cells 52000 1049 Not reported Drop-seq Seurat Monocle 2 Seurat 16 Y Y http://geschwindlab.dgsom.ucla.edu/pages/codexviewer
31363221 2019 Aug Gene expression atlas of a developing tissue by single cell expression correlation analysis 106 all Drosophila 7227 Wing disc Wing disc Larva W1118 1644 Cells Not reported 1134 Not reported Drop-seq Seurat None Seurat 5 Y N GSE127832 https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/geo/query/acc.cgi?acc=GSE127832
31413257 2019 Aug 14 A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing 101 all Human 9606 Bone marrow Bone marrow Adult - 89827 Cells 192427 1851 20090 10x Genomics Seurat None Not reported 19 N Y https://github.com/genome/scrna_mutations
31418408 2019 Aug 16 Testis Single-Cell RNA-seq Reveals the Dynamics of De Novo Gene Transcription and Germline Mutational Bias in Drosophila 58 all Drosophila 7227 Testis Testis DGRP-RAL517 5000 Cells 85312 4185 426563073 10x Genomics Seurat Monocle Not reported 9 Y N
31455604 2019 Sep 20 Single cell transcriptomic landscapes of pattern formation, proliferation and growth in Drosophila wing imaginal discs 95 all Drosophila 7227 Wing disc Wing disc Larva FRT82B 5202 Cells 109258 2948 Not reported 10x Genomics Seurat None Not reported 6 Y Y http://drosophilayanlab-virtual-wingdisc.ust.hk:3838/v2/ GSE133204 https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/geo/query/acc.cgi?acc=GSE133204
31506348 2019 Sep 24 The single-cell transcriptomic landscape of early human diabetic nephropathy 103 all Human 9606 Kidney Kidney Adult - 23980 Nuclei Not reported 2541 Not reported 10x Genomics Seurat None Not reported 12 Y Y http://humphreyslab.com/SingleCell/ Â GSE131882 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131882
31689386 2019 Nov 4 Single-Cell Profiling Reveals Sex, Lineage, and Regional Diversity in the Mouse Kidney 41 all Mouse 10090 Kidney Kidney C57BL6/J 31265 Cells 70446 1395 Not reported 10x Genomics Seurat None Not reported 31 Y Y https://cello.shinyapps.io/kidneycellexplorer/ GSE129798 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE129798
31746739 2019 Nov 20 Single cell transcriptome atlas of the Drosophila larval brain. 5,6,15 WT,starved,combined Drosophila 7227 Brain Brain Larva Canton-S 4645 Cells 545512 1962 Not reported 10x Genomics Seurat N Seurat R 27 Y N GSE134722 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134722
31753849 2020 Feb 3 Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine 114,115,116,117 Rectum,Intestine,Ileum,Colon Human 9606 Intestine Intestine 7
31851941 2019 Dec 17 The Cellular Diversity and Transcription Factor Code of Drosophila Enteroendocrine Cells 4 WT Drosophila 7227 Intestine Midgut Adult CG32547-KI-GAL4; UAS-GFP 4661 Cells 36000 1350 Not reported 10x Genomics Seurat None Not reported 11 N Y https://xilab.shinyapps.io/database/ GSE132274 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132274
31915294 2020 Jan 21 A cell atlas of the adult Drosophila midgut. 8 WT Drosophila 7227 Intestine Midgut esg:GFP/+; pros-Gal4, UAS-RFP/+ 10605 Cells Not reported 442 7651 10x Genomics Seurat, Slingshot Slingshot Seurat 22 Y Y https://www.flyrnai.org/scRNA/ GSE120537 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE120537
31919193 2020 Feb 1 A single-cell atlas of the developing Drosophila ovary identifies follicle stem cell progenitors 3,13 low resolution,high resolution Drosophila 7227 Ovary Ovary Larva - 1747 Cells Not reported 3230 10610 10x Genomics Seurat G-TRACE Not reported 7 Y N N/A GSE131971 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131971
32092251 2020 Mar 17 Single-Cell RNA Sequencing Reveals Size-Dependent Effects of Polystyrene Microplastics on Immune and Secretory Cell Populations from Zebrafish Intestines 112 all zebrafish 7955 Intestine Intestine 12
32162708 2020 Jun 17 Temporal specificity and heterogeneity of Drosophila immune cells 1,2,14 WT,wasp,combined Drosophila 7227 Blood Hemolymph Larva Oregon-R 8058 Cells 32365 1250 Not reported 10x Genomics Seurat, SCENIC RNA velocity, Monocle Not reported 16 Y N N/A E-MTAB-8690 www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-8698/
32175841 2020 Mar 16 An abundant quiescent stem cell population in Drosophila Malpighian tubules protects principal cells from kidney stones 7 WT Drosophila 7227 Malpighian Tubules Malpighian tubule Adult Oregon-R 710 Cells Not reported 1611 Not reported 10x Genomics Seurat N Not reported 5 Y Y https://www.ncbi.nlm.nih.gov/bioproject/PRJNA595625
32339165 2020 Apr A single-cell atlas of adult Drosophila ovary identifies transcriptional programs and somatic cell lineage regulating oogenesis 76 all Drosophila 7227 Ovary Ovary 32
32396065 2020 May 12 A single-cell survey of Drosophila blood 12,17,18,19 combined,wounded,unwounded,wasp infestation Drosophila 7227 Blood Hemolymph 17
32487456 2020 Apr 20 Single-cell RNA sequencing identifies novel cell types in Drosophila 98 all Drosophila 7227 Blood Blood Larva W1118 3424 Cells 12134 1211 Not reported 10x Genomics Seurat Monocle Not reported 5 N N
32815271 2020 Oct 5 A cell atlas of adult muscle precursors uncovers early events in fibre-type divergence in Drosophila 107,120,121 merged,Notum,Cherry Drosophila 7227 Wing disc Wing disc Larva 1151‐GAL4; 1151>mCherry‐RNAi 11527 Cells Not reported 500 Not reported Drop-seq Seurat None Not reported 26 Y N GSE138626 https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/geo/query/acc.cgi?acc=GSE138626
32855340 2020 Aug 28 Mosquito cellular immunity at single-cell resolution 108,119 aedes,anopheles Mosquito 7165 Blood Hemolymph Adult M-form (An. coluzzii) 5383 Cells Not reported Not reported Not reported 10x Genomics Seurat None Not reported 9 Y Y https://hemocytes.cellgeni.sanger.ac.uk/
32900993 2020 Sep 8 Single-cell transcriptome maps of myeloid blood cell lineages in Drosophila 84,85,86,87 merged,72hr,96hr,120hr Drosophila 7227 Lymph gland Embryonic/larval lymph gland Larva Oregon R 22645 Cells Not reported 1477 15540 Drop-seq Seurat Monocle 3 Seurat 11 Y N GSE141273 https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/geo/query/acc.cgi?acc=GSE141273
33159074 2020 Nov 6 A Single-Cell Atlas and Lineage Analysis of the Adult Drosophila Ovary 93 all Drosophila 7227 Ovary Ovary Adult Canton S 14000 Cells Not reported Not reported Not reported 10x Genomics CellFindR, Seurat Monocle Not reported 26 Y N GSE136162 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE136162
9000000002 2020 Sep Novel Human Kidney Cell Subsets Identified by Mux-Seq 110 all Human 9606 Kidney Kidney Adult - 45411 Cells 107863 1222 33694 10x Genomics Seurat Monocle 2 Not reported 37 Y Y www.kpmp.org https://www.biorxiv.org/content/10.1101/2020.03.02.973925v1.full