SCC Publications

Publications that have resulted from projects with the Single Cell Core or using the inDrops method.

Please notify us if your publications that involve the use of the Single Cell Core is not listed here.

2020

  • Sanmarco LM, Wheeler MA, Gutiérrez-Vázquez C, Polonio CM, Linnerbauer M, Pinho-Ribeiro FA, Li Z, Giovannoni F, Batterman KV, Scalisi G, Zandee SEJ, Heck ES, Alsuwailm M, Rosene DL, Becher B, Chiu IM, Prat A, Quintana FJ. Gut-licensed IFNγ+ NK cells drive LAMP1+TRAIL+ anti-inflammatory astrocytes. Nature [Internet]. 2021 Jan 6; Available from: http://dx.doi.org/10.1038/s41586-020-03116-4 PMID: 33408417

  • Renthal W, Tochitsky I, Yang L, Cheng Y-C, Li E, Kawaguchi R, Geschwind DH, Woolf CJ. Transcriptional Reprogramming of Distinct Peripheral Sensory Neuron Subtypes after Axonal Injury. Neuron. 2020 Oct 14;108(1):128–144.e9. PMCID: PMC7590250

  • Kalish BT, Kim E, Finander B, Duffy EE, Kim H, Gilman CK, Yim YS, Tong L, Kaufman RJ, Griffith EC, Choi GB, Greenberg ME, Huh JR. Maternal immune activation in mice disrupts proteostasis in the fetal brain. Nat Neurosci [Internet]. 2020 Dec 23; Available from: http://dx.doi.org/10.1038/s41593-020-00762-9 PMID: 33361822

  • Yap E-L, Pettit NL, Davis CP, Nagy MA, Harmin DA, Golden E, Dagliyan O, Lin C, Rudolph S, Sharma N, Griffith EC, Harvey CD, Greenberg ME. Bidirectional perisomatic inhibitory plasticity of a Fos neuronal network. Nature [Internet]. 2020 Dec 9; Available from: http://dx.doi.org/10.1038/s41586-020-3031-0 PMID: 33299180

  • Dost AFM, Moye AL, Vedaie M, Tran LM, Fung E, Heinze D, Villacorta-Martin C, Huang J, Hekman R, Kwan JH, Blum BC, Louie SM, Rowbotham SP, Sainz de Aja J, Piper ME, Bhetariya PJ, Bronson RT, Emili A, Mostoslavsky G, Fishbein GA, Wallace WD, Krysan K, Dubinett SM, Yanagawa J, Kotton DN, Kim CF. Organoids Model Transcriptional Hallmarks of Oncogenic KRAS Activation in Lung Epithelial Progenitor Cells. Cell Stem Cell. 2020 Oct 1;27(4):663–678.e8. PMCID: PMC7541765

  • Rodriguez-Fraticelli AE, Weinreb C, Wang S-W, Migueles RP, Jankovic M, Usart M, Klein AM, Lowell S, Camargo FD. Single-cell lineage tracing unveils a role for TCF15 in haematopoiesis [Internet]. Nature. 2020. Available from: http://dx.doi.org/10.1038/s41586-020-2503-6

  • Tanoury ZA, Al Tanoury Z, Rao J, Tassy O, Gobert B, Gapon S, Garnier J-M, Wagner E, Hick A, Hall A, Gussoni E, Pourquié O. Differentiation of the human PAX7-positive myogenic precursors/satellite cell lineage in vitro [Internet]. Development. 2020. p. dev187344. Available from: http://dx.doi.org/10.1242/dev.187344

  • Kalish BT, Barkat TR, Diel EE, Zhang EJ, Greenberg ME, Hensch TK. Single-nucleus RNA sequencing of mouse auditory cortex reveals critical period triggers and brakes. Proc Natl Acad Sci U S A [Internet]. 2020 May 13; Available from: http://dx.doi.org/10.1073/pnas.1920433117 PMID: 32404418

  • Tattikota SG, Cho B, Liu Y, Hu Y, Barrera V, Steinbaugh MJ, Yoon S-H, Comjean A, Li F, Dervis F, Hung R-J, Nam J-W, Ho Sui S, Shim J, Perrimon N. A single-cell survey of Drosophila blood. Elife [Internet]. 2020 May 12;9. Available from: http://dx.doi.org/10.7554/eLife.54818 PMID: 32396065

  • Huang KW, Sabatini BL. Single-Cell Analysis of Neuroinflammatory Responses Following Intracranial Injection of G-Deleted Rabies Viruses. Front Cell Neurosci. 2020 Mar 20;14:65. PMCID: PMC7098990

  • Wallace ML, Huang KW, Hochbaum D, Hyun M, Radeljic G, Sabatini BL. Anatomical and single-cell transcriptional profiling of the murine habenular complex. Elife [Internet]. 2020 Feb 11;9. Available from: http://dx.doi.org/10.7554/eLife.51271 PMCID: PMC7012610

  • Ghazizadeh Z, Kiviniemi T, Olafsson S, Plotnick D, Beerens ME, Zhang K, Gillon L, Steinbaugh MJ, Barrera V, Sui SH, Werdich AA, Kapur S, Eranti A, Gunn J, Jalkanen J, Airaksinen J, Kleber AG, Hollmén M, MacRae CA. Metastable Atrial State Underlies the Primary Genetic Substrate for MYL4 Mutation-Associated Atrial Fibrillation. Circulation. 2020 Jan 28;141(4):301–312. PMID: 31735076

  • Hurley K, Ding J, Villacorta-Martin C, Herriges MJ, Jacob A, Vedaie M, Alysandratos KD, Sun YL, Lin C, Werder RB, Huang J, Wilson AA, Mithal A, Mostoslavsky G, Oglesby I, Caballero IS, Guttentag SH, Ahangari F, Kaminski N, Rodriguez-Fraticelli A, Camargo F, Bar-Joseph Z, Kotton DN. Reconstructed Single-Cell Fate Trajectories Define Lineage Plasticity Windows during Differentiation of Human PSC-Derived Distal Lung Progenitors. Cell Stem Cell [Internet]. 2020 Jan 27; Available from: http://dx.doi.org/10.1016/j.stem.2019.12.009 PMID: 32004478

  • Weinreb C, Rodriguez-Fraticelli A, Camargo FD, Klein AM. Lineage tracing on transcriptional landscapes links state to fate during differentiation. Science [Internet]. 2020 Jan 23; Available from: http://dx.doi.org/10.1126/science.aaw3381 PMID: 31974159

  • Hung R-J, Hu Y, Kirchner R, Liu Y, Xu C, Comjean A, Tattikota SG, Li F, Song W, Ho Sui S, Perrimon N. A cell atlas of the adult Drosophila midgut. Proc Natl Acad Sci U S A [Internet]. 2020 Jan 8; Available from: http://dx.doi.org/10.1073/pnas.1916820117 PMID: 31915294

  • Diaz-Cuadros M, Wagner DE, Budjan C, Hubaud A, Tarazona OA, Donelly S, Michaut A, Al Tanoury Z, Yoshioka-Kobayashi K, Niino Y, Kageyama R, Miyawaki A, Touboul J, Pourquié O. In vitro characterization of the human segmentation clock. Nature [Internet]. 2020 Jan 8; Available from: http://dx.doi.org/10.1038/s41586-019-1885-9 PMID: 31915384

2019

  • A. Pratama, A. Schnell, D. Mathis, C. Benoist, Developmental and cellular age direct conversion of CD4+ T cells into RORγ+ or Helios+ colon Treg cells. J. Exp. Med. (2019) https:/doi.org/10.1084/jem.20190428.

  • Hrvatin S, Tzeng CP, Nagy MA, Stroud H, Koutsioumpa C, Wilcox OF, Assad EG, Green J, Harvey CD, Griffith EC, Greenberg ME. A scalable platform for the development of cell-type-specific viral drivers. Elife [Internet]. 2019 Sep 23;8. Available from: http://dx.doi.org/10.7554/eLife.48089 PMID: 31545165

  • Huang KW, Ochandarena NE, Philson AC, Hyun M, Birnbaum JE, Cicconet M, Sabatini BL. Molecular and anatomical organization of the dorsal raphe nucleus. Elife [Internet]. 2019 Aug 14;8. Available from: http://dx.doi.org/10.7554/eLife.46464 PMID: 31411560

  • Wolock SL, Krishnan I, Tenen DE, Matkins V, Camacho V, Patel S, Agarwal P, Bhatia R, Tenen DG, Klein AM, Welner RS. Mapping Distinct Bone Marrow Niche Populations and Their Differentiation Paths. Cell Rep. 2019 Jul 9;28(2):302–311.e5. PMID: 31291568

  • Pepe-Mooney BJ, Dill MT, Alemany A, Ordovas-Montanes J, Matsushita Y, Rao A, Sen A, Miyazaki M, Anakk S, Dawson PA, Ono N, Shalek AK, van Oudenaarden A, Camargo FD. Single-Cell Analysis of the Liver Epithelium Reveals Dynamic Heterogeneity and an Essential Role for YAP in Homeostasis and Regeneration. Cell Stem Cell. 2019 Jul 3;25(1):23–38.e8. PMID: 31080134

  • Gunner G, Cheadle L, Johnson KM, Ayata P, Badimon A, Mondo E, Nagy MA, Liu L, Bemiller SM, Kim K-W, Lira SA, Lamb BT, Tapper AR, Ransohoff RM, Greenberg ME, Schaefer A, Schafer DP. Sensory lesioning induces microglial synapse elimination via ADAM10 and fractalkine signaling. Nat Neurosci. 2019 Jul;22(7):1075–1088. PMCID: PMC6596419

  • Saatcioglu HD, Kano M, Horn H, Zhang L, Samore W, Nagykery N, Meinsohn M-C, Hyun M, Suliman R, Poulo J, Hsu J, Sacha C, Wang D, Gao G, Lage K, Oliva E, Morris Sabatini ME, Donahoe PK, Pépin D. Single-cell sequencing of neonatal uterus reveals an endometrial progenitor indispensable for fertility. Elife [Internet]. 2019 Jun 24;8. Available from: http://dx.doi.org/10.7554/eLife.46349 PMID: 31232694

  • Pellin D, Loperfido M, Baricordi C, Wolock SL, Montepeloso A, Weinberg OK, Biffi A, Klein AM, Biasco L. A comprehensive single cell transcriptional landscape of human hematopoietic progenitors. Nat Commun. 2019 Jun 3;10(1):2395. PMCID: PMC6546699

  • Zilionis R, Engblom C, Pfirschke C, Savova V, Zemmour D, Saatcioglu HD, Krishnan I, Maroni G, Meyerovitz CV, Kerwin CM, Choi S, Richards WG, De Rienzo A, Tenen DG, Bueno R, Levantini E, Pittet MJ, Klein AM. Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and Species. Immunity. 2019 May 21;50(5):1317–1334.e10. PMCID: PMC6620049

  • Mandelbaum G, Taranda J, Haynes TM, Hochbaum DR, Huang KW, Hyun M, Umadevi Venkataraju K, Straub C, Wang W, Robertson K, Osten P, Sabatini BL. Distinct Cortical-Thalamic-Striatal Circuits through the Parafascicular Nucleus. Neuron. 2019 May 8;102(3):636–652.e7. PMID: 30905392

  • Spallanzani RG, Zemmour D, Xiao T, Jayewickreme T, Li C, Bryce PJ, Benoist C, Mathis D. Distinct immunocyte-promoting and adipocyte-generating stromal components coordinate adipose tissue immune and metabolic tenors. Sci Immunol [Internet]. 2019 May 3;4(35). Available from: http://dx.doi.org/10.1126/sciimmunol.aaw3658 PMID: 31053654

  • Veres A, Faust AL, Bushnell HL, Engquist EN, Kenty JH-R, Harb G, Poh Y-C, Sintov E, Gürtler M, Pagliuca FW, Peterson QP, Melton DA. Charting cellular identity during human in vitro β-cell differentiation. Nature. 2019 May;569(7756):368–373. PMID: 31068696

  • Russell MA, Redick SD, Blodgett DM, Richardson SJ, Leete P, Krogvold L, Dahl-Jørgensen K, Bottino R, Brissova M, Spaeth JM, Babon JAB, Haliyur R, Powers AC, Yang C, Kent SC, Derr AG, Kucukural A, Garber MG, Morgan NG, Harlan DM. HLA Class II Antigen Processing and Presentation Pathway Components Demonstrated by Transcriptome and Protein Analyses of Islet β-Cells From Donors With Type 1 Diabetes. Diabetes. 2019 May;68(5):988–1001. PMCID: PMC6477908

 

2018

  • Hinohara K, Wu H-J, Vigneau S, McDonald TO, Igarashi KJ, Yamamoto KN, Madsen T, Fassl A, Egri SB, Papanastasiou M, Ding L, Peluffo G, Cohen O, Kales SC, Lal-Nag M, Rai G, Maloney DJ, Jadhav A, Simeonov A, Wagle N, Brown M, Meissner A, Sicinski P, Jaffe JD, Jeselsohn R, Gimelbrant AA, Michor F, Polyak K. KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance. Cancer Cell. 2018 Dec 10;34(6):939–953.e9. PMCID: PMC6310147

  • Leigh ND, Dunlap GS, Johnson K, Mariano R, Oshiro R, Wong AY, Bryant DM, Miller BM, Ratner A, Chen A, Ye WW, Haas BJ, Whited JL. Transcriptomic landscape of the blastema niche in regenerating adult axolotl limbs at single-cell resolution. Nat Commun. 2018 Dec 4;9(1):5153. PMCID: PMC6279788

  • Renthal W, Boxer LD, Hrvatin S, Li E, Silberfeld A, Nagy MA, Griffith EC, Vierbuchen T, Greenberg ME. Characterization of human mosaic Rett syndrome brain tissue by single-nucleus RNA sequencing. Nat Neurosci. 2018 Dec;21(12):1670–1679. PMCID: PMC6261686

  • Cheadle L, Tzeng CP, Kalish BT, Harmin DA, Rivera S, Ling E, Nagy MA, Hrvatin S, Hu L, Stroud H, Burkly LC, Chen C, Greenberg ME. Visual Experience-Dependent Expression of Fn14 Is Required for Retinogeniculate Refinement. Neuron. 2018 Aug 8;99(3):525–539.e10. PMCID: PMC6101651

  • Plasschaert LW, Žilionis R, Choo-Wing R, Savova V, Knehr J, Roma G, Klein AM, Jaffe AB. A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte. Nature. 2018 Aug;560(7718):377–381. PMCID: PMC6108322

  • La Manno G, Soldatov R, Zeisel A, Braun E, Hochgerner H, Petukhov V, Lidschreiber K, Kastriti ME, Lönnerberg P, Furlan A, Fan J, Borm LE, Liu Z, van Bruggen D, Guo J, He X, Barker R, Sundström E, Castelo-Branco G, Cramer P, Adameyko I, Linnarsson S, Kharchenko PV. RNA velocity of single cells. Nature. 2018 Aug;560(7719):494–498. PMCID: PMC6130801

  • Briggs JA, Weinreb C, Wagner DE, Megason S, Peshkin L, Kirschner MW, Klein AM. The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution. Science [Internet]. 2018 Jun 1;360(6392). Available from: http://dx.doi.org/10.1126/science.aar5780 PMCID: PMC6038144

  • Wagner DE, Weinreb C, Collins ZM, Briggs JA, Megason SG, Klein AM. Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo. Science. 2018 Jun 1;360(6392):981–987. PMCID: PMC6083445

  • Zemmour D, Zilionis R, Kiner E, Klein AM, Mathis D, Benoist C. Single-cell gene expression reveals a landscape of regulatory T cell phenotypes shaped by the TCR. Nat Immunol. 2018 Mar;19(3):291–301. PMCID: PMC6069633

  • Tusi BK, Wolock SL, Weinreb C, Hwang Y, Hidalgo D, Zilionis R, Waisman A, Huh JR, Klein AM, Socolovsky M. Population snapshots predict early haematopoietic and erythroid hierarchies. Nature. 2018 Mar 1;555(7694):54–60. PMCID: PMC5899604

  • Kalish BT, Cheadle L, Hrvatin S, Nagy MA, Rivera S, Crow M, Gillis J, Kirchner R, Greenberg ME. Single-cell transcriptomics of the developing lateral geniculate nucleus reveals insights into circuit assembly and refinement. Proc Natl Acad Sci U S A. 2018 Jan 30;115(5):E1051–E1060. PMCID: PMC5798372

  • Rodriguez-Fraticelli AE, Wolock SL, Weinreb CS, Panero R, Patel SH, Jankovic M, Sun J, Calogero RA, Klein AM, Camargo FD. Clonal analysis of lineage fate in native haematopoiesis. Nature. 2018 Jan 11;553(7687):212–216. PMCID: PMC5884107

  • Hrvatin S, Hochbaum DR, Nagy MA, Cicconet M, Robertson K, Cheadle L, Zilionis R, Ratner A, Borges-Monroy R, Klein AM, Sabatini BL, Greenberg ME. Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex. Nat Neurosci; 2018 Jan;21(1):120–129. PMCID: PMC5742025

 

2017

  • Schelker M, Feau S, Du J, Ranu N, Klipp E, MacBeath G, Schoeberl B, Raue A. Estimation of immune cell content in tumour tissue using single-cell RNA-seq data. Nat Commun.; 2017 Dec 11;8(1):2032. PMCID: PMC5725570

  • King KR, Aguirre AD, Ye Y-X, Sun Y, Roh JD, Ng RP Jr, Kohler RH, Arlauckas SP, Iwamoto Y, Savol A, Sadreyev RI, Kelly M, Fitzgibbons TP, Fitzgerald KA, Mitchison T, Libby P, Nahrendorf M, Weissleder R. IRF3 and type I interferons fuel a fatal response to myocardial infarction. Nat Med.; 2017 Dec;23(12):1481–1487. PMCID: PMC6477926

  • Briggs JA, Li VC, Lee S, Woolf CJ, Klein A, Kirschner MW. Mouse embryonic stem cells can differentiate via multiple paths to the same state. Elife [Internet]. 2017 Oct 9;6. Available from: http://dx.doi.org/10.7554/eLife.26945 PMCID: PMC5648529

  • Kadoki M, Patil A, Thaiss CC, Brooks DJ, Pandey S, Deep D, Alvarez D, von Andrian UH, Wagers AJ, Nakai K, Mikkelsen TS, Soumillon M, Chevrier N. Organism-Level Analysis of Vaccination Reveals Networks of Protection across Tissues. Cell. 2017 Oct 5;171(2):398–413.e21. PMID: 28942919

  • Tang Q, Iyer S, Lobbardi R, Moore JC, Chen H, Lareau C, Hebert C, Shaw ML, Neftel C, Suva ML, Ceol CJ, Bernards A, Aryee M, Pinello L, Drummond IA, Langenau DM. Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing. J Exp Med; 2017 Oct 2;214(10):2875–2887. PMCID: PMC5626406

  • Sugimura R, Jha DK, Han A, Soria-Valles C, da Rocha EL, Lu Y-F, Goettel JA, Serrao E, Rowe RG, Malleshaiah M, Wong I, Sousa P, Zhu TN, Ditadi A, Keller G, Engelman AN, Snapper SB, Doulatov S, Daley GQ. Haematopoietic stem and progenitor cells from human pluripotent stem cells. Nature; 2017 May 25;545(7655):432–438. PMCID: PMC587214

2016

  • Baron M, Veres A, Wolock SL, Faust AL, Gaujoux R, Vetere A, Ryu JH, Wagner BK, Shen-Orr SS, Klein AM, Melton DA, Yanai I. A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure. Cell Syst. 2016 Oct 26;3(4):346–360.e4. PMCID: PMC5228327

2015

  • Klein AM, Mazutis L, Akartuna I, Tallapragada N, Veres A, Li V, Peshkin L, Weitz DA, Kirschner MW. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell. 2015;161(5):1187–1201. PMCID: PMC4441768