메뉴 건너뛰기




Volumn 17, Issue 1, 2016, Pages

Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction

Author keywords

Metadata; Proximity extension assay; Single cell multi omics; Single cell proteomics; Single cell transcriptomics

Indexed keywords

CELL PROTEIN; COMPLEMENTARY DNA; DNA POLYMERASE; EXCISION REPAIR CROSS COMPLEMENTING PROTEIN; PROTEOME; RECOMBINANT PROTEIN; RNA DIRECTED DNA POLYMERASE; TRANSCRIPTOME; UNCLASSIFIED DRUG; RNA;

EID: 84988014533     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-016-1045-6     Document Type: Article
Times cited : (130)

References (53)
  • 2
    • 84872195205 scopus 로고    scopus 로고
    • Methods for qPCR gene expression profiling applied to 1440 lymphoblastoid single cells
    • Livak KJ, Wills QF, Tipping AJ, Datta K, Mittal R, Goldson AJ, et al. Methods for qPCR gene expression profiling applied to 1440 lymphoblastoid single cells. Methods. 2013;59:71-9.
    • (2013) Methods. , vol.59 , pp. 71-79
    • Livak, K.J.1    Wills, Q.F.2    Tipping, A.J.3    Datta, K.4    Mittal, R.5    Goldson, A.J.6
  • 4
    • 84903185013 scopus 로고    scopus 로고
    • Single-cell RNA-seq reveals dynamic paracrine control of cellular variation
    • Shalek AK, Satija R, Shuga J, Trombetta JJ, Gennert D, Lu D, et al. Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. Nature. 2014;510:363-9.
    • (2014) Nature. , vol.510 , pp. 363-369
    • Shalek, A.K.1    Satija, R.2    Shuga, J.3    Trombetta, J.J.4    Gennert, D.5    Lu, D.6
  • 6
    • 84900529199 scopus 로고    scopus 로고
    • Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq
    • Treutlein B, Brownfield DG, Wu AR, Neff NF, Mantalas GL, Espinoza FH, et al. Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. Nature. 2014;509:371-5.
    • (2014) Nature. , vol.509 , pp. 371-375
    • Treutlein, B.1    Brownfield, D.G.2    Wu, A.R.3    Neff, N.F.4    Mantalas, G.L.5    Espinoza, F.H.6
  • 7
    • 84929684998 scopus 로고    scopus 로고
    • Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells
    • Klein AM, Mazutis L, Akartuna I, Tallapragada N, Veres A, Li V, et al. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell. 2015;161:1187-201.
    • (2015) Cell. , vol.161 , pp. 1187-1201
    • Klein, A.M.1    Mazutis, L.2    Akartuna, I.3    Tallapragada, N.4    Veres, A.5    Li, V.6
  • 8
    • 84929684999 scopus 로고    scopus 로고
    • Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets
    • Macosko EZ, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M, et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell. 2015;161:1202-14.
    • (2015) Cell. , vol.161 , pp. 1202-1214
    • Macosko, E.Z.1    Basu, A.2    Satija, R.3    Nemesh, J.4    Shekhar, K.5    Goldman, M.6
  • 9
    • 84922311090 scopus 로고    scopus 로고
    • Combinatorial labeling of single cells for gene expression cytometry
    • Fan HC, Fu GK, Fodor SPA. Combinatorial labeling of single cells for gene expression cytometry. Science. 2015;347:1258367.
    • (2015) Science. , vol.347 , pp. 1258367
    • Fan, H.C.1    Fu, G.K.2    Fodor, S.P.A.3
  • 10
    • 84899929564 scopus 로고    scopus 로고
    • Heterogeneity in immune responses: from populations to single cells
    • Satija R, Shalek AK. Heterogeneity in immune responses: from populations to single cells. Trends Immunol. 2014;35:219-29.
    • (2014) Trends Immunol. , vol.35 , pp. 219-229
    • Satija, R.1    Shalek, A.K.2
  • 11
    • 79955750055 scopus 로고    scopus 로고
    • Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum
    • Bendall SC, Simonds EF, Qiu P, Amir E-aD, Krutzik PO, Finck R, et al. Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science. 2011;332:687-96.
    • (2011) Science , vol.332 , pp. 687-696
    • Bendall, S.C.1    Simonds, E.F.2    Qiu, P.3    Amir, E.-A.4    Krutzik, P.O.5    Finck, R.6
  • 13
    • 78649875958 scopus 로고    scopus 로고
    • Single-cell quantification of IL-2 response by effector and regulatory T cells reveals critical plasticity in immune response
    • Feinerman O, Jentsch G, Tkach KE, Coward JW, Hathorn MM, Sneddon MW, et al. Single-cell quantification of IL-2 response by effector and regulatory T cells reveals critical plasticity in immune response. Mol Syst Biol. 2010;6:437.
    • (2010) Mol Syst Biol. , vol.6 , pp. 437
    • Feinerman, O.1    Jentsch, G.2    Tkach, K.E.3    Coward, J.W.4    Hathorn, M.M.5    Sneddon, M.W.6
  • 14
    • 77950809059 scopus 로고    scopus 로고
    • A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations
    • Sharma SV, Lee DY, Li B, Quinlan MP, Takahashi F, Maheswaran S, et al. A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations. Cell. 2010;141:69-80.
    • (2010) Cell. , vol.141 , pp. 69-80
    • Sharma, S.V.1    Lee, D.Y.2    Li, B.3    Quinlan, M.P.4    Takahashi, F.5    Maheswaran, S.6
  • 15
    • 77955102352 scopus 로고    scopus 로고
    • Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells
    • Taniguchi Y, Choi PJ, Li G-W, Chen H, Babu M, Hearn J, et al. Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science. 2010;329:533-8.
    • (2010) Science , vol.329 , pp. 533-538
    • Taniguchi, Y.1    Choi, P.J.2    Li, G.-W.3    Chen, H.4    Babu, M.5    Hearn, J.6
  • 17
    • 84859641038 scopus 로고    scopus 로고
    • Using gene expression noise to understand gene regulation
    • Munsky B, Neuert G, van Oudenaarden A. Using gene expression noise to understand gene regulation. Science. 2012;336:183-7.
    • (2012) Science. , vol.336 , pp. 183-187
    • Munsky, B.1    Neuert, G.2    Oudenaarden, A.3
  • 20
    • 84958078627 scopus 로고    scopus 로고
    • The heterogeneity of human CD127(+) innate lymphoid cells revealed by single-cell RNA sequencing
    • Björklund ÅK, Forkel M, Picelli S, Konya V, Theorell J, Friberg D, et al. The heterogeneity of human CD127(+) innate lymphoid cells revealed by single-cell RNA sequencing. Nat Immunol. 2016;17:451-60.
    • (2016) Nat Immunol. , vol.17 , pp. 451-460
    • Björklund, K.1    Forkel, M.2    Picelli, S.3    Konya, V.4    Theorell, J.5    Friberg, D.6
  • 21
    • 84941333786 scopus 로고    scopus 로고
    • Pathogen cell-to-cell variability drives heterogeneity in host immune responses
    • Avraham R, Haseley N, Brown D, Penaranda C, Jijon HB, Trombetta JJ, et al. Pathogen cell-to-cell variability drives heterogeneity in host immune responses. Cell. 2015;162:1309-21.
    • (2015) Cell. , vol.162 , pp. 1309-1321
    • Avraham, R.1    Haseley, N.2    Brown, D.3    Penaranda, C.4    Jijon, H.B.5    Trombetta, J.J.6
  • 22
    • 84949252174 scopus 로고    scopus 로고
    • Single-cell genomics unveils critical regulators of Th17 cell pathogenicity
    • Gaublomme JT, Yosef N, Lee Y, Gertner RS, Yang LV, Wu C, et al. Single-cell genomics unveils critical regulators of Th17 cell pathogenicity. Cell. 2015;163:1400-12.
    • (2015) Cell. , vol.163 , pp. 1400-1412
    • Gaublomme, J.T.1    Yosef, N.2    Lee, Y.3    Gertner, R.S.4    Yang, L.V.5    Wu, C.6
  • 24
    • 84950290139 scopus 로고    scopus 로고
    • Transcriptional heterogeneity and lineage commitment in myeloid progenitors
    • Paul F, Arkin Y, Giladi A, Jaitin DA, Kenigsberg E, Keren-Shaul H, et al. Transcriptional heterogeneity and lineage commitment in myeloid progenitors. Cell. 2015;163:1663-77.
    • (2015) Cell. , vol.163 , pp. 1663-1677
    • Paul, F.1    Arkin, Y.2    Giladi, A.3    Jaitin, D.A.4    Kenigsberg, E.5    Keren-Shaul, H.6
  • 27
    • 84955681537 scopus 로고    scopus 로고
    • Fixed single-cell transcriptomic characterization of human radial glial diversity
    • Thomsen ER, Mich JK, Yao Z, Hodge RD, Doyle AM, Jang S, et al. Fixed single-cell transcriptomic characterization of human radial glial diversity. Nat Methods. 2016;13:87-93.
    • (2016) Nat Methods. , vol.13 , pp. 87-93
    • Thomsen, E.R.1    Mich, J.K.2    Yao, Z.3    Hodge, R.D.4    Doyle, A.M.5    Jang, S.6
  • 28
  • 32
    • 84870357009 scopus 로고    scopus 로고
    • Quantitative PCR analysis of DNA, RNAs, and proteins in the same single cell
    • Ståhlberg A, Thomsen C, Ruff D, Åman P. Quantitative PCR analysis of DNA, RNAs, and proteins in the same single cell. Clin Chem. 2012;58:1682-91.
    • (2012) Clin Chem. , vol.58 , pp. 1682-1691
    • Ståhlberg, A.1    Thomsen, C.2    Ruff, D.3    Åman, P.4
  • 34
    • 84939162152 scopus 로고    scopus 로고
    • Scalable microfluidics for single-cell RNA printing and sequencing
    • Bose S, Wan Z, Carr A, Rizvi AH, Vieira G, Pe'er D, et al. Scalable microfluidics for single-cell RNA printing and sequencing. Genome Biol. 2015;16:120.
    • (2015) Genome Biol. , vol.16 , pp. 120
    • Bose, S.1    Wan, Z.2    Carr, A.3    Rizvi, A.H.4    Vieira, G.5    Pe'er, D.6
  • 35
    • 33745072443 scopus 로고    scopus 로고
    • A microengraving method for rapid selection of single cells producing antigen-specific antibodies
    • Love JC, Ronan JL, Grotenbreg GM, van der Veen AG, Ploegh HL. A microengraving method for rapid selection of single cells producing antigen-specific antibodies. Nat Biotechnol. 2006;24:703-7.
    • (2006) Nat Biotechnol. , vol.24 , pp. 703-707
    • Love, J.C.1    Ronan, J.L.2    Grotenbreg, G.M.3    Veen, A.G.4    Ploegh, H.L.5
  • 37
    • 42349086630 scopus 로고    scopus 로고
    • Probing the active site steric flexibility of HIV-1 reverse transcriptase: different constraints for DNA- versus RNA-templated synthesis
    • Silverman AP, Garforth SJ, Prasad VR, Kool ET. Probing the active site steric flexibility of HIV-1 reverse transcriptase: different constraints for DNA- versus RNA-templated synthesis. Biochemistry. 2008;47:4800-7.
    • (2008) Biochemistry. , vol.47 , pp. 4800-4807
    • Silverman, A.P.1    Garforth, S.J.2    Prasad, V.R.3    Kool, E.T.4
  • 38
    • 80053301165 scopus 로고    scopus 로고
    • ProteinSeq: high-performance proteomic analyses by proximity ligation and next generation sequencing
    • Darmanis S, Nong RY, Vänelid J, Siegbahn A, Ericsson O, Fredriksson S, et al. ProteinSeq: high-performance proteomic analyses by proximity ligation and next generation sequencing. PLoS One. 2011;6:e25583.
    • (2011) PLoS One. , vol.6
    • Darmanis, S.1    Nong, R.Y.2    Vänelid, J.3    Siegbahn, A.4    Ericsson, O.5    Fredriksson, S.6
  • 39
    • 84866891364 scopus 로고    scopus 로고
    • Phorbol esters from jatropha meal triggered apoptosis, activated PKC-δ, caspase-3 proteins and down-regulated the proto-oncogenes in MCF-7 and HeLa cancer cell lines
    • Oskoueian E, Abdullah N, Ahmad S. Phorbol esters from jatropha meal triggered apoptosis, activated PKC-δ, caspase-3 proteins and down-regulated the proto-oncogenes in MCF-7 and HeLa cancer cell lines. Molecules. 2012;17:10816-30.
    • (2012) Molecules. , vol.17 , pp. 10816-10830
    • Oskoueian, E.1    Abdullah, N.2    Ahmad, S.3
  • 42
    • 84874321000 scopus 로고    scopus 로고
    • Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments
    • McDavid A, Finak G, Chattopadyay PK, Dominguez M, Lamoreaux L, Ma SS, et al. Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments. Bioinformatics. 2013;29:461-7.
    • (2013) Bioinformatics. , vol.29 , pp. 461-467
    • McDavid, A.1    Finak, G.2    Chattopadyay, P.K.3    Dominguez, M.4    Lamoreaux, L.5    Ma, S.S.6
  • 43
    • 0032546028 scopus 로고    scopus 로고
    • Intron-exon structure of the MET gene and cloning of an alternatively-spliced Met isoform reveals frequent exon-skipping of a single large internal exon
    • Lin JC, Naujokas M, Zhu H, Nolet S, Park M. Intron-exon structure of the MET gene and cloning of an alternatively-spliced Met isoform reveals frequent exon-skipping of a single large internal exon. Oncogene. 1998;16:833-42.
    • (1998) Oncogene. , vol.16 , pp. 833-842
    • Lin, J.C.1    Naujokas, M.2    Zhu, H.3    Nolet, S.4    Park, M.5
  • 44
    • 0142242172 scopus 로고    scopus 로고
    • Epidermal growth factor receptor down-regulation induced by UVA in human keratinocytes does not require the receptor kinase activity
    • He YY, Huang JL, Gentry JB, Chignell CF. Epidermal growth factor receptor down-regulation induced by UVA in human keratinocytes does not require the receptor kinase activity. J Biol Chem. 2003;278:42457-65.
    • (2003) J Biol Chem. , vol.278 , pp. 42457-42465
    • He, Y.Y.1    Huang, J.L.2    Gentry, J.B.3    Chignell, C.F.4
  • 45
    • 6344279932 scopus 로고    scopus 로고
    • Caspase inhibition blocks human T cell proliferation by suppressing appropriate regulation of IL-2, CD25, and cell cycle-associated proteins
    • Falk M, Ussat S, Reiling N, Wesch D, Kabelitz D, Adam-Klages S. Caspase inhibition blocks human T cell proliferation by suppressing appropriate regulation of IL-2, CD25, and cell cycle-associated proteins. J Immunol. 2004;173:5077-85.
    • (2004) J Immunol. , vol.173 , pp. 5077-5085
    • Falk, M.1    Ussat, S.2    Reiling, N.3    Wesch, D.4    Kabelitz, D.5    Adam-Klages, S.6
  • 46
    • 11144356134 scopus 로고    scopus 로고
    • The histone deacetylase inhibitor MS-275 interacts synergistically with fludarabine to induce apoptosis in human leukemia cells
    • Maggio SC, Rosato RR, Kramer LB, Dai Y, Rahmani M, Paik DS, et al. The histone deacetylase inhibitor MS-275 interacts synergistically with fludarabine to induce apoptosis in human leukemia cells. Cancer Res. 2004;64:2590-600.
    • (2004) Cancer Res. , vol.64 , pp. 2590-2600
    • Maggio, S.C.1    Rosato, R.R.2    Kramer, L.B.3    Dai, Y.4    Rahmani, M.5    Paik, D.S.6
  • 47
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2008;4:44-57.
    • (2008) Nat Protoc. , vol.4 , pp. 44-57
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 49
    • 84878935042 scopus 로고    scopus 로고
    • Nanobodies: natural single-domain antibodies
    • Muyldermans S. Nanobodies: natural single-domain antibodies. Annu Rev Biochem. 2013;82:775-97.
    • (2013) Annu Rev Biochem. , vol.82 , pp. 775-797
    • Muyldermans, S.1
  • 51
    • 34548154323 scopus 로고    scopus 로고
    • Detecting antigens by quantitative immuno-PCR
    • Niemeyer CM, Adler M, Wacker R. Detecting antigens by quantitative immuno-PCR. Nat Protoc. 2007;2:1918-30.
    • (2007) Nat Protoc. , vol.2 , pp. 1918-1930
    • Niemeyer, C.M.1    Adler, M.2    Wacker, R.3
  • 52


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.