-
1
-
-
84891677425
-
Full-length RNA-seq from single cells using Smart-seq2
-
Picelli,S., Faridani,O.R., Björklund,A.K., Winberg,G., Sagasser,S. and Sandberg,R. (2014) Full-length RNA-seq from single cells using Smart-seq2. Nat. Protoc., 9, 171-181.
-
(2014)
Nat. Protoc
, vol.9
, pp. 171-181
-
-
Picelli, S.1
Faridani, O.R.2
Björklund, A.K.3
Winberg, G.4
Sagasser, S.5
Sandberg, R.6
-
2
-
-
84900529199
-
Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq
-
Treutlein,B., Brownfield,D.G., Wu,A.R., Neff,N.F., Mantalas,G.L., Espinoza,F.H., Desai,T.J., Krasnow,M.A. and Quake,S.R. (2014) Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. Nature, 509, 371-375.
-
(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
Desai, T.J.7
Krasnow, M.A.8
Quake, S.R.9
-
3
-
-
84931274624
-
A survey of human brain transcriptome diversity at the single cell level
-
Darmanis,S., Sloan,S.A., Zhang,Y., Enge,M., Caneda,C., Shuer,L.M., Hayden Gephart,M.G., Barres,B.A. and Quake,S.R. (2015) A survey of human brain transcriptome diversity at the single cell level. Proc. Natl. Acad. Sci. U.S.A., 112, 7285-7290.
-
(2015)
Proc. Natl. Acad. Sci. U.S.A
, vol.112
, pp. 7285-7290
-
-
Darmanis, S.1
Sloan, S.A.2
Zhang, Y.3
Enge, M.4
Caneda, C.5
Shuer, L.M.6
Hayden Gephart, M.G.7
Barres, B.A.8
Quake, S.R.9
-
4
-
-
79959403670
-
Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq
-
Islam,S., Kjällquist,U., Moliner,A., Zajac,P., Fan,J.-B., Lönnerberg,P. and Linnarsson,S. (2011) Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res., 21, 1160-1167.
-
(2011)
Genome Res
, vol.21
, pp. 1160-1167
-
-
Islam, S.1
Kjällquist, U.2
Moliner, A.3
Zajac, P.4
Fan, J.-B.5
Lönnerberg, P.6
Linnarsson, S.7
-
5
-
-
84895069488
-
Quantitative single-cell RNA-seq with unique molecular identifiers
-
Islam,S., Zeisel,A., Joost,S., La Manno,G., Zajac,P., Kasper,M., Lönnerberg,P. and Linnarsson,S. (2014) Quantitative single-cell RNA-seq with unique molecular identifiers. Nat. Methods, 11, 163-166.
-
(2014)
Nat. Methods
, vol.11
, pp. 163-166
-
-
Islam, S.1
Zeisel, A.2
Joost, S.3
La Manno, G.4
Zajac, P.5
Kasper, M.6
Lönnerberg, P.7
Linnarsson, S.8
-
6
-
-
85049606172
-
NanoCAGE: a high-resolution technique to discover and interrogate cell transcriptomes
-
Salimullah,M., Sakai,M., Mizuho,S., Plessy,C. and Carninci,P. (2011) NanoCAGE: a high-resolution technique to discover and interrogate cell transcriptomes. Cold Spring Harb. Protoc., 2011, 96-110.
-
(2011)
Cold Spring Harb. Protoc
, vol.2011
, pp. 96-110
-
-
Salimullah, M.1
Sakai, M.2
Mizuho, S.3
Plessy, C.4
Carninci, P.5
-
7
-
-
9144233601
-
Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage
-
Shiraki,T., Kondo,S., Katayama,S., Waki,K., Kasukawa,T., Kawaji,H., Kodzius,R., Watahiki,A., Nakamura,M., Arakawa,T. et al. (2003) Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc. Natl. Acad. Sci. U.S.A., 100, 15776-15781.
-
(2003)
Proc. Natl. Acad. Sci. U.S.A
, vol.100
, pp. 15776-15781
-
-
Shiraki, T.1
Kondo, S.2
Katayama, S.3
Waki, K.4
Kasukawa, T.5
Kawaji, H.6
Kodzius, R.7
Watahiki, A.8
Nakamura, M.9
Arakawa, T.10
-
8
-
-
84946780209
-
Progressive chromatin condensation and H3K9 methylation regulate the differentiation of embryonic and hematopoietic stem cells
-
Ugarte,F., Sousae,R., Cinquin,B., Martin,E.W., Krietsch,J., Sanchez,G., Inman,M., Tsang,H., Warr,M., Passegué,E. et al. (2015) Progressive chromatin condensation and H3K9 methylation regulate the differentiation of embryonic and hematopoietic stem cells. Stem Cell Rep., 5, 728-740.
-
(2015)
Stem Cell Rep
, vol.5
, pp. 728-740
-
-
Ugarte, F.1
Sousae, R.2
Cinquin, B.3
Martin, E.W.4
Krietsch, J.5
Sanchez, G.6
Inman, M.7
Tsang, H.8
Warr, M.9
Passegué, E.10
-
9
-
-
84922547230
-
ROBO4-mediated vascular integrity regulates the directionality of hematopoietic stem cell trafficking
-
Smith-Berdan,S., Nguyen,A., Hong,M.A. and Forsberg,E.C. (2015) ROBO4-mediated vascular integrity regulates the directionality of hematopoietic stem cell trafficking. Stem Cell Rep., 4, 255-268.
-
(2015)
Stem Cell Rep
, vol.4
, pp. 255-268
-
-
Smith-Berdan, S.1
Nguyen, A.2
Hong, M.A.3
Forsberg, E.C.4
-
10
-
-
84897801113
-
Flk2/Flt3 promotes both myeloid and lymphoid development by expanding non-self-renewing multipotent hematopoietic progenitor cells
-
Beaudin,A.E., Boyer,S.W. and Forsberg,E.C. (2014) Flk2/Flt3 promotes both myeloid and lymphoid development by expanding non-self-renewing multipotent hematopoietic progenitor cells. Exp. Hematol., 42, 218-229.
-
(2014)
Exp. Hematol
, vol.42
, pp. 218-229
-
-
Beaudin, A.E.1
Boyer, S.W.2
Forsberg, E.C.3
-
11
-
-
84913593681
-
Tn5 transposase and tagmentation procedures for massively scaled sequencing projects
-
Picelli,S., Björklund,A.K., Reinius,B., Sagasser,S., Winberg,G. and Sandberg,R. (2014) Tn5 transposase and tagmentation procedures for massively scaled sequencing projects. Genome Res., 24, 2033-2040.
-
(2014)
Genome Res
, vol.24
, pp. 2033-2040
-
-
Picelli, S.1
Björklund, A.K.2
Reinius, B.3
Sagasser, S.4
Winberg, G.5
Sandberg, R.6
-
12
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
ENCODE Project Consortium
-
ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
13
-
-
84905049901
-
Trimmomatic: a flexible trimmer for Illumina sequence data
-
Bolger,A.M., Lohse,M. and Usadel,B. (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30, 2114-2120.
-
(2014)
Bioinformatics
, vol.30
, pp. 2114-2120
-
-
Bolger, A.M.1
Lohse, M.2
Usadel, B.3
-
14
-
-
80255127234
-
Cutadapt removes adapter sequences from high-throughput sequencing reads
-
Martin,M. (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. Journal., 17, 10-12.
-
(2011)
EMBnet. Journal
, vol.17
, pp. 10-12
-
-
Martin, M.1
-
15
-
-
84871809302
-
STAR: ultrafast universal RNA-seq aligner
-
Dobin,A., Davis,C.A., Schlesinger,F., Drenkow,J., Zaleski,C., Jha,S., Batut,P., Chaisson,M. and Gingeras,T.R. (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 29, 15-21.
-
(2013)
Bioinformatics
, vol.29
, pp. 15-21
-
-
Dobin, A.1
Davis, C.A.2
Schlesinger, F.3
Drenkow, J.4
Zaleski, C.5
Jha, S.6
Batut, P.7
Chaisson, M.8
Gingeras, T.R.9
-
16
-
-
84897397058
-
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
-
Liao,Y., Smyth,G.K. and Shi,W. (2014) featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30, 923-930.
-
(2014)
Bioinformatics
, vol.30
, pp. 923-930
-
-
Liao, Y.1
Smyth, G.K.2
Shi, W.3
-
17
-
-
84860771820
-
SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing
-
Bankevich,A., Nurk,S., Antipov,D., Gurevich,A.A., Dvorkin,M., Kulikov,A.S., Lesin,V.M., Nikolenko,S.I., Pham,S., Prjibelski,A.D. et al. (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol., 19, 455-477.
-
(2012)
J. Comput. Biol
, vol.19
, pp. 455-477
-
-
Bankevich, A.1
Nurk, S.2
Antipov, D.3
Gurevich, A.A.4
Dvorkin, M.5
Kulikov, A.S.6
Lesin, V.M.7
Nikolenko, S.I.8
Pham, S.9
Prjibelski, A.D.10
-
18
-
-
84883563447
-
IgBLAST: an immunoglobulin variable domain sequence analysis tool
-
Ye,J., Ma,N., Madden,T.L. and Ostell,J.M. (2013) IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Res., 41, W34-W40.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. W34-W40
-
-
Ye, J.1
Ma, N.2
Madden, T.L.3
Ostell, J.M.4
-
19
-
-
2642551345
-
IMGT-ONTOLOGY for immunogenetics and immunoinformatics
-
Lefranc,M.-P., Giudicelli,V., Ginestoux,C., Bosc,N., Folch,G., Guiraudou,D., Jabado-Michaloud,J., Magris,S., Scaviner,D., Thouvenin,V. et al. (2004) IMGT-ONTOLOGY for immunogenetics and immunoinformatics. In Silico Biol., 4, 17-29.
-
(2004)
Silico Biol
, vol.4
, pp. 17-29
-
-
Lefranc, M.-P.1
Giudicelli, V.2
Ginestoux, C.3
Bosc, N.4
Folch, G.5
Guiraudou, D.6
Jabado-Michaloud, J.7
Magris, S.8
Scaviner, D.9
Thouvenin, V.10
-
20
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li,H. and Durbin,R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
21
-
-
34247493236
-
Matplotlib: a 2D graphics environment
-
Hunter,J.D. (2007) Matplotlib: a 2D graphics environment. Comput. Sci. Eng., 9, 90-95.
-
(2007)
Comput. Sci. Eng
, vol.9
, pp. 90-95
-
-
Hunter, J.D.1
-
22
-
-
34247500374
-
Python for scientific computing
-
Oliphant,T.E. (2007) Python for scientific computing. Comput. Sci. Eng., 9, 10-20.
-
(2007)
Comput. Sci. Eng
, vol.9
, pp. 10-20
-
-
Oliphant, T.E.1
-
23
-
-
79952595565
-
The NumPy array: a structure for efficient numerical computation
-
van der Walt,S., Colbert,S.C. and Varoquaux,G. (2011) The NumPy array: a structure for efficient numerical computation. Comput. Sci. Eng., 13, 22-30.
-
(2011)
Comput. Sci. Eng
, vol.13
, pp. 22-30
-
-
van der Walt, S.1
Colbert, S.C.2
Varoquaux, G.3
-
25
-
-
85025142062
-
Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells
-
Byrne,A., Beaudin,A.E., Olsen,H.E., Jain,M., Cole,C., Palmer,T., DuBois,R.M., Forsberg,E.C., Akeson,M. and Vollmers,C. (2017) Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells. Nat. Commun., 8, 16027.
-
(2017)
Nat. Commun
, vol.8
, pp. 16027
-
-
Byrne, A.1
Beaudin, A.E.2
Olsen, H.E.3
Jain, M.4
Cole, C.5
Palmer, T.6
DuBois, R.M.7
Forsberg, E.C.8
Akeson, M.9
Vollmers, C.10
-
26
-
-
85012271992
-
Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput
-
2nd, and
-
Gierahn,T.M., Wadsworth,M.H. 2nd, Hughes,T.K., Bryson,B.D., Butler,A., Satija,R., Fortune,S., Love,J.C. and Shalek,A.K. (2017) Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput. Nat. Methods, 14, 395-398.
-
(2017)
Nat. Methods
, vol.14
, pp. 395-398
-
-
Gierahn, T.M.1
Wadsworth, M.H.2
Hughes, T.K.3
Bryson, B.D.4
Butler, A.5
Satija, R.6
Fortune, S.7
Love, J.C.8
Shalek, A.K.9
-
27
-
-
85009446777
-
Massively parallel digital transcriptional profiling of single cells
-
Zheng,G.X.Y., Terry,J.M., Belgrader,P., Ryvkin,P., Bent,Z.W., Wilson,R., Ziraldo,S.B., Wheeler,T.D., McDermott,G.P., Zhu,J. et al. (2017) Massively parallel digital transcriptional profiling of single cells. Nat. Commun., 8, 14049.
-
(2017)
Nat. Commun
, vol.8
, pp. 14049
-
-
Zheng, G.X.Y.1
Terry, J.M.2
Belgrader, P.3
Ryvkin, P.4
Bent, Z.W.5
Wilson, R.6
Ziraldo, S.B.7
Wheeler, T.D.8
McDermott, G.P.9
Zhu, J.10
-
28
-
-
84893905629
-
Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types
-
Jaitin,D.A., Kenigsberg,E., Keren-Shaul,H., Elefant,N., Paul,F., Zaretsky,I., Mildner,A., Cohen,N., Jung,S., Tanay,A. et al. (2014) Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science, 343, 776-779.
-
(2014)
Science
, vol.343
, pp. 776-779
-
-
Jaitin, D.A.1
Kenigsberg, E.2
Keren-Shaul, H.3
Elefant, N.4
Paul, F.5
Zaretsky, I.6
Mildner, A.7
Cohen, N.8
Jung, S.9
Tanay, A.10
-
29
-
-
85008473053
-
Intrinsic transcriptional heterogeneity in B cells controls early class switching to IgE
-
Wu,Y.L., Stubbington,M.J.T., Daly,M., Teichmann,S.A. and Rada,C. (2017) Intrinsic transcriptional heterogeneity in B cells controls early class switching to IgE. J. Exp. Med., 214, 183-196.
-
(2017)
J. Exp. Med
, vol.214
, pp. 183-196
-
-
Wu, Y.L.1
Stubbington, M.J.T.2
Daly, M.3
Teichmann, S.A.4
Rada, C.5
-
30
-
-
84964556059
-
Pooling across cells to normalize single-cell RNA sequencing data with many zero counts
-
Lun,A.T.L., Bach,K. and Marioni,J.C. (2016) Pooling across cells to normalize single-cell RNA sequencing data with many zero counts. Genome Biol., 17, 75.
-
(2016)
Genome Biol
, vol.17
, pp. 75
-
-
Lun, A.T.L.1
Bach, K.2
Marioni, J.C.3
-
31
-
-
0021255196
-
Changes in J chain and mu chain RNA expression as a function of B cell differentiation
-
Lamson,G. and Koshland,M.E. (1984) Changes in J chain and mu chain RNA expression as a function of B cell differentiation. J. Exp. Med., 160, 877-892.
-
(1984)
J. Exp. Med
, vol.160
, pp. 877-892
-
-
Lamson, G.1
Koshland, M.E.2
-
32
-
-
84954476936
-
Multifunctional role of the transcription factor Blimp-1 in coordinating plasma cell differentiation
-
Minnich,M., Tagoh,H., Bönelt,P., Axelsson,E., Fischer,M., Cebolla,B., Tarakhovsky,A., Nutt,S.L., Jaritz,M. and Busslinger,M. (2016) Multifunctional role of the transcription factor Blimp-1 in coordinating plasma cell differentiation. Nat. Immunol., 17, 331-343.
-
(2016)
Nat. Immunol
, vol.17
, pp. 331-343
-
-
Minnich, M.1
Tagoh, H.2
Bönelt, P.3
Axelsson, E.4
Fischer, M.5
Cebolla, B.6
Tarakhovsky, A.7
Nutt, S.L.8
Jaritz, M.9
Busslinger, M.10
-
33
-
-
84923829724
-
The generation of antibody-secreting plasma cells
-
Nutt,S.L., Hodgkin,P.D., Tarlinton,D.M. and Corcoran,L.M. (2015) The generation of antibody-secreting plasma cells. Nat. Rev. Immunol., 15, 160-171.
-
(2015)
Nat. Rev. Immunol
, vol.15
, pp. 160-171
-
-
Nutt, S.L.1
Hodgkin, P.D.2
Tarlinton, D.M.3
Corcoran, L.M.4
-
34
-
-
10344227714
-
Analysis of the major patterns of B cell gene expression changes in response to short-term stimulation with 33 single ligands
-
Zhu,X., Hart,R., Chang,M.S., Kim,J.-W., Lee,S.Y., Cao,Y.A., Mock,D., Ke,E., Saunders,B., Alexander,A. et al. (2004) Analysis of the major patterns of B cell gene expression changes in response to short-term stimulation with 33 single ligands. J. Immunol., 173, 7141-7149.
-
(2004)
J. Immunol
, vol.173
, pp. 7141-7149
-
-
Zhu, X.1
Hart, R.2
Chang, M.S.3
Kim, J.-W.4
Lee, S.Y.5
Cao, Y.A.6
Mock, D.7
Ke, E.8
Saunders, B.9
Alexander, A.10
-
35
-
-
0042470566
-
Regulatory mechanisms that determine the development and function of plasma cells
-
Calame,K.L., Lin,K.-I. and Tunyaplin,C. (2003) Regulatory mechanisms that determine the development and function of plasma cells. Annu. Rev. Immunol., 21, 205-230.
-
(2003)
Annu. Rev. Immunol
, vol.21
, pp. 205-230
-
-
Calame, K.L.1
Lin, K.-I.2
Tunyaplin, C.3
-
36
-
-
44449118948
-
Rapid cloning of high-affinity human monoclonal antibodies against influenza virus
-
Wrammert,J., Smith,K., Miller,J., Langley,W.A., Kokko,K., Larsen,C., Zheng,N.-Y., Mays,I., Garman,L., Helms,C. et al. (2008) Rapid cloning of high-affinity human monoclonal antibodies against influenza virus. Nature, 453, 667-671.
-
(2008)
Nature
, vol.453
, pp. 667-671
-
-
Wrammert, J.1
Smith, K.2
Miller, J.3
Langley, W.A.4
Kokko, K.5
Larsen, C.6
Zheng, N.-Y.7
Mays, I.8
Garman, L.9
Helms, C.10
-
37
-
-
85050262766
-
BASIC: BCR assembly from single cells
-
Canzar,S., Neu,K.E., Tang,Q., Wilson,P.C. and Khan,A.A. (2017) BASIC: BCR assembly from single cells. Bioinformatics, 33, 425-427.
-
(2017)
Bioinformatics
, vol.33
, pp. 425-427
-
-
Canzar, S.1
Neu, K.E.2
Tang, Q.3
Wilson, P.C.4
Khan, A.A.5
-
38
-
-
84884752287
-
Comparison of RNA- or LNA-hybrid oligonucleotides in template-switching reactions for high-speed sequencing library preparation
-
Harbers,M., Kato,S., de Hoon,M., Hayashizaki,Y., Carninci,P. and Plessy,C. (2013) Comparison of RNA- or LNA-hybrid oligonucleotides in template-switching reactions for high-speed sequencing library preparation. BMC Genomics, 14, 665.
-
(2013)
BMC Genomics
, vol.14
, pp. 665
-
-
Harbers, M.1
Kato, S.2
de Hoon, M.3
Hayashizaki, Y.4
Carninci, P.5
Plessy, C.6
|