Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex. Pollen, A. A, Nowakowski, T. J, Shuga, J., Wang, X., Leyrat, A. A, Lui, J. H, Li, N., Szpankowski, L., Fowler, B., Chen, P., Ramalingam, N., Sun, G., Thu, M., Norris, M., Lebofsky, R., Toppani, D., Kemp, 2., Wong, M., Clerkson, B., Jones, B. N, Wu, S., Knutsson, L., Alvarado, B., Wang, J., Weaver, L. S, May, A. P, Jones, R. C, Unger, M. A, Kriegstein, A. R, & West, J. A A Nat Biotechnol, 32(10):1053–1058, August, 2014. abstract bibtex Large-scale surveys of single-cell gene expression have the potential to reveal rare cell populations and lineage relationships but require efficient methods for cell capture and mRNA sequencing. Although cellular barcoding strategies allow parallel sequencing of single cells at ultra-low depths, the limitations of shallow sequencing have not been investigated directly. By capturing 301 single cells from 11 populations using microfluidics and analyzing single-cell transcriptomes across downsampled sequencing depths, we demonstrate that shallow single-cell mRNA sequencing ( 50,000 reads per cell) is sufficient for unbiased cell-type classification and biomarker identification. In the developing cortex, we identify diverse cell types, including multiple progenitor and neuronal subtypes, and we identify EGR1 and FOS as previously unreported candidate targets of Notch signaling in human but not mouse radial glia. Our strategy establishes an efficient method for unbiased analysis and comparison of cell populations from heterogeneous tissue by microfluidic single-cell capture and low-coverage sequencing of many cells.
@ARTICLE{Pollen2014-ow,
title = "Low-coverage single-cell {mRNA} sequencing reveals cellular
heterogeneity and activated signaling pathways in developing
cerebral cortex",
author = "Pollen, Alex A and Nowakowski, Tomasz J and Shuga, Joe and Wang,
Xiaohui and Leyrat, Anne A and Lui, Jan H and Li, Nianzhen and
Szpankowski, Lukasz and Fowler, Brian and Chen, Peilin and
Ramalingam, Naveen and Sun, Gang and Thu, Myo and Norris, Michael
and Lebofsky, Ronald and Toppani, Dominique and Kemp, 2nd,
Darnell W and Wong, Michael and Clerkson, Barry and Jones,
Brittnee N and Wu, Shiquan and Knutsson, Lawrence and Alvarado,
Beatriz and Wang, Jing and Weaver, Lesley S and May, Andrew P and
Jones, Robert C and Unger, Marc A and Kriegstein, Arnold R and
West, Jay A A",
abstract = "Large-scale surveys of single-cell gene expression have the
potential to reveal rare cell populations and lineage
relationships but require efficient methods for cell capture and
mRNA sequencing. Although cellular barcoding strategies allow
parallel sequencing of single cells at ultra-low depths, the
limitations of shallow sequencing have not been investigated
directly. By capturing 301 single cells from 11 populations using
microfluidics and analyzing single-cell transcriptomes across
downsampled sequencing depths, we demonstrate that shallow
single-cell mRNA sequencing (~50,000 reads per cell) is
sufficient for unbiased cell-type classification and biomarker
identification. In the developing cortex, we identify diverse
cell types, including multiple progenitor and neuronal subtypes,
and we identify EGR1 and FOS as previously unreported candidate
targets of Notch signaling in human but not mouse radial glia.
Our strategy establishes an efficient method for unbiased
analysis and comparison of cell populations from heterogeneous
tissue by microfluidic single-cell capture and low-coverage
sequencing of many cells.",
journal = "Nat Biotechnol",
volume = 32,
number = 10,
pages = "1053--1058",
month = aug,
year = 2014,
language = "en"
}
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A A"],"bibdata":{"bibtype":"article","type":"article","title":"Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex","author":[{"propositions":[],"lastnames":["Pollen"],"firstnames":["Alex","A"],"suffixes":[]},{"propositions":[],"lastnames":["Nowakowski"],"firstnames":["Tomasz","J"],"suffixes":[]},{"propositions":[],"lastnames":["Shuga"],"firstnames":["Joe"],"suffixes":[]},{"propositions":[],"lastnames":["Wang"],"firstnames":["Xiaohui"],"suffixes":[]},{"propositions":[],"lastnames":["Leyrat"],"firstnames":["Anne","A"],"suffixes":[]},{"propositions":[],"lastnames":["Lui"],"firstnames":["Jan","H"],"suffixes":[]},{"propositions":[],"lastnames":["Li"],"firstnames":["Nianzhen"],"suffixes":[]},{"propositions":[],"lastnames":["Szpankowski"],"firstnames":["Lukasz"],"suffixes":[]},{"propositions":[],"lastnames":["Fowler"],"firstnames":["Brian"],"suffixes":[]},{"propositions":[],"lastnames":["Chen"],"firstnames":["Peilin"],"suffixes":[]},{"propositions":[],"lastnames":["Ramalingam"],"firstnames":["Naveen"],"suffixes":[]},{"propositions":[],"lastnames":["Sun"],"firstnames":["Gang"],"suffixes":[]},{"propositions":[],"lastnames":["Thu"],"firstnames":["Myo"],"suffixes":[]},{"propositions":[],"lastnames":["Norris"],"firstnames":["Michael"],"suffixes":[]},{"propositions":[],"lastnames":["Lebofsky"],"firstnames":["Ronald"],"suffixes":[]},{"propositions":[],"lastnames":["Toppani"],"firstnames":["Dominique"],"suffixes":[]},{"propositions":[],"lastnames":["Kemp"],"firstnames":["2nd"],"suffixes":["Darnell","W"]},{"propositions":[],"lastnames":["Wong"],"firstnames":["Michael"],"suffixes":[]},{"propositions":[],"lastnames":["Clerkson"],"firstnames":["Barry"],"suffixes":[]},{"propositions":[],"lastnames":["Jones"],"firstnames":["Brittnee","N"],"suffixes":[]},{"propositions":[],"lastnames":["Wu"],"firstnames":["Shiquan"],"suffixes":[]},{"propositions":[],"lastnames":["Knutsson"],"firstnames":["Lawrence"],"suffixes":[]},{"propositions":[],"lastnames":["Alvarado"],"firstnames":["Beatriz"],"suffixes":[]},{"propositions":[],"lastnames":["Wang"],"firstnames":["Jing"],"suffixes":[]},{"propositions":[],"lastnames":["Weaver"],"firstnames":["Lesley","S"],"suffixes":[]},{"propositions":[],"lastnames":["May"],"firstnames":["Andrew","P"],"suffixes":[]},{"propositions":[],"lastnames":["Jones"],"firstnames":["Robert","C"],"suffixes":[]},{"propositions":[],"lastnames":["Unger"],"firstnames":["Marc","A"],"suffixes":[]},{"propositions":[],"lastnames":["Kriegstein"],"firstnames":["Arnold","R"],"suffixes":[]},{"propositions":[],"lastnames":["West"],"firstnames":["Jay","A","A"],"suffixes":[]}],"abstract":"Large-scale surveys of single-cell gene expression have the potential to reveal rare cell populations and lineage relationships but require efficient methods for cell capture and mRNA sequencing. Although cellular barcoding strategies allow parallel sequencing of single cells at ultra-low depths, the limitations of shallow sequencing have not been investigated directly. By capturing 301 single cells from 11 populations using microfluidics and analyzing single-cell transcriptomes across downsampled sequencing depths, we demonstrate that shallow single-cell mRNA sequencing ( 50,000 reads per cell) is sufficient for unbiased cell-type classification and biomarker identification. In the developing cortex, we identify diverse cell types, including multiple progenitor and neuronal subtypes, and we identify EGR1 and FOS as previously unreported candidate targets of Notch signaling in human but not mouse radial glia. Our strategy establishes an efficient method for unbiased analysis and comparison of cell populations from heterogeneous tissue by microfluidic single-cell capture and low-coverage sequencing of many cells.","journal":"Nat Biotechnol","volume":"32","number":"10","pages":"1053–1058","month":"August","year":"2014","language":"en","bibtex":"@ARTICLE{Pollen2014-ow,\n title = \"Low-coverage single-cell {mRNA} sequencing reveals cellular\n heterogeneity and activated signaling pathways in developing\n cerebral cortex\",\n author = \"Pollen, Alex A and Nowakowski, Tomasz J and Shuga, Joe and Wang,\n Xiaohui and Leyrat, Anne A and Lui, Jan H and Li, Nianzhen and\n Szpankowski, Lukasz and Fowler, Brian and Chen, Peilin and\n Ramalingam, Naveen and Sun, Gang and Thu, Myo and Norris, Michael\n and Lebofsky, Ronald and Toppani, Dominique and Kemp, 2nd,\n Darnell W and Wong, Michael and Clerkson, Barry and Jones,\n Brittnee N and Wu, Shiquan and Knutsson, Lawrence and Alvarado,\n Beatriz and Wang, Jing and Weaver, Lesley S and May, Andrew P and\n Jones, Robert C and Unger, Marc A and Kriegstein, Arnold R and\n West, Jay A A\",\n abstract = \"Large-scale surveys of single-cell gene expression have the\n potential to reveal rare cell populations and lineage\n relationships but require efficient methods for cell capture and\n mRNA sequencing. Although cellular barcoding strategies allow\n parallel sequencing of single cells at ultra-low depths, the\n limitations of shallow sequencing have not been investigated\n directly. By capturing 301 single cells from 11 populations using\n microfluidics and analyzing single-cell transcriptomes across\n downsampled sequencing depths, we demonstrate that shallow\n single-cell mRNA sequencing (~50,000 reads per cell) is\n sufficient for unbiased cell-type classification and biomarker\n identification. In the developing cortex, we identify diverse\n cell types, including multiple progenitor and neuronal subtypes,\n and we identify EGR1 and FOS as previously unreported candidate\n targets of Notch signaling in human but not mouse radial glia.\n Our strategy establishes an efficient method for unbiased\n analysis and comparison of cell populations from heterogeneous\n tissue by microfluidic single-cell capture and low-coverage\n sequencing of many cells.\",\n journal = \"Nat Biotechnol\",\n volume = 32,\n number = 10,\n pages = \"1053--1058\",\n month = aug,\n year = 2014,\n language = \"en\"\n}\n\n","author_short":["Pollen, A. A","Nowakowski, T. J","Shuga, J.","Wang, X.","Leyrat, A. A","Lui, J. H","Li, N.","Szpankowski, L.","Fowler, B.","Chen, P.","Ramalingam, N.","Sun, G.","Thu, M.","Norris, M.","Lebofsky, R.","Toppani, D.","Kemp, 2.","Wong, M.","Clerkson, B.","Jones, B. N","Wu, S.","Knutsson, L.","Alvarado, B.","Wang, J.","Weaver, L. S","May, A. P","Jones, R. C","Unger, M. 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