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Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue. / Hardwick, Simon A.; Hu, Wen; Joglekar, Anoushka; Fan, Li; Collier, Paul G.; Foord, Careen; Balacco, Jennifer; Lanjewar, Samantha; Sampson, Maureen Mc Guirk; Koopmans, Frank; Prjibelski, Andrey D.; Mikheenko, Alla; Belchikov, Natan; Jarroux, Julien; Lucas, Anne Bergstrom; Palkovits, Miklós; Luo, Wenjie; Milner, Teresa A.; Ndhlovu, Lishomwa C.; Smit, August B.; Trojanowski, John Q.; Lee, Virginia M.Y.; Fedrigo, Olivier; Sloan, Steven A.; Tombácz, Dóra; Ross, M. Elizabeth; Jarvis, Erich; Boldogkői, Zsolt; Gan, Li; Tilgner, Hagen U.

в: Nature Biotechnology, Том 40, № 7, 07.2022, стр. 1082-1092.

Результаты исследований: Научные публикации в периодических изданиях › статья › Рецензирование

Harvard

Hardwick, SA, Hu, W, Joglekar, A, Fan, L, Collier, PG, Foord, C, Balacco, J, Lanjewar, S, Sampson, MMG, Koopmans, F, Prjibelski, AD, Mikheenko, A, Belchikov, N, Jarroux, J, Lucas, AB, Palkovits, M, Luo, W, Milner, TA, Ndhlovu, LC, Smit, AB, Trojanowski, JQ, Lee, VMY, Fedrigo, O, Sloan, SA, Tombácz, D, Ross, ME, Jarvis, E, Boldogkői, Z, Gan, L & Tilgner, HU 2022, 'Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue', Nature Biotechnology, Том. 40, № 7, стр. 1082-1092. https://doi.org/10.1038/s41587-022-01231-3

APA

Hardwick, S. A., Hu, W., Joglekar, A., Fan, L., Collier, P. G., Foord, C., Balacco, J., Lanjewar, S., Sampson, M. M. G., Koopmans, F., Prjibelski, A. D., Mikheenko, A., Belchikov, N., Jarroux, J., Lucas, A. B., Palkovits, M., Luo, W., Milner, T. A., Ndhlovu, L. C., ... Tilgner, H. U. (2022). Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue. Nature Biotechnology, 40(7), 1082-1092. https://doi.org/10.1038/s41587-022-01231-3

Vancouver

Hardwick SA, Hu W, Joglekar A, Fan L, Collier PG, Foord C и пр. Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue. Nature Biotechnology. 2022 Июль;40(7):1082-1092. https://doi.org/10.1038/s41587-022-01231-3

Author

Hardwick, Simon A. ; Hu, Wen ; Joglekar, Anoushka ; Fan, Li ; Collier, Paul G. ; Foord, Careen ; Balacco, Jennifer ; Lanjewar, Samantha ; Sampson, Maureen Mc Guirk ; Koopmans, Frank ; Prjibelski, Andrey D. ; Mikheenko, Alla ; Belchikov, Natan ; Jarroux, Julien ; Lucas, Anne Bergstrom ; Palkovits, Miklós ; Luo, Wenjie ; Milner, Teresa A. ; Ndhlovu, Lishomwa C. ; Smit, August B. ; Trojanowski, John Q. ; Lee, Virginia M.Y. ; Fedrigo, Olivier ; Sloan, Steven A. ; Tombácz, Dóra ; Ross, M. Elizabeth ; Jarvis, Erich ; Boldogkői, Zsolt ; Gan, Li ; Tilgner, Hagen U. / Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue. в: Nature Biotechnology. 2022 ; Том 40, № 7. стр. 1082-1092.

BibTeX

@article{e0ff5be312d944b19d6108dbf8d62d3d,
title = "Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue",
abstract = "Single-nuclei RNA sequencing characterizes cell types at the gene level. However, compared to single-cell approaches, many single-nuclei cDNAs are purely intronic, lack barcodes and hinder the study of isoforms. Here we present single-nuclei isoform RNA sequencing (SnISOr-Seq). Using microfluidics, PCR-based artifact removal, target enrichment and long-read sequencing, SnISOr-Seq increased barcoded, exon-spanning long reads 7.5-fold compared to naive long-read single-nuclei sequencing. We applied SnISOr-Seq to adult human frontal cortex and found that exons associated with autism exhibit coordinated and highly cell-type-specific inclusion. We found two distinct combination patterns: those distinguishing neural cell types, enriched in TSS-exon, exon-polyadenylation-site and non-adjacent exon pairs, and those with multiple configurations within one cell type, enriched in adjacent exon pairs. Finally, we observed that human-specific exons are almost as tightly coordinated as conserved exons, implying that coordination can be rapidly established during evolution. SnISOr-Seq enables cell-type-specific long-read isoform analysis in human brain and in any frozen or hard-to-dissociate sample.",
keywords = "Alternative Splicing/genetics, Brain/metabolism, Exons/genetics, Humans, Protein Isoforms/genetics, RNA/genetics, Sequence Analysis, RNA",
author = "Hardwick, {Simon A.} and Wen Hu and Anoushka Joglekar and Li Fan and Collier, {Paul G.} and Careen Foord and Jennifer Balacco and Samantha Lanjewar and Sampson, {Maureen Mc Guirk} and Frank Koopmans and Prjibelski, {Andrey D.} and Alla Mikheenko and Natan Belchikov and Julien Jarroux and Lucas, {Anne Bergstrom} and Mikl{\'o}s Palkovits and Wenjie Luo and Milner, {Teresa A.} and Ndhlovu, {Lishomwa C.} and Smit, {August B.} and Trojanowski, {John Q.} and Lee, {Virginia M.Y.} and Olivier Fedrigo and Sloan, {Steven A.} and D{\'o}ra Tomb{\'a}cz and Ross, {M. Elizabeth} and Erich Jarvis and Zsolt Boldogk{\H o}i and Li Gan and Tilgner, {Hagen U.}",
note = "Hardwick, S.A., Hu, W., Joglekar, A. et al. Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue. Nat Biotechnol (2022). https://doi.org/10.1038/s41587-022-01231-3",
year = "2022",
month = jul,
doi = "10.1038/s41587-022-01231-3",
language = "English",
volume = "40",
pages = "1082--1092",
journal = "Nature Biotechnology",
issn = "1087-0156",
publisher = "Nature Publishing Group",
number = "7",

}

RIS

TY - JOUR

T1 - Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue

AU - Hardwick, Simon A.

AU - Hu, Wen

AU - Joglekar, Anoushka

AU - Fan, Li

AU - Collier, Paul G.

AU - Foord, Careen

AU - Balacco, Jennifer

AU - Lanjewar, Samantha

AU - Sampson, Maureen Mc Guirk

AU - Koopmans, Frank

AU - Prjibelski, Andrey D.

AU - Mikheenko, Alla

AU - Belchikov, Natan

AU - Jarroux, Julien

AU - Lucas, Anne Bergstrom

AU - Palkovits, Miklós

AU - Luo, Wenjie

AU - Milner, Teresa A.

AU - Ndhlovu, Lishomwa C.

AU - Smit, August B.

AU - Trojanowski, John Q.

AU - Lee, Virginia M.Y.

AU - Fedrigo, Olivier

AU - Sloan, Steven A.

AU - Tombácz, Dóra

AU - Ross, M. Elizabeth

AU - Jarvis, Erich

AU - Boldogkői, Zsolt

AU - Gan, Li

AU - Tilgner, Hagen U.

N1 - Hardwick, S.A., Hu, W., Joglekar, A. et al. Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue. Nat Biotechnol (2022). https://doi.org/10.1038/s41587-022-01231-3

PY - 2022/7

Y1 - 2022/7

N2 - Single-nuclei RNA sequencing characterizes cell types at the gene level. However, compared to single-cell approaches, many single-nuclei cDNAs are purely intronic, lack barcodes and hinder the study of isoforms. Here we present single-nuclei isoform RNA sequencing (SnISOr-Seq). Using microfluidics, PCR-based artifact removal, target enrichment and long-read sequencing, SnISOr-Seq increased barcoded, exon-spanning long reads 7.5-fold compared to naive long-read single-nuclei sequencing. We applied SnISOr-Seq to adult human frontal cortex and found that exons associated with autism exhibit coordinated and highly cell-type-specific inclusion. We found two distinct combination patterns: those distinguishing neural cell types, enriched in TSS-exon, exon-polyadenylation-site and non-adjacent exon pairs, and those with multiple configurations within one cell type, enriched in adjacent exon pairs. Finally, we observed that human-specific exons are almost as tightly coordinated as conserved exons, implying that coordination can be rapidly established during evolution. SnISOr-Seq enables cell-type-specific long-read isoform analysis in human brain and in any frozen or hard-to-dissociate sample.

AB - Single-nuclei RNA sequencing characterizes cell types at the gene level. However, compared to single-cell approaches, many single-nuclei cDNAs are purely intronic, lack barcodes and hinder the study of isoforms. Here we present single-nuclei isoform RNA sequencing (SnISOr-Seq). Using microfluidics, PCR-based artifact removal, target enrichment and long-read sequencing, SnISOr-Seq increased barcoded, exon-spanning long reads 7.5-fold compared to naive long-read single-nuclei sequencing. We applied SnISOr-Seq to adult human frontal cortex and found that exons associated with autism exhibit coordinated and highly cell-type-specific inclusion. We found two distinct combination patterns: those distinguishing neural cell types, enriched in TSS-exon, exon-polyadenylation-site and non-adjacent exon pairs, and those with multiple configurations within one cell type, enriched in adjacent exon pairs. Finally, we observed that human-specific exons are almost as tightly coordinated as conserved exons, implying that coordination can be rapidly established during evolution. SnISOr-Seq enables cell-type-specific long-read isoform analysis in human brain and in any frozen or hard-to-dissociate sample.

KW - Alternative Splicing/genetics

KW - Brain/metabolism

KW - Exons/genetics

KW - Humans

KW - Protein Isoforms/genetics

KW - RNA/genetics

KW - Sequence Analysis, RNA

UR - http://www.scopus.com/inward/record.url?scp=85125715810&partnerID=8YFLogxK

UR - https://www.mendeley.com/catalogue/27215911-a652-3079-acda-b801a4ec1a4d/

U2 - 10.1038/s41587-022-01231-3

DO - 10.1038/s41587-022-01231-3

M3 - Article

C2 - 35256815

AN - SCOPUS:85125715810

VL - 40

SP - 1082

EP - 1092

JO - Nature Biotechnology

JF - Nature Biotechnology

SN - 1087-0156

IS - 7

ER -

ID: 94683191