Defining a personal, allele-specific, and single-molecule long-read transcriptome
Open accessAbstract
Significance: RNA molecules of higher eukaryotes can be thousands of nucleotides long and are expressed from two distinct alleles, which can differ by single nucleotide variations (SNVs) in the mature RNA molecule. The de facto standard in RNA biology is short (≤101 bp) read sequencing, which, although very useful, does not cover the entire molecule in a read. We show that using amplification-free long-read sequencing one can often ( i ) cover the entire molecule, ( ii ) determine the allele it originated from, and ( iii ) record its entire exon-intron structure within a single read, thus producing a full-length, allele-specific view of an individual’s transcriptome. By enhancing existing gene annotations using long reads and quantifying this enhanced annotation using >100 million 101-bp paired-end reads, we overcome the smaller number of long reads.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
PacBio RNA-seq has proven useful for unraveling isoform diversity at complex loci and for determining allele-specific expression from single reads.
“The technology has proven useful for unraveling isoform diversity at complex loci [186], and for determining allele-specific expression from single reads [187].”
From A survey of best practices for RNA-seq data analysis (2016) · cites this paper as [187]
61.6% of CCS contained a T9, broadly consistent with the previous estimation of 67%.
“61.6% of CCS contained a T9, broadly consistent with our previous estimation (67%) 1,4 .”
From Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells (2018) · cites this paper as [4]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
R: A Language and Environment for Statistical Computing
R Core Team (2000) · doi:10.32614/r.manuals · Cited by 355,706 · see citing works
STAR: ultrafast universal RNA-seq aligner
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709 · see citing works
Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556 · see citing works
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696 · see citing works
RNA-Seq: a revolutionary tool for transcriptomics
Wang, Z., Gerstein, M., & Snyder, M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2484 · Cited by 13,174 · see citing works
Self-citationLandscape of transcription in human cells
Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., et al. (2012) · Nature · doi:10.1038/nature11233 · Cited by 5,187 · see citing works
Self-citationAlternative isoform regulation in human tissue transcriptomes
Wang, E. T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S. F., Schroth, G. P., & Burge, C. B. (2008) · Nature · doi:10.1038/nature07509 · Cited by 5,181 · see citing works
GENCODE: The reference human genome annotation for The ENCODE Project
Harrow, J., Frankish, A., Gonzalez, J. M., Tapanari, E., Diekhans, M., Kokocinski, F., Aken, B. L., Barrell, D., Zadissa, A., Searle, S., et al. (2012) · Genome Research · doi:10.1101/gr.135350.111 · Cited by 4,585 · see citing works
Real-Time DNA Sequencing from Single Polymerase Molecules
Eid, J., Fehr, A., Gray, J., Luong, K., Lyle, J., Otto, G., Peluso, P., Rank, D., Baybayan, P., Bettman, B., et al. (2009) · Science · doi:10.1126/science.1162986 · Cited by 3,732 · see citing works
The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing
Nagalakshmi, U., Wang, Z., Waern, K., Shou, C., Raha, D., Gerstein, M., & Snyder, M. (2008) · Science · doi:10.1126/science.1158441 · Cited by 2,479 · see citing works
Self-citationQuail, M., Smith, M. E., Coupland, P., Otto, T. D., Harris, S. R., Connor, T. R., Bertoni, A., Swerdlow, H. P., & Gu, Y. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-341 · Cited by 2,031 · see citing works
Sultan, M., Schulz, M. H., Richard, H., Magen, A., Klingenhoff, A., Scherf, M., Seifert, M., Borodina, T., Soldatov, A., Parkhomchuk, D., et al. (2008) · Science · doi:10.1126/science.1160342 · Cited by 1,293 · see citing works
Hybrid error correction and de novo assembly of single-molecule sequencing reads
Koren, S., Schatz, M. C., Walenz, B. P., Martin, J. V., Howard, J. T., Ganapathy, G., Wang, Z., Rasko, D. A., McCombie, W. R., Jarvis, E. D., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2280 · Cited by 993 · see citing works
Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution
Wilhelm, B. T., Marguerat, S., Watt, S. B., Schubert, F., Wood, V., Goodhead, I., Penkett, C. J., Rogers, J., & Bähler, J. (2008) · Nature · doi:10.1038/nature07002 · Cited by 974 · see citing works
A single-molecule long-read survey of the human transcriptome
Sharon, D., Tilgner, H., Grubert, F., & Snyder, M. (2013) · Nature Biotechnology · doi:10.1038/nbt.2705 · Cited by 701 · see citing works
Self-citationAssessment of transcript reconstruction methods for RNA-seq
The RGASP Consortium, Steijger, T., Abril, J. F., Engström, P. G., Kokocinski, F., Hubbard, T. J., Guigó, R., Harrow, J., & Bertone, P. (2013) · Nature Methods · doi:10.1038/nmeth.2714 · Cited by 699 · see citing works
Characterization of the human ESC transcriptome by hybrid sequencing
Au, K. F., Sebastiano, V., Afshar, P. T., Durruthy, J. D., Lee, L., Williams, B. A., van Bakel, H., Schadt, E. E., Reijo-Pera, R. A., Underwood, J. G., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1320101110 · Cited by 341 · see citing works
Noisy Splicing Drives mRNA Isoform Diversity in Human Cells
Pickrell, J. K., Pai, A. A., Gilad, Y., & Pritchard, J. K. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001236 · Cited by 311 · see citing works
Accurate Identification and Analysis of Human mRNA Isoforms Using Deep Long Read Sequencing
Tilgner, H., Raha, D., Habegger, L., Mohiuddin, M., Gerstein, M., & Snyder, M. P. (2013) · G3 Genes Genomes Genetics · doi:10.1534/g3.112.004812 · Cited by 65 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
A survey of best practices for RNA-seq data analysis
Conesa, A., Madrigal, P., Tarazona, S., Gomez-Cabrero, D., Cervera, A., McPherson, A., Szcześniak, M. W., Gaffney, D. J., Elo, L. L., Zhang, X., et al. (2016) · Genome Biology · doi:10.1186/s13059-016-0881-8 · Cited by 2,794 · see citing works
Opportunities and challenges in long-read sequencing data analysis
Amarasinghe, S. L., Su, S., Dong, X., Zappia, L., Ritchie, M. E., & Gouil, Q. (2020) · Genome Biology · doi:10.1186/s13059-020-1935-5 · Cited by 2,530 · see citing works
A draft human pangenome reference.
Liao, W.-W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J. K., Monlong, J., Abel, H. J., et al. (2023) · Nature · doi:10.1038/s41586-023-05896-x · Cited by 1,129 · see citing works
“(SRR1153470) (Tilgner et al., 2014) and the ENCODE project (ENCSR000AED, replicate 1) (Davis et al.”
BackgroundMethodAshley, E. A. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.86 · Cited by 1,116 · see citing works
Sahraeian, S. M. E., Mohiyuddin, M., Sebra, R., Tilgner, H., Afshar, P. T., Au, K. F., Bani Asadi, N., Gerstein, M. B., Wong, W. H., Snyder, M. P., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-00050-4 · Cited by 376 · see citing works
Self-citationSingle-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells
Gupta, I., Collier, P. G., Haase, B., Mahfouz, A., Joglekar, A., Floyd, T., Koopmans, F., Barres, B., Smit, A. B., Sloan, S. A., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4259 · Cited by 343 · see citing works
Self-citationTilgner, H., Jahanbani, F., Blauwkamp, T., Moshrefi, A., Jaeger, E., Chen, F., Harel, I., Bustamante, C. D., Rasmussen, M., & Snyder, M. P. (2015) · Nature Biotechnology · doi:10.1038/nbt.3242 · Cited by 223 · see citing works
Self-citationA spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain
Joglekar, A., Prjibelski, A., Mahfouz, A., Collier, P., Lin, S., Schlusche, A. K., Marrocco, J., Williams, S. R., Haase, B., Hayes, A., et al. (2021) · Nature Communications · doi:10.1038/s41467-020-20343-5 · Cited by 229 · see citing works
Self-citationAnvar, S. Y., Allard, G., Tseng, E., Sheynkman, G. M., de Klerk, E., Vermaat, M., Yin, R. H., Johansson, H. E., Ariyurek, Y., den Dunnen, J. T., et al. (2018) · Genome Biology · doi:10.1186/s13059-018-1418-0 · Cited by 118 · see citing works
Microfluidic isoform sequencing shows widespread splicing coordination in the human transcriptome
Tilgner, H., Jahanbani, F., Gupta, I., Collier, P., Wei, E., Rasmussen, M., & Snyder, M. (2018) · Genome Research · doi:10.1101/gr.230516.117 · Cited by 71 · see citing works
Self-citation
- Authors
- Tilgner, H., Grubert, F., Sharon, D., & Snyder, M. P.
- Affiliations
- Stanford University (US)
- Yale University (US)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2014-06-24
- Volume
- 111
- Issue
- 27
- Pages
- 9869-9874
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC4103364
- OpenAlex
- W2136899396
- Cited by
- 266
- References
- 19
- Citations by year
- 2026: 11 · 2025: 9 · 2024: 13 · 2023: 31 · 2022: 23 · 2021: 29 · 2020: 29 · 2019: 33 · 2018: 24 · 2017: 20 · 2016: 24 · 2015: 17 · 2014: 2 · 2012: 1
- FWCI
- 8.62
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Heart, Lung, and Blood Institute (U01HL107393)
- National Institute of Diabetes and Digestive and Kidney Diseases (U54DK102556)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Keywords
- single-molecule long-read sequencing, splice site detection, HLA haplotypes, differential allelic expression, transcriptome annotation
- MeSH terms
- Alleles, Haplotypes, Humans, RNA, Gene Expression, Polymorphism, Single Nucleotide, Transcriptome
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
