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Cited by 116Genomics and Phylogenetic StudiesGene expression and cancer classificationSingle-cell and spatial transcriptomics

A mouse atlas of gene expression: Large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells

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Siddiqui, Asim S., Khattra, Jaswinder, Delaney, Allen D., Zhao, Yongjun, Astell, Caroline, Asano, Jennifer, Babakaiff, Ryan, Barber, Sarah +42 more·2005·Proceedings of the National Academy of Sciences
DOI 10.1073/pnas.0509455102PMC PMC1311911
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Abstract

We analyzed 8.55 million LongSAGE tags generated from 72 libraries. Each LongSAGE library was prepared from a different mouse tissue. Analysis of the data revealed extensive overlap with existing gene data sets and evidence for the existence of ≈24,000 previously undescribed genomic loci. The visual cortex, pancreas, mammary gland, preimplantation embryo, and placenta contain the largest number of differentially expressed transcripts, 25% of which are previously undescribed loci.

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  • Many of the tag-sequences can be mapped by allowing a one-basepair mismatch, insertion or deletion.

    “We have previously shown that many of these tag-sequences can be mapped by allowing a one-basepair mismatch, insertion or deletion [33].”

    From A systematic screen for genes expressed in definitive endoderm by Serial Analysis of Gene Expression (SAGE) (2007) · cites this paper as [33]

    The Results and Discussion (Data Overview and Quality Filtering; page unavailable) report that many tag sequences mapped to mouse sequence resources. The Tag-Sequence Mapping section (Materials and Methods; page unavailable) describes the resources used, but neither passage says that mapping allowed a one-base-pair mismatch, insertion, or deletion. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

  • A total of 322,208 tags were sequenced from the three longSAGE endoderm libraries.

    “A total of 322,208 tags were sequenced from these three longSAGE endoderm libraries [33].”

    From A systematic screen for genes expressed in definitive endoderm by Serial Analysis of Gene Expression (SAGE) (2007) · cites this paper as [33]

    Materials and Methods reports that the authors sequenced approximately 100,000 LongSAGE tags per library, and the Abstract reports 72 libraries in total (page numbers unavailable). Our copy does not identify three endoderm libraries or give a combined count of 322,208 tags, so the specific figure cannot be verified from it. (LLM, conf=0.77)

    Experimental — accuracy not yet measured

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Cited by

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Authors
Siddiqui, A. S., Khattra, J., Delaney, A. D., Zhao, Y., Astell, C., Asano, J., Babakaiff, R., Barber, S., Beland, J., Bohacec, S., Brown-John, M., Chand, S., Charest, D., Charters, A. M., Cullum, R., Dhalla, N., Featherstone, R., Gerhard, D. S., Hoffman, B., Holt, R. A., Hou, J., Kuo, B. Y.-L., Lee, L. L. C., Lee, S., Leung, D., Ma, K., Matsuo, C., Mayo, M., McDonald, H., Prabhu, A.-L., Pandoh, P., Riggins, G. J., de Algara, T. R., Rupert, J. L., Smailus, D., Stott, J., Tsai, M., Varhol, R., Vrljicak, P., Wong, D., Wu, M. K., Xie, Y.-Y., Yang, G., Zhang, I., Hirst, M., Jones, S. J. M., Helgason, C. D., Simpson, E. M., Hoodless, P. A., & Marra, M. A.
Affiliations
  • BC Cancer Agency (CA)
  • Canada's Michael Smith Genome Sciences Centre, Terry Fox Laboratory, and Cancer Endocrinology, British Columbia Cancer Research Centre, British Columbia Cancer Agency, Vancouver, BC, Canada V5Z 4S6; Centre for Molecular Medicine and Therapeutics, British Columbia Research Institute for Children's and Women's Health, Vancouver, BC, Canada V6H 3N1; Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; Department of Neurosurgery, The Johns Hopkins...
ORCID
Venue
Proceedings of the National Academy of Sciences
Publisher
National Academy of Sciences
Published
2005-12-13
Volume
102
Issue
51
Pages
18485-18490
ISSN
  • 0027-8424 (ISSN-L)
  • 1091-6490
DOI
10.1073/pnas.0509455102
PMC
PMC1311911
OpenAlex
W2038303935
Cited by
116
References
3
Citations by year
2026: 1 · 2025: 1 · 2024: 1 · 2023: 3 · 2022: 1 · 2020: 3 · 2017: 1 · 2016: 2 · 2015: 3 · 2014: 6 · 2013: 4 · 2012: 9
FWCI
6.76
Type
journal article
Language
en
Open access
Locations
  • Proceedings of the National Academy of Sciences (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
U.S. Public Health Service (N01C012400)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
Keywords
gene expression atlas, LongSAGE, C57BL/6J mice, tissue-specific gene expression, differentially expressed transcripts, visual cortex, pancreas, mammary gland, preimplantation embryo, placenta, mouse development
MeSH terms
Animals, Multigene Family, Mice, Inbred C57BL, Transcription, Genetic, Reproducibility of Results, Alternative Splicing, Gene Expression Regulation, Developmental, Gene Expression Profiling, RNA, Untranslated, Mice

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