The DOI matches its Crossref record; 22 of the 22 references it cites were found in a registry or an index.
Design of 240,000 orthogonal 25mer DNA barcode probes
Open accessAbstract
DNA barcodes linked to genetic features greatly facilitate screening these features in pooled formats using microarray hybridization, and new tools are needed to design large sets of barcodes to allow construction of large barcoded mammalian libraries such as shRNA libraries. Here we report a framework for designing large sets of orthogonal barcode probes. We demonstrate the utility of this framework by designing 240,000 barcode probes and testing their performance by hybridization. From the test hybridizations, we also discovered new probe design rules that significantly reduce cross-hybridization after their introduction into the framework of the algorithm. These rules should improve the performance of DNA microarray probe designs for many applications.
Overview
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
Verification
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?
The check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“Finally, avoiding spurious amplification of off-target files due to crosstalk of PCR primers with incorrect barcodes or main file sequences requires careful primer design20.”
From Random access DNA memory using Boolean search in an archival file storage system (2021) · cites this paper as [20]
Experimental — accuracy not yet measuredIn the citing paper
“which allows for individual selection of up to ~1015 possible distinct files using only three unique barcodes per file20”
From Random access DNA memory using Boolean search in an archival file storage system (2021) · cites this paper as [20]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
EMBOSS: the European molecular biology open software suite.
Rice, P., Longden, I., & Bleasby, A. (2000) · Trends in Genetics · doi:10.1016/s0168-9525(00)02024-2 · Cited by 9,466
Functional profiling of the Saccharomyces cerevisiae genome
Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Véronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., André, B., et al. (2002) · Nature · doi:10.1038/nature00935 · Cited by 4,316
Functional Characterization of the S. cerevisiae Genome by Gene Deletion and Parallel Analysis
Winzeler, E. A., Shoemaker, D. D., Astromoff, A., Liang, H., Anderson, K., Andre, B., Bangham, R., Benito, R., Boeke, J. D., Bussey, H., et al. (1999) · Science · doi:10.1126/science.285.5429.901 · Cited by 3,953
A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics.
SantaLucia, J. (1998) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.95.4.1460 · Cited by 2,791
Markham, N. R., & Zuker, M. (2008) · Methods in molecular biology · doi:10.1007/978-1-60327-429-6_1 · Cited by 1,026
The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes
Hillenmeyer, M. E., Fung, E., Wildenhain, J., Pierce, S. E., Hoon, S. S., Lee, W., Proctor, M. J., St.Onge, R. P., Tyers, M., Koller, D., et al. (2008) · Science · doi:10.1126/science.1150021 · Cited by 978
Second-generation shRNA libraries covering the mouse and human genomes
Silva, J. M., Li, M. Z., Chang, K. C. N., Ge, W., Golding, M. C., Rickles, R. J., Siolas, D., Hu, G., Paddison, P. J., Schlabach, M. R., et al. (2005) · Nature Genetics · doi:10.1038/ng1650 · Cited by 625
Self-citationAssessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays
Kane, M. D. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.22.4552 · Cited by 618
Shoemaker, D. D., Lashkari, D. A., Morris, D., Mittmann, M., & Davis, R. W. (1996) · Nature Genetics · doi:10.1038/ng1296-450 · Cited by 569
OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach
Rouillard, J. M. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg426 · Cited by 419
Cited by
Sorted by citations
RNA-Guided Human Genome Engineering via Cas9
Mali, P., Yang, L., Esvelt, K. M., Aach, J., Guell, M., DiCarlo, J. E., Norville, J. E., & Church, G. M. (2013) · Science · doi:10.1126/science.1232033 · Cited by 9,210
Spatially resolved, highly multiplexed RNA profiling in single cells
Chen, K. H., Boettiger, A. N., Moffitt, J. R., Wang, S., & Zhuang, X. (2015) · Science · doi:10.1126/science.aaa6090 · Cited by 2,969
Random access in large-scale DNA data storage
Organick, L., Ang, S. D., Chen, Y.-J., Lopez, R., Yekhanin, S., Makarychev, K., Racz, M. Z., Kamath, G., Gopalan, P., Nguyen, B., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4079 · Cited by 775
Moffitt, J. R., Hao, J., Wang, G., Chen, K. H., Babcock, H. P., & Zhuang, X. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1612826113 · Cited by 568
SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues
Kishi, J. Y., Lapan, S. W., Beliveau, B. J., West, E. R., Zhu, A., Sasaki, H. M., Saka, S. K., Wang, Y., Cepko, C. L., & Yin, P. (2019) · Nature Methods · doi:10.1038/s41592-019-0404-0 · Cited by 446
Metadata
- Authors
- Xu, Q., Schlabach, M. R., Hannon, G. J., & Elledge, S. J.
- Affiliations
- Brigham and Women's Hospital (US)
- Howard Hughes Medical Institute (US)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2009-02-17
- Volume
- 106
- Issue
- 7
- Pages
- 2289-2294
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC2631075
- OpenAlex
- W2091266578
- Cited by
- 170
- References
- 22
- Citations by year
- 2026: 13 · 2025: 16 · 2024: 13 · 2023: 13 · 2022: 13 · 2021: 22 · 2020: 12 · 2019: 11 · 2018: 6 · 2017: 10 · 2016: 8 · 2015: 5 · 2014: 3 · 2013: 5 · 2012: 6
- FWCI
- 2.68
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
- Funders
- Howard Hughes Medical Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced biosensing and bioanalysis techniques
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- DNA barcodes, probe design, microarray hybridization, cross-hybridization, shRNA library
- MeSH terms
- Algorithms, Electronic Data Processing, DNA, Nucleic Acid Conformation, Nucleic Acid Hybridization, RNA, Software, Temperature, DNA Probes, Oligonucleotide Probes, Sequence Analysis, DNA, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling
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
