Recovering Supplementary Materials

image credit: Airborne (Andrew Wyeth, 1996)

Supplementary materials include information that is relevant to a paper but is not included in the paper itself -- underlying datasets, additional materials and methods information, large data tables, multimedia files, etc. If they are not available it becomes much more difficult for others to replicate, or even understand, the research. And yet as researchers move on, and publishers revamp websites, these data can be lost.

Diana Kwon has written about "The Push to Replace Journal Supplements with Repositories" in The Scientist, and Guy Plunkett posted a blog entry about "Zombie Sites and Lost Resources." For several years we have been hosting a copy of their Supplementary Materials for a group of retired colleagues, as well as making some of our own additional data available on this site.

During a recent link check we discovered that supplementary materials for a number of papers from this laboratory were no longer available from the publishers' websites, or at least not discoverable. With this page we are attempting to gather data that has been scattered to the winds and make them available once again.

  • Y. Kang, T. Durfee, J. D. Glasner, Y. Qiu, D. Frisch, K. M. Winterberg, & F. R. Blattner (2004) Systematic mutagenesis of the Escherichia coli genome. J Bacteriol 186(15):4921-4930. [PMID: 15262929]
        Table S1 - Genes previously identified as being potentially essential for which we obtained an insertion allele (MS Word document)

  • M. B. Łobocka, D. J. Rose, G. Plunkett III, M. Rusin, A. Samojedny, H. Lehnherr, M. B. Yarmolinsky, & F. R. Blattner (2004) Genome of bacteriophage P1. J Bacteriol 186(21):7032-7068. [PMID: 15489417]
        Table S1 - P1 gene products (MS Word document)

  • Y. Kang, K. D. Weber, Y. Qiu, P. J. Kiley, & F. R. Blattner (2005) Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function. J Bacteriol 187(3):1135-1160. [PMID: 15659690]
        Supplemental File 1 - Table S2, Published Fnr binding sites (MS Word document)
        Supplemental File 2 - Normalized array data (Zipped Excel file)
        CEL files

  • S.S. Fong, A. P. Burgard, C. D. Herring, E. M. Knight, F. R. Blattner, C. D. Maranas, & B. O. Palsson (2005) In silico design and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnol Bioeng 91(5):643-648. Epub June 16, 2005. [PMID: 15962337]
        Supplemental Table 1 (PDF)

  • M. Liu, T. Durfee, J. E. Cabrera, K. Zhao, D. J. Jin, & F. R. Blattner (2005) Global transcriptional programs reveal a carbon source foraging strategy by Escherichia coli. J Biol Chem 280(16):15921-15927. Epub February 10, 2005. [PMID: 15705577]
        Supplemental Data (PDF)
        CEL files

  • M. Riley, T. Abe, M. B. Arnaud, M. K. Berlyn, F. R. Blattner, R. R. Chaudhuri, J. D. Glasner, T. Horiuchi, I. M. Keseler, T. Kosuge, H. Mori, N. T. Perna, G. Plunkett III, K. E. Rudd, M. H. Serres, G. H. Thomas, N. R. Thomson, D. Wishart, & B. L. Wanner (2006) Escherichia coli K-12: a cooperatively developed annotation snapshot--2005. Nucleic Acids Res 34(1):1-9. [PMID: 16397293]
        Supplementary Data (PDF)
        Supplementary Table 1 - E. coli Genes (Text file)
        Supplementary Table 1 - E. coli Genes (Excel file)
        Supplementary Table 2 - Enzymes (Text file)
        Supplementary Table 2 - Enzymes (Excel file)
        Supplementary Table 3 - Transporters (Text file)
        Supplementary Table 3 - Transporters (Excel file)
        Supplementary Table 4 - Regulators (Text file)
        Supplementary Table 4 - Regulators (Excel file)
        Supplementary Table 5 - Other Annotations (Text file)
        Supplementary Table 5 - Other Annotations (Excel file)
        Supplementary Table 6 - Genes removed from MG1655 (Text file)
        Supplementary Table 6 - Genes removed from MG1655 (Excel file)

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