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RL-SAGE Data Description
RL-SAGE libraries were produced at Ohio State University. The sequencing was done at Arizona Genomics Institute, University of Arizona.

  Statistics   Analysis   References  

Library Summary
Tag Summary
Library Tag Frequency
≥ 500 499-100 99-50 49-10 9-2 1
OSJNGb 17 330 797 5274 3176 21433
OSJNGd 15 535 737 2627 3705 20464
OSJNGf 6 35 92 1295 10207 24401
OSJNGg 7 101 190 2421 15437 39514
MG_SGa 36 220 273 2096 13957 35345

Analysis [ Top ]
Rules used in ditag and tag isolation process:
  • Un-trimmed sequence reads are used in ditag extraction.
  • The ditag must have a CATG site at both ends.
  • The ditag must be between 40 to 43 bp.
  • If there is a forward and reverse read, the overlapping tag with the best quality is used.
  • Tags with one or more N's in sequence are ignored.
  • Note: due to a request by Gui-liang Wang, the following is not done:

  • Low quality tags are not discarded.
  • Duplicate ditags are not discarded.
    As per request by Gui-liang, ALL singletons are submitted to Genbank, even if all their quality scores are below 5.

    Since low quality singletons should be ignored, we have included the average quality value for each tag on the far right column of the tag table. The rules we are using are:

  • When there are multiple instances of a tag, the highest average is shown.
  • If a subset of the libraries is displayed, the highest average from the subset is shown.

  •    References [ Top ]

    [1] Malali Gowda, Chatchawan Jantasuriyarat, Ralph A. Dean, and Guo-Liang Wang (2004). Robust-LongSAGE (RL-SAGE): A Substantially Improved LongSAGE Method for Gene Discovery and Transcriptome Analysis. Plant Physiology 134: 890-897.

    [2] Gowda M, Venu RC, Jia Y, Stahlberg E, Pampanwar V, Soderlund C, Wang GL (2007). Use of robust-long serial analysis of gene expression to identify novel fungal and plant genes involved in host-pathogen interactions. Methods Mol Biol 354: 131-44.