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RL-SAGE Data Description

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  
Statistics
Library Summary
Library Treatment Reaction Stage Tissue Unique Tags Genbank Accession
MG_SGa Fungus grown on a minimum medium [0.2% (w/v) yeast extract, and 1%(w/v) Sucrose at 28C at 200 rpm] RLiquid grown mycelium 3 days 3 days old mycelia 51927 GSM34286
OSJNGb Che8061 Susceptible 24 hr after infection with fungus 21 days leaf 31027 GSM34282
OSJNGd C9249-1 Resistant 24 hr after infection with fungus 21 days leaf 28083 GSM34283
OSJNGf Water +Tween20 (0.1%) Normal 24 hr after water spray 21 days leaf 35974 GSM34284
OSJNGg Che8061 Susceptible 96 hr after infection with fungus 21 days leaf 57670 GSM34285
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] Romualdi C, Bortoluzzi S, D'Alessi F, Danieli GA. IDEG6: a web tool for detection of differentially expressed genes in multiple tag sampling experiments. Physiol Genomics. (2003) 12(2):159-62

    [3] Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389-3402.

    [4] Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS (2005) The Universal Protein Resource (UniProt) Nucleic Acids Res. 33: D154-159.

    [5] Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8: 175-185

    [6] Li S, Chou HH (2004) LUCY2: an interactive DNA sequence quality trimming and vector removal tool. Bioinformatics 20: 2865-2866