Serial Analysis of Gene Expression (Sage): Methods and Protocols

Contents.Preface ContributorsPart 1: Experimental Procedures1. SAGE and LongSAGE.Annabeth Laursen Høgh and Kåre Lehmann Nielsen.2. Robust-LongSAGE (RL-SAGE): an improved LongSAGE method for high-throughput transcriptome analysis.Malali Gowda and Guo-Liang Wang.3. aRNALongsAGE: SAGE with Antisense RNA.Anna M. Heidenblut.4. SuperSAGEHideo Matsumura, Monika Reuter, Detlev H. Krüger, Peter Winter, Günter Kahl and Ryohei Terauchi.5. Low Cost Medium Throughput Sanger Dideoxy-Sequencing.Kåre Lehmann Nielsen.6. DeepSAGE-Higher Sensitivity and Multiplexing of Samples Using a Simpler Experimental Protocol.Kåre Lehmann Nielsen.7. High-Resolution Genome-wide Mapping of Chromatin Modifications by GMATTae-Young Roh and Keji Zhao.8. 5'-and 3'-RACE from LongSAGE tags.Kåre Lehmann Nielsen.Part 2: Tag Extraction and Analysis.9. Extraction and Annotation of SAGE tags using Sequence Quality values.Jeppe Emmersen.10. Correction of technology-Related artifacts in Serial Analysis of Gene Expression.Viatcheslav R. Akmaev.11. Duplicate Ditag analysis in LongSAGEJeppe Emmersen.12. Statistical Comparison of Two or More SAGE Libraries: One Tag at the Time.Gerben J. Schaaf, Fred van Ruissen, Antoine van Kampen, Marcel Kool and Jan M. Ruijter.13. Scaling of Gene Expression Data Allowing the Comparison of Different Gene Expression Platforms.Fred van Ruissen, Gerben J. Schaaf, Marcel Kool, Frank Baas and Jan M. Ruijter.14. Clustering Analysis of SAGE Transcription Profiles Using a Poisson Approach.Haiyan Huang, Li Cai and Wing H. Wong.15. Identifying Non-specific SAGE tags by Context of Gene Expression.Xijin Ge and San Ming Wang.