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CAGE-TSSchip: promoter-based expression profiling using the 5'-leading label of capped transcripts

Shintaro Katayama1, Mutsumi Kanamori-Katayama1, Kazumi Yamaguchi12, Piero Carninci13 and Yoshihide Hayashizaki13*

Author Affiliations

1 Laboratory for Genome Exploration Research Group, Genomic Sciences Center, RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan

2 Bioinformatics Solutions Division, Nittetsu Hitachi Systems Engineering, Inc., Akashi-cho, Chuo-ku, Tokyo 104-6591, Japan

3 Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Main Campus, Hirosawa, Wako 351-0198, Japan

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Genome Biology 2007, 8:R42  doi:10.1186/gb-2007-8-3-r42

Published: 26 March 2007

Additional files

Additional data file 1:

TSSchip probe annotation and experimental results. Some probe-sequences from the Agilent Catalog Array are not included in this data file because of a material transfer agreement between RIKEN and Agilent. (Please contact Agilent if you need these probe sequences.)

Format: XLS Size: 5.1MB Download file

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Open Data

Additional data file 2:

Shown is the performance of 5'-leading label in dye swap experiments.

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Open Data

Additional data file 3:

Shown are the details of a sensitivity check with the qRT-PCR.

Format: XLS Size: 33KB Download file

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Open Data

Additional data file 4:

Summarized is the sensitivity check with the qRT-PCR.

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Additional data file 5:

Details of the alternative promoter check with qRT-PCR are given.

Format: XLS Size: 21KB Download file

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Open Data

Additional data file 6:

Shown are CAGE expression clustering results of Bdh alternative promoters.

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Open Data

Additional data file 7:

Shown are over-expressed promoters in Hepa1-6 and liver

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Additional data file 8:

Supplementary Methods regarding the array probe design and whole protocols of wet experiments are given.

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Additional data file 9:

Shown are details of cross-validation by qRT-PCR and CAGE in mouse liver versus E17.5.

Format: XLS Size: 14KB Download file

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Open Data