Supplemental data for:

Yeast Isw1p Forms Two Separable Complexes In Vivo. Vary JC Jr, Gangaraju VK, Qin J, Landel CC, Kooperberg C, Bartholomew B, Tsukiyama T. Mol Cell Biol 2003, 23:80-91.

Isw1 complex mutants

RNA was harvested from isw1, ioc2, ioc3, and ioc2ioc3 and wild-type cultures grown to OD660=0.7. DNA microarray analyses were done using 30 mg total RNA from each strain labeled with Cy5 or Cy3 dyes and hybridized to ORF-based arrays containing all putative S. cerevisiae open reading frames. Four independent microarray hybridizations were performed for ioc2 vs. w.t., ioc3 vs. w.t., and ioc2ioc3 vs. w.t., samples. Three independent microarray hybridizations were performed for isw1 vs. w.t., samples

We utilized a number of different previously described methods to normalize our expression data. Briefly, a Bayesian background correction method was applied to reduce the variance of spots of low intensity (Kooperberg, 2002; Fazzio, 2001). This corrected data from each microarray slide was then normalized to account for bias due to spot intensity (Intensity-dependent normalization using a lowess smoother to account for nonlinearity) and each cDNA’s position on the array grid (Within-print-tip-group normalization). In addition, conversely labeled slide pairs were normalized to each other to account for dye-specific differences in labeling efficiency and/or dye stability (Paired-slides normalization); and separate slides were normalized to each other to reduce absolute expression differences that introduce bias when making slide to slide comparisons (Multiple slide normalizations) (Yang, 2001).

The expression changes for each gene were then determined by calculating the median value from these normalized values.

File is a tab-delimited text file.

isw1_ioc2_ioc3.txt

Platform: ORF-based array
Cell source: Cells grown in YEPD to OD660=0.7
RNA prep: Hot phenol extraction
Taxonomy: Saccharomyces cerevisiae
Submitter: Jay Vary
Submission Date: July 2002
Institution: Fred Hutchinson Cancer Research Center
Address: Tsukiyama Lab A1-175, 1100 Fairview Ave MS A1-162, Seattle, WA 98109, USA
E-mail: ttsukiya@fhcrc.org

• Kooperberg, C., T. G. Fazzio, J. J. Delrow, and T. T. Tsukiyama 2002. Improved background correction for spotted DNA microarrays J. Comp. Biol. 9:57-68.
• Fazzio, T. G., C. Kooperberg, J. P. Goldmark, C. Neal, R. Basom, J. Delrow, and T. Tsukiyama 2001. Widespread collaboration of Isw2 and Sin3-Rpd3 chromatin remodeling complexes in transcriptional repression Mol Cell Biol. 21:6450-60.
• Yang, Y. H., S. Dudoit, P. Luu, and T. P. Speed 2001. Normalization for cDNA microarray data. In M. L. Bittner, Y. Chen, A. N. Dorsel, and E. R. Dougherty (eds), Proceedings of SPIE, vol. 4266, San Jose, CA.

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