Open Access Highly Accessed Research article

Elucidating a normal function of huntingtin by functional and microarray analysis of huntingtin-null mouse embryonic fibroblasts

Hua Zhang1, Sudipto Das2, Quan-Zhen Li3, Ioannis Dragatsis4, Joyce Repa1, Scott Zeitlin5, György Hajnóczky2 and Ilya Bezprozvanny1*

1 Department of Physiology, UT Southwestern Medical Center at Dallas, Dallas, TX 75390, USA

2 Department of Pathology and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA

3 Department of Immunology, UT Southwestern Medical Center at Dallas, Dallas, TX 75390, USA

4 Department of Physiology, The University of Tennessee Health Science Center, Memphis, TN 38163, USA

5 Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, VA 22908, USA

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BMC Neuroscience 2008, 9:38 doi:10.1186/1471-2202-9-38

Published: 15 April 2008

Additional files

Additional file 1:

Supplementary Table 1. The list of annotated genes significantly affected in Hdh-KO MEF cells. The genes are classified into significant GO categories (classes) as explained in the text. The official gene symbol and protein name are shown. Also shown is average intensity of microarray signal for Hdh-HET and Hdh-KO samples and the calculated Diff score and p-values. Negative Diff scores correspond to genes underexpressed in Hdh-KO cells, positive Diff Scores correspond to genes overexpressed in Hdh-KO cells. The fold change is calculated by dividing average Hdh-HET and Hdh-KO signals. The transcripts which are not detected in Hdh-HET samples are shown as "up", the samples not detected in Hdh-KO samples are shown as "down". The Genebank accession numbers are also shown.

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Additional file 2:

Excell file with Supplementary Table 1. The microarray data for 821 differentially expressed probes are presented in the Excell file. The data listed for each probe are as follows: an Illumina beads target ID, an average signal from 6 chips with Hdh-HET samples, the probability of detection of a probe in Hdh-HET samples, an average signal from 6 chips with Hdh-KO samples, the probability of detection of a probe in Hdh-KO samples, the Diff Score obtained by comparing Hdh-HET and Hdh-HET samples, the P value calculated from the Diff score, an official gene symbol and definition (when available), the sequence of the probe, and the genebank accession number (when available). The results are sorted by the Diff score with negative Diff scores corresponding to the probes downregulated in Hdh-KO cells (366 probes) and positive Diff scores corresponding to the probes upregulated in Hdh-KO cells (455 probes).

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