Agilent RNA Gels - Samples 1 through 12

Agilent RNA Gels Run By University of Texas Molecular Genomics Laboratory (Thomas Wood, Ph.D., Laboratory Director)

Agilent RNA gels were run after a column purification step and band resolution is improved over the preliminary results obtained prior to purification.

Samples 1 through 12 in consecutive order on the Agilent RNA gel

WM-A1-01 WM-A2-02 WM-A3-03 WM-A4-04 WM-A5-05 WM-A6-06 ¶ WM-B1-07** WM-B2-08 WM-B3-09 WM-B4-10 WM-B5-11** ¶ WM-B6-12** ¶

** Denotes that the isolated RNA contained degradation that has the potential to adversely affect results on the array. After the results of the hybridization signals were screened for evidence that signal patterns were adversely affected, some degraded specimens were affected adversely ( ¶ ), and some were not.

¶ Denotes that the hybridization signal pattern of this sample was influenced by RNA degradation when it was analyzed. One or more outcomes were used to screen for anomalous hybridization on a particular chip. See 6.0 for details. Briefly, a hybridization signal was present in a relatively high percentage of all the probe sets, or signal intensities were weak across the board and required a high scaling factor for calibration. Both of those measures generally indicate that probe sets that did not produce a significant hybridization signal in most of the samples as a whole may erroneously report a signal being present on these particular chips. As well spiked control RNA may have shown an uneven distribution of cDNA representation due to uneven conversion to cDNA. This means that the effectiveness of hybridization of some transcripts on the chip, but not all transcripts on the chip, may have been corrupted due to RNA degradation. These errors can produce over- or under-representation of certain signal intensities relative to the other transcripts on the array.

** ¶ Both of the above

BOLD denotes that this case was added to compensate for cases that had preliminary evidence of potentially substantial RNA degradation

Gel traces for samples 1 through 12 in consecutive order on the Agilent RNA gel

Agilent RNA gels were run after a column purification step

Gel traces from samples that ended up being adversely affected on the gene array are indicated by including the full NNTC identification number.