Agilent RNA Gels - Samples 12 through 22

Samples 12 through 22 in consecutive order on the Agilent RNA gel

#12 is a repeated assay. See above for first run. Both runs showed degradation.

WM-B6-12** ¶ (repeated) WM-C1-13 WM-C2-14 WM-C3-15** WM-C4-16 WM-C5-17 WM-C6-18** WM-C7-19** WM-D1-20 WM-D2-21 WM-D3-22

Sample in the run not related:

** 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. On this gel, four of the specimens have apparent degradation that was substantial (12, 15, 18, 19). Three of them produced interpretable hybridization signals, while just one sample (#12) showed an adverse effect on the array. See below.

¶ 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

Traces for samples 12 through 22 in consecutive order on the Agilent RNA gel

Agilent RNA gels were run after a column purification step

One sample (hela) is not related to this study.

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