Experiment filename

Sample Name – To edit the Sample Name see Edit projects.

Scorecard Result – The result icons , , or (positive, borderline, or negative for the sample type tested) are displayed color coded to the test type (below). The pass/fail thresholds in the hPSC Scorecard™ Analysis Software are set by comparing the distributions of undifferentiated and Day 5 EB samples for the 13 pluripotent stem cell lines in the reference set. A "positive" result icon for self-renewal (previously labeled pluripotent) indicates that the gene expression levels of the self-renewal markers for that sample match or exceed that of the undifferentiated reference set. A "negative" result means the expression levels are lower than the undifferentiated reference set. Failure of the self-renewal test does not necessarily imply that your cell line is not pluripotent. It means only that the levels of self-renewal gene expression in your sample are lower than the hPSC Scorecard™ Assay reference set.

A "positive" result for any of the three germ layers indicates that the gene expression profile of those markers has a high probability of matching or exceeding that of the Day 5 EB samples derived from the 13 reference lines. A "negative" result for any of the three germ layers means that the expression profile for that gene set more closely matches that of the undifferentiated reference set than the Day 5 EB samples used to set the result thresholds.

• Green, Self-renewal = markers of the undifferentiated state (previously labeled pluripotency). Test for the expression of self-renewal markers.

• Blue, Ectoderm = ectoderm expression

• Orange, Mesoderm = mesoderm expression

• Purple, Endoderm = endoderm expression

Borderline result: Scores that lie very near the intersection of the undifferentiated and EB populations are now labeled "borderline" to emphasize that the result is as likely to match the scores range for the undifferentiated reference set as it is to match the scores range for the EB reference set. The gene expression profiles of these two populations are not completely distinct, so the tails of the two distributions show varying amounts of overlap, depending on the gene set.

Red Flag Warning – The hPSC Scorecard™ Analysis Software performs a set of quality control checks upon data import to ensure the quality of the results. A red flag appears to provide additional information about a sample.

Hover the cursor over the warning flag to view the message.

Warning messages and their meaning:

• Well produced very low or no fluorescence

  The sample is excluded from analysis and should be repeated.

• Low control gene expression

  The expression levels of internal positive control genes were low. Results will be displayed, however, sample should be repeated.

• High control gene expression

  The expression levels of internal positive control genes were high. Results will be displayed, however, sample should be repeated.

• Abnormal control gene expression

  The expression levels of internal positive control genes were mixed. Results will be displayed, however, sample should be repeated.

• Passive reference signal is abnormal

  The passive reference signal may not be acceptable for normalization of the target signal. This may explain why a particular assay is not showing the anticipated gene expression level.

• Sendai detected

  The hPSC Scorecard™ panel includes a control to look for Sendai virus expression. Samples are flagged if a C_t value of <30 is observed for this control. Rarely, the SEV oligonucleotide cross-reacts with other genes resulting in a false positive in differentiated cells. You may want to repeat the sample or look at the amplification plot (TaqMan^® hPSC Scorecard™ Panel 96-well plate: well B9; in the 384-well plate format: wells D3, D9, D15, and D21) to see if the automated C_t value call is real, or in error.

• Endoderm QC failure

  Many wells containing endoderm gene expression values are undetermined and/or omitted. For best results, samples should be repeated.

• Mesoderm QC failure

  Many wells containing mesoderm gene expression values are undetermined and/or omitted. For best results, samples should be repeated.

• Ectoderm QC failure

  Many wells containing ectoderm gene expression values are undetermined and/or omitted. For best results, samples should be repeated.

• Self-renewal QC failure

  Many wells containing self-renewal gene expression values are undetermined and/or omitted. For best results, samples should be repeated.

• Insufficient data for analysis

  The hPSC Scorecard™ Analysis Software requires that a minimum number of genes amplify to accurately analyze the data. In cases where less than the minimum number of genes amplify, or if data has been omitted by the user, the sample is excluded from analysis. The sample should be repeated.

Show/Hide all details – Click Hide all details to collapse the scorecard view. Click on the Show all details icon , to expand the scorecards for more detail. See Expanded Scorecard Results for more information. Scorecards display in show all details view by default.