[measurement] Does any study report AP+ and TRA-1-60+ colony counts on the same reprogramming material without first pre-selecting colonies by hESC-like morphology, so AP's known tendency to mark partially reprogrammed colonies can actually be measured against TRA-1-60?

Answer

The supplied verified evidence does not yet provide a qualifying matched measurement of AP+ and TRA-1-60+ colony counts on the same unselected reprogramming material. A later BRD2 study is a promising candidate because it describes whole-well counts of both markers without stated morphology screening, but the cited AP and TRA-1-60 panels use OSKM and OSK respectively. Those unmatched factor sets cannot quantify AP's excess counting relative to TRA-1-60 2275b121.

This is a bounded result about the records examined, not proof that no qualifying study exists. Earlier searches found relevant qualitative marker evidence, morphology-conditioned staining, or cell-flow measurements rather than paired colony counts fb5c9ab0; 1b582220; c5912b30.

Summary

The newly supplied Wang record adds another distinct failure to meet the measurement requirement: numerical TRA-1-60 colony counts paired with qualitative AP images, rather than AP colony totals. It reinforces the bounded negative without changing the answer a4146610.

A usable comparison must preserve both the experimental material and the counting unit: unselected colonies, paired AP and TRA-1-60 endpoints, and matched factor conditions. Whole-well staining alone does not repair a cocktail mismatch. TRA-1-60-positive cell fractions, TRA-1-81 colony assays and unstated figure counts are not interchangeable with the requested paired colony counts 1b582220; c5912b30; 2275b121.

Evidence

• Chan et al. 2009: accessible abstract evidence says AP is insufficient to identify fully reprogrammed colonies and TRA-1-60 is more discriminating. The record does not provide paired counts and notes hESC-like morphology selection. Full text was unavailable to that search, so this is neither a numerical AP-bias estimate nor a full-paper negative fb5c9ab0.

• Seven-paper full-text search, 2026-10-06: no qualifying pair was extracted. Zhang 2011 reports that all AP-positive colonies subsequently stained were TRA-1-60-positive, but labels the result data not shown and does not exclude morphology selection. Other candidates count AP alone, use TRA-1-81, or assay TRA-1-60 by flow cytometry. The reported result is seven papers searched, with main text and legends inspected; supplements were not read 1b582220.

• Six-paper screen, 2026-10-03: no qualifying pair was identified. Phactr3 2024 counts ALP-positive colonies and quantifies SSEA-4/TRA-1-60-positive cells by flow cytometry in the same culture. A cell fraction is not a colony count, even when material is shared. Other screened cases use one marker, pre-sort cells, or do not establish the required human paired-colony design c5912b30.

• Cevallos et al. 2026, PMC13639006: whole-well ALP and TRA-1-60 counts are described at day 20, with phase-contrast counting and no morphology screening stated. Figure 1c is ALP under OSKM; Figure 1e is TRA-1-60 under OSK. Numeric values are not printed in the retrieved text. Extracting the two plotted means would therefore still leave a cocktail mismatch, rather than produce the requested matched AP-versus-TRA-1-60 estimate 2275b121.

• Wang et al. 2019 (10.1242/bio.047225): human umbilical-cord-derived MSCs are reprogrammed with retroviral OSKM and added factors. The study quantifies homogeneous and heterogeneous TRA-1-60-positive colonies, with three replicates and mean ± SD, while AP is presented as representative staining images described as correlating with TRA-1-60 results. The verified record supplies no numerical AP colony count. Thus two stains are used, but a qualitative correlation does not provide the paired colony totals needed to estimate AP over-counting. No prior hESC-like morphology filter is described for the TRA-1-60 enumeration; this alone does not make the AP images a quantitative endpoint a4146610.

Methodology

All five supplied verified records are cited. The earlier report is retained with the new Wang evidence integrated. Primary-text checking in this revision read Wang's Results, Methods and main figure legends, and rechecked the BRD2 Methods and Figure 1 legend through Europe PMC article XML. Supplemental count files were not opened, so the previously raised Supplementary Data 3 question remains unresolved. A candidate qualifies only if both outcomes are colony counts on matching reprogramming material with no prior morphology filter established by the methods. Search populations and dates are retained; the seven-paper and six-paper searches overlap and are not combined into a new denominator. Abstract-only access, figure-only values, marker substitutions and cell-versus-colony units remain explicit. This synthesis does not claim a fresh systematic search or calculate a ratio from unmatched panels.

Limitations

No morphology screening described is weaker than an explicit statement that every colony was scored without filtering. The BRD2 candidate remains provisional on that point and unmatched on factor cocktail. Chan full-text counts and supplementary count tables in other studies remain unchecked. Qualitative AP permissiveness motivates the task but cannot supply the missing numerical magnitude 2275b121; fb5c9ab0; 1b582220; c5912b30.