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We evaluate the batch effect after scaling normalization by assessing expression of commonly used housekeeping genes, including Actb, Actg1, B2m, Rps6, and Rpl13 (all of these genes are expressed in >20% of cells in each batch) and confirmed that our normalization procedure reduced differences between batches (Supplementary Figure 23c).
Cultures were also evaluated for cell cycle status by assessing expression of Ki-67 and p27.
Equal loading was ensured by assessing expression of tubulin and was similar in all the samples.
Measurements were normalized by assessing expression of glyceraldehyde-3-phosphate dehydrogenase (GAPDH, from Biodesign International, Saco, ME, USA).
The cell cycle analysis data were confirmed by assessing expression of the proliferation and apoptosis markers in studied cell populations.
In addition, characterization of mismatch repair competency by assessing expression of four main mismatch repair proteins corroborated these results.
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Erythroid development was determined by assessing expression levels of transferrin receptor (CD71) and glycophorin A (CD235a) by flow cytometry.
Since the most important TGFβ isoform in humans is represented by TGFβ1, we assessed expression of this particular molecule in our study.
The phenotype of the tendon derived cells had not demonstrated significant drift as evidence by the gene expression pattern by assessing the expression of gene for scleraxis and genes for collagens α1(I), α2(I) and α1 III) in real-time PCR assays with specific primers (data not shown).
We ruled out that the lack of myotube formation was caused by the non-myogenic origin of the SCCs by assessing the expression of MyoD in a subset of clones that did not respond to the differentiation treatment (n = 14).
We therefore analyzed tumors induced by PDGF-B in NG2-KO mice by assessing the expression of a panel of markers which allow distinguishing between different neural cell types.
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by assessing phosphorylation of
by assessing completeness of
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