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Some key approaches to understanding the molecular basis of pluripotency and early differentiation are the analysis of transcription factor binding site mapping [ 3], epigenetics studies (reviewed in [ 4]), as well as in-depth assessments of transcripts expressed in ES cells.
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Both quantitative expression data (adjusted signal intensity) as well as qualitative expression data (present/absent) are included to facilitate rapid assessments of transcript abundance in target tissues.
Microarray analysis and assessment of transcripts from B lymphocyte-related genes were performed as previously described.
The PLA used in this context is both an assessment of transcripts, portfolios etc. and performance in an Objective Structures Clinical Examination (OSCE).
Gene specific assessment of transcripts showed approximately 2.5 fold higher expression of SCGB1A1A than SCGB1A1 in lung and uterus of control animals, and an increased ratio in lung tissue of animals with RAO, an asthma-like condition.
PS developed the study design, carried out the preparation of RNA, the quantification and assessment of transcript integrity, the RNA amplifications and reverse transcriptions, supervised the T-UCR qPCR reactions, participated in data analysis, drafted the manuscript.
Tests for heterogeneity used the natural log for assessment of transcript levels.
Assessment of transcript gene sets containing specific cis-regulatory elements that were upregulated by UAG in muscle are detailed in Table S7.
Assessment of transcript gene sets containing specific cis-regulatory elements that were upregulated by UAG in liver (Table S9) include ATF, CREBP1 and RSRF4.
The cDNAs used here were not experimentally normalized, so as to allow assessment of transcript abundance and thus it is not surprising to find that transcripts from the mitochondrial genome are prominent.
The public repository Gene Expression Omnibus [39] contains tens of thousands of 3'-end targeted expression microarray datasets (Table 5), many of which have been analyzed only for assessment of transcript abundance.
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