The single primer assay design shows how insignificant peaks could easily be wrongly interpreted as clonal T-cell receptor-γ gene rearrangements.
miRNA-specific RT-PCRs were performed using the miScript primer assay according to the manufacturer's protocol (Qiagen, Hilden, Germany).
Primer sets for Oct-3/4, Utf1 and Nanog were purchased from Qiagen (QuantiTect Primer Assay Kits) and added according to manufacturer's protocols.
The one-step QuantiFast SYBR Green RT-PCR Kit (Qiagen) was used in combination with primers from the QuantiTect Primer Assay (Qiagen).
Cycle threshold values were determined automatically by iCycler software and normalized by those for β-actin transcripts amplified using the Mm_Actb_2_SG QuantiTect Primer Assay (Qiagen).
Primers for crystallin α A (Cryaa) and crystallin γ f (Crygf) were purchased from Qiagen (Quantitect primer assay, codes 12954 and 12969 respectively).
Quantitative PCR was performed with the ABI Prism 7000, the SYBR Green PCR kt (Qiagen) and the QuantiTect Primer Assay (Quiagen) for specific genes.
As internal control, mRNA expression of housekeeping genes Gapdh (Rn_Gapd_1_SG QuantiTect Primer Assay QT00199633, Qiagen, Hilden, Germany) or B2m (Table S4) were monitored.
SMN2: Quantitect primer assay QT01673679 (Qiagen), ß-actin: Quantitect primer assay QT00095431 (Qiagen), MeCP2: Quantitect primer assay QT00039361 (Qiagen).
(Rn_Actb_1_SG, QuantiTect Primer Assay QT00193473, Qiagen).
Other primers were ordered 'on demand' with the following order names: Rn_Col3a1_2_SG QuantiTect primer assay (QT01083537), Rn_Tgfb1_1_SG QuantiTect primer assay (QT00187796), Rn-Vcam1-1-SG QuantiTect primer assay (QT00178500) and Rat-Spp-1 RT2 qPCR Primer assay (osteopontin) (PPR44222B).
