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BMS performed probe preparation, hybridisations, microscopy and data analysis and prepared the manuscript.
Two separate RNA extracts were prepared from each sample, one for microarray probe preparation and the second for QPCR.
More complete shRNA probe preparation and hybridization protocols are included in Additional file 2. PCR product was prepared as described above for GMAP shRNA probe preparation except that 27 cycles of PCR were employed when amplifying from pooled plasmid DNA.
For target probe preparation, 5 μl of gDNA was used.
Current colloidal probe preparation techniques face several challenges in the production of functional probes using particles ⩽5 μm.
Probe preparation, membrane hybridization, and signal detection followed the instructions of the ECL direct nucleic acid labeling and detection system (Amersham Pharmacia Biotech).
Xist probe preparation was carried out as described [19].
Total RNA was isolated from cells using Trizol (invitrogen) and used for cDNA probe preparation.
Cell sorting, RNA isolation, probe preparation and quantitative real time PCR (qRTPCR) were described previously [19].
The EST LD20463 was used as a template for RNA probe preparation.
cDNA probe preparation and microarray hybridization were performed as described previously [51].
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