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Complementary DNA was prepared using the Primer Script RT Reagent (TaKaRa, Tokyo, Japan).
cDNA synthesis was performed at 37°C for 15 min and 85°C for 5 sec using the Primer Script RT reagent Kit (TaKaRa Biotechnology, Dalian, China) in a total volume of 20 μL according to the manufacturer's instructions.
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RNA was reversed transcribed into cDNAs using the Primer-Script one step RT-PCR kit (TaKaRa, Dalian, China).
Primers were designed using the Primer Premier 5 software.
For cDNA synthesis, 5 µg of DNase-treated total RNA was reverse transcribed with oligo d(T) primers using the Invitrogen Super Script II First Strand cDNA synthesis kit according to manufacturer protocols (Carlsbad, CA).
Through reverse transcription, using the Super Script Preamplification System (Life Technologies, Inc ., cDNA was generated with oligo-dT primers from 5 μg of total RNA per sample (Life Technologies, Inc .. Total RNA was extracted from cells using Trizol.
Python scripts can also be written and executed within MorphoGraphX using the Python Script process.
The alignments were concatenated using the perl script concatenate_alignments.pl.pl
The porcupine plot was plotted using the VMD script.
Oligo-dT primer-directed cDNA was synthesized using the Super-Script III First-Strand Synthesis System for RT-PCR kit from Invitrogen.
Reverse transcriptase reactions were performed with 1μg RNA from patient and control using the Super-Script II Reverse Transcriptase Synthesis Kit (Invitrogen) with hexamers random primers.
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