Supplementary Methods
RNA extraction and purification
Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA),
purified using RNeasy columns (Qiagen, Valencia, USA). After processing with
DNase digestion, clean-up procedures, RNA samples were quantified, aliquot and
stored at -80°C until use. Total RNA was amplified and purified using the Ambion
Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA. After
purification, the cRNA was quantified using the ND-1000 Spectrophotometer
(NanoDrop, Wilmington, USA).
Publicly available mRNA datasets
To construct GEO-GPL96 and 570 set, we used the following GSE entries,
GSE11121, GSE12093, GSE1456, GSE1561, GSE15852, GSE20192, GSE20271,
GSE2034, GSE24185, GSE24509, GSE25066, GSE2603, GSE31519, GSE3494,
GSE5462, GSE5849, GSE6532, GSE6883, GSE7390, GSE10281, GSE10780,
GSE12276, GSE16446, GSE18931, GSE19615, GSE20685, GSE2109, GSE22035,
GSE23177, GSE23593, GSE25407, GSE29431, GSE31448, GSE33658,
GSE35925, GSE3744, GSE5460, GSE5764, GSE6532, and GSE8977.
Primer information
The following primer pairs were used: GAPDH, 5΄-ACCCAGAAGACTGTGGATGG-3΄
and 5΄-TTTCTAGACGGCAGGTCAGG-3΄; PHLDA2, 5΄ACTTCACCATCGTCACCACC-3΄ and 5́-TCTGGAAATCGATGAGCGCC-3΄; TKT, 5́CTCCCAGATGGCCCTAGAAG-3΄ and 5́-TCCGGATGAAGCAGATACCC-3΄; P4HA2,
5΄-GACTACCTGCCTGAGAGGGA-3΄and 5΄-ATCCGACGATTTACTCGGGC-3΄.
Relative levels of mRNA were normalized to the values of GAPDH mRNA for each
reaction