7 protocols
normalization data transformation protocol
We use Cufflinks to make assembly from Tophat result and Cuffidff to identify differentially expressed genes. The normalization method is RPKM
high throughput sequence alignment protocol
I use Tophat command line for read alignment, the reference is Aspergillus Fumigatus af293. I use command line with default parameter
nucleic acid sequencing protocol
TruSeq RNA sample preparation kit (Illumina)
treatment protocol
nothing v.s. 1 mM DTT or 10 ug/ml TM for 1 h
growth protocol
a 250 ml flask containing 50 ml of YG medium (0.5% yeast extract, 2% glucose) was inoculated with 5 X 107 conidia and incubated for 16 h with shaking (200 rpm) at 37 degrees C
nucleic acid extraction protocol
TRIZOL method
nucleic acid library construction protocol
Illumina HiSeq 50nt single-end reads