7 protocols
AccessionType
bioassay_data_transformation
ID_REF = VALUE = RMA-normalized, averaged gene-level signal intensity
feature_extraction
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis), quantile normalization and background correction as implemented in the NimbleScan software package.
image_aquisition
Scanning was performed following NimbleGen's standard operating protocol. See www.nimblegen.com.
hybridization
Hybridization was performed following NimbleGen's standard operating protocol. See www.nimblegen.com.
labeling
Labelling was performed following NimbleGen's standard operating protocol. See www.nimblegen.com.
grow
wild-type SL1344 and SL1344 (R27) were grown at 25oC and 37oC to mid-exponential growth (OD600 0.6) and early stationary phase (OD600 2.0) in Luria-Bertani (LB) medium (10 g NaCl, 10 g tryptone and 5 g yeast extract per litre).
nucleic_acid_extraction
Total RNA was purified using an SV Total RNA Isolation System (Promega) according to the manufacturer's directions. The RNA was DNase treated with TURBO DNA-free (Ambion) and purified and concentrated again with RNeasy Minielute Clean-up kit (Qiagen). The purity and quality of the purified RNA was tested by Bionalyser 2100 (Agilent Technologies).