7 protocols
AccessionNameType
P-GSE45347-1
bioassay_data_transformation
ID_REF = VALUE = RMA-normalized, averaged gene-level signal intensity
P-GSE45347-7
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.
P-GSE45347-6
image_aquisition
Scanning was performed following NimbleGen's standard operating protocol. See www.nimblegen.com.
P-GSE45347-5
hybridization
Hybridization was performed following NimbleGen's standard operating protocol. See www.nimblegen.com.
P-GSE45347-4
labeling
Labelling was performed following NimbleGen's standard operating protocol. See www.nimblegen.com.
P-GSE45347-2
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).
P-GSE45347-3
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).