8 protocols
AccessionNameType
P-AFFY-6
feature_extraction
Title: Affymetrix CEL analysis. Description:
P-AFFY-3
nucleic acid hybridization to array protocol
GeneChip hybridization
 
P-MTAB-35154
normalization data transformation protocol
GeneSpring software (Agilent) was used to compare groups of triplicate datasets for (i) wild-type cells grown with vs without arabinose, (ii) wild-type vs delta araC cells grown in the presence arabinose, and (iii) wild-type vs delta araC cells grown in the absence of arabinose. Analysis incorporates replicates. Each value is a comparison of 3 replicates for one strain/condition to 3 replicates for another strain/condition.
P-MTAB-35153
nucleic acid labeling protocol
cDNA synthesis, labeling, hybridization to Affymetrix GeneChip E. coli Genome 2.0 microarrays, washing and scanning were performed according to the manufacturer’s (Affymetrix) instructions
P-MTAB-35151
treatment protocol
In some cases cells were grown with 0.2% arabinose throughout the culture growth
P-MTAB-35152
nucleic acid extraction protocol
1 ml cells were mixed with 400 ul ice-cold 95% ethanol and 5% phenol/chloroform/isoamyl alcohol (25:24:21 mix). Cells were pelleted in a microcentrifuge for 1 minute at full speed and washed once with TBS. Cell pellets were resuspended in 400 ul RNA lysis buffer (2% SDS, 4 mM EDTA) and boiled for 3 minutes. 400 ul acid phenol/choroform/isoamyl alcohol mix (pH 4.3) was added and incubated at 65 degrees C for 6 minutes and on ice for 5 minutes. Samples were centrifuged and the aqueous layer was extracted once more with phenol/choroform/isoamyl alcohol mix (pH 4.3). RNA was precipitated with 1 ml 100% ethanol and 40 ul 3 M sodium acetate. RNA was pelleted in a microcentrifuge for 10 minutes at full speed and washed once with room-temperature 75% ethanol. RNA pellets were air-dried and resuspended in water and treated with 10 units of DNase I (NEB) in 500 ul for 1 hour at 37 degrees C. RNA was then phenol extracted and ethanol precipitated. For each sample we generated three independent biological replicates labeled B, C or D.
P-MTAB-35150
growth protocol
RNA was purified from wild-type MG1655 or MG1655 delta araC cells grown in LB at 37 degrees C to an OD600 of 0.6-0.8.