7 protocols
AccessionNameType
P-GSE47975-1
normalization data transformation protocol
Raw data was extracted using the Agilent Feature Extraction Software (Version 10.7.3.1). Array quality was monitored using the Agilent QC tool with the metric set Ge2_107_Sep09. ID_REF = VALUE = Normalized log10 ratio Cy5/Cy3.
P-GSE47975-7
array scanning protocol
Scanned on an Agilent G2565AA microarray scanner at 5 µm resolution.
P-GSE47975-6
hybridization protocol
Hybridization was performed onto 4 x 44k microarray slides, containing oligonucleotide 60mers designed with the Agilent eArray online platform, using the Agilent Gene Expression Kit according to the manufacturer's protocol.
P-GSE47975-5
labelling protocol
80 ng of total RNA were amplified, reverse transcribed and labelled using the Agilent Two-color Low Input Quick Amp Labeling Kit according to the manufacturer's protocol. As a minor modification, random hexamers with attached T7 promotor were added.
P-GSE47975-2
sample treatment protocol
F. vesiculosus pieces were or were not grazed by Idotea baltica for 15 and 18 days.
P-GSE47975-3
growth protocol
Fucus vesiculosus pieces were kept in 25L aquaria at a mean (± SD) seawater flow rate of 184 (± 17) ml min-1. Mean (± SD) water temperature was 19.7 (± 1.0) °C. Light was provided in a light/dark cycle of 12/12 h at a mean (± SD) photon flow rate of 121.1 (± 2.9) µmol m-2 s-1 (PAR) during light periods.
P-GSE47975-4
nucleic acid extraction protocol
Total RNA was isolated with using 1 ml of a CTAB extraction buffer (2% CTAB, 1 M NaCl, 100 mM Tris pH 8, 50 mM EDTA pH 8) and 25 µl DTT 2 M. After incubation at 45°C for 15 min, an equal volume of chloroform:isoamylalcohol (24:1) was added, vortexed vigorously for 5 min and afterwards centrifugated for 20 min at RT and 12,000 g. Subsequently, the aqueous phase was transferred and 0.3 volumes of EtOH 96% were added. After mixing gently, a second chloroform extraction was performed. Subsequently, total RNA was extracted using the Qiagen Plant Mini Kit accoding to the manufacturer's protocol.