7 protocols
AccessionType
array scanning and feature extraction protocol
Scanning of Affymetrix GeneChip microarrays was carried out according to the manufacturer’s standard protocol
hybridization protocol
Affymetrix Generic Hybridization
nucleic acid labeling protocol
Labeling of samples was carried out according to the manufacturer’s standard protocol
bioassay_data_transformation
Background correction,quantile normalization, and gene expression analysis were performed using RMA (Bolstad, B.M., Irizarry R. A., Astrand, M., and Speed, T.P. (2003)A Comparison of Normalization Methods for High Density Oligonucleotide Array Data Based on Bias and Variance. Bioinformatics 19(2):185-193).
pool
Six inflorescence stems from the same pot were dissected out and the top half discarded. RNA was then isolated from the upper half of the remaining tissue using TRIzol Reagent (Invitrogen). i.e. 6 samples pooled per extract.
nucleic_acid_extraction
Six inflorescence stems from the same pot were dissected out and the top half discarded. RNA was then isolated from the upper half of the remaining tissue using TRIzol Reagent (Invitrogen).
(Parameters: Extracted product = total_RNA, Amplification = none)
grow
For comparison of wild type and pxy transcriptomes, previously described Col-0 (wild type) and pxy-3 (mutation of At5g61480) lines were used (Fisher K, Turner S (2007) PXY, a receptor-like kinase essential for maintaining polarity during plant vascular-tissue development. Current Biology 17: 1061-1066). For each replicate, plants were germinated on MS agar plates prior to transfer to soil (6 plants per 10cm pot), where they were grown on for 5 weeks under long day conditions. Pots were randomised and rotated daily. For each replicate, 6 inflorescence stems from one pot were dissected out and the top half discarded. RNA was then isolated from the upper half of the remaining tissue using TRIzol Reagent (Invitrogen).
(Parameters: time unit = seconds, min temperature = 22, temperature unit = C)