7 protocols
AccessionNameType
P-AFFY-6
feature_extraction
Title: Affymetrix CEL analysis. Description:
Affymetrix:Protocol:Hybridization-Unknown
hybridization
P-AFFY-2
labeling
P-MTAB-13513
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).
P-MTAB-13511
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.
P-MTAB-13510
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)
P-MTAB-13512
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)