Velvetleaf was sown on May 8, 2006 alone or with corn (DKC46-22) at Aurora, SD on a Brandt silty clay loam soil (fine-silty, mixed superactive, frigid Calcic Hapludoll). The sand, silt, and clay contents were 390, 383, and 226 g kg-1, respectively, with a pH of 6.0 and organic matter content of 35 g kg-1. Velvetleaf seed was planted about 1.5 cm deep using a seed drill either alone or in the interrow area of corn about 20 cm from the crop row. Granular urea was broadcast at 224 kg N ha-1 after planting. Weed management for species other than velvetleaf consisted of a glyphosate application as a burn-down treatment prior to plant emergence and hand removal for the rest of the season. There was some variability in the density of velvetleaf between plots due to uneven germination, however, in general, velvetleaf density was about 6 plants m-2 (ranging from 4 to 8 plants m-2) after germination. Treatments were placed in randomized complete block design with four replicates. Plots were six m long by four rows wide with a row spacing of 76 cm with four replications per treatment. On June 22nd between 1:00 and 2:00 PM, the apical meristem and all of the young leaves (up to 6 cm in diameter) were collected from 4 individual velvetleaf plants within each treatment plot. The samples from within each plot were pooled and immediately frozen in liquid N¬2.
Extracted molecule
total RNA
Extraction protocol
Chang, S., J. Puryear, and J. Cairney. 1993. A simple and efficient method for isolating RNA from pine trees. Plant Mol. Biol. Rep. 11:113-116.
Label
Cy5
Label protocol
Two step labeling of 30 ug total RNA using invitrogen ARES alexa Fluor labeling kit according to manufacturers protocol.
Velvetleaf was sown on May 8, 2006 alone or with corn (DKC46-22) at Aurora, SD on a Brandt silty clay loam soil (fine-silty, mixed superactive, frigid Calcic Hapludoll). The sand, silt, and clay contents were 390, 383, and 226 g kg-1, respectively, with a pH of 6.0 and organic matter content of 35 g kg-1. Corn was planted at a population of about 24,000 plants ha-1. Velvetleaf seed was planted about 1.5 cm deep using a seed drill either alone or in the interrow area of corn about 20 cm from the crop row. Granular urea was broadcast at 224 kg N ha-1 after planting. Weed management for species other than velvetleaf consisted of a glyphosate application as a burn-down treatment prior to plant emergence and hand removal for the rest of the season. There was some variability in the density of velvetleaf between plots due to uneven germination, however, in general, velvetleaf density was about 6 plants m-2 (ranging from 4 to 8 plants m-2) after germination. Treatments were placed in randomized complete block design with four replicates. Plots were six m long by four rows wide with a row spacing of 76 cm with four replications per treatment. On June 22nd between 1:00 and 2:00 PM, the apical meristem and all of the young leaves (up to 6 cm in diameter) were collected from 4 individual velvetleaf plants within each treatment plot. The samples from within each plot were pooled and immediately frozen in liquid N¬2.
Extracted molecule
total RNA
Extraction protocol
Chang, S., J. Puryear, and J. Cairney. 1993. A simple and efficient method for isolating RNA from pine trees. Plant Mol. Biol. Rep. 11:113-116.
Label
Cy3
Label protocol
Two step labeling of 30 ug total RNA using invitrogen ARES alexa Fluor labeling kit according to manufacturers protocol.
Hybridization protocol
Probe was resuspended in 24.6 ul water, 7.2 ul of 2%SDS, 7.65 ul 20XSSC, and 3.75 ul of yeast tRNA (2ug/ul). Probe was denatured at 95 C for 5 minutes and placed on array. Array was hybridized overnight at 60 C. Array was washed 2X in 0.1XSSC, 0.1% SDS at room temp for 5 min. and 2X in 0.1XSSC for 5 min at room temp. The array was spun dry.
Scan protocol
Array was scanned in an Affy 428 scanner using Jaguar software.
Description
NA
Data processing
Raw data was loess normalized using the GeneMaths XT software program and the log2 of the normalized ratio was generated.
