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Sample GSM282027 Query DataSets for GSM282027
Status Public on Mar 05, 2009
Title Malting_day1_Legacy_rep2
Sample type RNA
Source name Barley seed day 1 germination, Legacy
Organism Hordeum vulgare
Characteristics Genotype: Legacy
Treatment protocol Samples were frozen in liquid nitrogen and stored at -80°C until use.
Growth protocol Fifty to 100 g seeds of each variety were micro-malted at Busch Agricultural Resources, LLC, Fort Collins, CO. The micromalting conditions were as follows: steeping at 12°C for 37 h, germination at 12°C for 5 h, 17°C for 65 h, 18°C for 23 h, and kilning stages consisting of 55°C for 10 h, 60°C for 4 h, 68°C for 3 h, 80°C for 2 h and 90°C for 3 h.
Extracted molecule total RNA
Extraction protocol Frozen barley malt was ground and incubated with RNA purification reagent from Invitrogen (Carlsbad, CA) at room temperature for 10 minutes. Total RNA was extracted using Qiagen RNeasy Plant Mini Kit with RNase Free/DNase (Qiagen, Valencia, CA) following the manufacturer's instructions.
Label biotin
Label protocol The BioArray High-Yield RNA Transcript labeling kit (Enzo Diagnostics) was used to synthesize biotin-labeled cRNA from template cDNA by in vitro transcription.
Hybridization protocol 10 µg labeled, fragmented cRNA was hybridized at 45°C with rotation for 16 h in an Affymetrix GeneChio Hybridization Oven 320 on Affymetrix Barley1 GeneChip arrays. The arrays were washed and stained using streptavidin phycoerythrin on an Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the GeneChip Scanner 3000.
Description Probe synthesis, labeling and hybridization were perfomed according to manufacturer's protocols (Affymetrix, Santa Clara, CA) at the UCI Microarray Core Facility, Irvine, CA.
Data processing Different quality control checks were performed including inspection of hybridized images, boxplots and histograms of log2(PM) values, examination of hybridization and PolyA controls. Based on the results of the quality control screening, some chips were discarded from the analysis. Twenty-two arrays were retained for further analysis, with two replications per cultivar per time point, with the exception of Harrington day 1, where one of the replicates was discarded. Data analysis was carried out using Bioconductor in R (Gentleman et al. 2004). Data preprocessing and summarization were performed using Robust Multichip Average (RMA) (Irizarry et al. 2003).
Submission date Apr 17, 2008
Last update date Mar 05, 2009
Contact name Nora L Lapitan
E-mail(s) Nora.Lapitan@ColoState.EDU
Phone 970 491-1921
Fax 970 491-0564
Organization name Colorado State University
Department Soil and Crop Sciences
Lab Crop Genomics Lab
Street address Plant Science Bldg
City Fort Collins
State/province CO
ZIP/Postal code 80523
Country USA
Platform ID GPL1340
Series (1)
GSE11200 Expression data from malting barley seeds

Data table header descriptions
VALUE RMA values

Data table
1200459_Reg_88-1740_at 5.503645 P
1289374_Reg_826-1545_at 5.779681 A
149174_Reg_66-1115_at 6.226094 A
150775_Reg_211-1236_at 4.899863 A
23381122_R_1101-1898_at 7.837042 A
2623978_R_1403-2212_at 6.272239 P
40321-46140.AF427791_x_at 3.977496 A
48446_Reg_1231-2205_at 6.178662 A
48446_Reg_137-1204_at 5.081277 A
74797-75570.AF427791_x_at 5.086997 A
8829-9073.AF427791_x_at 4.209528 A
9507414_R_4264-4644_at 7.966943 A
A00196.1_at 6.554687 A
A06498.1_s_at 5.043881 A
AB011264_at 6.791904 A
AB011266_at 5.203731 A
AB019525_at 4.960973 A
AB024007_at 5.018486 A
AF016328_at 8.06408 A
AF026538_at 6.946439 A

Total number of rows: 22840

Table truncated, full table size 582 Kbytes.

Supplementary file Size Download File type/resource
GSM282027.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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