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Sample GSM238433 Query DataSets for GSM238433
Status Public on Dec 20, 2007
Title Embryo 0 h; Seed germination; Rep 2
Sample type RNA
Source name Barley Embryos from germinating seeds, 0h imbibed
Organism Hordeum vulgare
Characteristics Genotype: Barke cultivar
Age: 0h after imbibition
Treatment protocol endosperm+aleurone (e/a) and embryo+scutellum (em) fractions were dissected from germinating seeds 0, 24, 48 and 72 after imbibition
Growth protocol Seeds were germinated on a moist filter paper in Microclima 1000 growth chambers (Snijders Scientific B.V., Tilburg, Holland) with 16 h light (17oC; 337-377 mmol m-2 s-1 light intensity measured by Sky Quantium light sensor) and 8 h darkness (12oC), 80% humidity.
Extracted molecule total RNA
Extraction protocol PURESCRIPT® RNA isolation kits (Gentra Systems, Inc., Minneapolis, MN) , followed by Rneasy spincolumn cleanup
Label Probe synthesis, labelling and hybridisation were performed according to manufacturer’s protocols (Affymetrix, Santa Clara, CA) at the UCI MicroArray Core Facility, Irvine, Ca.]
Label protocol The BioArray High-Yield RNA Transcript Labeling Kit (Enzo Diagnostics) was then used to synthesize biotin-labeled cRNA from template cDNA by in vitro transcription.
Hybridization protocol 10 µg labeled, fragmented cRNA was then hybridized at 45°C with rotation for 16 hours in an Affymetrix GeneChip 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 Gene expression data from germinationg barley embryo 0h after imbibition
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
Submission date Oct 18, 2007
Last update date Aug 14, 2011
Contact name Björn Usadel
Organization name Max Planck Institute of Molecular Plant Physiology
Street address Am Mühlenberg 1
City Potsdam
ZIP/Postal code 14476
Country Germany
Platform ID GPL1340
Series (1)
GSE9365 Expression data from barley maturing and germinating grains

Data table header descriptions
VALUE MAS5-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
1200459_Reg_88-1740_at 15.50688624 A 0.164032396
1289374_Reg_826-1545_at 5.313007872 A 0.788201896
149174_Reg_66-1115_at 5.762654332 A 0.788201896
150775_Reg_211-1236_at 6.491166875 A 0.570568468
23381122_R_1101-1898_at 11.36277947 A 0.429431532
2623978_R_1403-2212_at 50.01484341 P 0.010397582
40321-46140.AF427791_x_at 22.03362576 P 0.011454516
48446_Reg_1231-2205_at 12.01923648 A 0.856998271
48446_Reg_137-1204_at 1.037700175 A 0.638946097
74797-75570.AF427791_x_at 3.188612754 A 0.788201896
8829-9073.AF427791_x_at 22.22506769 A 0.399429748
9507414_R_4264-4644_at 161.7149946 A 0.143001729
A00196.1_at 12.40827543 A 0.788201896
A06498.1_s_at 33.3099853 A 0.53542366
AB011264_at 43.84702549 A 0.186972371
AB011266_at 31.44361975 A 0.186972371
AB019525_at 39.52212385 A 0.570568468
AB024007_at 9.049844524 A 0.46457634
AF016328_at 145.6368825 A 0.238453215
AF026538_at 99.18186365 A 0.065332572

Total number of rows: 22840

Table truncated, full table size 914 Kbytes.

Supplementary file Size Download File type/resource
GSM238433.CEL.gz 2.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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