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Sample GSM238437 Query DataSets for GSM238437
Status Public on Dec 20, 2007
Title Embryo 48 h; Seed germination; Rep 2
Sample type RNA
Source name Barley Embryos from germinating seeds, 48h imbibed
Organism Hordeum vulgare
Characteristics Genotype: Barke cultivar
Age: 48h 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 48h 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 102.5882638 P 0.006396093
1289374_Reg_826-1545_at 4.736227553 A 0.570568468
149174_Reg_66-1115_at 19.18851817 A 0.570568468
150775_Reg_211-1236_at 11.78601557 A 0.570568468
23381122_R_1101-1898_at 125.4828508 A 0.328321007
2623978_R_1403-2212_at 59.14042932 P 0.010397582
40321-46140.AF427791_x_at 5.084334554 A 0.240088382
48446_Reg_1231-2205_at 38.78946065 A 0.46457634
48446_Reg_137-1204_at 2.143503098 A 0.761546785
74797-75570.AF427791_x_at 3.770060756 A 0.671678993
8829-9073.AF427791_x_at 7.242148376 A 0.560759124
9507414_R_4264-4644_at 236.485971 A 0.065332572
A00196.1_at 11.28252883 A 0.788201896
A06498.1_s_at 3.740800306 A 0.813027629
AB011264_at 21.49743573 A 0.296855833
AB011266_at 38.39058704 A 0.106611564
AB019525_at 5.99871053 A 0.703144167
AB024007_at 11.22972299 A 0.361053903
AF016328_at 170.3891385 A 0.186972371
AF026538_at 105.768118 A 0.361053903

Total number of rows: 22840

Table truncated, full table size 914 Kbytes.

Supplementary file Size Download File type/resource
GSM238437.CEL.gz 2.4 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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