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Sample GSM238421 Query DataSets for GSM238421
Status Public on Dec 20, 2007
Title Endosperm 0 h; Seed germination Rep 2
Sample type RNA
Source name Barley Enodsperm 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 endosperm 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 113.6680663 A 0.077429964
1289374_Reg_826-1545_at 14.0382529 A 0.703144167
149174_Reg_66-1115_at 27.93415464 A 0.788201896
150775_Reg_211-1236_at 43.94964989 A 0.394837628
23381122_R_1101-1898_at 84.0838237 A 0.394837628
2623978_R_1403-2212_at 119.4505125 P 0.006396093
40321-46140.AF427791_x_at 32.28438022 P 0.035594564
48446_Reg_1231-2205_at 67.7632196 A 0.394837628
48446_Reg_137-1204_at 2.500580186 A 0.605162372
74797-75570.AF427791_x_at 57.19484347 A 0.186972371
8829-9073.AF427791_x_at 46.70656087 A 0.253812115
9507414_R_4264-4644_at 257.4816744 A 0.091157283
A00196.1_at 17.67731441 A 0.813027629
A06498.1_s_at 43.99299869 A 0.46457634
AB011264_at 65.44754546 A 0.091157283
AB011266_at 65.6694072 A 0.328321007
AB019525_at 6.743588773 A 0.73315269
AB024007_at 57.8920891 P 0.020429855
AF016328_at 174.6191469 P 0.020429855
AF026538_at 150.2894338 A 0.238453215

Total number of rows: 22840

Table truncated, full table size 914 Kbytes.

Supplementary file Size Download File type/resource
GSM238421.CEL.gz 2.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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