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Sample GSM238420 Query DataSets for GSM238420
Status Public on Dec 20, 2007
Title Endosperm 0 h; Seed germination; Rep 1
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 78.81347103 P 0.037684072
1289374_Reg_826-1545_at 13.3122269 A 0.671678993
149174_Reg_66-1115_at 28.51428097 A 0.761546785
150775_Reg_211-1236_at 37.84801586 A 0.500000024
23381122_R_1101-1898_at 105.771653 A 0.361053903
2623978_R_1403-2212_at 145.8884575 P 0.013115575
40321-46140.AF427791_x_at 9.890705408 A 0.194093165
48446_Reg_1231-2205_at 80.09631594 A 0.361053903
48446_Reg_137-1204_at 1.799984416 A 0.671678993
74797-75570.AF427791_x_at 105.6276024 A 0.211798104
8829-9073.AF427791_x_at 48.553051 A 0.399429748
9507414_R_4264-4644_at 228.2042314 A 0.123873163
A00196.1_at 13.03616831 A 0.761546785
A06498.1_s_at 35.20199852 A 0.500000024
AB011264_at 56.25096044 A 0.091157283
AB011266_at 39.06217272 A 0.296855833
AB019525_at 34.85049612 A 0.429431532
AB024007_at 63.20774986 A 0.123873163
AF016328_at 213.1633703 A 0.065332572
AF026538_at 174.525077 A 0.211798104

Total number of rows: 22840

Table truncated, full table size 914 Kbytes.

Supplementary file Size Download File type/resource
GSM238420.CEL.gz 2.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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