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Sample GSM238416 Query DataSets for GSM238416
Status Public on Dec 20, 2007
Title Endosperm 16DAF; Seed development; Rep 1
Sample type RNA
Source name Barley Endosperm 16DAF
Organism Hordeum vulgare
Characteristics Genotype: Barke cultivar
Age: 16DAF
Treatment protocol From the early stages of developing caryopsis, the maternal tissues, i.e. mostly pericarp (p), and the filial endosperm/embryo fraction as embryo sac (es) were separated by manual dissection as described by Sreenivasulu et al. (2002). At later stages 16 and 25 DAF endosperm+aleurone (e/a) and embryo+scutellum (em) fractions were prepared.
Growth protocol Barley plants were cultivated in growth chambers at 20oC/18°C under a 16 h light/8 h dark cycle until seed set. The developmental stage of a caryopsis was determined from the mid-region of the ear and assigned as 4, 8, 16 and 25 days after flowering (DAF).
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions, 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 barley endosperm 16 DAF
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 67.9652602 A 0.123873163
1289374_Reg_826-1545_at 10.02591659 A 0.605162372
149174_Reg_66-1115_at 8.926160972 A 0.813027629
150775_Reg_211-1236_at 3.841157304 A 0.703144167
23381122_R_1101-1898_at 77.97094456 A 0.296855833
2623978_R_1403-2212_at 93.5520845 P 0.016427052
40321-46140.AF427791_x_at 2.576865899 A 0.406972737
48446_Reg_1231-2205_at 20.30361623 A 0.671678993
48446_Reg_137-1204_at 2.995841371 A 0.671678993
74797-75570.AF427791_x_at 20.59893387 A 0.570568468
8829-9073.AF427791_x_at 3.419165037 A 0.520323228
9507414_R_4264-4644_at 158.5030932 A 0.077429964
A00196.1_at 27.01985118 A 0.570568468
A06498.1_s_at 26.59705347 A 0.638946097
AB011264_at 40.23755247 A 0.186972371
AB011266_at 34.83225395 A 0.123873163
AB019525_at 5.486968583 A 0.605162372
AB024007_at 19.99162532 A 0.26684731
AF016328_at 283.0579873 A 0.123873163
AF026538_at 93.40895943 A 0.361053903

Total number of rows: 22840

Table truncated, full table size 914 Kbytes.

Supplementary file Size Download File type/resource
GSM238416.CEL.gz 3.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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