NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM238425 Query DataSets for GSM238425
Status Public on Dec 20, 2007
Title Endosperm 48 h; Seed germination; Rep 2
Sample type RNA
 
Source name Barley Enodsperm 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 endosperm 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
E-mail(s) usadel@mpimp-golm.mpg.de
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
ID_REF
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
ID_REF VALUE ABS_CALL DETECTION P-VALUE
1200459_Reg_88-1740_at 90.58086345 A 0.091157283
1289374_Reg_826-1545_at 6.802478983 A 0.73315269
149174_Reg_66-1115_at 6.696232489 A 0.570568468
150775_Reg_211-1236_at 23.08459224 A 0.500000024
23381122_R_1101-1898_at 148.7188228 A 0.238453215
2623978_R_1403-2212_at 78.2048117 P 0.020429855
40321-46140.AF427791_x_at 8.162357484 A 0.318935115
48446_Reg_1231-2205_at 31.39657408 A 0.53542366
48446_Reg_137-1204_at 1.500994228 A 0.605162372
74797-75570.AF427791_x_at 47.24952901 A 0.091157283
8829-9073.AF427791_x_at 14.67789607 A 0.676768867
9507414_R_4264-4644_at 159.8305267 A 0.123873163
A00196.1_at 9.850674708 A 0.835967604
A06498.1_s_at 8.243803656 A 0.703144167
AB011264_at 34.13579211 A 0.123873163
AB011266_at 41.58470032 A 0.238453215
AB019525_at 47.41981866 A 0.46457634
AB024007_at 40.21431849 A 0.091157283
AF016328_at 165.2972759 P 0.037684072
AF026538_at 137.4571865 A 0.211798104

Total number of rows: 22840

Table truncated, full table size 914 Kbytes.




Supplementary file Size Download File type/resource
GSM238425.CEL.gz 2.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap