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Sample GSM147939 Query DataSets for GSM147939
Status Public on Apr 26, 2007
Title Laser capture microdissected (LCM) endosperm at the globular stage, biological replicate 1
Sample type RNA
 
Source name Soybean globular stage endosperm captured by LCM
Organism Glycine max
Characteristics Soybean cv. Asgrow A3237
Treatment protocol Pods with lengths between 0.5 and 1.2 cm containing seeds with globular-stage embryos were fixed in 3:1(v/v) ethanol:acetic acid and embedded in paraffin (Kerk et al., Plant Physiol.132. 27-35 (2003)). Seed compartment was captured from six-micron sections using a Leica AS LMD System.
Growth protocol Soybean cv. Asgrow A3237 was grown in the UCLA Plant Growth Center using a 16:8 light-dark cycle at 22?C.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the PicoPure RNA Extraction Kit (Molecular Devices, Sunnyvale, CA).
Label biotin
Label protocol Two nanograms of total RNA was amplified using the RiboAmp OA Amplification Kit (Molecular Devices, Sunnyvale, CA). Biotinylated cRNAs were synthesized with the ENZO BioArray High Yield RNA Transcript Labeling Kit using all of the amplified RNA from the RiboAmp OA Kit.
 
Hybridization protocol Following fragmentation, Ten micrograms of cRNA were hybridized for 16 hr at 45?C with the GeneChip Soybean Genome Array. GeneChips were washed and stained using the EukGE-WS2V4_450 protocol in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G System.
Description Endosperm regions from globular stage seeds were microdissected using the LEICA AS LMD system.
Data processing The data were analyzed with the Affymetrix GeneChip Operating System 1.3 (GCOS 1.3) using default analysis settings and global scaling as a normalization method. The trimmed mean target intensity of each array was set to 500.
 
Submission date Dec 01, 2006
Last update date Apr 26, 2007
Contact name Bob Goldberg
E-mail(s) bobglab@mcdb.ucla.edu
Phone 310-825-3270
Organization name University of California, Los Angeles
Department Molecular, Cell and Developmental Biology
Street address 610 Charles E Young Drive East
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platform ID GPL4592
Series (1)
GSE6414 Expression data from soybean seed compartments with embryos at the globular stage

Data table header descriptions
ID_REF
VALUE GCOS 1.3 generated signal intensity.
ABS_CALL The call from the GCOS1.3 software analysis indicates if the transcript was present (P), absent (A), or marginal (M).
DETECTION P-VALUE p-value indicates the detection call significance level.

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 5369.9 P 0.000044
AFFX-BioB-M_at 11500.5 P 0.000044
AFFX-BioB-3_at 7549.4 P 0.000044
AFFX-BioC-5_at 14554.1 P 0.000044
AFFX-BioC-3_at 12861.2 P 0.000044
AFFX-BioDn-5_at 28427 P 0.000044
AFFX-BioDn-3_at 64601.4 P 0.000044
AFFX-CreX-5_at 189182.6 P 0.000052
AFFX-CreX-3_at 190379.2 P 0.000044
AFFX-DapX-5_at 85.8 A 0.52976
AFFX-DapX-M_at 34.4 A 0.617401
AFFX-DapX-3_at 15.1 A 0.979978
AFFX-LysX-5_at 13 A 0.749204
AFFX-LysX-M_at 41.1 A 0.712257
AFFX-LysX-3_at 14.8 A 0.852061
AFFX-PheX-5_at 21.1 A 0.860538
AFFX-PheX-M_at 109.8 A 0.425962
AFFX-PheX-3_at 22.3 A 0.9273
AFFX-ThrX-5_at 21.2 A 0.904333
AFFX-ThrX-M_at 99.2 A 0.617401

Total number of rows: 61170

Table truncated, full table size 2197 Kbytes.




Supplementary file Size Download File type/resource
GSM147939.CEL.gz 4.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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