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Sample GSM182032 Query DataSets for GSM182032
Status Public on Apr 20, 2007
Title Laser capture microdissected (LCM) suspensor at the heart stage, biological replicate 1
Sample type RNA
 
Source name Soybean heart stage suspensor captured by LCM
Organism Glycine max
Characteristics Soybean cv. Asgrow A3237
Treatment protocol Pods with lengths between 1.3 and 2.0 cm containing seeds with heart-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 eight-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 Suspensor regions from heart embryos 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 Apr 12, 2007
Last update date Apr 13, 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)
GSE7511 Expression data from soybean seed compartments with embryos at the heart 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 22851.6 P 0.000044
AFFX-BioB-M_at 34443.4 P 0.000044
AFFX-BioB-3_at 26253 P 0.000044
AFFX-BioC-5_at 60308.2 P 0.000044
AFFX-BioC-3_at 52765.1 P 0.000044
AFFX-BioDn-5_at 103287.5 P 0.000044
AFFX-BioDn-3_at 152810.8 P 0.000044
AFFX-CreX-5_at 407900.8 P 0.000052
AFFX-CreX-3_at 423395.4 P 0.000044
AFFX-DapX-5_at 169.9 A 0.645547
AFFX-DapX-M_at 238.1 A 0.396911
AFFX-DapX-3_at 38 A 0.868639
AFFX-LysX-5_at 27.9 A 0.749223
AFFX-LysX-M_at 160 A 0.382599
AFFX-LysX-3_at 11.6 A 0.980013
AFFX-PheX-5_at 25.4 A 0.883969
AFFX-PheX-M_at 66.7 A 0.749204
AFFX-PheX-3_at 287.9 A 0.60308
AFFX-ThrX-5_at 280.9 A 0.425962
AFFX-ThrX-M_at 85.1 A 0.804734

Total number of rows: 61170

Table truncated, full table size 2203 Kbytes.




Supplementary file Size Download File type/resource
GSM182032.CEL.gz 3.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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