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Sample GSM182046 Query DataSets for GSM182046
Status Public on Apr 20, 2007
Title Laser capture microdissected (LCM) outer integument at the heart stage, biological replicate 2
Sample type RNA
 
Source name Soybean heart stage outer integument 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 Outer integument regions from heart 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 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 3269.7 P 0.000044
AFFX-BioB-M_at 5546.2 P 0.000044
AFFX-BioB-3_at 3836.2 P 0.000044
AFFX-BioC-5_at 11053 P 0.000044
AFFX-BioC-3_at 10173.9 P 0.000044
AFFX-BioDn-5_at 21981.9 P 0.000044
AFFX-BioDn-3_at 32883.8 P 0.000044
AFFX-CreX-5_at 88325.9 P 0.000052
AFFX-CreX-3_at 91138.9 P 0.000044
AFFX-DapX-5_at 30.9 A 0.645547
AFFX-DapX-M_at 30.6 A 0.760937
AFFX-DapX-3_at 7.6 A 0.971543
AFFX-LysX-5_at 3.6 A 0.904333
AFFX-LysX-M_at 28.2 A 0.529762
AFFX-LysX-3_at 8.9 A 0.937071
AFFX-PheX-5_at 4.5 A 0.994435
AFFX-PheX-M_at 10.7 A 0.824693
AFFX-PheX-3_at 23.4 A 0.876448
AFFX-ThrX-5_at 7.6 A 0.995516
AFFX-ThrX-M_at 5 A 0.98333

Total number of rows: 61170

Table truncated, full table size 2187 Kbytes.




Supplementary file Size Download File type/resource
GSM182046.CEL.gz 4.3 Mb (ftp)(http) CEL
Processed data included within Sample table
Raw data provided as supplementary file

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