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Sample GSM201117 Query DataSets for GSM201117
Status Public on Jun 19, 2007
Title Laser capture microdissected (LCM) cotyledon vascular bundle at the early maturation stage, biological replicate 2
Sample type RNA
 
Source name Soybean early maturation-stage cotyledon vascular bundle captured by LCM
Organism Glycine max
Characteristics Soybean cv. Asgrow A3237
Treatment protocol Seeds with length between 6.0 and 7.0 mm containing early maturation-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 LMD6000 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 Cotyledon vascular bundle regions from early maturation-stage seeds were microdissected using the LEICA LMD6000 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 Jun 13, 2007
Last update date Aug 14, 2011
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)
GSE8112 Expression data from soybean seed compartments with embryos at the early maturation 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-3_at 805.1 P 0.000044
AFFX-BioB-5_at 713.4 P 0.000081
AFFX-BioB-M_at 1200 P 0.000044
AFFX-BioC-3_at 2246.8 P 0.000044
AFFX-BioC-5_at 2336.5 P 0.000044
AFFX-BioDn-3_at 9189.5 P 0.000044
AFFX-BioDn-5_at 4721.3 P 0.000044
AFFX-CreX-3_at 32293.1 P 0.000044
AFFX-CreX-5_at 27652.4 P 0.000052
AFFX-DapX-3_at 4.8 A 0.981719
AFFX-DapX-5_at 54.7 A 0.216524
AFFX-DapX-M_at 87.6 A 0.123572
AFFX-Gm_18SrRNA_at 28499.1 P 0.000219
AFFX-Gm_Actin_3_at 932.9 P 0.000266
AFFX-Gm_Actin_5_at 66.9 A 0.127645
AFFX-Gm_Actin_M_at 84.5 A 0.11716
AFFX-Gm_GlutTrans_3_r_at 10407 P 0.000219
AFFX-Gm_GlutTrans_5_s_at 339.6 P 0.02786
AFFX-Gm_GlutTrans_M_at 928.5 P 0.000219
AFFX-Gm_P450_3_s_at 7810 P 0.000219

Total number of rows: 61170

Table truncated, full table size 2184 Kbytes.




Supplementary file Size Download File type/resource
GSM201117.CEL.gz 4.8 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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