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Sample GSM191079 Query DataSets for GSM191079
Status Public on May 25, 2007
Title Soybean_Cotyledon_ES1
Sample type RNA
Source name Soybean cotyledon-stage endosperm captured by LCM
Organism Glycine max
Characteristics Laser capture microdissected (LCM) endosperm at the cotyledon stage, biological replicate 1
Soybean cv. Asgrow A3237
Treatment protocol Seeds with length between 2.5 and 3.0 mm containing cotyledon-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 Endosperm regions from cotyledon-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 May 23, 2007
Last update date May 23, 2007
Contact name Bob Goldberg
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)
GSE7881 Expression data from soybean seed compartments with embryos at the cotyledon stage

Data table header descriptions
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
AFFX-BioB-5_at 1302.8 P 0.000044
AFFX-BioB-M_at 1523.4 P 0.000044
AFFX-BioB-3_at 1165.1 P 0.000044
AFFX-BioC-5_at 3763.5 P 0.000044
AFFX-BioC-3_at 2921.3 P 0.000044
AFFX-BioDn-5_at 7900.4 P 0.000044
AFFX-BioDn-3_at 13746.1 P 0.000044
AFFX-CreX-5_at 47875.3 P 0.000052
AFFX-CreX-3_at 52786.9 P 0.000044
AFFX-DapX-5_at 54 M 0.054213
AFFX-DapX-M_at 51.7 A 0.16584
AFFX-DapX-3_at 3.7 A 0.922016
AFFX-LysX-5_at 4.6 A 0.916426
AFFX-LysX-M_at 38.7 A 0.603089
AFFX-LysX-3_at 3.8 A 0.945787
AFFX-PheX-5_at 3.6 A 0.963431
AFFX-PheX-M_at 37 A 0.5
AFFX-PheX-3_at 50.3 A 0.52976
AFFX-ThrX-5_at 5.1 A 0.969024
AFFX-ThrX-M_at 6.5 A 0.783476

Total number of rows: 61170

Table truncated, full table size 2183 Kbytes.

Supplementary file Size Download File type/resource
GSM191079.CEL.gz 4.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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