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Sample GSM311285 Query DataSets for GSM311285
Status Public on Aug 12, 2008
Title Laser capture microdissected (LCM) whole seed sections at the pre-globular stage, biological replicate 1
Sample type RNA
 
Source name Arabidopsis pre-globular stage whole seed sections captured by LCM
Organism Arabidopsis thaliana
Characteristics Genotype: Ws-0
Treatment protocol Siliques between 1.0 and 1.1 cm containing pre-globular stage seeds were collected from 38-46 day old plants. Siliques were sub-divided and fixed in 3:1 (v/v) ethanol to acetic acid and embedded in paraffin. Microdissection of compartments was carried out on sections using a Leica LMD6000 system.
Growth protocol Plants were grown in a Conviron chamber under continuous light with fluorescent lamps at 20°C and 50% - 70% relative humidity.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNaqueous Micro-Kit (Ambion, Austin, TX) using a modified protocol incorporating an on-column DNase treatment (Qiagen RNase-Free DNase Set) during column washes.
Label biotin
Label protocol 2 to 5 ng of total RNA was amplified using the WT-Ovation Pico RNA Amplification System (NuGEN, San Carlos, CA). cDNAs were fragmented and labeled with NuGEN FL-Ovation™ cDNA Biotin Module V2.
 
Hybridization protocol Following fragmentation, five micrograms of cDNA was hybridized for 18 hr at 45°C with the GeneChip ATH1 Arabidopsis 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 Serial sections of whole seeds collected from seeds containing pre-globular embryo propers of 2 to 8 cells as determined by median section using the LEICA LMD6000 system for microdissection.
Data processing The data were analyzed with the Affymetrix GeneChip Operating system 1.4 (GCOS) using default analysis settings and global scaling as a normalization method. The mean target intensity of each array was set to 500.
 
Submission date Aug 11, 2008
Last update date Aug 28, 2018
Contact name John J Harada
E-mail(s) jjharada@ucdavis.edu
Phone 530-752-0673
Organization name University of California, Davis
Department Plant Biology
Lab Harada
Street address One Shields Avenue
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
 
Platform ID GPL198
Series (2)
GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
GSE12404 Expression data from Arabidopsis Seed Compartments at 5 discrete stages of development
Relations
Reanalyzed by GSE118579
Reanalyzed by GSE119083

Data table header descriptions
ID_REF
VALUE Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 5473.92 P 4.42873e-05
AFFX-BioB-M_at 10106.6 P 4.42873e-05
AFFX-BioB-3_at 9282.75 P 5.16732e-05
AFFX-BioC-5_at 20164 P 4.42873e-05
AFFX-BioC-3_at 11895.3 P 4.42873e-05
AFFX-BioDn-5_at 24079 P 4.42873e-05
AFFX-BioDn-3_at 54137.5 P 4.42873e-05
AFFX-CreX-5_at 118585 P 4.42873e-05
AFFX-CreX-3_at 187205 P 4.42873e-05
AFFX-DapX-5_at 33.8636 A 0.470241
AFFX-DapX-M_at 8.44751 A 0.916408
AFFX-DapX-3_at 63.5077 A 0.340661
AFFX-LysX-5_at 32.9292 A 0.396911
AFFX-LysX-M_at 16.7237 A 0.699394
AFFX-LysX-3_at 10.2923 A 0.921998
AFFX-PheX-5_at 3.0864 A 0.992398
AFFX-PheX-M_at 4.24038 A 0.973889
AFFX-PheX-3_at 7.90736 A 0.99238
AFFX-ThrX-5_at 6.39704 A 0.737173
AFFX-ThrX-M_at 54.7895 A 0.300606

Total number of rows: 22810

Table truncated, full table size 671 Kbytes.




Supplementary file Size Download File type/resource
GSM311285.CEL.gz 1.8 Mb (ftp)(http) CEL
GSM311285.CHP.gz 126.1 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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