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Sample GSM378737 Query DataSets for GSM378737
Status Public on Mar 12, 2009
Title Laser capture microdissected (LCM) peripherial endosperm at the mature green stage, biological replicate 1
Sample type RNA
 
Source name Arabidopsis mature green stage peripherial endosperm captured by LCM
Organism Arabidopsis thaliana
Characteristics development stage: mature green stage
tissue: peripherial endosperm captured by LCM
genotype: Ws-0
Treatment protocol Siliques between 1.8-2.0 cm long containing mature green-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 5 to 6 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 Peripherial endosperm collected from seeds containing a mature green embryo proper as dermined by a medial embryo section showing cotyledons that have extended fully to the chalazal pole and possessing full and visible seed coat layers showing no collapse or senescence, when examined 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 Mar 10, 2009
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)
GSE12404 Expression data from Arabidopsis Seed Compartments at 5 discrete stages of development
GSE15165 Expression data from Arabidopsis seed compartments at the mature green stage.
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 6123.21 P 4.42873e-05
AFFX-BioB-M_at 11000 P 4.42873e-05
AFFX-BioB-3_at 9065.65 P 5.16732e-05
AFFX-BioC-5_at 18459.3 P 4.42873e-05
AFFX-BioC-3_at 10715.7 P 4.42873e-05
AFFX-BioDn-5_at 22861.6 P 4.42873e-05
AFFX-BioDn-3_at 52773.9 P 4.42873e-05
AFFX-CreX-5_at 126692 P 4.42873e-05
AFFX-CreX-3_at 154394 P 4.42873e-05
AFFX-DapX-5_at 120.281 P 0.0166701
AFFX-DapX-M_at 41.4671 A 0.327079
AFFX-DapX-3_at 14.183 A 0.783476
AFFX-LysX-5_at 3.68558 A 0.969024
AFFX-LysX-M_at 15.944 A 0.891041
AFFX-LysX-3_at 4.5207 A 0.989683
AFFX-PheX-5_at 8.85217 A 0.737173
AFFX-PheX-M_at 22.5198 A 0.617401
AFFX-PheX-3_at 16.0097 A 0.9273
AFFX-ThrX-5_at 3.89189 A 0.760956
AFFX-ThrX-M_at 22.3842 A 0.5

Total number of rows: 22810

Table truncated, full table size 669 Kbytes.




Supplementary file Size Download File type/resource
GSM378737.CEL.gz 1.8 Mb (ftp)(http) CEL
GSM378737.CHP.gz 127.0 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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