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Sample GSM378742 Query DataSets for GSM378742
Status Public on Mar 12, 2009
Title Laser capture microdissected (LCM) chalazal seed coat at the mature green stage, biological replicate 2
Sample type RNA
Source name Arabidopsis mature green stage chalazal seed coat captured by LCM
Organism Arabidopsis thaliana
Characteristics development stage: mature green stage
tissue: chalazal seed coat 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 Chalazal seed coat 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
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.
Reanalyzed by GSE118579
Reanalyzed by GSE119083

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

Data table
AFFX-BioB-5_at 8909.11 P 4.42873e-05
AFFX-BioB-M_at 15691.8 P 4.42873e-05
AFFX-BioB-3_at 13184.3 P 4.42873e-05
AFFX-BioC-5_at 28974.6 P 4.42873e-05
AFFX-BioC-3_at 17463.9 P 4.42873e-05
AFFX-BioDn-5_at 35017.3 P 4.42873e-05
AFFX-BioDn-3_at 75811.4 P 4.42873e-05
AFFX-CreX-5_at 199770 P 4.42873e-05
AFFX-CreX-3_at 220043 P 4.42873e-05
AFFX-DapX-5_at 83.4544 A 0.275146
AFFX-DapX-M_at 16.7021 A 0.860518
AFFX-DapX-3_at 39.5979 A 0.645547
AFFX-LysX-5_at 22.948 A 0.724871
AFFX-LysX-M_at 130.888 A 0.0956669
AFFX-LysX-3_at 18.3722 A 0.760937
AFFX-PheX-5_at 35.2766 A 0.631562
AFFX-PheX-M_at 4.06433 A 0.993129
AFFX-PheX-3_at 26.2879 A 0.937071
AFFX-ThrX-5_at 41.203 A 0.58862
AFFX-ThrX-M_at 7.31125 A 0.659339

Total number of rows: 22810

Table truncated, full table size 669 Kbytes.

Supplementary file Size Download File type/resource
GSM378742.CEL.gz 1.9 Mb (ftp)(http) CEL
GSM378742.CHP.gz 125.2 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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