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Sample GSM284396 Query DataSets for GSM284396
Status Public on Apr 25, 2008
Title Arabidopsis GPSc2
Sample type RNA
Source name Arabidopsis globular stage chalazal seed coat captured by LCM
Organism Arabidopsis thaliana
Characteristics Genotype: Ws-0
Treatment protocol Siliques with length between 1.1 and 1.4 cm containing globular stage seeds were collected from 38-46 day old plants. Seeds were either dissected out of siliques or left in sub-divided siliques and fixed in 3:1 (v/v) ethanol to acetic acid and embedded in paraffin. Microdissection of compartments was carried out on 5 or 7 um sections using a Leica LMD6000 system. Compartments were only captured from seeds with globular embryos 24-32 um in diameter, as determined by a medial section through the embryo proper.
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 4 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 Laser capture microdissected (LCM) chalazal seed coat at the globular stage, biological replicate 2
Chalazal seed coat collected from seeds containing globular embryos 24 to 32 um in diameter 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 Apr 25, 2008
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)
GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
GSE12404 Expression data from Arabidopsis Seed Compartments at 5 discrete stages of development
Reanalyzed by GSE118579
Reanalyzed by GSE119083

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

Data table
AFFX-BioB-5_at 7518.98 P 4.42873e-05
AFFX-BioB-M_at 13902.9 P 4.42873e-05
AFFX-BioB-3_at 10652.7 P 4.42873e-05
AFFX-BioC-5_at 24376.2 P 4.42873e-05
AFFX-BioC-3_at 16338.8 P 4.42873e-05
AFFX-BioDn-5_at 41037.6 P 4.42873e-05
AFFX-BioDn-3_at 70400.6 P 4.42873e-05
AFFX-CreX-5_at 142613 P 4.42873e-05
AFFX-CreX-3_at 216124 P 4.42873e-05
AFFX-DapX-5_at 72.0828 A 0.411373
AFFX-DapX-M_at 2.76524 A 0.998204
AFFX-DapX-3_at 39.7082 A 0.440646
AFFX-LysX-5_at 26.0679 A 0.5
AFFX-LysX-M_at 51.0164 A 0.724854
AFFX-LysX-3_at 36.4511 A 0.645547
AFFX-PheX-5_at 3.31747 A 0.960339
AFFX-PheX-M_at 4.0102 A 0.995983
AFFX-PheX-3_at 11.3519 A 0.904333
AFFX-ThrX-5_at 25.608 A 0.411373
AFFX-ThrX-M_at 5.23536 A 0.631562

Total number of rows: 22810

Table truncated, full table size 669 Kbytes.

Supplementary file Size Download File type/resource
GSM284396.CEL.gz 1.8 Mb (ftp)(http) CEL
GSM284396.CHP.gz 128.7 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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