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Sample GSM284391 Query DataSets for GSM284391
Status Public on Apr 25, 2008
Title Arabidopsis GPE3
Sample type RNA
Source name Arabidopsis globular stage peripherial endosperm 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) peripheral endosperm at the globular stage, biological replicate 2
Peripheral endosperm 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 6426.51 P 4.42873e-05
AFFX-BioB-M_at 13103.8 P 4.42873e-05
AFFX-BioB-3_at 11703.1 P 4.42873e-05
AFFX-BioC-5_at 25047.3 P 4.42873e-05
AFFX-BioC-3_at 15952 P 4.42873e-05
AFFX-BioDn-5_at 32411.3 P 4.42873e-05
AFFX-BioDn-3_at 67424.6 P 4.42873e-05
AFFX-CreX-5_at 142218 P 4.42873e-05
AFFX-CreX-3_at 218799 P 4.42873e-05
AFFX-DapX-5_at 77.5113 A 0.0676785
AFFX-DapX-M_at 8.23263 A 0.910541
AFFX-DapX-3_at 8.77953 A 0.910522
AFFX-LysX-5_at 2.22869 A 0.916408
AFFX-LysX-M_at 66.7545 A 0.772403
AFFX-LysX-3_at 54.1194 A 0.588635
AFFX-PheX-5_at 42.7933 A 0.275146
AFFX-PheX-M_at 4.7234 A 0.978135
AFFX-PheX-3_at 29.5932 A 0.772364
AFFX-ThrX-5_at 3.43067 A 0.804734
AFFX-ThrX-M_at 2.5687 A 0.957038

Total number of rows: 22810

Table truncated, full table size 664 Kbytes.

Supplementary file Size Download File type/resource
GSM284391.CEL.gz 1.7 Mb (ftp)(http) CEL
GSM284391.CHP.gz 130.6 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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