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Sample GSM284394 Query DataSets for GSM284394
Status Public on Apr 25, 2008
Title Arabidopsis GCE3
Sample type RNA
Source name Arabidopsis globular stage chalazal 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) chalazal endosperm at the globular stage, biological replicate 3
Chalazal 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 8256.73 P 4.42873e-05
AFFX-BioB-M_at 14511.6 P 5.16732e-05
AFFX-BioB-3_at 11320.4 P 4.42873e-05
AFFX-BioC-5_at 27539.5 P 4.42873e-05
AFFX-BioC-3_at 17300.5 P 4.42873e-05
AFFX-BioDn-5_at 44188 P 4.42873e-05
AFFX-BioDn-3_at 73600.7 P 4.42873e-05
AFFX-CreX-5_at 148382 P 4.42873e-05
AFFX-CreX-3_at 224819 P 4.42873e-05
AFFX-DapX-5_at 77.4449 M 0.0629128
AFFX-DapX-M_at 11.3573 A 0.843268
AFFX-DapX-3_at 24.4669 A 0.686277
AFFX-LysX-5_at 13.6587 A 0.724854
AFFX-LysX-M_at 9.64533 A 0.949771
AFFX-LysX-3_at 9.36461 A 0.916482
AFFX-PheX-5_at 23.7555 A 0.617411
AFFX-PheX-M_at 48.5154 A 0.631562
AFFX-PheX-3_at 21.9593 A 0.916408
AFFX-ThrX-5_at 30.9244 A 0.52976
AFFX-ThrX-M_at 62.2842 A 0.131361

Total number of rows: 22810

Table truncated, full table size 664 Kbytes.

Supplementary file Size Download File type/resource
GSM284394.CEL.gz 1.7 Mb (ftp)(http) CEL
GSM284394.CHP.gz 128.6 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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