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Sample GSM311278 Query DataSets for GSM311278
Status Public on Aug 12, 2008
Title Laser capture microdissected (LCM) peripheral endosperm at the pre-globular stage, biological replicate 2
Sample type RNA
Source name Arabidopsis pre-globular stage cellularized endosperm captured by LCM
Organism Arabidopsis thaliana
Characteristics Genotype: Ws-0
Treatment protocol Siliques between 1.0 and 1.1 cm containing pre-globular 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 2 to 5 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 cellularized endosperm collected from seeds containing pre-globular embryo propers of 2 to 8 cells 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 Aug 11, 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)
GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular 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 Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)

Data table
AFFX-BioB-5_at 7324.44 P 4.42873e-05
AFFX-BioB-M_at 12742.1 P 4.42873e-05
AFFX-BioB-3_at 10043.5 P 4.42873e-05
AFFX-BioC-5_at 24041.3 P 4.42873e-05
AFFX-BioC-3_at 14314.5 P 4.42873e-05
AFFX-BioDn-5_at 32820.2 P 4.42873e-05
AFFX-BioDn-3_at 66031.7 P 4.42873e-05
AFFX-CreX-5_at 123911 P 4.42873e-05
AFFX-CreX-3_at 163305 P 4.42873e-05
AFFX-DapX-5_at 35.627 A 0.455413
AFFX-DapX-M_at 53.6047 A 0.48511
AFFX-DapX-3_at 12.5941 A 0.904333
AFFX-LysX-5_at 23.2134 A 0.603124
AFFX-LysX-M_at 10.4423 A 0.876428
AFFX-LysX-3_at 7.83975 A 0.976071
AFFX-PheX-5_at 33.0984 A 0.58862
AFFX-PheX-M_at 16.5099 A 0.916408
AFFX-PheX-3_at 11.3814 A 0.966323
AFFX-ThrX-5_at 20.0164 A 0.5
AFFX-ThrX-M_at 27.9942 A 0.300591

Total number of rows: 22810

Table truncated, full table size 668 Kbytes.

Supplementary file Size Download File type/resource
GSM311278.CEL.gz 1.8 Mb (ftp)(http) CEL
GSM311278.CHP.gz 127.4 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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