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Sample GSM311292 Query DataSets for GSM311292
Status Public on Aug 12, 2008
Title Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 2
Sample type RNA
Source name Arabidopsis linear-cotyledon stage chalazal endosperm captured by LCM
Organism Arabidopsis thaliana
Characteristics Genotype: Ws-0
Treatment protocol Siliques between 1.6 and 1.9 cm long containing linear-cotyledon 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 Chalazal endosperm collected from seeds containing linear-cotyledon embryos 175 (+/- 11) microns in length 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)
GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
GSE12404 Expression data from Arabidopsis Seed Compartments at 5 discrete stages of development
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 7268.69 P 4.42873e-05
AFFX-BioB-M_at 11225.5 P 4.42873e-05
AFFX-BioB-3_at 9202.6 P 4.42873e-05
AFFX-BioC-5_at 23473 P 4.42873e-05
AFFX-BioC-3_at 14252.9 P 4.42873e-05
AFFX-BioDn-5_at 33145.5 P 4.42873e-05
AFFX-BioDn-3_at 66057.3 P 4.42873e-05
AFFX-CreX-5_at 129306 P 4.42873e-05
AFFX-CreX-3_at 187577 P 4.42873e-05
AFFX-DapX-5_at 67.0233 A 0.262791
AFFX-DapX-M_at 20.2686 A 0.916408
AFFX-DapX-3_at 11.0463 A 0.804734
AFFX-LysX-5_at 20.2337 A 0.783476
AFFX-LysX-M_at 22.9509 A 0.783476
AFFX-LysX-3_at 17.7102 A 0.761014
AFFX-PheX-5_at 12.2104 A 0.724871
AFFX-PheX-M_at 9.15764 A 0.852082
AFFX-PheX-3_at 88.7898 A 0.574044
AFFX-ThrX-5_at 4.72464 A 0.953533
AFFX-ThrX-M_at 25.2844 A 0.749242

Total number of rows: 22810

Table truncated, full table size 665 Kbytes.

Supplementary file Size Download File type/resource
GSM311292.CEL.gz 1.8 Mb (ftp)(http) CEL
GSM311292.CHP.gz 128.5 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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