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Sample GSM311293 Query DataSets for GSM311293
Status Public on Aug 12, 2008
Title Laser capture microdissected (LCM) chalazal seed coat at the linear-cotyledon stage, biological replicate 1
Sample type RNA
Source name Arabidopsis linear-cotyledon stage chalazal seed coat 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 seed coat 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 8840 P 4.42873e-05
AFFX-BioB-M_at 15155.2 P 4.42873e-05
AFFX-BioB-3_at 11716.6 P 4.42873e-05
AFFX-BioC-5_at 27601.5 P 4.42873e-05
AFFX-BioC-3_at 15143.5 P 4.42873e-05
AFFX-BioDn-5_at 36692 P 4.42873e-05
AFFX-BioDn-3_at 82138.8 P 4.42873e-05
AFFX-CreX-5_at 166595 P 4.42873e-05
AFFX-CreX-3_at 219864 P 4.42873e-05
AFFX-DapX-5_at 91.0304 A 0.440641
AFFX-DapX-M_at 5.62406 A 0.9989
AFFX-DapX-3_at 60.0704 A 0.544587
AFFX-LysX-5_at 9.06283 A 0.860538
AFFX-LysX-M_at 41.4866 A 0.58862
AFFX-LysX-3_at 16.3051 A 0.672935
AFFX-PheX-5_at 14.0404 A 0.672921
AFFX-PheX-M_at 10.6049 A 0.737191
AFFX-PheX-3_at 76.6474 A 0.783496
AFFX-ThrX-5_at 75.5978 A 0.147918
AFFX-ThrX-M_at 39.6207 A 0.814869

Total number of rows: 22810

Table truncated, full table size 665 Kbytes.

Supplementary file Size Download File type/resource
GSM311293.CEL.gz 1.7 Mb (ftp)(http) CEL
GSM311293.CHP.gz 128.5 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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