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Sample GSM311291 Query DataSets for GSM311291
Status Public on Aug 12, 2008
Title Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 1
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
E-mail(s) jjharada@ucdavis.edu
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
Relations
Reanalyzed by GSE118579
Reanalyzed by GSE119083

Data table header descriptions
ID_REF
VALUE GCOS normalized signal intensity
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 7924.86 P 4.42873e-05
AFFX-BioB-M_at 13161.6 P 4.42873e-05
AFFX-BioB-3_at 10261.2 P 4.42873e-05
AFFX-BioC-5_at 26049.9 P 4.42873e-05
AFFX-BioC-3_at 14586.5 P 4.42873e-05
AFFX-BioDn-5_at 37424.3 P 4.42873e-05
AFFX-BioDn-3_at 69162.3 P 4.42873e-05
AFFX-CreX-5_at 128475 P 4.42873e-05
AFFX-CreX-3_at 165654 P 4.42873e-05
AFFX-DapX-5_at 48.1123 A 0.340661
AFFX-DapX-M_at 4.89327 A 0.922016
AFFX-DapX-3_at 16.7312 A 0.686292
AFFX-LysX-5_at 34.9529 A 0.340661
AFFX-LysX-M_at 19.3771 A 0.544587
AFFX-LysX-3_at 4.38892 A 0.986196
AFFX-PheX-5_at 24.9219 A 0.51489
AFFX-PheX-M_at 6.79757 A 0.978098
AFFX-PheX-3_at 12.4716 A 0.988616
AFFX-ThrX-5_at 37.1714 A 0.455413
AFFX-ThrX-M_at 9.53664 A 0.852061

Total number of rows: 22810

Table truncated, full table size 667 Kbytes.




Supplementary file Size Download File type/resource
GSM311291.CEL.gz 1.8 Mb (ftp)(http) CEL
GSM311291.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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