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Sample GSM311289 Query DataSets for GSM311289
Status Public on Aug 12, 2008
Title Laser capture microdissected (LCM) cellularized endosperm at the linear-cotyledon stage, biological replicate 1
Sample type RNA
 
Source name Arabidopsis linear-cotyledon stage cellularized 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 Cellularized 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 4413.1 P 4.42873e-05
AFFX-BioB-M_at 7446.83 P 4.42873e-05
AFFX-BioB-3_at 6269.57 P 4.42873e-05
AFFX-BioC-5_at 14438.6 P 4.42873e-05
AFFX-BioC-3_at 8292.56 P 4.42873e-05
AFFX-BioDn-5_at 22765.8 P 4.42873e-05
AFFX-BioDn-3_at 41009.5 P 4.42873e-05
AFFX-CreX-5_at 83574.6 P 4.42873e-05
AFFX-CreX-3_at 103987 P 4.42873e-05
AFFX-DapX-5_at 15.4894 A 0.574038
AFFX-DapX-M_at 2.9506 A 0.981728
AFFX-DapX-3_at 22.1653 A 0.686277
AFFX-LysX-5_at 30.6185 A 0.617401
AFFX-LysX-M_at 9.16184 A 0.921998
AFFX-LysX-3_at 29.319 A 0.645547
AFFX-PheX-5_at 7.74207 A 0.58862
AFFX-PheX-M_at 3.80957 A 0.994435
AFFX-PheX-3_at 5.089 A 0.960352
AFFX-ThrX-5_at 31.6448 A 0.455413
AFFX-ThrX-M_at 27.3941 A 0.156732

Total number of rows: 22810

Table truncated, full table size 671 Kbytes.




Supplementary file Size Download File type/resource
GSM311289.CEL.gz 1.8 Mb (ftp)(http) CEL
GSM311289.CHP.gz 127.8 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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