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Sample GSM368745 Query DataSets for GSM368745
Status Public on Feb 10, 2009
Title gapcp1gapcp2, biological rep2
Sample type RNA
 
Source name 15 day old whole seedling
Organism Arabidopsis thaliana
Characteristics mutant
Growth protocol Seeds were germinated and grown vertically in MS 1/5 with Gamborg vitamins. Light condicitions: 16 hours light, 8 hours dark. Temperature: 22ºC. Light 100 μmol m−2 s−1.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy plant mini kit (Qiagen).RNA was extracted from three sets of gapcp double mutants and wild type plants grown at the same time. RNA integrity was determined using RNA 6000 Nano Labchips® in an Agilent 2100 Bioanalyzer following the manufactures protocol. The purified RNA (8 μg) was used to generate first-strand cDNA in a reverse transcription reaction (One-Cycle Target Labeling and Control Reagents; Affymetrix). After second-strand synthesis, the double-stranded cDNAs were used to generate cRNA via an in vitro transcriptional reaction.
Label biotin
Label protocol The cRNA was labeled with biotin, and 20 μg of the labeled cRNA was fragmented. The size distribution of the cRNAs and fragmented cRNAs was assessed using an Eppendorf Biophotometer and electrophoresis.
 
Hybridization protocol Fragmented cRNA (15 μg) was added to 300 μL of hybridization solution, and 200 μL of this mixture was used for hybridization on Arabidopsis ATH1 Genome Arrays for 16 h at 45°C. The standard wash and double-stain protocols (EukGE-WS2v5-450) were applied using an Affymetrix GeneChip Fluidics Station 450.
Scan protocol The arrays (three replicates of each treatment) were scanned on an Affymetrix GeneChip scanner 3000.
Description Gene expression data from embryos in slow phase of cellularisation.
Data processing Fluorescence images were normalized with the software GCOS from Affymetrix. Data were analyzed and compared using the dChip software ( http://www.hsph.harvard.edu/~cli/complab/dchip/). A threshold criteria of 2 fold; P value <0.05 was used.
 
Submission date Feb 09, 2009
Last update date Aug 28, 2018
Contact name Roc Ros
E-mail(s) roc.ros@uv.es
Organization name Universitat de Valencia
Department Biologia Vegetal
Street address Vicent Andres Estelles
City Burjassot
State/province valencia
ZIP/Postal code 46100
Country Spain
 
Platform ID GPL198
Series (1)
GSE14765 Expression data from Arabidopsis gapcp mutant
Relations
Reanalyzed by GSE119083

Data table header descriptions
ID_REF
VALUE signal intensity

Data table
ID_REF VALUE
261585_at 72.42
261568_at 22.04
261584_at 222.38
261579_at 1140.55
261569_at 30.19
261576_at 158.78
261577_at 714.04
261583_at 1713.35
261578_at 3822.07
261580_at 30.06
261570_at 581.84
261575_at 60.37
261581_at 479.32
261571_at 9.94
261582_at 312.21
261572_at 1672.58
261573_at 15.7
261574_at 31.73
261042_at 43.6
261043_at 143.85

Total number of rows: 22746

Table truncated, full table size 367 Kbytes.




Supplementary file Size Download File type/resource
GSM368745.CEL.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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