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Sample GSM261045 Query DataSets for GSM261045
Status Public on Apr 29, 2009
Title after 3 days in mannitol medium rep1
Sample type RNA
 
Source name 100904A_DH46_4d1
Organism Hordeum vulgare
Characteristics after 3 days in mannitol medium
Treatment protocol Anthers extracted from the spikes under a stereoscopic microscope were inoculated in a treatment medium containing 0.7 M mannitol, 40 mM CaCl2, and 8 g/l agarose, and kept at 25 C in the dark for 4 days (Cistue´et al. 2003). Samples were collected before and after 4 days in mannitol medium. Three samples from each step were harvested and used for microarray analysis.
Growth protocol Donor plants were grown in growth chambers with controlled temperature (18-21ºC), relative humidity (70-80%) and photoperiod (16 h light), as described by Cistué et al. (2003).
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using TRIzol reagent (Invitrogen) from frozen crown samples taken from above soil tissue excluding most fully extended lamina. The protocol is available on the Arabidopsis Information Resource website at http://www.arabidopsis.org/info/2010_projects/comp_proj/AFGC/RevisedAFGC/site2RnaL.htm. RNA was purified using Qiagen RNeasy spin columns with DNase treatment. Quality was assessed by running 25-250 ng on a RNA Lab-On-A-Chip (Caliper Technologies) using an Agilent Bioanalyzer 2100 (Agilent Technologies).
Label biotin
Label protocol The BioArray High-Yield RNA Transcript Labeling Kit (Enzo Diagnostics) was then used to synthesize biotin-labeled cRNA from template cDNA by in vitro transcription.
 
Hybridization protocol 10 µg labeled, fragmented cRNA was hybridized at 45°C with rotation for 16 hours in an Affymetrix GeneChip Hybridization Oven 320 on Affymetrix Barley1 Genechip arrays. The arrays were washed and stained using streptavidin phycoerythrin on an Affymetrix Fluidics Station 400.
Scan protocol The arrays were scanned on a Hewlett-Packard GeneArray scanner.
Description after 3 days in mannitol medium
Data processing GCOS MAS 5
 
Submission date Jan 30, 2008
Last update date Apr 28, 2009
Contact name Livia Tommasini
E-mail(s) liviat@ucr.edu
Phone 951 827 3808
Fax 951 827 4437
URL http://plantbiology.ucr.edu/research_areas/?genomics
Organization name University of California, Riverside
Department Botany and Plant Science
Lab Tim Close
Street address 2150 Batchelor Hall
City Riverside
State/province CA
ZIP/Postal code 92521-0124
Country USA
 
Platform ID GPL1340
Series (1)
GSE10330 Transcriptome analysis of barley anthers: effect of mannitol treatment on microspore embryogenesis

Data table header descriptions
ID_REF
VALUE Signal
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 124.655 P 0.00618711
AFFX-BioB-M_at 77.4764 P 0.002867
AFFX-BioB-3_at 84.8725 P 0.00499819
AFFX-BioC-5_at 280.051 P 0.00010954
AFFX-BioC-3_at 389.636 P 5.16732e-05
AFFX-BioDn-5_at 673.586 P 7.00668e-05
AFFX-BioDn-3_at 1651.16 P 0.000146581
AFFX-CreX-5_at 3287.66 P 4.42873e-05
AFFX-CreX-3_at 7979.79 P 4.42873e-05
AFFX-DapX-5_at 41.4513 P 0.00933744
AFFX-DapX-M_at 110.271 P 0.000972149
AFFX-DapX-3_at 294.338 P 0.00010954
AFFX-LysX-5_at 16.3771 A 0.354453
AFFX-LysX-M_at 50.0703 A 0.250796
AFFX-LysX-3_at 86.115 P 9.4506e-05
AFFX-PheX-5_at 14.8346 A 0.52976
AFFX-PheX-M_at 6.61406 A 0.772364
AFFX-PheX-3_at 62.7775 P 0.0200219
AFFX-ThrX-5_at 21.1036 A 0.48511
AFFX-ThrX-M_at 56.0611 P 0.0396608

Total number of rows: 22840

Table truncated, full table size 792 Kbytes.




Supplementary file Size Download File type/resource
GSM261045.CEL.gz 2.3 Mb (ftp)(http) CEL
GSM261045.CHP.gz 122.7 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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