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Sample GSM159173 Query DataSets for GSM159173
Status Public on Mar 19, 2007
Title Rice coleoptiles, 4 days old, aerobic, replicate N.2 (sample#10)
Sample type RNA
Source name Rice coleoptiles, 4 days old, aerobic
Organism Oryza sativa
Characteristics Rice coleoptiles, free of leaf tissue. Rice cultivar: Nipponbare Age: 4 days Germination: aerobic, 28°C, darkness
Treatment protocol This is the control: aerobic samples to be compared to anoxic samples
Growth protocol Rice (Oryza sativa L. cv Nipponbare) seeds were sterilized with diluted bleach (15-min incubation in 1.7% sodium hypochlorite, rinsing and washing in sterile water 10 times) and germinated for four days in air on sterile filter paper at 28°C in the dark. The primary leaf was removed from the coleoptiles of air-germinated seedlings (the leaf is absent in anoxia-germinated seedlings). All the air/anoxia treatments were performed in the dark at 28°C.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the seedling samples using the Ambion RNAqueous kit (Ambion). RNA quality was assessed by agarose gel electrophoresis and spectrophotometry. RNA was processed for use on Affymetrix Rice Genome GeneChip arrays.
Label Biotin
Label protocol Affymetrix standard labeling protocol
Hybridization protocol Affymetrix standard hybridization protocol
Scan protocol Affymetrix standard scan protocol
Description no additional description required
Data processing GC-RMA algorithm
Submission date Jan 29, 2007
Last update date Mar 19, 2007
Contact name Pierdomenico Perata
Phone +39050881901
Organization name Sant'Anna School of Advanced Studies
Department Institute of Life Sciences
Lab PlantLab
Street address Via Guidiccioni 8-10
City San Giuliano Terme
State/province Pisa
ZIP/Postal code 56010
Country Italy
Platform ID GPL2025
Series (1)
GSE6908 Transcript Profiling of the Aerobic and Anoxic Rice Coleoptile

Data table header descriptions
VALUE Signal value

Data table
AFFX-BioB-3_at 76.18800569
AFFX-BioB-5_at 57.14953147
AFFX-BioB-M_at 89.86253789
AFFX-BioC-3_at 246.6433124
AFFX-BioC-5_at 184.124995
AFFX-BioDn-3_at 1245.900902
AFFX-BioDn-5_at 579.4554771
AFFX-CreX-3_at 5981.647615
AFFX-CreX-5_at 5358.923312
AFFX-DapX-3_at 6.357957209
AFFX-DapX-5_at 6.513998208
AFFX-DapX-M_at 6.799521829
AFFX-LysX-3_at 7.618313595
AFFX-LysX-5_at 6.530533721
AFFX-LysX-M_at 5.931258575
AFFX-Mgr-actin-3_at 5.006996186
AFFX-Mgr-actin-5_at 6.897517187
AFFX-Mgr-actin-M_at 3.85135968
AFFX-Mgr-ef1a-3_at 4.862267656
AFFX-Mgr-ef1a-3_x_at 4.826117735

Total number of rows: 57381

Table truncated, full table size 1728 Kbytes.

Supplementary file Size Download File type/resource
GSM159173.CEL.gz 7.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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