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Sample GSM290554 Query DataSets for GSM290554
Status Public on Jul 22, 2009
Title WS2 with array type maize from Affymetrix
Sample type RNA
Source name WS2
Organism Zea mays
Characteristics Zea mays, maize, corn - dev.stage (Boyes et al. Plant Cell 2001):7 or 8 leaves
Treatment protocol Name:Early - environmental treatment - hydrometry,drought:time 36hour . short time at REW 20-30 percent
Growth protocol aerial - Maize plants were grown in culture room conditions with a thermoperiod of 25 celsius day/22 celsius night and a photoperiod of 16h day/8h night. Seeds were sown in pots containing compost (H4-TREF) and fertilized one time a week with Algoflash solution. At 6-7-leaf stage samples (young piled-up internodes) were collected individually and immediatly frozen.
Extracted molecule total RNA
Extraction protocol Pool of extract, 130-L:1ug, 131-L:1ug, 133-L:1ug, WS2:215ug.
Label Biotin
Label protocol labelling Biotin direct, amplification=yes, RNAa 20 ug.
Hybridization protocol labelled extract quantity: 10ug
Scan protocol GCOS, Biotin:pmt voltage 570nm,650V,laser power 1
Description Cinnamoyl-CoA reductase (CCR) catalyzes a key step in monolignol biosynthesis. We show that downregulation of CCR in maize was associated with lower lignin content and a strong decrease in H units. Concomitantly, these cell wall modifications were associated with higher digestibility. On another hand, immunocytochemistry indicated a modification of lignification pattern and cellulose content. Transcript profiling was used as comprehensive phenotyping tools to investigate how CCR downregulation impacted metabolism and the biosynthesis of other cell wall polymers.
Data processing The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).
Submission date May 22, 2008
Last update date May 12, 2009
Contact name sandrine balzergue
Organization name INRA
Street address Rue G. Morel
City Beaucouze
ZIP/Postal code 49000
Country France
Platform ID GPL4032
Series (1)
GSE11531 Downregulation of cinnamoyl-coenzyme A reductase in maize (affy_ccr_maize)

Data table header descriptions
ID_REF ID number
VALUE Normalized data by GCRMA

Data table
AFFX-BioB-3_at 4.89
AFFX-BioB-5_at 4.98
AFFX-BioB-M_at 6.21
AFFX-BioC-3_at 8.19
AFFX-BioC-5_at 7.17
AFFX-BioDn-3_at 10.36
AFFX-BioDn-5_at 9.44
AFFX-CreX-3_at 13.10
AFFX-CreX-5_at 12.98
AFFX-DapX-3_at 10.94
AFFX-DapX-5_at 9.61
AFFX-DapX-M_at 10.91
AFFX-LysX-3_at 8.04
AFFX-LysX-5_at 6.31
AFFX-LysX-M_at 6.09
AFFX-PheX-3_at 7.23
AFFX-PheX-5_at 7.33
AFFX-PheX-M_at 7.21
AFFX-r2-Bs-dap-3_at 11.60
AFFX-r2-Bs-dap-5_at 9.94

Total number of rows: 17734

Table truncated, full table size 396 Kbytes.

Supplementary file Size Download File type/resource
GSM290554.CEL.gz 2.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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