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Sample GSM146821 Query DataSets for GSM146821
Status Public on Oct 24, 2008
Title Xylem Pole Pericycle Cells at T2, biological rep2
Sample type RNA
Source name Arabidopsis roots at 72 HAG on NPA + 2h NAA
Organism Arabidopsis thaliana
Characteristics Genotype: J0121 (for more information, please see the Dept. of Plant Sciences website of GAL4-GFP expressino patterns at the University of Cambridge)
Age seedlings: 74 HAG
Treatment protocol Roots were treated according to Birnbaum et al (2002, 2005) to isolate xylem pole pericycle cells, which were frozen in RLT buffer
Growth protocol Seedlings were grown on MS supplemented with 10 microM NPA (as described by Himanen et al., 2002) on top of nylon mesh. The seedlings were grown in 16h/8h day/night conditions at 22 C. At 72 HAG the seedlings were transfered to 10 microM NAA for 2h.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from frozen material using the Qiagen RNeasy kit (Valencia, California, United States) according to the manufacturer's instructions
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from undetectable amouns of total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Hybridization protocol Following fragmentation, cRNA was hybridized on GeneChip Arabidopsis ATH1 Genome Array. Treatments were done according to the protocol on the Duke Microarray Facility web site
Scan protocol GeneChips were scanned using the Axon GenePix 4000B scanner (Molecular Devices)
Description Gene expression data from xylem pole pericycle cells from 72-HAG-old Arabidopsis roots grown on NPA and 2h NAA
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0)
Submission date Nov 22, 2006
Last update date Oct 14, 2008
Contact name Ive De Smet
Organization name University of Tübingen - Center for Plant Molecular Biology
Street address Auf der Morgenstelle 3
City Tuebingen
ZIP/Postal code D-72076
Country Germany
Platform ID GPL198
Series (1)
GSE6349 Expression data from xylem pole pericycle cells of Arabidopsis roots undergoing lateral root initiation

Data table header descriptions
VALUE MAS5-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
AFFX-BioB-5_at 1047.6 P 0.00006
AFFX-BioB-M_at 1841.7 P 0.00006
AFFX-BioB-3_at 1228.6 P 0.000044
AFFX-BioC-5_at 3685.5 P 0.00007
AFFX-BioC-3_at 2262 P 0.000052
AFFX-BioDn-5_at 2901.9 P 0.000044
AFFX-BioDn-3_at 11390.1 P 0.000044
AFFX-CreX-5_at 30703.8 P 0.000044
AFFX-CreX-3_at 40799.8 P 0.000044
AFFX-DapX-5_at 4.6 A 0.617401
AFFX-DapX-M_at 5.9 A 0.868639
AFFX-DapX-3_at 2.4 A 0.960339
AFFX-LysX-5_at 22.8 A 0.41138
AFFX-LysX-M_at 3.2 A 0.949771
AFFX-LysX-3_at 18.7 A 0.617401
AFFX-PheX-5_at 4.3 A 0.904372
AFFX-PheX-M_at 26.9 A 0.470241
AFFX-PheX-3_at 9.7 A 0.783476
AFFX-ThrX-5_at 14.6 A 0.41138
AFFX-ThrX-M_at 4.1 A 0.916408

Total number of rows: 22810

Table truncated, full table size 580 Kbytes.

Supplementary file Size Download File type/resource
GSM146821.CEL.gz 579.0 Kb (ftp)(http) CEL

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