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Sample GSM146819 Query DataSets for GSM146819
Status Public on Oct 24, 2008
Title Xylem Pole Pericycle Cells at T0, biological rep2
Sample type RNA
Source name Arabidopsis roots at 72 HAG on NPA
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: 72 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
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
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 519.7 P 0.00006
AFFX-BioB-M_at 1059.5 P 0.000052
AFFX-BioB-3_at 481.3 P 0.00006
AFFX-BioC-5_at 1458 P 0.000044
AFFX-BioC-3_at 921.4 P 0.000052
AFFX-BioDn-5_at 1392.2 P 0.000044
AFFX-BioDn-3_at 4879.9 P 0.000044
AFFX-CreX-5_at 14510.3 P 0.000044
AFFX-CreX-3_at 16795.4 P 0.000044
AFFX-DapX-5_at 8.2 A 0.617401
AFFX-DapX-M_at 5.1 A 0.712257
AFFX-DapX-3_at 1.5 A 0.997727
AFFX-LysX-5_at 20.5 A 0.58862
AFFX-LysX-M_at 4 A 0.876428
AFFX-LysX-3_at 1.9 A 0.824672
AFFX-PheX-5_at 2.7 A 0.932322
AFFX-PheX-M_at 3.2 A 0.876428
AFFX-PheX-3_at 46.4 A 0.287743
AFFX-ThrX-5_at 1.6 A 0.957038
AFFX-ThrX-M_at 1.6 A 0.897835

Total number of rows: 22810

Table truncated, full table size 582 Kbytes.

Supplementary file Size Download File type/resource
GSM146819.CEL.gz 576.0 Kb (ftp)(http) CEL

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