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Sample GSM226538 Query DataSets for GSM226538
Status Public on Nov 05, 2007
Title L8SB
Sample type RNA
Source name root tissue
Organism Arabidopsis thaliana
Characteristics Columbia ecotype
Age: Seedling roots, 7 days after germination
Growth media: standard media
Treatment protocol Samples were prepared as in Birnbaum et al. (2005) Nat. Methods for roots grown under standard conditions.
Growth protocol Seeds were surface sterilized with 50% Bleach and 0.1% Tween for 5 minutes and then rinsed 3 times with sterile water. Seeds were stratified at 4˚C for 2 days before being planted on standard media. Standard media is 1X concentration Murashige and Skoog salt mixture (Caisson laboratories), 0.5g/L MES, 1% sucrose, 1% agar and adjusted to pH 5.7 with KOH. Nylon mesh was placed on top of the solidified media and seeds were evenly placed on the mesh.
Extracted molecule total RNA
Extraction protocol RNA was extracted using the RNAeasy Micro Kit (Qiagen GmbH).
Label biotin
Label protocol Fragmented cRNA probes were prepared using the two-cycle amplification protocol by Affymetrix.
Hybridization protocol Samples were submitted to Expression Analysis Inc. (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.
Scan protocol Samples were submitted to Expression Analysis Inc. (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.
Description Arabidopsis, root cells, cross-section, 1/2 of elongation zone, second elongation section from root tip, standard conditions, root2
Gene expression data from a cross-section of 1/2 of the root elongation zone, the second section from the root tip
Data processing Software described in Levesque et al. (2006), PLoS Biology, 4:e143 was used for normalization. This uses the global normalization/linear modeling approach described in Chu et al. (2001). This method simultaneously considers the perfect match probeset data across all chips in an experiment. Normalization across all chips was performed as follows: [Log2(IntensityPROBE, ARRAY) = logarithmic meanALLARRAY INTENSITY VALUES + residualsPROBE, ARRAY]. For each array, all probes were removed that were greater than two standard deviations from the probeset mean. For all remaining probe values across replicates in a treatment, expression indices are calculated as: 2^r1 + 2^r2 + 2^rN/N
Submission date Aug 31, 2007
Last update date Aug 28, 2018
Contact name Siobhan M Brady
Fax (919)660-7293
Organization name Duke University
Department Biology
Lab Benfey Lab
Street address Box 90338
City Durham
State/province NC
ZIP/Postal code 27708
Country USA
Platform ID GPL198
Series (1)
GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
Reanalyzed by GSE119083

Data table header descriptions
VALUE 2^Residuals for all probesets

Data table
244901_at 0.975402756
244902_at 0.864912302
244903_at 1.280426833
244904_at 3.652813813
244905_at 0.934289593
244906_at 1.075957599
244907_at 1.395429603
244908_at 1.163581676
244909_at 0.849575535
244910_s_at 0.816756521
244911_at 0.960323105
244912_at 1.315927696
244913_at 1.473330915
244914_at 1.126594303
244915_s_at 1.282417361
244916_at 1.428752635
244917_at 1.350612936
244918_at 0.822110001
244919_at 0.796921059
244920_s_at 2.035207965

Total number of rows: 22746

Table truncated, full table size 488 Kbytes.

Supplementary file Size Download File type/resource
GSM226538.CEL.gz 3.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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