|
| 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 |
| E-mail(s) |
chevybra@duke.edu
|
| 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 |
|
| Relations |
| Reanalyzed by |
GSE119083 |
