|
| Status |
Public on Feb 28, 2011 |
| Title |
Seedlings, mutant, rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Above ground apart of 15-day old seedlings of pcfs4-1
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Seedlings
genotype: pcfs4-1
age: 15-day old
|
| Treatment protocol |
Wild type Col and mutant pcfs4-1 were grown in a randomized block design.
|
| Growth protocol |
The imbibed seeds were first stratified at 4°C in the dark for two days and then grown in growth chamber at 22°C, under 16h/8h light/dark cycles. The above ground tissue of 15-day old seedlings was collected 8 hours after dawn
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using Concert Plant RNA reagent (Invitrogen) and further treated with Turbo DNA-free (Ambion) following the manufacture’s instructions.
|
| Label |
biotin
|
| Label protocol |
The fragmented, double-stranded cDNA were prepared using the Affymetrix GeneChip WT Double-Stranded Target Assay kit (Affymetrix, PN900813) and further end-labeled with the biotin-labeled DLR (dual luciferase reporter) using Terminal Deoxynucleotidyl Transferase (Affymetrix, PN900812)
|
| |
|
| Hybridization protocol |
The labeled targets were hybridized to the Arabidopsis Tiling 1.0R array (Affymetrix, PN900594) using GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix, PN 900720). Hybridization was carried out on Affymetrix GeneChip Hybridization Oven 640, washed and post-hybridization stained on Affymetrix GeneChip Fluidics Station 450.
|
| Scan protocol |
Hybridization signals were collected using an Affymetrix GCS 3000 7G scanner and processed with GeneChip Operating Software
|
| Description |
Gene expression data from 15-day old seedlings of pcfs4-1.
|
| Data processing |
The data were normalized with VSN of Bioconductor and further analyzed with a newly developed protocol, RADPRE, from our lab. In RADPRE, ratios of normalized probe intensities between control and treatment were first generated. With the probe ratios as inputs, a hierarchy of statistical tests was carried out to identify differentially processed genes (DPG) and differentially expressed genes (DEG). The false discovery rate (FDR) of this analysis was estimated by using the balanced random combinations of Control/treatment and treatment/Control ratios as inputs. The Arabidopsis*.txt files represent the data 'normalized with VSN of Bioconductor'.
The mapping information between 'bpmap' vs. 'NomralizedData' and the ratio data files:
pmindex (in the NormalizedData or Ratio) ＝ [PMX (in bpmap) ＋PMY(in bpmap)*2560+1] or [MMX (in bpmap)+MMY(in bpmap)*2560+1]
|
| |
|
| Submission date |
Apr 07, 2010 |
| Last update date |
Mar 01, 2011 |
| Contact name |
Quinn Li |
| E-mail(s) |
[email protected]
|
| Phone |
513 5294200
|
| Organization name |
Miami University
|
| Department |
Botany
|
| Lab |
Quinn Li
|
| Street address |
316, Person Hall, High Str.
|
| City |
Oxford |
| State/province |
OH |
| ZIP/Postal code |
45056 |
| Country |
USA |
| |
|
| Platform ID |
GPL10298 |
| Series (1) |
| GSE21250 |
Expression data of Arabidopsis wild type Col and mutant pcfs4-1 |
|
