|
| Status |
Public on Mar 05, 2013 |
| Title |
Sm1021 innoculated roots-40dpi-biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Medicago truncatula roots were innoculated with Sm1021 WT rhizobia, and nodulated roots were harvested after 40 days.
|
| Organism |
Medicago truncatula |
| Characteristics |
plant age: 45 days
treatment: inoculated with Sinorhizobium meliloti Sm1021
treatment-time: 40 days
tissue: roots
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on to the AtMtDEFL custom Array. GeneChips were washed and stained using the MAUI 12-bay hybridization system.
|
| Scan protocol |
GeneChips were scanned using the MAUI 12-bay hybridization system.
|
| Description |
Gene expression data from 40 dpi root segments excluding the root tip of plants innoculated with Sm1021 WT rhizobia.
|
| Data processing |
Microarray normalizations and initial analyses were performed in R using custom scripts that made use of Bioconductor routines. To implement the Stable-genes Based Quantile (SBQ) normalization (Sato et al., 2007), we first combined expression data from all 11 probes within a probe set into a single expression measure using the Bioconductor expression command, using RMA-style background correction and median polish probe summarization. These summarized values were output from R and used as input to the SBQ perl script (Sato et al., 2007).For statistical analysis, SBQ normalized signal intensity values were Log2 transformed and statistical analysis was based on a t-test or ANOVA (P<0.05) with Benjamini and Hochberg false discovery rate multiple testing correction (Benjamini and Hochberg, 1995), and the corrected p values were designated as q values.
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| |
|
| Submission date |
Jan 03, 2012 |
| Last update date |
Mar 06, 2013 |
| Contact name |
Kevin A Silverstein |
| Organization name |
Universtiy of Minnesota
|
| Department |
Minnesota Supercomuting Institute
|
| Street address |
599 Walter Library, 117 Pleasant St SE
|
| City |
Minneapolis |
| State/province |
MN |
| ZIP/Postal code |
55455 |
| Country |
USA |
| |
|
| Platform ID |
GPL14988 |
| Series (1) |
| GSE34803 |
Expression data of Nodule Cysteine-Rich (NCR) Defensin-Like (DEFL) genes in different stages of nodule development in Medicago truncatula |
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