|
| Status |
Public on Jan 01, 2006 |
| Title |
Maize juvenile leaf ND101/W23 vs W23 replicate 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Maize ND101/W23 juvenile leaf sample 2
|
| Organism |
Zea mays |
| Characteristics |
Maize ND101/W23 juvenile leaf
|
| Growth protocol |
Plants grown and dissected at Stanford field; tissue collected and frozen in liquid nitrogen immediately.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted from 30 - 60 mg of frozen tissues with Qiagen RNeasy Mini kit, digested with DNase I, and cleaned up with RNeasy columns.
|
| Label |
Cy5
|
| Label protocol |
Total RNA (500 ng) was amplified & labeled with Cy5 using Agilent Low RNA Input Fluorescent Linear Amplification Kit.
|
| |
|
| Channel 2 |
| Source name |
Maize W23 juvenile leaf sample 2
|
| Organism |
Zea mays |
| Characteristics |
Maize W23 juvenile leaf
|
| Growth protocol |
Plants grown and dissected at Stanford field; tissue collected and frozen in liquid nitrogen immediately.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted from 30 - 60 mg of frozen tissues with Qiagen RNeasy Mini kit, digested with DNase I, and cleaned up with RNeasy columns.
|
| Label |
Cy3
|
| Label protocol |
Total RNA (500 ng) was amplified & labeled with Cy3 using Agilent Low RNA Input Fluorescent Linear Amplification Kit.
|
| |
|
| |
| Hybridization protocol |
750 ng of each labeled target cRNA were hybed for 17 h at 60¡ãC.
|
| Scan protocol |
Data were acquired with an Agilent G2565BA scanner with default settings (100% PMT). Images processed by Agilent Feature Extraction v0.75.
|
| Description |
Maize juvenile leaf ND101/W23 vs W23 biological replicate 2
|
| Data processing |
After removing saturated spot flagged by Feature Extraction, non-specific hybridizations were estimated by internal negative controls and an iterative approach given the presence of lots of anti-sense probes on the array. Probes with signals (median with background subtracted) above a calculated threshold for at least 2 of the 3 biological replicates were normalized by a combined approach of the rank invariant method (Tseng et al. 2001) and a loess fitness method. Normalized expressions were scaled and outliers flagged. Log base 2 expression ratios were calculated from the normalized expression of the test tissue (A619 or ND101/W23) divided by that of the reference W23 tissue regardless of the dye label of the two samples.
|
| |
|
| Submission date |
Nov 20, 2005 |
| Last update date |
Nov 21, 2005 |
| Contact name |
Jiong Ma |
| E-mail(s) |
jiongm@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Biological Sciences
|
| Lab |
Walbot
|
| Street address |
385 Serra Mall
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL3099 |
| Series (1) |
| GSE3640 |
Comparative Transcriptome Profiling of Maize Lines |
|
| Data table header descriptions |
| ID_REF |
|
| Ch2MeanSignal |
Channel 2 (Cy3) mean intensity |
| Ch1MeanSignal |
Channel 1 (Cy5) mean intensity |
| Ch2MedianSignal |
Channel 2 (Cy3) median intensity |
| Ch1MedianSignal |
Channel 1 (Cy5) median intensity |
| Ch2BGMeanSignal |
Channel 2 (Cy3) background mean intensity |
| Ch1BGMeanSignal |
Channel 1 (Cy5) background mean intensity |
| Ch2BGMedianSignal |
Channel 2 (Cy3) background median intensity |
| Ch1BGMedianSignal |
Channel 1 (Cy5) background median intensity |
| Ch2IsSaturated |
1 if channel 2 (Cy5) is saturated, 0 otherwise |
| Ch1IsSaturated |
1 if channel 1 (Cy3) is saturated, 0 otherwise |
| Ch1_Norm |
Normalized channel 1 (Cy5) intensity |
| Ch2_Norm |
Normalized channel 2 (Cy3) intensity |
| VALUE |
log2 ratios of normalized Ch1 intensity (Ch1_Norm) divided by Ch2 (Ch2_Norm) |
