|
| Status |
Public on Feb 29, 2008 |
| Title |
mibta52b 48h (AH_WT48hVsta52b48h_BRI_TR1_135) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
mib mutant embryos
|
| Organism |
Danio rerio |
| Characteristics |
mib mutant embryos
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction using Trizol followed by Qiagen RNeasy Mini Kit extraction
|
| Label |
Cy-5 d-UTP
|
| Label protocol |
20ug of total RNA was reverse transcribed to produce Cy-5 d-UTP (Sample) cDNA targets
|
| |
|
| Channel 2 |
| Source name |
wild type embryos
|
| Organism |
Danio rerio |
| Characteristics |
wild type siblings
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction using Trizol followed by Qiagen RNeasy Mini Kit extraction
|
| Label |
Cy3 d-UTP
|
| Label protocol |
20ug of total RNA was reverse transcribed to produce Cy3 d-UTP (Reference) cDNA targets
|
| |
|
| |
| Hybridization protocol |
Standard procedure (Mathavan et al., 2005)
|
| Scan protocol |
GenePix 4000B microarray scanner (Axon Instruments)
|
| Description |
RNA from mib mutant embryos and their wild type siblings at three different time points
|
| Data processing |
The intensity-based log ratio median method (Yang et al./, 2003)
|
| |
|
| Submission date |
Jul 19, 2007 |
| Last update date |
Oct 26, 2007 |
| Contact name |
Govindarajan Kunde Ramamoorthy |
| E-mail(s) |
mathavans@gis.a-star.edu.sg
|
| Phone |
+65-64788059
|
| Fax |
+65-64789058
|
| Organization name |
Genome Institute of Singapore
|
| Department |
Research Computing Group
|
| Street address |
60, Biopolis Street, Genome
|
| City |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL2715 |
| Series (1) |
| GSE8522 |
RNA from 3 d and 2 d old embryos of mibta52b, mibm132 and mibtfi91, and RNA from 3 d, 2d and 1 d old embryos of mibta52b |
|
| Data table header descriptions |
| ID_REF |
Unique ID |
| VALUE |
Normalized log2 ratio of means defined by CH1/CH2 |
| CH1_Median |
CH1(F635) median fluorescence intensity |
| CH1_MEAN |
CH1 (F635) mean fluorescence intensity |
| CH1_SD |
CH1 (F635) fluorescence intensity standard deviation |
| CH1_BKD_Median |
CH1 (F635) background median fluorescence intensity |
| CH1_BKD_MEAN |
CH1 (F635) background mean fluorescence intensity |
| CH1_BKD_SD |
CH1 (F635) background fluorescence intensity standard deviation |
| %>CH1_BKD_+2SD |
% of feature pixels greater than two standard deviations over the background |
| CH2_Median |
CH2(F532) median fluorescence intensity |
| CH2_MEAN |
CH2 (F532) mean fluorescence intensity |
| CH2_SD |
CH2 (F532) fluorescence intensity standard deviation |
| CH2_BKD_Median |
CH2 (F532) background median fluorescence intensity |
| CH2_BKD_MEAN |
CH2 (F532) background mean fluorescence intensity |
| CH2_BKD_SD |
CH2 (F532) background fluorescence intensity standard deviation |
| %>CH2_BKD_+2SD |
% of feature pixels greater than two standard deviations over the background |
| Ratio_of_Means |
Unnormalized ratio of means defined by CH1/CH2 |
| AREA |
Number of feature pixels |
| BKD_AREA |
Number of feature background pixels |
| CH1_Median-CH1_BKD |
Channel 1 median signal |
| CH2_Median-CH2_BKD |
Channel 2 median signal |
| CH1_Mean-CH1_BKD |
Channel 1 mean signal |
| CH2_Mean-CH2_BKD |
Channel 2 mean signal |
