|
| Status |
Public on Feb 01, 2011 |
| Title |
Sample3_chip1_experimentA_replicate3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Total RNA from juveniles of experiment A condition X
|
| Organism |
Daphnia pulex |
| Characteristics |
Sex: female
developmental stage: juvenile
tissue: whole body
strain: TCO
|
| Treatment protocol |
AX
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue was homogenized using Trizol reagent (Invitrogen), and extracted RNA was purified using the Qiagen RNeasy protocol with on-column DNase treatment from specific tissues. Total RNA amplified using MessageAmp II aRNA Kit (Ambion). aRNA converted to ds cDNA using SuperScript cDNA Synthesis Kit (Invitrogen).
|
| Label |
Cy3
|
| Label protocol |
DNA labeling using 1 O.D. Cy-labeled random nonomer primer and 100U Klenow fragment (3>5 exo) per 1 μg double-stranded cDNA in triplicate.
|
| |
|
| Channel 2 |
| Source name |
Total RNA from juveniles of experiment A condition Y
|
| Organism |
Daphnia pulex |
| Characteristics |
Sex: female
developmental stage: juvenile
tissue: whole body
strain: TCO
|
| Treatment protocol |
AY
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue was homogenized using Trizol reagent (Invitrogen), and extracted RNA was purified using the Qiagen RNeasy protocol with on-column DNase treatment from specific tissues. Total RNA amplified using MessageAmp II aRNA Kit (Ambion). aRNA converted to ds cDNA using SuperScript cDNA Synthesis Kit (Invitrogen).
|
| Label |
Cy5
|
| Label protocol |
DNA labeling using 1 O.D. Cy-labeled random nonomer primer and 100U Klenow fragment (3>5 exo) per 1 μg double-stranded cDNA in triplicate.
|
| |
|
| |
| Hybridization protocol |
Labeled products were pooled to serve as a Master Mix for Array set. The products were dried in a speedvac then resuspended in water prior to hybridization, which was performed with the NimbleGen hybridization kit. A single hybridization master for a given source and biological replicate.
|
| Scan protocol |
Axon GenePix 4200 Professional, 5 micron resolution.
|
| Data processing |
Raw signal intensity extract with NimbleScan 2.4 Software (Roche NimbleGen) in PAIR files. Quantile normalization to convert raw to processed data.
|
| |
|
| Submission date |
Dec 05, 2010 |
| Last update date |
Jun 25, 2012 |
| Contact name |
Jacqueline Lopez |
| E-mail(s) |
jacqueline.ann.lopez@gmail.com
|
| Phone |
574-631-1902
|
| Organization name |
University of Notre Dame
|
| Department |
Biology
|
| Lab |
Pfrender Laboratory
|
| Street address |
019 Galvin Life Science Center
|
| City |
Notre Dame |
| State/province |
Indiana |
| ZIP/Postal code |
46556 |
| Country |
USA |
| |
|
| Platform ID |
GPL11200 |
| Series (2) |
| GSE25823 |
The Ecoresponsive Genome of Daphnia pulex: Empirical annotation of the Daphnia pulex genome |
| GSE25855 |
Empirical Annotation of the Daphnia pulex genome; Experiment A |
|
