|
| Status |
Public on Jun 07, 2013 |
| Title |
8 wk CD-1 mice estrus uterus /8 wk CD-1 mice proestrus uterus /Replicates#1 and #2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
CD-1 mouse uterus in estrus
|
| Organism |
Mus musculus |
| Characteristics |
strain: CD-1
gender: Female
age: 8 wk
estrus cycle stage: estrus
tissue: uterine horns
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of RNA
|
| Label |
Alexa 555, Alexa 647
|
| Label protocol |
RNA samples were amplified as antisense-RNA (aRNA) while incorporating aminoallyl modified bases using the TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 per the vendor’s protocol (Epicentre, Madison, WI). Five µg of each aminoallyl-aRNA sample was fluorescent labeled using Alexa 555 or Alexa 647 by incubating with an amine-reactive dye conjugate for 1 hr at room temperature. Unincorporated dye was removed using an RNeasy column (Qiagen, Valencia, CA). Dye incorporation efficiency was determined using a Nanodrop spectrophotometer.
|
| |
|
| Channel 2 |
| Source name |
CD-1 mouse uterus in proestrus
|
| Organism |
Mus musculus |
| Characteristics |
strain: CD-1
gender: Female
age: 8 wk
estrus cycle stage: proestrus
tissue: uterine horns
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of RNA
|
| Label |
Alexa 555, Alexa 647
|
| Label protocol |
RNA samples were amplified as antisense-RNA (aRNA) while incorporating aminoallyl modified bases using the TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 per the vendor’s protocol (Epicentre, Madison, WI). Five µg of each aminoallyl-aRNA sample was fluorescent labeled using Alexa 555 or Alexa 647 by incubating with an amine-reactive dye conjugate for 1 hr at room temperature. Unincorporated dye was removed using an RNeasy column (Qiagen, Valencia, CA). Dye incorporation efficiency was determined using a Nanodrop spectrophotometer.
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed using 0.825 µg of Alexa 555-labeled aRNA and 0.825 µg of Alexa 647-labeled aRNA. Agilent’s SureHyb hybridization chambers were used in a hybridization oven and rotation rack for 17 hr at 65° C at 10 rpm. After hybridization, the slides were washed per Agilent’s SSPE wash protocol.
|
| Scan protocol |
Slides were scanned using an Agilent dual laser scanner using the extended dynamic range option, which utilizes two 5 um scans of each slide at settings of PMT 100% and PMT 10% to increase signal dynamic range and avoid feature saturation. TIFF images were analyzed using Agilent’s feature extraction software (version 10.7.1.1, protocol GE2_107_Sep09).
|
| Description |
Estrus/Proestrus_reps1and2
dyeswap
12-02-2010_252665510407_S01_GE2_107_Sep09_1_4.txt: Alexa647_estrus; Alexa555_proestrus
12-02-2010_252665510408_S01_GE2_107_Sep09_1_4.txt: Alexa647_proestrus; Alexa555_estrus
Each RNA sample was a pool of RNA extracted from uterine horns of 4-6 individual mice.
|
| Data processing |
Linear and LOWESS normalization and analysis using Rosetta Resolver pipeline (version 5.1)
|
| |
|
| Submission date |
Dec 20, 2012 |
| Last update date |
Jun 07, 2013 |
| Contact name |
David J. Waxman |
| E-mail(s) |
[email protected]
|
| Organization name |
Boston University
|
| Department |
Department of Biology and Bioinformatics Program
|
| Street address |
5 Cummington Mall
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL11202 |
| Series (2) |
| GSE43064 |
Changes in Mouse Uterine Transcriptome in Estrus and Proestrus |
| GSE46814 |
Mouse Uterine Transcriptome in Estrus and Proestrus: whole uterine tissue and isolated lumenal epithelial cells |
|
