|
| Status |
Public on Mar 23, 2021 |
| Title |
Mammary tumor vs. adjacent normal mammary gland, replicate 1 dye swap |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
adjacent normal mammary gland
|
| Organism |
Mus musculus |
| Characteristics |
tissue: normal
strain: BK5.ATF3 transgenic
|
| Treatment protocol |
Females were allowed to breed and raise one litter of pups. Mammary tumors arose in most transgenic mice between 6 months and 12 months of age. When tumors reached 1.5 cm in length, animals were sacrificed under CO2 and the tumor was quickly dissected. Adjacent normal mammary glands were obtained from each tumor-bearing mouse.
|
| Growth protocol |
Transgenic female BK5.ATF3 mice were bred and raised in an A AALAC-accredited facility on standard lab chow.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol following manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
RNA molecules labeled using Hy5 or Hy3 fluorescent-labed using miRCURY LNA microRNA Array.
|
| |
|
| Channel 2 |
| Source name |
mammary tumor
|
| Organism |
Mus musculus |
| Characteristics |
tissue: tumor
strain: BK5.ATF3 transgenic
|
| Treatment protocol |
Females were allowed to breed and raise one litter of pups. Mammary tumors arose in most transgenic mice between 6 months and 12 months of age. When tumors reached 1.5 cm in length, animals were sacrificed under CO2 and the tumor was quickly dissected. Adjacent normal mammary glands were obtained from each tumor-bearing mouse.
|
| Growth protocol |
Transgenic female BK5.ATF3 mice were bred and raised in an A AALAC-accredited facility on standard lab chow.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
RNA molecules labeled using Hy5 or Hy3 fluorescent-labed using miRCURY LNA microRNA Array.
|
| |
|
| |
| Hybridization protocol |
Labeled samples were mixed pairwise and Hybridized to the array (provided slides by Exiqon) using Tecan HS400 following the manufacturer's instructions.
|
| Scan protocol |
Scanned with GenePix 4200A 01 scanner. Images were quantified using GenePix Pro 6.0.1.25 software.
|
| Description |
Biological replicate 1 of 4 dye swap. Mammary tumors arose in parous BK5.ATF3 transgenic females between 6 and 12 months of age, and animals were sacrificed when their tumors reached 1.5 cm in their longest dimension. Mammary tumor was directly compared to adjacent normal mammary gland.
|
| Data processing |
R limma package used as follows: Low quality and control spots removed, between array normalization using vsn performed on background subtracted data. After within-array duplicate spot correlation was determined, fold change estimates and standard errors calculated with lmFit. Empirical Bayes smoothing was applied to standard error values and p-values were adjusted with Benjamini and Hochberg method.
|
| |
|
| Submission date |
Dec 07, 2020 |
| Last update date |
Mar 23, 2021 |
| Contact name |
Yue Lu |
| E-mail(s) |
ylu4@mdanderson.org
|
| Phone |
7135637960
|
| Organization name |
The University of Texas MD Anderson Cancer Center
|
| Department |
Epigenetics & Molecular Carcinogenesis
|
| Street address |
1881 East Road
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
|
| Platform ID |
GPL29478 |
| Series (1) |
| GSE162793 |
BK5.ATF3-induced mammary tumors compared to normal mammary glands |
|
