|
| Status |
Public on May 05, 2017 |
| Title |
Subpopulation P4 (CD24+CD29hi) from virgin wild type FVB mice, replicate 3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
MaSC enriched P4 population of wild type virgin mice
|
| Organism |
Mus musculus |
| Characteristics |
strain: FVB/N-J
genotype/variation: wild type
mg condition: Virgin
enrichment: MaSC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell preparation protocol: Single cell suspensions were prepared from the mammary glands of virgin wild type and transgenic mice using mechanical and enzymatic dissociation as detail described in Tiede BJ et al., 2009, PLoS ONE 4(11): e8035. doi:10.1371/journal.pone.0008035
FACS sorting protocol: Various subpopulations of mammary epithelial cells were sorted using flow cytometry based on combination of a set of surface markers. The marker profiles and FACS gating parameters are detailed in Tiede BJ et al., 2009, PLoS ONE 4(11): e8035. doi:10.1371/journal.pone.0008035
Total RNA were extracted using RNAeasy mini-prep kit from Qiagen
|
| Label |
Cy5
|
| Label protocol |
The testing RNA samples and universal mouse reference RNA (Agilent) were labeled with CTP-cy5 and CTP-cy3, respectively, Using Agilent Quick Amp Labeling Kit.
|
| |
|
| Channel 2 |
| Source name |
Universal Mouse Reference RNA
|
| Organism |
Mus musculus |
| Characteristics |
cell lines: Mix of 11 mouse cell lines
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell preparation protocol: Single cell suspensions were prepared from the mammary glands of virgin wild type and transgenic mice using mechanical and enzymatic dissociation as detail described in Tiede BJ et al., 2009, PLoS ONE 4(11): e8035. doi:10.1371/journal.pone.0008035
FACS sorting protocol: Various subpopulations of mammary epithelial cells were sorted using flow cytometry based on combination of a set of surface markers. The marker profiles and FACS gating parameters are detailed in Tiede BJ et al., 2009, PLoS ONE 4(11): e8035. doi:10.1371/journal.pone.0008035
Total RNA were extracted using RNAeasy mini-prep kit from Qiagen
|
| Label |
Cy3
|
| Label protocol |
The testing RNA samples and universal mouse reference RNA (Agilent) were labeled with CTP-cy5 and CTP-cy3, respectively, Using Agilent Quick Amp Labeling Kit.
|
| |
|
| |
| Hybridization protocol |
Each cy5 labeled testing sample was mixed with equal amount cy3-labeled reference sample and fragmented and blocked (Agilent Gene Expression Hybridization Kit), and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential
|
| Scan protocol |
Scanned on an Agilent G2565BA scanner.
Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1).
|
| Description |
See Agilent Cat#740100 for product details
|
| Data processing |
Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and linear Lowess normalization.
|
| |
|
| Submission date |
Aug 15, 2016 |
| Last update date |
Feb 29, 2024 |
| Contact name |
Yong Wei |
| E-mail(s) |
yongwei@princeton.edu
|
| Organization name |
Princeton University
|
| Department |
Molecular Biology
|
| Lab |
Kang
|
| Street address |
LTL227 Wathington Road
|
| City |
Plainsboro |
| State/province |
NJ |
| ZIP/Postal code |
08536 |
| Country |
USA |
| |
|
| Platform ID |
GPL7202 |
| Series (2) |
| GSE85635 |
Transcriptome profiles of mouse mammary stem cells and progenitor cells 2 |
| GSE85808 |
miR-199a-LCOR axis regulation of mammary gland stem cell and breast cancer stem cell transcriptional programs |
|
