|
| Status |
Public on Feb 08, 2012 |
| Title |
Adult_Mammary_Lineage_depleted_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Flow sorted lineage depleated (CD31, CD45 and Ter119 neg) adult mouse mammary cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Flow sorted lineage depleated (CD31, CD45 and Ter119 neg) adult mouse mammary cells
strain: CD-1
gender: Female
tissue source: Mammary gland
Stage: Adult
processing: 2 rounds of polyA-primed linear T7 amplification of total RNA
quality control notes: Pass
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNAqueous-Micro kit (Ambion Cat # AM1931) according to the manufacturers' instructions.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by the Gene Chip Microarray Core through the UCSD: Rebecca and John Moores Cancer Center, following the standard operating protocol described by NimbleGen Systems Inc., Madison, WI USA. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed by the UCSD Gene Chip Microarray Core according to their standard operating protocol and instructions from NimbleGen Systems Inc., Madison, WI for the 12x135k array format. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by the UCSD Gene Chip Core following their standard operating protocol and instructions for NimbleGen arrays. See www.nimblegen.com.
|
| Description |
Four #4 (inguinal) mammaries from two nulliparous females were combined in this sample
Dissected mammary tissue from adult and fetal mice was dissociated according to StemCell technologies' EasySep procedure (product #29008) with minor modifications. Briefly, fetal rudiments were dissociated for only 90min in collagenase/hyaluronidase containing media and trypsinization was omitted.
Cells were labeled with Anti-CD49f-FITC, Anti-CD24-PE and a biotinylated antibody cocktail against CD31,CD45 and Ter119 (StemCell Technologies CAT# 19757).Secondary labeling was achieved using Streptavidin conjugated PerCPCy5.5. Cells were sorted into RNA Lysis solution (Ambion Cat# 8540G12) using a FACS Vantage SE DiVa sorter.
|
| Data processing |
The raw data (.pair files) were subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package using the default settings, version 2.4.27 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
Feb 02, 2011 |
| Last update date |
Feb 08, 2012 |
| Contact name |
Benjamin T Spike |
| E-mail(s) |
bspike@salk.edu
|
| Organization name |
The Salk Institute
|
| Department |
Gene Expression Laboratory
|
| Lab |
Geoffrey M. Wahl
|
| Street address |
10010 N Torrey Pines Rd
|
| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL10192 |
| Series (1) |
| GSE27027 |
Expression profiling of mammary stem cell enriched fractions and other fractions from fetal and adult mouse. |
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