|
| Status |
Public on Oct 05, 2024 |
| Title |
Lung macrophages from MMTV-HER2 late lung |
| Sample type |
SRA |
| |
|
| Source name |
MMTV-HER2 late lung
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Lung
cell line: Primary cells
cell type: Primary lung macrophages
strain: wild type and MMTV-HER2
age: 32-weeks
|
| Treatment protocol |
Single cell suspensions were obtained from lungs by digestion with 0.15% Collagenase 1A (SIGMA, C-9891) 2.5% bovine serum al- bumin (BSA) at 37?C with agitation for 30 min followed by passing through a 70mm cell strainer and RBC lysis (RBC lysis buffer, BioLegend) for 5 min at room temperature. For flow cytometry or fluorescence-activated cell sorting (FACS), cells were stained in FACS buffer (PBS supplemented with 10% BSA and 2mM EDTA) with BD Brilliant Stain Buffer Plus and rat monoclonal antibodies (see Dalla et al. for detailed list of antibodies used).
|
| Growth protocol |
Mice were maintained at specified pathogen free health status in individually ventilated cages at 21-22?C and 39-50% humidity. All animal procedures were approved by the Institutional Animal Care and Use Committee (IACUC) of Icahn School of Medicine at Mount Sinai and Albert Einstein College of Medicine. 16-week-old female mice were used as early (‘early lesion’) stage mice and 32-week-old females with palpable tumor(s) were used as late stage of cancer progression. Female littermates were randomly assigned to experimental groups.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells loaded onto 10x Genomics NextGen 3’ v.1.2 assay.
10x Genomics NextGen 3’ v.1.2 assay, as per manufacturer’s instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Data processed with cellranger-5.0.1
Assembly: mm10-2020-A
Supplementary files format and content: comma separated values file containing average UMI values
|
| |
|
| Submission date |
Oct 04, 2024 |
| Last update date |
Oct 05, 2024 |
| Contact name |
Michael Papanicolaou |
| E-mail(s) |
papanicolaou.michael@gmail.com
|
| Phone |
9296930014
|
| Organization name |
Albert Einstein College of Medicine
|
| Department |
Cell Biology
|
| Lab |
Julio Aguirre-Ghiso
|
| Street address |
1300 Morris Park Avenue
|
| City |
The Bronx |
| State/province |
New York |
| ZIP/Postal code |
10461 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE278454 |
Gene expression profile at single cell level of lung alveolar macrophages (AM) and interstital macrophages (IM) in MMTV-HER2 and wildtype early stage (16-week) or late stage (32-week) mice. |
| GSE278455 |
The effect of co-culture on MMTV-HER2 early lesion or primary tumor cell and alveolar macrophages |
|
| Relations |
| BioSample |
SAMN44063090 |
| SRA |
SRX26292663 |
