|
| Status |
Public on May 03, 2023 |
| Title |
CD45-Ter119- bone marrow niche cells [XZ21487] |
| Sample type |
SRA |
| |
|
| Source name |
CD45-Ter119- bone marrow niche cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Bone marrow
cell type: Bone marrow niche cells
inoculated tumor cell line: PyMT-N
sample type: Tumor-bearing
|
| Extracted molecule |
total RNA |
| Extraction protocol |
To isolate the BM niche and HSPC cells, the muscle tissue on the tibia and femur were completely removed, then flushed out the BM cells. The remaining bone were cut and crashed into fragments and digest in DMEM containing 1 mg/mL Collagenase 1, 1 mg/mL Collagenase 2 , 4 mg/mL Dispase 2 , 0.1 mg/mL DNase 1 , 1 mg/mL BSA, 1% HEPES and antibiotics for 45 min at 37°C. Flushed BM cells also incubate in the same digest buffer for 15 min at 37°C. After digestion, bone cells and BM cells are filtered through a 70 µm strainer and resuspended in RBC lysis buffer, then combined into one sample (per mouse) for subsequent step analysis. Lin-cKit+ or CD45-Ter119- from the same batch of experiment were sorted into single-cell suspension and immediately submitted to the Single Cell Genomics Core at Baylor College of Medicine.
The single-cell gene expression library was prepared according to the Chromium Single Cell Gene Expression 3v3.1 kit (10x Genomics).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The mm10 genome was used for reads mapping. Raw sequencing files were imported into 10x Genomics Cell Ranger toolkit (v3.1.0) with default settings for quantifications.
Genome_build: mm10
Supplementary_files_format_and_content: *filtered_feature_bc_matrix.tar.gz files contains the filtered_feature_bc_matrix output folder from Cellranger. Each .gz file contains a .mtx file which is the count matrix and two .tsv files that list the feature names and sample annotations.
|
| |
|
| Submission date |
Nov 11, 2021 |
| Last update date |
May 03, 2023 |
| Contact name |
Xiang Zhang |
| E-mail(s) |
xiangz@bcm.edu
|
| Organization name |
Baylor College of Medicine
|
| Department |
Molecular and Cellular Biology
|
| Street address |
One Baylor Plaza
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE188648 |
The impact of remote solid tumors on bone marrow ecosystem at single-cell resolution |
|
| Relations |
| BioSample |
SAMN23075121 |
| SRA |
SRX13114877 |
