 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 14, 2023 |
| Title |
Type_H_Metaphysis |
| Sample type |
SRA |
| |
|
| Source name |
CD31+CD45- cells from metaphysis
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Femurs from wild-type mice were collected in PBS. Epiphysis, metaphysis and diaphysis were crushed separately with pestle in DMEM (+ Collagenase IV 10μl/ml, + Dispase 4μ/ml, + DNase 0.2μ/ml), and incubated 30min at 37°. The cells were dissociated to a single-cell suspension by filtering thorough 40μm nylon mesh. To eliminate red blood cells, we used RBC Lysis Buffer (pluriSelect 60-00050-11). Cells are FC-blocked and stained with FITC anti-mouse CD31 antibody (Biolegend 102506; 1:200), and APC anti mouse CD45 antibody (Biolegend 103112;1:200) for 40 min. Cell sorting was performed with Cell Sorter SH800S (SONY, Tokyo,Japan).
Libraries were constructed using a Chromium Single Cell 3’ v3.1 (10×Genomics, Pleasanton, CA) according to the manufacturer’s instructions.
single cell RNA-Seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Data processing |
Sequenced reads were aligned to the reference genome (mm10) using Cell Ranger v3.0.2 software (10×Genomics).
Sequenced reads with low quality and PCR duplicates were removed.
Data analysis was performed using Loupe Cell Browser (10× Genomics)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include cell barcode
Supplementary_files_format_and_content: tab-delimited text files include gene features
Supplementary_files_format_and_content: tab-delimited matrix files
|
| |
|
| Submission date |
Dec 17, 2020 |
| Last update date |
Jul 14, 2023 |
| Contact name |
Tsukasa Sanosaka |
| E-mail(s) |
sanosaka@keio.jp
|
| Organization name |
Keio University School of Medicine
|
| Department |
Department of Physiology
|
| Street address |
35 Shinanomachi
|
| City |
Shinjuku-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
1608582 |
| Country |
Japan |
| |
|
| Platform ID |
GPL28457 |
| Series (1) |
| GSE163451 |
Single cell RNA sequencing for bone marrow CD31+CD45- cells |
|
| Relations |
| BioSample |
SAMN17106452 |
| SRA |
SRX9698916 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4979486_type_H_barcodes.tsv.gz |
4.8 Kb |
(ftp)(http) |
TSV |
| GSM4979486_type_H_features.tsv.gz |
272.8 Kb |
(ftp)(http) |
TSV |
| GSM4979486_type_H_matrix.mtx.gz |
8.2 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
