|
| Status |
Public on Dec 22, 2021 |
| Title |
p75 conditional knockout mice (p75PDGFRα) |
| Sample type |
SRA |
| |
|
| Source name |
Total cells in the defect site from p75 conditional knockout mice (p75PDGFRα) calvarial tissue
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: p75 conditional knockout mice (p75PDGFR{alpha})
stimulation: Tamoxifen injection; 1.8 mm Calvarial defect
|
| Treatment protocol |
For p75 deletion, tamoxifen (TM; Sigma-Aldrich) was dissolved in sunflower seed oil (Sigma-Aldrich) and injected intraperitoneally (TM: 150 mg/kg/d for 5 d).
|
| Growth protocol |
Skull defects were microdissected 7 days after injury (1.8 mm defect). The cells in the defect site were obtained by collagenase Type I/II (1 mg/mL) digestion (six sequential enzymatic digestions). Cell fractions (from sequential digestions 1-6) were collected and filtered at 40 μm and centrifuged. Cells were resuspended in resuspended in HBSS. Cell viability was assessed with Trypan blue exclusion on a Countess II (ThermoFisher Scientific) automated counter and showed a >85% viability.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Calvarial defects were created after 14 d of the last TM administration. A 1.8 mm diameter, full-thickness, circular frontal bone defect was created in the non-suture associated frontal bone (right side) using a micro surgical drill and a trephine drill bit.
10X mRNA Library V3.1 Prep Kit using standard paired-end protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
JXu-WT1
|
| Data processing |
CellRanger v5.0.0
Seurat
Genome_build: mm10 "refdata-gex-mm10-2020-A" modifed to include EGFP and tdTomato to capture transgene expression
Supplementary_files_format_and_content: 10x multiplex barcode, feature and matrix .gz files
|
| |
|
| Submission date |
Jul 11, 2021 |
| Last update date |
Dec 22, 2021 |
| Contact name |
Aaron W James, MD, PhD |
| Organization name |
Johns Hopkins University School of Medicine
|
| Department |
Pathology
|
| Lab |
Ross 524
|
| Street address |
600 North Wolfe Street
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21287 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE179890 |
Myeloid-to-mesenchymal NGF-p75 signaling coordinates cell migration during bone repair [scRNA-seq] |
| GSE179891 |
Myeloid-to-mesenchymal NGF-p75 signaling coordinates cell migration during repair. |
|
| Relations |
| BioSample |
SAMN20166698 |
| SRA |
SRX11407659 |
