|
| Status |
Public on Jun 06, 2021 |
| Title |
PTH |
| Sample type |
SRA |
| |
|
| Source name |
metaphyseal mesenchymal progenitors
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Bone mesenchymal progenitor
strain: Mix background
treatment: Teriparatide 400ng/g body weight i.p. injection for 3 dyas
|
| Treatment protocol |
Gli1-CreERT2; Ai9 mice at 1 month of age were administrated Tamoxifen for three consecutive days once daily followed by three daily injections of teriparatide or vehicle.
|
| Growth protocol |
This is a mouse work and cells were freshly isolated.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells from the cancellous bone region of the femur were isolated as follows. Upon removal of the epiphysis, the metaphyseal bone region extending about 5 mm below the growth plate was dissected and crushed with mortar and pestle in FACS Buffer, followed by digestion with 0.25% collagenase type I (C0130, Sigma-Aldrich) in PBS (Gibco) for 20 min at 37 °C with gentle shaking. The cells were then centrifuged and re-suspended with FACS Buffer and filtered with a 70-μm cell strainer. The tdTomato+CD31-CD45-Ter119- cells were sorted with Navios EX (Beckman Coulter). Cell viability and number were determined with a cell counter (Biorad).
10x Genomics Chromium platform was used to capture and barcode cells to generate single-cell Gel Beads-in-Emulsion (GEMs) by following the manufacturer’s protocol. The oligonucleotides coating the gel beds enable mRNA capture by 30 bp oligo-dT and provide barcodes to index cells (16 bp) as well as transcripts (10 bp unique molecular identifier; UMI). Following reverse transcription, cDNAs with both barcodes were amplified, and a library was constructed using the Single Cell 3’ Reagent Kit (v2 chemistry) for each sample. The resulting libraries were sequenced on an Illumina NovaSeq 6000 System.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sample demultiplexing, barcode processing and UMI counting were performed by using the official 10x Genomics pipeline Cell Ranger v2.1.0 (https://support.10xgenomics.com). Briefly, FASTQs generated from Illumina sequencing output were aligned to the mouse reference genome (mm10). Next, Gene-Barcode matrices were generated for each individual sample by counting unique molecular identifiers (UMIs) and filtering non-cell associated barcodes. Finally, we generated a gene-barcode matrix containing the barcoded cells and gene expression counts.
Genome_build: mm10
|
| |
|
| Submission date |
Mar 24, 2021 |
| Last update date |
Mar 07, 2024 |
| Contact name |
Yu Shi |
| E-mail(s) |
yushi1105@scu.edu.cn
|
| Organization name |
Sichuan University
|
| Street address |
NO.14 South Renmin Road
|
| City |
Chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
600000 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE169560 |
Gli1+ progenitors mediate bone anabolic function of teriparatide via Hh and Igf signaling |
|
| Relations |
| BioSample |
SAMN18474734 |
| SRA |
SRX10437494 |
