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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 20, 2021 |
| Title |
scRNAseq_Sp7_cKO |
| Sample type |
SRA |
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| Source name |
tdTomato positve cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: Osteoblasts and osteocytes
strain: C57BL/6
tissue: tdTomato positve cells
age: post natal day 28
genotype: Sp7 cKO: Dmp1-Cre; Sp7 f/f; tdTm+
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| Extracted molecule |
total RNA |
| Extraction protocol |
4-week old mice were sacrificed and tibiae, femura, and calvariae were dissected. Soft tissue was removed through scraping, and the epiphysis was cut off. Bone marrow cells were flushed out with cold PBS using a syringe. Bones were cut into 1- to 2-mm lengths and subjected to 8 serial digestions of type I collagenase/EDTA. The final three collagenase fractions were collected by centrifuging the supernatant at 4ºC/300 rcf/8 min. Cell pellets were resuspended with 2% FACS buffer containing RNAse inhibitor and were filtered through a 100 µm cell strainer.
tdTomato+/DAPI- cells were sorted (Sony SH800s Cell Sorter) into a new PCR tube containing 2% FACS buffer. Single cells were encapsulated into emulsion droplets using Chromium Controller (10x Genomics). scRNA-seq libraries were constructed using Chromium Single Cell 3’ v3 Reagent Kit according to the manufacturer’s protocol. Briefly, ~ 15,000 cells were loaded in each channel with a target output of 2,000 cells. Reverse transcription and library preparation were performed on C1000 Touch Thermal cycler with 96-Deep Well Reaction Module (Bio-Rad). Amplified cDNA and final libraries were evaluated on an Agilent BioAnalyzer using a High Sensitivity DNA Kit (Agilent Technologies). Libraries were sequenced with PE100 on the DNBSEQTM NGS technology platform (BGI, China) to reach ~ 450 million reads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
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| Data processing |
Raw reads obtained from scRNA-seq experiments were demultiplexed, aligned to the mouse genome, version mm10 (with tdTomato gene inserted), and collapsed into unique molecular identifiers (UMIs) with the Cellranger toolkit (version 3.1.0, 10X Genomics)
Libraries were batch-corrected to achieve a similar average read count using the CellRanger aggr function. Using a cutoff of 1000 UMIs, cell type annotation were performed iteratively through two rounds of dimensionality reduction, clustering, and removal of putative doublets across all cells.
Genome_build: mm10
Supplementary_files_format_and_content: gene-barcode matrices; genes; barcodes
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| Submission date |
Jul 20, 2020 |
| Last update date |
Sep 21, 2021 |
| Contact name |
Jialiang Wang |
| E-mail(s) |
jialiang.wang@utsouthwestern.edu
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| Organization name |
University of Texas Southwestern Medical Center
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| Street address |
5323 Harry Hines Blvd
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| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
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| Platform ID |
GPL28457 |
| Series (2) |
| GSE154718 |
Control of osteocyte dendrite formation by Sp7 and its target gene osteocrin [scRNA-Seq] |
| GSE154719 |
Control of osteocyte dendrite formation by Sp7 and its target gene osteocrin |
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| Relations |
| BioSample |
SAMN15581618 |
| SRA |
SRX8771909 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4677820_Sp7_cKO_barcodes.tsv.gz |
20.0 Mb |
(ftp)(http) |
TSV |
| GSM4677820_Sp7_cKO_features.tsv.gz |
417.3 Kb |
(ftp)(http) |
TSV |
| GSM4677820_Sp7_cKO_matrix.mtx.gz |
41.0 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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