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| Status |
Public on Sep 06, 2019 |
| Title |
Cxcl12GFPCxcl12CE#2 |
| Sample type |
SRA |
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| Source name |
Femurs
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| Organism |
Mus musculus |
| Characteristics |
genotype: Cxcl12(GFP/+); Cxcl12-iCreER; R26R(tdTomato/+)
cells: GFP+ bone marrow mesenchymal cells
treatment: Postnatal day 28, tamoxifen injection at P21
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| Extracted molecule |
total RNA |
| Extraction protocol |
Femurs were dissected, distal epiphyseal growth plates were removed and proximal ends were cut off. Remaining bones were cut roughly, and cells were enzymatically dissociated. tdTomato+ cells were FACS-isolated. ~18,000 cells were loaded onto 10X Genomic Chromium Single Cell Solution v3
10X Genomic Chromium Single Cell 3' v3 Libraries
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
FACS-sorted at P28
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| Data processing |
The sequencing data was first pre-processed using the 10X Genomics Cell Ranger software.
For alignment purposes, we generated and used a custom genome fasta and index file by including the sequences of eGFP and tdTomato_WPRE to the mouse genome (mm10).
Further downstream analysis steps were performed using the Seurat R package.
We filtered out cells with less than 1000 genes per cell and with more than 15% mitochondrial read content.
The downstream analysis steps include normalization, identification of highly variable genes across the single cells, scaling based on number of UMI, dimensionality reduction (PCA, and UMAP), unsupervised clustering, and the discovery of differentially expressed cell-type specific markers.
Genome_build: mm10_trans_nono
Supplementary_files_format_and_content: raw_feature_bc_matrix/barcodes.tsv.gz, features.tsv.gz & matrix.mtx.gz
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| Submission date |
Sep 05, 2019 |
| Last update date |
Sep 06, 2019 |
| Contact name |
Noriaki Ono |
| E-mail(s) |
noriaki.ono@uth.tmc.edu
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| Phone |
7134860539
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| Organization name |
University of Texas Health Science Center at Houston
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| Department |
School of Dentistry
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| Lab |
Ono lab
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| Street address |
1941 East Rd, Rm 5322
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| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77054 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE136970 |
Single cell RNAseq analysis of Cxcl12-GFP+ bone marrow stromal cells |
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| Relations |
| BioSample |
SAMN12702608 |
| SRA |
SRX6808863 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4064137_Sample_135167_barcodes.tsv.gz |
20.0 Mb |
(ftp)(http) |
TSV |
| GSM4064137_Sample_135167_features.tsv.gz |
245.3 Kb |
(ftp)(http) |
TSV |
| GSM4064137_Sample_135167_matrix.mtx.gz |
101.5 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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