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| Status |
Public on Sep 08, 2020 |
| Title |
NICHE_VC |
| Sample type |
SRA |
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| Source name |
bone marrow LepR+ cells and Ecs
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| Organism |
Mus musculus |
| Characteristics |
tissue: bone marrow
strain: C57Bl/6JCrl
genotype: Cdh5CreERT2;Vegfc flox/flox
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| Treatment protocol |
For sample 1-3, mice received tamoxifen via gavage.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
the mice were injected intravenously with VE-Cadherin A647 (BioLegend, CA). WBM plug was obtained by flushing tibias and digestion with Collagenase I (Worthington Biochemical Corporation, NJ), Dispase II (Roche Applied Science, Swizerland) and DNase I (Sigma-Aldrich) in HBSS with calcium and magnesium. The digested marrow was pooled with staining buffer (HBSS +2% FBS +2mM EDTA) to stop the enzymatic reaction. The red cell-depleted WBM cells were stained with antibodies against CD45 eFluor 450, Ter119 eFluor 450, and biotinylated LepR (1:100, R&D Systems, CA) on ice for 30 minutes followed by streptavidin PE-Cy5 on ice for 15 minutes.
use the Chromium Single-Cell 3′RNA-sequencing system (10x Genomics, Pleasanton, CA) with the Reagent Kit v3.1 according to the manufacturer’s instructions
Sample libraries were sequenced on the Illumina NovaSeq 6000 system using S2 flow cell (Illumina)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The Cell Ranger v 2.1.1 mkfastq and count pipelines (10x Genomics, Pleasanton, CA) were used to demultiplex and convert Chromium single-cell 3’ RNA-sequencing barcodes and read data to FASTQ files and to generate aligned reads and gene-cell matrices.
Reads were aligned to mouse reference genome mm10
We used the Seurat R package (v3.1) for QC, filtering and analysis of the aggregated data (Butler et al. Nature Biotechnology 2018)
Cells were filtered based on the number of genes and the percentage of mitochondrial genes.
For further analysis, Seurat R package was used.
Genome_build: mm10
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| Submission date |
Jan 28, 2020 |
| Last update date |
Sep 09, 2020 |
| Contact name |
Shentong Fang |
| E-mail(s) |
shentong.fang@helsinki.fi
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| Organization name |
Wihuri Research Institute and University of Helsinki
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| Street address |
Haartmaninkatu 8
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| City |
Helsinki |
| ZIP/Postal code |
00290 |
| Country |
Finland |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE144420 |
Single cell analysis in the adult bone marrow vascular niche after Vegfc deletion |
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| Relations |
| BioSample |
SAMN13938369 |
| SRA |
SRX7644760 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4287859_NICHE_VC_barcodes.tsv.gz |
15.4 Kb |
(ftp)(http) |
TSV |
| GSM4287859_NICHE_VC_features.tsv.gz |
244.7 Kb |
(ftp)(http) |
TSV |
| GSM4287859_NICHE_VC_matrix.mtx.gz |
27.9 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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