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| Status |
Public on Jul 29, 2019 |
| Title |
wt_SMC_baseline_031617 |
| Sample type |
SRA |
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| Source name |
wt_SMC_baseline
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| Organism |
Mus musculus |
| Characteristics |
genotype/variation: Myh11(cre), ROSA(tdT), ApoE(-/-)
treatment/timepoint: baseline
number of animals included in sample: 1
tissue: aortic root and ascending aorta
smc lineage status: SMC lineage
sample number in processed data: 1
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were enzymatically dissociated from the aortic root and ascending aorta (to the level of the brachiocephalic artery) of experimental mice
Cells were captured on a 10x Chromium instrument (10x Genomics, Pleasanton, CA) using either the V2 or V3 chemistry for 3' whole transcriptome analysis. Manufacturer's instructions for GEM (Gelbead EMulsion) generation, downstream reverse transcription, cDNA isolation, PCR amplification and library preparation were followed without any significant alterations
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
sample_1
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| Data processing |
FASTQ files were generated by demultiplexing the Illumina sequencer's base call files (BCLs) using 10X CellRanger 'mkfastq' command.
For cell-gene matrix files, individual matrices were first generated using 10X Cell Ranger 'count' command. Individual matrices were then aggregated using the 10X Cell Ranger 'aggr' command. Sparse matrix was read into Seurat and a dense matrix was exported.
Genome_build: mm10
Supplementary_files_format_and_content: cell-gene readcount matrix; sample identity, corresponding to the 'sample number in processed data' numbers, is appended to each cell barcode column name
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| Submission date |
May 27, 2019 |
| Last update date |
Jul 29, 2019 |
| Contact name |
Thomas Quertermous |
| E-mail(s) |
tomq1@stanford.edu
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| Phone |
650-723-5012
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| Organization name |
Stanford University
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| Department |
Medicine Cardiology
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| Lab |
Quertermous
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| Street address |
300 Pasteur Drive
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE131776 |
Single cell analysis of smooth muscle cell phenotypic modulation in vivo during disease in mice and humans [mouse scRNA-seq] |
| GSE131780 |
Single cell analysis of smooth muscle cell phenotypic modulation in vivo during disease in mice and humans |
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| Relations |
| BioSample |
SAMN11867222 |
| SRA |
SRX5904089 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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