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| Status |
Public on Jul 29, 2019 |
| Title |
wt_SMC_16wk_citeseq_antibody |
| Sample type |
SRA |
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| Source name |
wt_SMC_16wk
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| Organism |
Mus musculus |
| Characteristics |
genotype/variation: Myh11(cre), ROSA(tdT), ApoE(-/-)
timepoint: 16 weeks high-fat diet
smc lineage status: SMC-lineage
tissue: aortic root and ascending aorta
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 were followed. Prior to library construction, cDNA was separated using size selection into mRNA and antibody barcode fractions and PCR amplification and library preparation were conducted separately. For the mRNA fraction, PCR amplification and library preparation were performed following the manufacturer's instructions. For the antibody barcode fraction, PCR and library construction was performed according to the standard CITE-seq protocol (https://cite-seq.com/protocol/). Both library fractions were pooled together prior to sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
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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 -antibody barcode-derived reads were read from the 'undetermined' FASTQ files. 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: *RNA_wirka_et_al_GEO.txt: mRNA gene-cell matrix. Sample identity, corresponding to the 'sample number in processed data' numbers, is appended to each cell barcode column name
Supplementary_files_format_and_content: *ADT_wirka_et_al_GEO.txt: Antibody-derived tag(ADT)-cell 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 |
GPL21626 |
| Series (2) |
| GSE131777 |
Single cell analysis of smooth muscle cell phenotypic modulation in vivo during disease in mice and humans [mouse CITE-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 |
SAMN11867219 |
| SRA |
SRX5904132 |
| 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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