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Sample GSM4879345 Query DataSets for GSM4879345
Status Public on Nov 01, 2021
Title Single-cell transcriptomes of macrophages isolated from atherosclerotic lesions of nt-LNA-treated mice
Sample type SRA
 
Source name nt-LNA-treated CD45+/CD3- Cells
Organism Mus musculus
Characteristics treatment: nt-LNA
Treatment protocol Apoe-/- mice were treated with saline or nt-LNA (30 mg/kg) for 4 weeks in combination with a western diet. The aortic arch and thoracic aorta were removed and processed to yield a single cell suspension that was processed by FACS to yield a CD45+/CD3- population.
Growth protocol n/a
Extracted molecule total RNA
Extraction protocol 10X Chromium system.
3' RNA Seq, P/N 1000006, 1000080, 1000020.
NovaSeq6000, 150 bp paired-end.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing RTA (version 2.4.11; Illumina) was used for base calling and analysis was completed using 10X Genomics Cell Ranger software v2.1.1.
scRNABatchQC software package was used for assessment of scSEQ data quality control,
Clustering analysis was generated by Seurat
Initial cell type classification (i.e. myeloid/macrophage, B cells, T cells, NK cells) of complete datasets was based on cell activity database (PanglaoDB).
Genome_build: mm9
Supplementary_files_format_and_content: Mouse_aortas_4187_2nd_ur.html: output from scRNABatchQC
Supplementary_files_format_and_content: Mouse_aortas_4187_2nd.cluster.summary.csv: # of cells from each treatment/cluster
Supplementary_files_format_and_content: Mouse_aortas_4187_2nd.cluster.csv: barcoding of individual cells and assignment to cluster by gene activity database
Supplementary_files_format_and_content: Mouse_aortas_4187_2nd.cluster.count.csv: raw gene expression in each cluster
Supplementary_files_format_and_content: Mouse_aortas_4187_2nd.cluster.normByUpQuantile.csv: normalized gene expression in each cluster
 
Submission date Nov 04, 2020
Last update date Nov 01, 2021
Contact name Ryan M Allen
E-mail(s) ryan.m.allen@vumc.org
Phone 3146109328
Organization name Vanderbilt University Medical Center
Department Medicine
Lab Vickers
Street address 2220 Pierce Ave
City Nashville
State/province TN
ZIP/Postal code 37232
Country USA
 
Platform ID GPL24247
Series (2)
GSE160791 The influence of nt-LNA on cell composition and phenotypees in the atherosclerotic lesion.
GSE206859 LDL delivery of microbial small RNAs drives atherosclerosis through macrophage TLR8
Relations
BioSample SAMN16659285
SRA SRX9430520

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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