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Sample GSM4192692 Query DataSets for GSM4192692
Status Public on Mar 01, 2020
Title Apoe ND
Sample type SRA
 
Source name ascending aorta
Organism Mus musculus
Characteristics genotype: Apoe-/-
diet: ND
Treatment protocol mice were fed with HFD for 1 to 4 months
Extracted molecule total RNA
Extraction protocol Digest the mice ascending aorta and sort GFP positive cells (smooth muscle cells)
Libraries were prepared for sequencing at Yale using Chromium™ system (10x Genomics)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description ApoE mice feed with ND
apoe_dko_0m_combined_count_tmm_relaxed_filter_noApoeTgfbr2.csv
Data processing UMI-tools is used for the end to end processing of scRNA-Seq data
Identified cell barcodes and UMI in the read sequence, which are then extracted from Read 1 and added to Read 2 read name. STAR,was used to map extracted reads from Read 2 to the reference mouse genome build 38 (GRCm38), followed by assigning reads to genes using featureCounts tool from the subread package (version 1.6.0). Quantification was performed using UMI-tools count function to find the number of unique UMIs mapping to each gene (GENCODE mouse annotation, release M15).
Count data was filtered by: removing cells for which UMI count was less than 3,000 or total number of detected genes was less than 1,500; removing genes that were not expressed in less than or equal to 5% of the remaining cells in at least one sample
ApoE and TGFβR2 UMI counts were removed from the processed data matrix
Genome_build: GRCm38, version M15 (Ensembl 90)
Supplementary_files_format_and_content: CSV files include raw and TMM values for all samples
 
Submission date Nov 26, 2019
Last update date Mar 02, 2020
Contact name Michael Simons
E-mail(s) michael.simons@yale.edu
Organization name Yale University
Department Department: Internal Medicine Cardiology
Lab Yale Cardiovascular Research Center
Street address 3oo George St, Suite 773
City New Haven
State/province CT
ZIP/Postal code 06511
Country USA
 
Platform ID GPL21273
Series (2)
GSE141031 Smooth muscle cell reprogramming in aortic aneurysms [scRNA-Seq]
GSE141032 Smooth muscle cell reprogramming in aortic aneurysms
Relations
BioSample SAMN13389454
SRA SRX7217602

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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