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Sample GSM5129125 Query DataSets for GSM5129125
Status Public on Mar 02, 2024
Title WWv SMC 3
Sample type SRA
 
Source name Primary SMCs extracted from Aorta
Organism Mus musculus
Characteristics cell type: Primary SMCs
genotype: WWv
Treatment protocol primary SMCs were extracted from the aortas of five KitW/WV mice and five Wild type mice through collagenase digestion then grown until passage 2
Extracted molecule total RNA
Extraction protocol RNA was extracted using Omega EZNA RNA isolation kit
Libraries were prepared for seuencing with the Nugen Universal Plus mRNA-Seq Library Preparation Kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 8W
Data processing FASTQ files were created with the Illumina supplied scripts in the BCL2FASTQ software (v2.17)
Illumina adapters trimmed with Trim Galore! v0.4.3
FASTQs aligned to the mm10 reference genome with STAR v2.5.2a using default parameters
--quantMode GeneCounts option in STAR used to count genes against the GENCODE vM19 GTF annotation file
Genome_build: mm10
Supplementary_files_format_and_content: Processed file is a tab delimited matrix file with the first column representing the Ensembl gene name and subsequent columns raw gene counts generated by --quantMode GeneCounts option in STAR. A read is counted if it overlaps (1bp or more) with an exon of only one gene on the appropriate strand.
 
Submission date Mar 02, 2021
Last update date Mar 02, 2024
Contact name Anthony Griswold
E-mail(s) agriswold@med.miami.edu
Organization name University of Miami
Street address 1501 NW 10th Ave, BRB 318
City Miami
State/province FL
ZIP/Postal code 33136
Country USA
 
Platform ID GPL24247
Series (1)
GSE168110 Next generation sequencing facilliates quantitative analysis of Wild type and KitW/Wv Smooth muscle cells transcriptomes
Relations
BioSample SAMN18114507
SRA SRX10212249

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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