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Sample GSM3317486 Query DataSets for GSM3317486
Status Public on Aug 03, 2018
Title vena_porta2_vSMC
Sample type SRA
 
Source name vena_porta_vSMC
Organism Canis lupus familiaris
Characteristics tissue: vena_porta
cell type: vascular smooth muscle cell
Extracted molecule total RNA
Extraction protocol cells were trypsinized and stored in RLT. Total RNA was isolated using a RNeasy Mini Kit (Qiagen).
Sequencing libraries were prepared using the Rapid Directional RNA-Seq Kit (NEXTflex)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description readCounts_raw.txt
processed data file column: SMCvpISO2
Data processing RNA-seq reads were aligned to the reference genome using STAR version 2.4.2a
Read groups were added to the BAM files with Picard's AddOrReplaceReadGroups
The BAM files are sorted with Sambamba v0.4.5 and transcript abundances were quantified with HTSeq-count version 0.6.1p1, using the union mode.
Genome_build: canfam3.1
Supplementary_files_format_and_content: readCounts_raw.txt
 
Submission date Aug 02, 2018
Last update date Aug 03, 2018
Contact name Frank van Steenbeek
E-mail(s) f.g.vansteenbeek@uu.nl
Phone 0302532848
Organization name Utrecht University
Street address Yalelaan 104
City Utrecht
State/province Select State/Province
ZIP/Postal code 3584 CM
Country Netherlands
 
Platform ID GPL21400
Series (1)
GSE118029 Characterization of endothelial and smooth muscle cells from different canine vessels
Relations
BioSample SAMN09760107
SRA SRX4501268

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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