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Sample GSM3315892 Query DataSets for GSM3315892
Status Public on Sep 19, 2018
Title Bulk RNA-seq AA replicate 2
Sample type SRA
 
Source name Medial layer of mouse aorta
Organism Mus musculus
Characteristics region: Aortic arch
genotype: wild type
cell type: Vascular smooth muscle cells
background: C57Bl/6
Extracted molecule total RNA
Extraction protocol Aortas from healthy male mice (8-14 weeks) were dissected free of fat and connective tissue. Dissected aortas were immediately transferred to RNAlater solution (Ambion) followed by isolation of AA and DT segments before manual removal of the adventitial and endothelial cell layers. The cleaned medial layer from 3-5 animals was then lysed in Trizol (Thermo-Fisher) and total RNA isolated. The extracted RNA was cleaned on a RNeasy column (Qiagen) and quality-assessed on a Bioanalyzer (Agilent, RNA integrity number [RIN] 7.8-9)
Sequencing libraries were made from 550 ng total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina MiSeq
 
Description bulk RNA-seq
normalised_bulk_counts.txt
Data processing Samples 1 - 313: Raw reads were trimmed using TrimGalore and Cutadapt. Alignment of the reads to the GRCm38 genome was performed using TopHat. Reads per gene were counted using htseq-count (single-cell RNA-seq) or Seqmonk (bulk RNA-seq). Reads were normalised using DESeq2 (bulk RNA-seq) or the scran Bioconductor R package (sinlge-cell RNA-seq) using the computeSumFactors function.
Samples 314 - 317: Raw sequencing data were processed through the 10X genomics Cellranger pipeline (v2). Cellranger demultiplexed the raw sequencing data, produced the fastq files, aligned the reads to the mouse genome (mm10, STAR aligner) performed unique molecular identifier (UMI) counting.
Genome_build: mm10
Supplementary_files_format_and_content: Samples 1 - 313: Tab separated text files contain normalised read counts with genes in rows and cells/samples in columns. Samples 314 - 317: Filtered gene barcode matrices output by the 10X genomics Cellranger pipeline in the h5 format (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices)
 
Submission date Jul 31, 2018
Last update date Sep 19, 2018
Contact name Steven William Wingett
E-mail(s) steven.wingett@mrc-lmb.cam.ac.uk
Organization name MRC Laboratory of Molecular Biology
Department Cell Biology
Street address Francis Crick Avenue, Cambridge Biomedical Campus
City Cambridge
State/province Cambs
ZIP/Postal code CB2 0QH
Country United Kingdom
 
Platform ID GPL16417
Series (1)
GSE117963 Disease-relevant transcriptional signatures identified in individual smooth muscle cells from healthy mouse vessels
Relations
BioSample SAMN09745527
SRA SRX4493174

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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