|
| Status |
Public on Sep 19, 2018 |
| Title |
Bulk RNA-seq AA replicate 3 |
| 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 |
SAMN09745526 |
| SRA |
SRX4493175 |
