|
| Status |
Public on Sep 19, 2018 |
| Title |
10X Whole aorta |
| Sample type |
SRA |
| |
|
| Source name |
Mouse aorta
|
| Organism |
Mus musculus |
| Characteristics |
region: Aorta
genotype: Myh11-CreERt2/Rosa26-Confetti
cell type: Vascular cell
background: C57Bl/6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Aortas from three male animals were dissected free of fat and connective tissue and subjected to enzymatic digestion. Single cell suspensions were pooled, filtered through a 40 um filter and 20,000 singlet cells isolated by FACS-sorting on an Aria-Fusion flow cytometer (BD Bioscience).
Libraries were prepared using the 10X Chromium platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Single-cell RNA seq, 10X Chromium
10X_whole_aorta_filtered_gene_bc_matrices_h5.h5
|
| 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 |
GPL21103 |
| Series (1) |
| GSE117963 |
Disease-relevant transcriptional signatures identified in individual smooth muscle cells from healthy mouse vessels |
|
| Relations |
| BioSample |
SAMN09745694 |
| SRA |
SRX4493488 |
