|
| Status |
Public on Mar 29, 2018 |
| Title |
L1700166 |
| Sample type |
SRA |
| |
|
| Source name |
Leukocytes
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6J
genotype/variation: Ldlr-/-
Sex: male
tissue: aorta
cell type: leukocytes
cell marker: CD45+
treatment: 20 weeks high fat, high cholesterol diet
|
| Extracted molecule |
total RNA |
| Extraction protocol |
We sorted total viable CD45+ leukocytes from the aortas of male Ldlr-/- mice. Three samples were tested: control, after 11 and 20 weeks of a high fat, high cholesterol diet.
Chromium™ Controller was used for partitioning single cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs) and Single Cell 3’ reagent kit v2 for reverse transcription, cDNA amplification and library construction (10x Genomics). The detailed protocol was provided by 10x Genomics.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Single-cell RNA-Seq
|
| Data processing |
Data were analyzed using Cell Ranger™ v1.3 pipelines and were visualized by Loupe™ Cell Browser. Both are available in 10x Genomics website.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: csv format: Files include mean UMI counts, log2 fold changes and adjusted p-values for the differentially expressed genes among the identified cell clusters.
Supplementary_files_format_and_content: h5 format: Contains the per molecule read information from Cell Ranger. The instructions to read the matrix in hdf5 format can be found here: https://support.10xgenomics.com/single-cell/software/pipelines/latest/advanced/h5_matrices
|
| |
|
| Submission date |
Apr 02, 2017 |
| Last update date |
Aug 22, 2019 |
| Contact name |
Antoine-Emmanuel Saliba |
| E-mail(s) |
emmanuel.saliba@helmholtz-hzi.de
|
| Phone |
+49-931-31-81341
|
| Organization name |
Helmholtz Institute for RNA-based Infection Research
|
| Street address |
Josef-Schneider-Straße 2 / D15
|
| City |
Würzburg |
| ZIP/Postal code |
97080 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE97310 |
Single-cell RNA-seq reveals the transcriptional landscape and heterogeneity of aortic macrophages in murine atherosclerosis |
|
| Relations |
| BioSample |
SAMN06674999 |
| SRA |
SRX2699460 |
