|
| Status |
Public on Sep 01, 2022 |
| Title |
CF2 BALB/c Naïve |
| Sample type |
SRA |
| |
|
| Source name |
Pleural macrophages
|
| Organism |
Mus musculus |
| Characteristics |
cell type: naive BALB/c pleural cavity macrophages
strain: BALB/c
Sex: female
age: 113 days old
infection: naive
|
| Treatment protocol |
Cells were FACS purified in 2% FBS and 2 mMEDTA and washed with PBS
|
| Growth protocol |
Cells were obtained from pleural lavage with dPBS containing 2% FBS and 2mM EDTA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
10x genomics protocol (15.7K cells were loaded per each sample)
10x genomics v2 chemistry
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Whole cells
|
| Data processing |
Illumina Novaseq S1 software used for basecalling
Initial processing was done using Cell Ranger (v3.0.1) mkfastq and count
Futher processing done using Cell Ranger aggr to create merged counts files
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary files: merged dataset created using Cell Ranger (v3.0.1) aggr;R object for singlecellexperiment; R object for seurat;python anndata object
|
| |
|
| Submission date |
Nov 17, 2021 |
| Last update date |
Sep 01, 2022 |
| Contact name |
Conor M Finlay |
| E-mail(s) |
cofinlay@tcd.ie, conor.finlay@manchester.ac.uk
|
| Organization name |
Trinity College Dublin
|
| Department |
School of Medicine
|
| Street address |
Trinity Translational Medicine Institute, Trinity College Dublin, St. James' Hospital Campus, Trinity College Dublin, Dublin 8
|
| City |
Dublin |
| ZIP/Postal code |
D08 W9RT |
| Country |
Ireland |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE189031 |
Single cell RNA-sequencing of pleural cavity macrophages naïve and nematode-infected C57BL/6 and BALB/c mice |
|
| Relations |
| BioSample |
SAMN23243012 |
| SRA |
SRX13158151 |
