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Sample GSM5693444 Query DataSets for GSM5693444
Status Public on Sep 01, 2022
Title CF1 C57BL/6 Naïve
Sample type SRA
Source name Pleural macrophages
Organism Mus musculus
Characteristics cell type: naive C57BL/6 pleural cavity macrophages
strain: C57BL/6
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
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
BioSample SAMN23243013
SRA SRX13158150

Supplementary file Size Download File type/resource
GSM5693444_CF1_B6N_filtered_feature_bc_matrix.tar.gz 36.4 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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