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Sample GSM4233281 Query DataSets for GSM4233281
Status Public on May 15, 2020
Title scRNA Mouse Spleen IFN alpha
Sample type SRA
 
Source name Spleen
Organism Mus musculus
Characteristics genotype: WT
tissue: Spleen
cell type: Immune cells
treatment: IFN alpha
Extracted molecule total RNA
Extraction protocol Spleens were isolated and smashed through a 70uM sterile filter to obtain single cell suspensions. Red blood cells (RBCs) were lysed using ACK lysing buffer. Cells were resuspended in RPMI supplemented with 10% FBS and 1% Pen/Strep. For human samples, cells were isolated from whole blood of healthy volunteers using ErythroClear RBC depletion kit (STEMCELL). Cells were resuspended in RPMI supplemented with 10% FBS and 1% Pen/Strep. Cells were treated with recombinant interferon for 4 hours as indicated.
Isolated cells were encapsulated using microfluidics technology, and barcoded using a unique molecular identifier (UMI).
scRNAseq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description mouse_spl_ifnalpha
WT Mouse
Exp ID: 190822_0270_E3
Lab data ID: SWTA
mRNA
read1_26/i7index_8/read2_98
Data processing Raw sequencing data were processed with Cell Ranger software (version 3.0.2). Cell Ranger output files were loaded into R for analysis using the Seurat package. Low quality cells were removed based on % mitochondrial gene expression. Data were integrated, normalized, and transformed for downstream analysis. Clustering was performed using the UMAP algorithm. Cell clusters were annotated using the SingleR algorithm. Unclassified cells were removed from downstream analysis. Gene expression was subsequently determined in each cluster. Data were visualized using ggplot2.
Genome_build: Mouse: mm10 (GRCm38); Human: GRCh38
Supplementary_files_format_and_content: barcodes.tsv: Cell Ranger count raw_feature_bc_matrix barcodes.
Supplementary_files_format_and_content: features.tsv: Cell Ranger count raw_feature_bc_matrix features.
Supplementary_files_format_and_content: matrix.mtx: Cell Ranger count raw_feature_bc_matrix matrix.
 
Submission date Dec 26, 2019
Last update date May 15, 2020
Contact name Hong-wei Sun
Organization name NIAMS
Department Office of Science & Technology
Lab Biodata Mining & Discovery Section
Street address 9000 Rockville Pile
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL21493
Series (1)
GSE142637 Interferon lambda promotes immune dysregulation and tissue inflammation in TLR7-induced lupus [scRNA-seq]
Relations
BioSample SAMN13683681
SRA SRX7443303

Supplementary file Size Download File type/resource
GSM4233281_mouse_spl_ifnalpha.barcodes.tsv.gz 36.5 Kb (ftp)(http) TSV
GSM4233281_mouse_spl_ifnalpha.features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSM4233281_mouse_spl_ifnalpha.matrix.mtx.gz 33.3 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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