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Sample GSM7919060 Query DataSets for GSM7919060
Status Public on May 21, 2024
Title wild type IL33 D7 SiglecF positive bone marrow leukocytes
Sample type SRA
 
Source name Bone Marrow
Organism Mus musculus
Characteristics tissue: Bone Marrow
strain: C57BL6
cell type: SiglecF positive bone marrow leukocytes
genotype: wild type
treatment: daily intraperitoneal injections of 400ng IL-33 in 200µl PBS for 7 days
Extracted molecule total RNA
Extraction protocol SiglecF positive bone marrow leukocytes were sorted using a BD FACSAria III (BD Biosciences) cell sorter and were resuspended in Ca and Mg free PBS containing 0.4mg/ml of UltraPure™ BSA (Thermofisher, AM2616).In total, 16,000 sorted cells were submitted to the 10X Genomics pipeline for encapsulation aiming for a recovery of 10,000 sequenced single cells as described in the manufacturer’s instructions.
Sequencing libraries were prepared using Chromium Single Cell 3' Reagent Kit V3 (10X Genomics) as per manufacturer’s instructions and cDNA quality and quantity were controlled using Agilent High Sensitivity DNA Kit (Agilent) on a 2100 Bioanalyser (Agilent).
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 10x Genomics
Data processing Demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Data analysis was performed using Seurat V4 (v4.3.0) in R (v4.0.3)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
 
Submission date Nov 27, 2023
Last update date May 21, 2024
Contact name Christophe J Desmet
E-mail(s) christophe.desmet@uliege.be
Organization name University of Liege
Lab Cellular and Molecular Immunology
Street address B34, Avenue de l'Hopital 1
City Liege
ZIP/Postal code 4000
Country Belgium
 
Platform ID GPL24247
Series (2)
GSE248716 Gene expression profile at single cell level of SiglecF positive bone marrow leukocytes.
GSE249011 Bulk and single-cell RNA sequencing of human and murine eosinophil lineage cells
Relations
BioSample SAMN38452875
SRA SRX22654396

Supplementary file Size Download File type/resource
GSM7919060_barcodes.tsv.gz 20.0 Mb (ftp)(http) TSV
GSM7919060_features.tsv.gz 191.1 Kb (ftp)(http) TSV
GSM7919060_matrix.mtx.gz 15.5 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA

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