|
| 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 |
