GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE223059 Query DataSets for GSE223059
Status Public on Oct 02, 2023
Title Bone marrow derived macrophages RNA-Seq (WT vs SIRPa KO)
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary RNA transcriptome difference between WT and SIRPa knockout (KO) bone marrow derived macrophages (BMDMs). To understand how SIRPa inhibits the phagocytotic capacity of macrophages, a mouse lacking SIRPa was generated, and the transcriptional profiles of BMDMs from wild-type and SIRPa KO mice were compared, using RNA sequencing.
Overall design BMDMs from WT and SIRPa KO mice were generated by growing freshly isolated bone marrow cells for 7 days in medium supplemented with 30% (vol/vol) L929 cell-conditioned medium. Total RNA was isolated from WT and SIRPa KO macrophage using the RNeasy Plus Mini Kit (Cat# 74134, Qiagen). RNA-Seq library preparation was performed using the Illumina TruSeq Stranded mRNA Kit, according to manufacturer’s instructions, and sequenced with Illumina HiSeq 2000 Sequencer. Read quality was confirmed using FastQC v0.10.1 before alignment using TopHat v2.0.10 on the mouse GRCm38/mm10 genome.
Contributor(s) Tang Z, Veillette A
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Jan 17, 2023
Last update date Oct 02, 2023
Contact name André Veillette
Phone 5149875605
Organization name IRCM
Department Molecular Oncology
Lab Veillette
Street address 110 Des Pins Ouest Rm1065
City Montreal
State/province QC
ZIP/Postal code H2W 1R7
Country Canada
Platforms (1)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (6)
GSM6939022 SIRPa KO BMDMs rep1
GSM6939023 SIRPa KO BMDMs rep2
GSM6939024 SIRPa KO BMDMs rep3
BioProject PRJNA924770

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE223059_ko_vs_wt_counts_normalized_relative_to_library_size.xlsx 5.6 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap