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Sample GSM6939023 Query DataSets for GSM6939023
Status Public on Oct 02, 2023
Title SIRPa KO BMDMs rep2
Sample type SRA
Source name Bone marrow derived macrophages
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: bone marrow cells
age: 8 weeks
genotype: SIRPa KO
Treatment protocol No treatment.
Growth protocol Bone marrow derived macrophages were generated by growing freshly isolated bone marrow cells for 7 days in medium supplemented with 30% (vol/vol) L929. cell-conditioned medium, as a source of colony-stimulating factor-1.
Extracted molecule total RNA
Extraction protocol RNA was isolated from wild-type and SIRPa KO BMDMs using the RNeasy Plus Mini Kit (Cat# 74134, Qiagen), according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
Description ko_2_sirpa
Data processing Basecalls performed using CASAVA version 1.4
Reads were aligned to the reference mouse genome version GRCm38 using STAR version 2.5.1b
Raw counts for each feature from GRCm38 ENSEMBL v93 annotation file were extracted using FeatureCounts v1.6.0  
DESeq2 version 1.22.2 was used to normalize gene readcounts and compute differential expression between conditions
Assembly: GRCm38
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample
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
Platform ID GPL21103
Series (1)
GSE223059 Bone marrow derived macrophages RNA-Seq (WT vs SIRPa KO)
BioSample SAMN32769864
SRA SRX19051730

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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