|
| Status |
Public on Oct 02, 2023 |
| Title |
SIRPa KO BMDMs rep1 |
| 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_1_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 |
| E-mail(s) |
Andre.Veillette@ircm.qc.ca
|
| 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) |
|
| Relations |
| BioSample |
SAMN32769865 |
| SRA |
SRX19051729 |
