|
| Status |
Public on Jul 22, 2023 |
| Title |
Irf1-Stim-R1_sorted |
| Sample type |
SRA |
| |
|
| Source name |
Bone Marrow
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Bone Marrow
cell type: Macrophage
genotype: IRF1-KO
treatment: stimulation with IFNgamma
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted from cells using RNAeasy (Qiagen) kit as per manufacturers instructions
Quant-seq 3′ mRNA-seq Library Prep Kit for Illumina (Lexogen) as per manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina Casava1.8.2 software used for basecalling.
The RNA sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using Hisat2 to the mouse reference genome (mm10)
Read counting was performed with featureCounts from the subread package (v1.6.4)
Assembly: mm10
Supplementary files format and content: count file generated by featureCounts
|
| |
|
| Submission date |
Jul 21, 2023 |
| Last update date |
Jul 22, 2023 |
| Contact name |
Kevin C sek |
| E-mail(s) |
kevin.sek@petermac.org
|
| Phone |
0432960331
|
| Organization name |
Peter MacCallum Cancer Centre
|
| Department |
Cancer Immunology
|
| Lab |
Beavis Lab
|
| Street address |
305 Grattan Street
|
| City |
Melbourne |
| State/province |
VIC |
| ZIP/Postal code |
3000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE237973 |
A novel CRISPR/Cas9 screening platform identifies an IRF1-SOCS1-mediated negative feedback loop that limits CXCL9 expression and anti-tumor immunity (Mouse RNA-Seq) |
| GSE237974 |
A novel CRISPR/Cas9 screening platform identifies an IRF1-SOCS1-mediated negative feedback loop that limits CXCL9 expression and anti-tumor immunity |
|
| Relations |
| BioSample |
SAMN36678446 |
| SRA |
SRX21125986 |
