|
| Status |
Public on Aug 24, 2021 |
| Title |
COM rep3 |
| Sample type |
SRA |
| |
|
| Source name |
CD11b+ FACS sorted
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
treatment: COMB
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
GL261 luc+ tdT+ implanted mice
|
| Data processing |
Illumina-specific adapters, short reads and low quality 5' and 3' bases were filtered out in the FASTQ format files using Trimmomatic tool.
Resulting RNA sequencing reads were aligned to a reference mouse genome sequence (mm10) with the STAR aligner using the twopassMode Basic option.
Duplicate reads were identified and marked using Picard Tools and mapped read quantification and summarization by genes was perform employing HTSeq-count, enabling paired mode (-p), reverse stranded mode (-s reverse) and only considering reads with MapQ values of 10 or higher.
Low-expressed features were pre-filtered out and a differential expressed genes analysis was performed using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample - HTSeq_raw_counts.tab
|
| |
|
| Submission date |
May 04, 2021 |
| Last update date |
Aug 24, 2021 |
| Contact name |
Adria-Jaume Roura |
| E-mail(s) |
a.canalda@nencki.edu.pl
|
| Organization name |
Nencki Institute of Experimental Biology, Polish Academy of Sciences
|
| Street address |
Ludwika Pasteura 3
|
| City |
Warsaw |
| ZIP/Postal code |
02-093 |
| Country |
Poland |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE173865 |
A novel oral arginase 1/2 inhibitor enhances the antitumor effect of PD-1 inhibition in murine experimental gliomas by altering the immunosuppressive environment. |
|
| Relations |
| BioSample |
SAMN19014319 |
| SRA |
SRX10774882 |
