|
| Status |
Public on Jul 09, 2021 |
| Title |
Cgas-/- rep1 |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: bone marrow
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from single cell suspensions using the SPLIT RNA Extraction kit (Lexogen)
RNA libraries were prepared for sequencing using the Lexogen QuantSeq 3’-mRNA-Seq Library Prep Kit (FWD)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
4250
DESeq2_results_BM_CgasKO_vs_dKO.csv
|
| Data processing |
Basecalling was performed with bcl2fastq 1.8.4
Adapter-trimmed raw reads were uploaded to Partek Genomics Suite (PGS, build 8.0.19.0819), trimmed for a Phred quality score > 20 and aligned to the mouse reference genome mm10 by STAR (version 2.6.1) with slightly modified standard settings (max mismatches = 14)
For mRNA quantification mm10 Ensembl transcripts (release 98) were used as annotation files
Raw gene counts were normalized and differentially expressed genes (defined by p value < 0.05) identified by DESeq2 (package version 1.25.16)
Genome_build: mm10
Supplementary_files_format_and_content: Comma separated value files contain DESeq2 results
|
| |
|
| Submission date |
Jun 06, 2021 |
| Last update date |
Jul 09, 2021 |
| Contact name |
Lino Lars Teichmann |
| E-mail(s) |
[email protected]
|
| Organization name |
University Hospital Bonn
|
| Department |
Department of Medicine III
|
| Street address |
Venusberg-Campus 1
|
| City |
Bonn |
| ZIP/Postal code |
53127 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE176225 |
Intercellular cGAMP transmission induces innate immune activation and tissue inflammation in Trex1 deficiency |
|
| Relations |
| BioSample |
SAMN19587800 |
| SRA |
SRX11078052 |
