|
| Status |
Public on Mar 29, 2019 |
| Title |
KO rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Spleen endothelial cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Spleen
cell type: Blood endothelial cells
genotype: Stab1-/-
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Spleens from WT and KO mice were removed, digested with collagenase and CD31+ CD45- endothelial cells were sorted and RNA was extracted. cDNA was synthesized with SMART-Seq v4 ultra low input RNA kit.
Sequencing libraries were generated from the amplified cDNA using Nextera XT (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Single-end 50 bp reads were aligned to the mm10 mouse genome with STAR version 2.5.2b. Read counting was performed with subreads package.
Read counts were normalized and RPKM was calculated using the TMM normalization method of the edgeR R/Bioconductor package.
The Bioconductor package Limma was used for differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited csv files include RPKM values for each Sample ...
|
| |
|
| Submission date |
Apr 06, 2018 |
| Last update date |
Mar 29, 2019 |
| Contact name |
Akira Takeda |
| E-mail(s) |
akira.takeda@utu.fi
|
| Organization name |
University of Turku
|
| Department |
Institute of Biomedicine
|
| Street address |
Tykistökatu 6A
|
| City |
Turku |
| State/province |
South-West Finland |
| ZIP/Postal code |
20520 |
| Country |
Finland |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE112805 |
Clever-1 controls site-specific interactions between vasculature and lymphocytes in mouse and human spleen |
|
| Relations |
| BioSample |
SAMN08875349 |
| SRA |
SRX3898494 |
