|
| Status |
Public on Jan 30, 2018 |
| Title |
Ctrl A |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: WT
tissue: spleen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Spleens pieces were cut, transferred to microcentrifuge tubes, snap frozen immediately in liquid nitrogen, and stored at -80C until RNA extraction. RLT buffer containing beta-mercaptoethanol was was used to lyse spleens, which were then homogenized. Qiagen RNeasy kit was used to isolate total RNA.
Illumina TruSeq stranded poly-A selection kit (Cat# NP-202-1001) was used to make libraries from 50ng of RNA using the NeoPrep system.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Alignment of mRNA-seq reads was aligned to mm10 genome using STAR_2.5.3a.
Read counts per gene files were genereated using using --quantMode GeneCounts and ENSEMBL mouse GRCm38.88 gtf file from ENSEMBL website.
Read counts betweeen different samples were normalized with LIMMA package in R.
Genome_build: mm10
Supplementary_files_format_and_content: .csv read counts per gene
|
| |
|
| Submission date |
Dec 20, 2017 |
| Last update date |
Jan 30, 2018 |
| Contact name |
Safiyyah Ziyad |
| E-mail(s) |
sziyad@ucla.edu
|
| Organization name |
University of California, Los Angeles
|
| Department |
Molecular, Cell and Developmental Biology
|
| Lab |
Dr Luisa Iruela-Arispe
|
| Street address |
621 Charles E. Young Drive, South
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE108353 |
A Forward Genetic Screen Targeting the Endothelium Reveals a Regulatory Role for the Lipid Kinase Pi4ka in Myelo- and Erythropoiesis [mutant] |
| GSE108355 |
A Forward Genetic Screen Targeting the Endothelium Reveals a Regulatory Role for the Lipid Kinase Pi4ka in Myelo- and Erythropoiesis |
|
| Relations |
| BioSample |
SAMN08214215 |
| SRA |
SRX3490070 |
