|
| Status |
Public on Oct 01, 2018 |
| Title |
Sample_1669 |
| Sample type |
SRA |
| |
|
| Source name |
KO_CD8+
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Spleen Dendritic Cells (DCs)
cell type: Ppef2-/- CD8+ DCs
sort: 2
|
| Treatment protocol |
Mice were not treated
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Spleen DCs were FACS-sorted in FCS, the purity was determined and RNA was isolated by resuspending the cells in TRIZOL (Invitrogen) following the manufacturers’ protocol
1µg of total RNA was converted to RNA-seq libraries according to manufacturers' protocol with Illumina TruSeq RNA Sample Preparation Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were demultiplexed, then aligned with TopHat2 (v2.0.3) against themm10 reference genome
Gene and transcript information was extracted with Partek Genomics Suite (v6.6). Annotated data was normalized using statistical software R (v3.0.2) including DESeq2 package. Normalized read counts lower than 1 were set to the floor value 1.Genes were defined as expressed with normalized RNA-seq values ≥ 10.
Genome_build: mm10
Supplementary_files_format_and_content: Processed DeSeq2 normalized RNA-seq tag counts annotated to the mm10 reference genome
|
| |
|
| Submission date |
Apr 26, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Joachim Schultze |
| E-mail(s) |
j.schultze@uni-bonn.de
|
| Organization name |
LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)
|
| Department |
Genomics and Immunoregulation
|
| Street address |
Carl-Troll-Strasse 31
|
| City |
Bonn |
| State/province |
NRW |
| ZIP/Postal code |
53115 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16173 |
| Series (1) |
| GSE98235 |
Ppef2 controls the survival and function of CD8+ dendritic cells |
|
| Relations |
| BioSample |
SAMN06835125 |
| SRA |
SRX2765877 |
