|
| Status |
Public on Dec 01, 2021 |
| Title |
1716 PD1 2h |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Mus musculus |
| Characteristics |
genotype: PD-1 KO
time: 2 h
treatment: no
|
| Treatment protocol |
Cells were cultivated for 2 or 8 hours with Amyloid-beta containing conditioned-medium.
|
| Growth protocol |
Primary microglial cell cultures were prepared from mouse brains. After 5–8 days of primary cultivation, microglial cells were harvested by shake off.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 100-500 ng of total RNA for the construction of sequencing libraries.
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 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were demultiplexed, then aligned with HISAT (v0.1.5-beta) 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 |
Feb 05, 2016 |
| Last update date |
Dec 01, 2021 |
| 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 |
GPL18480 |
| Series (1) |
| GSE77643 |
Loss of PD-1 aggravates plaque pathology by disrupting microglial phagocytosis in APP/PS1 mice |
|
| Relations |
| BioSample |
SAMN04461665 |
| SRA |
SRX1563542 |
