|
Status |
Public on Dec 01, 2021 |
Title |
1795 PD1 8h Ab |
Sample type |
SRA |
|
|
Source name |
brain
|
Organism |
Mus musculus |
Characteristics |
genotype: PD-1 KO time: 8 h treatment: Amyloid-beta
|
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 |
SAMN04461655 |
SRA |
SRX1563562 |