|
| Status |
Public on Jul 09, 2020 |
| Title |
X0152_APP.E4.Trem2ko.F.mRNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Mus musculus |
| Characteristics |
Sex: Female
tissue: brain
apoe: APOE4
app/ps1: APP
trem2: Trem2ko
|
| Treatment protocol |
We crossed 6.5 month olf male and female Trem2ko mice with APP/PSEN1dE9 mice expressing human APOE3 or APOE4 isoforms and assessed amyloid pathology, glial response, and whole-brain transcriptome.
|
| Growth protocol |
All animal experiments were approved by the University of Pittsburgh Institutional Animal Care and Use Committee. All procedures were carried out in accordance with the approved guidelines. APP23 transgenic mice (C57Bl6 background) expressing human APP751 familial Swedish AD mutation (APPK670N, M671L) were crossed to wild-type C57BL/6 mice to generate APP23 hemizygous mice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were anesthetized with Avertin (250 mg/kg of body weight, i.p.) and perfused transcardially with cold 0.1 M PBS, pH 7.4: left hemisphere fixed in 4% paraformaldehyde for histology. The cortex was dissected from the other and snap frozen on dry ice for RNA and protein isolation
RNA was isolated from cortex and purified using RNeasy mini kit (Qiagen) per the manufacturer’s protocol. RNA quality was assessed using 2100 Bioanalyzer (Agilent Technologies) and samples with RIN > 8 were further used for sequencing. Sequencing libraries were generated by Novogene.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
FASTQ TO BAM
FEATURECOUNTS
EDGER
Genome_build: mm10
Supplementary_files_format_and_content: raw expresison counts from featurecounts
|
| |
|
| Submission date |
Jan 23, 2020 |
| Last update date |
Jul 09, 2020 |
| Contact name |
Iliya Lefterov |
| E-mail(s) |
iliya.lefterov@pitt.edu
|
| Organization name |
University of Pittsburgh
|
| Department |
Enviromantal and Occupational health
|
| Lab |
Lefterov/Koldamova
|
| Street address |
130 De Soto Street
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15261 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE144125 |
Lack of TREM2 differentially affects the phenotype and transcriptome of mice expressing human APOE3 and APOE4 |
|
| Relations |
| BioSample |
SAMN13909321 |
| SRA |
SRX7623373 |
