|
| Status |
Public on Oct 15, 2021 |
| Title |
4mo Apoe(fl/fl) 5xFAD Csf1r-cre Hippocampus 2 |
| Sample type |
SRA |
| |
|
| Source name |
Hippocampus
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6, Apoe(fl/fl), 5xFAD, Csf1r-cre
brain region: Hippocampus
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Brains were removed, microdissected into cortex, hippocampus, and thalamus/striatum, and flash frozen on dry ice. RNA was extracted using Rneasy Mini Kit (Qiagen). cDNA synthesis, amplification, library construction and sequencing were performed by Novogene Inc. using Illumina NovaSeq and HiSeq platforms with paired-end 150 bp (PE 150) sequencing strategy.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
CH16
|
| Data processing |
Illumina HiSeq4000 was used to produce 50bp single-end reads.
Sequenced reads mapped to mm10 whole genome using STAR aligner.
featureCounts were calculated using function of the Rsubread package in R.
After filtering out low-count genes, count distributions were scaled using the calcNormFactors function of the edgeR package.
plotMDS function of the limma package in R was used to perform principal component analysis. Reads Per Kilobase of exon per Megabase of library size (RPKM) were prepared and fitted to linear models using the voom and lmfit functions.
Genome_build: mm10
Supplementary_files_format_and_content: Excel Workbook file includes RPKM values for all Samples.
|
| |
|
| Submission date |
Oct 10, 2021 |
| Last update date |
Oct 15, 2021 |
| Contact name |
Kim Green |
| E-mail(s) |
kngreen@uci.edu
|
| Phone |
9498243859
|
| Organization name |
University of California, Irvine
|
| Department |
Neurobiology and Behavior
|
| Street address |
3208 Biological Sciences 3
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92617 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE185622 |
Microglial-expressed Apoe does not modulate plaque pathogenesis |
|
| Relations |
| BioSample |
SAMN22208623 |
| SRA |
SRX12566474 |
