|
| Status |
Public on Dec 31, 2021 |
| Title |
MAD3 |
| Sample type |
SRA |
| |
|
| Source name |
hippocampus
|
| Organism |
Mus musculus |
| Characteristics |
tissue: hippocampus
strain: APPswePSEN1dE9
age: 8-month
Sex: male
treatment: MAD3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
A phenol-chloroform extraction
RNA libraries were prepared for sequencing using standard BGI-500 protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Filtering and trimming the reads using Trimmomatic v0.38 with parameters “HEADCROP:9 LEADING:20 TRAILING:20 SLIDINGWINDOW:5:20 MINLEN:50 AVGQUAL:20”.
Clean reads were mapped to the Mus musculus genome sequence (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/635/GCF_000001635.26_GRCm38.p6 ) using Hisat2 v2-2.1.0 with default parameters.
The reads of each sample were then assembled into transcripts and compared with reference gene models using StringTie v1.3.4d.
Merging the all transcripts to obtain a consensus transcript using StringTie-Merge program.
The gene expression FPKM values were calculated using StringTie based on the consensus transcript.
DEG analysis was performed using Ballgown v2.12.0.
Gene-set enrichment analysis (GSEA) was performed on genes ranked by their differential expression Signal2Noise using GSEA software (4.3.0 from Broad Institute). KEGG pathway database were downloaded from https://www.kegg.jp/kegg .bin/search_pathway_text?map=mmu&keyword=&mode=1&viewImage=truehttps://www.kegg.jp/kegg .
Genome_build: GCF_000001635.26_GRCm38
Supplementary_files_format_and_content: FPKM
|
| |
|
| Submission date |
Jan 08, 2021 |
| Last update date |
Dec 31, 2021 |
| Contact name |
Jin Xin |
| E-mail(s) |
jinxin1@genomics.cn
|
| Phone |
13419631327
|
| Organization name |
BGI
|
| Street address |
Beishan road
|
| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518120 |
| Country |
China |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE164461 |
Effects of intermittent fasting on the cognitive impairment in Alzheimer's disease mice: the roles of the gut brain axis regulation mechanism |
|
| Relations |
| BioSample |
SAMN17260889 |
| SRA |
SRX9807291 |
