|
| Status |
Public on Nov 26, 2019 |
| Title |
PrimaryNeuron_control_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
PrimaryNeuron_control
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell type: rat primary neuron
treatment: control
age: embryo
|
| Treatment protocol |
Mice were fed control diet and diet containing CAD031, CMS 121 and J147 for four months. Primary neurons were treated with 1μM of each compound for 24h.
|
| Growth protocol |
All experiments with the SAMP8 animals were performed in accordance with the US Public Health Service Guide for Care and Use of Laboratory Animals and protocols approved by the IACUC at the Salk Institute. Primary cortical neurons were prepared from day seventeen rat embryos and grown in culture as described in Soucek, T. Neuron. 2003 Jul 3;39(1):43-56.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA from both primary neurons and adult brain hippocampus was isolated using the RNeasy Plus Universal mini kit (Qiagen).
RNA-seq libraries were performed using stranded mRNA kit from Illumina and sequenced in an Illumina HiSeq 2500 device.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
PrimaryNeuron_FPKM.txt
|
| Data processing |
FastQC v0.11.5 with default parameter was used for quality test.
Reads were mapped to mm10/rn6 reference genome by STAR v2.5.1 with default parameters. Only uniquely mapped reads were considered for downstream analysis.
RNA-Seq gene expression was quantified by HOMER analyzeRepeats command, summing reads mapped across all gene exons of RefSeq genes.
RNA-Seq differential expression was carried out using edgeR v3.16.1 on the raw counts of replicates. FDR < 0.05 and logFC +/- 1.2 was used as cutoff to identify the DE genes.
Genome_build: mm10; rn6
Supplementary_files_format_and_content: tab delimited text file for RNA-Seq FPKM values.
|
| |
|
| Submission date |
Jul 10, 2017 |
| Last update date |
Mar 28, 2022 |
| Contact name |
April Elizabeth Williams |
| E-mail(s) |
apriljack06@gmail.com, awilliams@salk.edu
|
| Phone |
7345461645
|
| Organization name |
Salk Institute for Biological Studies
|
| Department |
IGC
|
| Street address |
10010 N Torrey Pines Rd
|
| City |
San Diego |
| State/province |
California |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE101112 |
Whole transcriptome analysis of brain hippocampal tissue from SAMP8 mice and rat primary neurons treated with the Alzheimer's disease drug candidates CMS121 and J147 |
|
| Relations |
| BioSample |
SAMN07340697 |
| SRA |
SRX2994511 |
