|
| Status |
Public on Sep 06, 2018 |
| Title |
Control_H |
| Sample type |
SRA |
| |
|
| Source name |
hippocampus
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
development stage: adult
Sex: male
treatment: saline
tissue: hippocampus
|
| Treatment protocol |
On Week 7, the hippocampi and PFC of the rat brains were dissected from one normal rat and two CUMS rats treated with either saline or 100 mM/kg MGO.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted and purified from ~30 mg tissue using the RNeasy mini kit (Qiagen, Germany) according to the manufacturer’s protocol. RNA-seq was performed at Genminix Informatics Ltd.,Co.(Shanghai, China) using Illumina HiSeq ×10 sequencing platform.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
R17014934-Control_H_combined
|
| Data processing |
Quality control of raw sequences from each sample was investigated using FastQC (v0.11.5).
Reads were then mapped to the Ensembl rat genome sequence (Rnor_6.0) using HISAT2 (v2.0.4) and assembled into transcripts by StringTie (v1.2.4) using a UCSC rn6 GTF (general transfer format) file.
FPKM (fragment per kilobase per million mapped reads) values were used to estimate the transcript abundance.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: FPKM values for all Samples
|
| |
|
| Submission date |
Sep 05, 2018 |
| Last update date |
Sep 06, 2018 |
| Contact name |
Yingxue Fu |
| E-mail(s) |
yingxue_fu@nwafu.edu.cn
|
| Organization name |
Northwest A&F University
|
| Street address |
Taicheng Road 3
|
| City |
Yangling |
| State/province |
Shaanxi |
| ZIP/Postal code |
712100 |
| Country |
China |
| |
|
| Platform ID |
GPL24688 |
| Series (1) |
| GSE119482 |
Methylglyoxal modification of TrkB enhances synaptic plasticity in prefrontal cortex and promotes resilience to chronic stress |
|
| Relations |
| BioSample |
SAMN09976650 |
| SRA |
SRX4643587 |
