|
| Status |
Public on Jan 17, 2022 |
| Title |
H1_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Prefrontal cortex
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Prefrontal cortex
strain: BALB/c
treatment: Duloxetine
behavior: Responder
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Prefrontal cortex tissues were removed, flash frozen on dry ice, and RNA was extracted using Direct-zol RNA kit. SureSelect Strand-Specific RNA Library Prep for Illumina (Agilent Technology) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Sequencing adaptors, low quality reads, and bases were trimmed with Trimmomatic-0.32 tool.
The sequence reads were aligned to the mouse reference genome (mm10) using Tophat 2.0.13 (bowtie2-2.2.3), which can adequately align reads onto the location including splice sites in the genome sequence.
The aligned reads were subjected to downstream analyses using StrandNGS 2.6 software (Agilent Technologies). The read counts allocated for each gene and transcript (UCSC version 2013.3.6) were quantified using a Trimmed Mean of M-value (TMM) method.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for every gene and every sample (all data are summarized in single file)
|
| |
|
| Submission date |
Mar 03, 2021 |
| Last update date |
Jan 17, 2022 |
| Contact name |
Shusaku Uchida |
| E-mail(s) |
uchida.shusaku.3n@kyoto-u.ac.jp
|
| Organization name |
Kyoto University
|
| Street address |
53 Kawaharamachi, Sakyo-ku
|
| City |
Kyoto |
| State/province |
Kyoto |
| ZIP/Postal code |
606-8507 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE168172 |
RNA sequencing analysis of gene expression in the prefrontal cortex of mice treated with antidepressant drugs |
|
| Relations |
| BioSample |
SAMN18128690 |
| SRA |
SRX10229630 |
