|
| Status |
Public on Oct 06, 2021 |
| Title |
Control (Emx-Cre) rep2 |
| Sample type |
SRA |
| |
|
| Source name |
hippocampus
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: hippocampus
age: 2-month old
genotype: EMX1-Cre
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hippocampus were removed and snap frozen in liquid nitrogen. RNA was prepared using Trizol reagent (Invitrogen), treated with DNase, and purified with RNA Cleanup kit (Qiagen). The KAPA Stranded mRNA-Seq Kit (KapaBioSystems) was used with 500 ng of total RNA for the construction of sequencing libraries.
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 |
| |
|
| Data processing |
TrimGalore toolkit which employed Cutadapt to trim low-quality bases and Illumina sequencing adapters from the 3’ end of the reads . Only reads that were 20 nt or longer after trimming were reserved for further analysis.
STAR RNA-Seq for alignment. Reads were reserved for subsequent analysis if they mapped to a single genomic location.
Gene counts were compiled using the HTSeq tool. Only genes that had at least 10 reads in any given library were used in subsequent analysis.
Normalization and differential expression were performed using the DESeq2 Bioconductor package with the R statistical programming environment .
Genome_build: GRCm38v68 version of the mouse genome
Supplementary_files_format_and_content: Excel file with normalized expression values.
|
| |
|
| Submission date |
Oct 27, 2020 |
| Last update date |
Oct 06, 2021 |
| Contact name |
Wei Yang |
| E-mail(s) |
[email protected]
|
| Organization name |
Duke University Medical Center
|
| Department |
Anesthesiology
|
| Lab |
152 Sands
|
| Street address |
303 Research Drive
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE160259 |
Effect of neuron-specific short-form ATF6 overexpression on gene expression in the mouse brain |
|
| Relations |
| BioSample |
SAMN16575697 |
| SRA |
SRX9381206 |
