|
| Status |
Public on Aug 24, 2020 |
| Title |
AB103 |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: CeA/BLA amygdala
Sex: male
timepoint: Acute
treatment: Blast
|
| Treatment protocol |
Rats were exposed to multiple BOP (blast overpressure) events using the Walter Reed Army Institute of Research (WRAIR) shock tube. The Subjects assigned to blast-exposed groups received a single 74.5 kPa (≈10.8 psi) BOP event every 24 hours for 72 hours. Control (i.e., sham blast) subjects were treated in an identical manner to blast-exposed subjects barring the BOP exposures.
|
| Growth protocol |
Male Long Evans rats weighing between 250-300 grams and approximately 10-12 weeks of age were utilized.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole brains were extracted and flash frozen in methylbutane chilled with dry ice. Frozen brains were subsequently coronally sectioned using a 1mm brain matrix. Sections were gently brushed onto slides and stored in -80°C. . Bihemispheric tissue samples of the central nucleus/ basolateral (CeA/BLA) amygdala were collected for each subject using 1.50-mm tissue punches and stored for downstream processing. Punches were taken between approximately -2.6mm and -3.2mm from Bregma (28)
RNA sequencing libraries were prepared using the KAPA Stranded RNA-Seq Kit with RiboErase (Kapa Biosystems) in accordance with the manufacturer’s instructions and sequenced on an Illumina HiSeq2500 sequencer (v4 chemistry) using 2 x 50bp cycles.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Alignment of sequenced reads was done with STAR 2.4.2a. STAR index was created using splice junction annotation database for guidance and both genome sequence and annotation files of Ensembl Rnor 6.0
Quantification of gene expression was achieved through featureCounts 1.4.3-p1 with Ensembl Rnor 6.0 annotation
Genome_build: Ensembl rnor 6.0
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt
|
| |
|
| Submission date |
Jul 29, 2020 |
| Last update date |
Aug 24, 2020 |
| Contact name |
Fatemeh Haghighi |
| E-mail(s) |
fatemeh.haghighi@mssm.edu
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Neuroscience
|
| Lab |
Haghighi Lab
|
| Street address |
1425 Madison Ave, 9-20D
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE155393 |
Blast-related mild TBI alters anxiety-like behavior and transcriptional signatures in the rat amygdala |
|
| Relations |
| BioSample |
SAMN15669921 |
| SRA |
SRX8845660 |
