 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 02, 2021 |
| Title |
29DPI-Hypo-Drug-TBI-1 |
| Sample type |
SRA |
| |
|
| Source name |
Hypothalamus
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
time point: 29 Days Post-Injury
drug treatment: Drug
tbi: TBI
|
| Treatment protocol |
All mice received their first dose of either candesartan (Tocris Bioscience, Minneapolis, MN # 4791) or vehicle (0.9% saline and 0.1N Na2CO3 at pH = 7.4) six hours after the CCI or sham procedure through intraperitoneal injection. Mice in the 3 day cohort received two subsequent i.p. injections at 24- and 48-hours after CCI, before sacrifice at 3 dpi. Mice in the 29-day cohort were surgically implanted with an osmotic pump (#1004, Alzet, Cupertino, CA) 24 hours after the CCI or sham procedure.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Animals were anesthetized and perfused with ice-cold filtered 0.9% saline solution, individual brain regions were removed (hypothalamus, thalamus, hippocampus), tissue triturated in Tri-reagent, RNA extracted utilizing Direct-zol RNA MiniPreps (Zymo Research, # R2025).
Total RNA integrity was assessed using automated capillary electrophoresis on a Fragment Analyzer (Roche). For all samples RQI > 8.0 and a total RNA amount of >75 ng was used as input for library preparation using the TruSeq Stranded mRNA Library Preparation Kit (Illumina, San Diego, CA, USA).
Sequencing libraries were quantified by PCR using KAPA Library Quantification Kit for NGS (Kapa, Wilmington, MA, USA) and assessed for size distribution on a Fragment Analyzer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
29DPI_samples_counts_table.txt
|
| Data processing |
Sequencing libraries were pooled and sequenced on a HiSeq 3000 System (Illumina) using a HiSeq 3000/4000 PE Cluster Kit and SBS Kit (150 cycles) with run conditions of paired-end reads at 75 bp length.
Raw sequencing data were demuxed using bcl2fastq2 conversion software 2.20.
Raw paired-end sequencing reads were aligned to the mouse reference genome (mm10) using MapSplice version 2.2.1.
Gene read counts against UCSC mouse gene models (obtained on February 21, 2016) were calculated by HTSeq version 0.9.1 with parameters: -m intersection-nonempty -i gene_id -s reverse
Gene read count normalization and differential expression analysis was performed with DESeq2 version 1.16.1.
Genome_build: mm10
Supplementary_files_format_and_content: 3DPI_samples_counts_table.txt - tab-delimited text file of gene raw counts for all 3DPI samples
Supplementary_files_format_and_content: 29DPI_samples_counts_table.txt - tab-delimited text file of gene raw counts for all 29DPI samples
|
| |
|
| Submission date |
Dec 17, 2020 |
| Last update date |
Feb 02, 2021 |
| Contact name |
Aviva Jane Symes |
| E-mail(s) |
[email protected]
|
| Organization name |
Uniformed Services University
|
| Department |
Pharmacology
|
| Street address |
4301 Jones Bridge Road
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20814 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE163415 |
Transcriptomic Analysis of mouse brain after traumatic brain injury reveals that the angiotensin receptor blocker candesartan acts through novel pathways |
|
| Relations |
| BioSample |
SAMN17103970 |
| SRA |
SRX9697944 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
