|
| Status |
Public on Jul 13, 2018 |
| Title |
SW6_L002 |
| Sample type |
SRA |
| |
|
| Source name |
Hypothalamus
|
| Organism |
Rattus norvegicus |
| Characteristics |
Sex: Male
strain: Sprague-Dawley
treatment: Water
|
| Treatment protocol |
All animals were subjected to either sham or fluid percussion injury (FPI). After 1 week of injury animals were tested for glucose tolerance (GTT) and were sacrificed immediately by decapitation. Body weight, food intake, water intake and calorie intake were measured throughout the study.
|
| Growth protocol |
Twenty-four Male Sprague–Dawley rats (Charles River Laboratories, Inc., Wilmington, MA) approximately 2 months old were housed in polyacrylic cages and maintained under standard housing conditions (room temperature 22–24C) with 12 h light/dark cycle. All experiments were performed in accordance with the United States National Institutes of Health Guide for the Care and Use of Laboratory Animals. The animal studies and experimental procedures were approved by the University of California at Los Angeles Chancellor's Animal Research Committee (ARC).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from hypothalamus tissue using Qiagen AllPrep DNA/RNA mini kit.
Libraries were constructed according to instructions of TruSeq Stranded Total RNA Ribo-Zero H/M/R Gold kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
HISAT was used to align the RNA-Seq reads against the Rattus norvegicus genome to discover the locations from which the reads originated and to determine the transcript sites.
StringTie was used to assemble the RNA-seq alignments into potential transcripts.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) for each transcript were obtained by Ballgown tool and used as the expression measure.
Genome_build: UCSC version rn6
Supplementary_files_format_and_content: Transcription abundances in terms of the FPKM measure of the expressed transcripts in each sample were obtained by using Ballgown R tool.
|
| |
|
| Submission date |
Jul 12, 2018 |
| Last update date |
Jul 13, 2018 |
| Contact name |
Xia Yang |
| E-mail(s) |
xyang123@ucla.edu
|
| Organization name |
UCLA
|
| Street address |
610 Charles E. Young Drive East
|
| City |
Los Angeles |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL22396 |
| Series (1) |
| GSE116980 |
Unwinding the interplay between brain and liver in the pathophysiology of brain trauma |
|
| Relations |
| BioSample |
SAMN09645057 |
| SRA |
SRX4383821 |
