|
| Status |
Public on May 31, 2023 |
| Title |
28.5_F3_Ctrl_NoRad |
| Sample type |
SRA |
| |
|
| Source name |
Muscle
|
| Organism |
Danio rerio |
| Characteristics |
tissue: Muscle
condition: Control
radiation (cgy): 0
temperature (c): 28.5
melatonin (um): 0
|
| Treatment protocol |
A melatonin group (28.5- melatonin) received melatonin daily for 10 days at a concentration of 24 µM for 10 days to reduce locomotion and arousal. A reduced temperature group (18.5-Ctrl) received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group (18.5-mel) was established with a 10°C reduction in ambient temperature and the addition of 24 µM melatonin. A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total mRNA was extracted from liver tissue of the zebrafish using Qiagen’s miRNeasy Mini kit (Qiagen, Hilden, Germany).
To prepare mRNA seq kit (poly A capture, KAPA RNA hyper)(Illumina, San Diego, CA, USA); was utilized; 100ng of total input muscle RNA was used in accordance with the manufacturer’s protocol.
High through-put RNA sequencing (RNAseq) was performed at the Queens University Belfast, Genomics Core Technology Unit on an Illumina Next SEQ 2000 instruments with the mRNA library sequenced to a minimum depth of 50 million reads using forward stranded PE50 strategy.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Sequence quality was assessed with FastQC to identify over-represented sequences and low quality reads
Low quality reads and over-represented sequences were removed with Cutadapt
The STAR aligner was utilised to align the RNA-Seq reads to the zebrafish genome (GRCz11)
HTSeq was used to determine the number of reads per transcript
DESeq2 was used for determination of differentially expressed genes
Assembly: zebrafish genome (GRCz11)
|
| |
|
| Submission date |
Jan 11, 2023 |
| Last update date |
May 31, 2023 |
| Contact name |
Thomas Cahill |
| E-mail(s) |
tcahill01@qub.ac.uk
|
| Organization name |
Queens university Belfast
|
| Street address |
19 Chlorine Gardens
|
| City |
Belfast |
| ZIP/Postal code |
BT95DL |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL30614 |
| Series (1) |
| GSE222614 |
Transcriptome Profiling Reveals Enhanced Mitochondrial Activity as a Cold Adaptive Strategy to Hypothermia in Zebrafish Muscle |
|
| Relations |
| BioSample |
SAMN32675794 |
| SRA |
SRX19001701 |
