|
| Status |
Public on Jul 31, 2024 |
| Title |
TAL-4, interbout euthermia, liver mitochondria |
| Sample type |
SRA |
| |
|
| Source name |
Liver mitochondria
|
| Organism |
Ictidomys tridecemlineatus |
| Characteristics |
tissue: Liver mitochondria
treatment: interbout euthermia
|
| Treatment protocol |
Squirrels were sampled during summer, torpor, and interbout euthermia to collect livers for mitochondrial isolation. Torpid squirrels were euthanized by cervical dislocation, while summer and interbout euthermia squirrels were euthanized using Euthanyl (0.5 ml of 240 mg/ml; Bimeda-MTC, Cambridge, ON, CAN) followed by cervical dislocation. Liver mitochondria were isolated using differential centrifugation and a Percoll density gradient, then stored at - 80 C.
|
| Growth protocol |
All squirrels were trapped in Carman, MB, CAN, or bred in captivity at Western University.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Qiagen miRNeasy kit.
Libraries were generated using the New England Biolabs (NEB) Small RNA Library Prep.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
TAL_4_cutadapt_trimm
|
| Data processing |
A quality control check on the raw data was completed using FastQC (version 0.11.9), then Cutadapt (version 1.3) was used to remove adapters, low-quality bases and reads, and to exclude any reads shorter than 18 nucleotides or longer than 35 nucleotides. A second quality control check using FastQC was completed after Cutadapt trimming.
Reads were analyzed using the miARma-seq pipeline (version 1.7.2). Reads were then mapped to the reference Ensembl genome for Ictidomys tridecemlineatus using Bowtie (version 1.1.1).
Assembly: Ensembl SpeTri2.0 (GCA_000236235.1)
Supplementary files format and content: Readcount file generated from the miARma-seq pipeline in .TAB format.
|
| |
|
| Submission date |
Jan 25, 2024 |
| Last update date |
Jul 31, 2024 |
| Contact name |
Karyn Robichaud |
| E-mail(s) |
[email protected], [email protected]
|
| Organization name |
University of Waterloo
|
| Department |
Biology
|
| Lab |
Paul Craig Lab
|
| Street address |
200 University Ave West, B1 171B
|
| City |
Waterloo |
| State/province |
ON |
| ZIP/Postal code |
N2L 3G1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL30340 |
| Series (1) |
| GSE254223 |
Mitochondrial microRNA profiles are altered in thirteen-lined ground squirrels (Ictidomys tridecemlineatus) during hibernation |
|
| Relations |
| BioSample |
SAMN39610054 |
| SRA |
SRX23391936 |
