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| Status |
Public on Oct 01, 2023 |
| Title |
Embryonic incubation temperature has a long-term effect on the microRNA transcriptome of adult zebrafish |
| Organism |
Danio rerio |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Zebrafish eggs were collected at 28 °C, and split into three temperature groups (24 °C, 28 °C, 32 °C) for incubation. When larvae reaching first feeding, the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C, and all fish were kept at 28 °C for later development until adulthood. At 100 d post-fertilization, seven replicates from each group were intraperitoneally (i.p.) injected with 2 μl of 50 mg/ml lipopolysaccharide (LPS) from Pseudomonas aeruginosa 10, while another seven replicates were i.p. injected with 2 μl phosphate-buffered saline as control. At 12 h post-injection, the spleen was dissected, and total RNA was isolated. Five LPS-treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures, 32 miRNAs (29 up-/3 down-regulated) were identified differentially expressed (DEmiRs, adjusted p-value < 0.05, |fold change| > 2.0, DESeq2) in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C, 3 DEmiRs (2 up-/1 down-regulated) were identified in response to LPS in fish kept at 28 °C. A total of 9,116 target genes were predicted using miRanda (v3.3a), including 8,224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs.
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| Overall design |
Thirty samples were analyzed, including five LPS-treated replicates and five controls from each of three embryonic incubation temperatures (24 °C, 28 °C, 32 °C).
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| Contributor(s) |
Zhang Q, Babiak I, Fernandes JM |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Oct 12, 2018 |
| Last update date |
Oct 01, 2023 |
| Contact name |
Jorge M.O. Fernandes |
| E-mail(s) |
jorge.m.fernandes@nord.no
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| Organization name |
Nord University
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| Department |
Faculty of Biosciences and Aquaculture
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| Street address |
Universitetsalleen 11
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| City |
Bodø |
| ZIP/Postal code |
8049 |
| Country |
Norway |
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| Platforms (1) |
| GPL20828 |
Illumina NextSeq 500 (Danio rerio) |
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| Samples (30)
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| This SubSeries is part of SuperSeries: |
| GSE121165 |
Embryonic incubation temperature effect adult zebrafish |
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| Relations |
| BioProject |
PRJNA495918 |
| SRA |
SRP165278 |
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