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Series GSE121164 Query DataSets for GSE121164
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
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.
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).
Contributor(s) Zhang Q, Babiak I, Fernandes JM
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Submission date Oct 12, 2018
Last update date Oct 01, 2023
Contact name Jorge M.O. Fernandes
Organization name Nord University
Department Faculty of Biosciences and Aquaculture
Street address Universitetsalleen 11
City Bodø
ZIP/Postal code 8049
Country Norway
Platforms (1)
GPL20828 Illumina NextSeq 500 (Danio rerio)
Samples (30)
GSM3427235 t24ct1 (miRNA-seq)
GSM3427236 t24ct3 (miRNA-seq)
GSM3427237 t24ct5 (miRNA-seq)
This SubSeries is part of SuperSeries:
GSE121165 Embryonic incubation temperature effect adult zebrafish
BioProject PRJNA495918
SRA SRP165278

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Supplementary file Size Download File type/resource
GSE121164_miRNA_readCounts.matrix.gz 53.7 Kb (ftp)(http) MATRIX
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Processed data are available on Series record

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