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| Status |
Public on Jul 19, 2023 |
| Title |
No treatment, rep 2 [miRNA-Seq] |
| Sample type |
SRA |
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| Source name |
whole larvae (30)
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| Organism |
Danio rerio |
| Characteristics |
tissue: whole larvae (30)
strain: AB strain
treatment: None
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| Treatment protocol |
anxiety (induced by a half hour exposure to 100 mg/liter caffeine [CAF], compared to no treatment [NO]) and obesity (induced by feeding 6 dpf larvae a high fat diet [HFD, egg yolk-based] until 15 dpf, compared to a standard diet [SD]).
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| Growth protocol |
Kept under 14 h light/10 h dark regimen. Water was pH7-7.7, 27.7-28.3 C, 490-510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle (20-G). Kit used was Nucleospin® miRNA kit (Macherey-Nagel GmbH & Co.)
Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center, Israel.
miRNA-seq, including other small RNAs. 75 nucleotide single-end runs
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Processing was by the Technion Genome Center, Israel and the online CLC Genomics Workbench 20.0.3.
Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench, which included removal of the Qiagen 3' adapter on the 3' end.
Reads without this adapter were discarded, and only sequences between 15 and 54 nucleotides were retained. These trimmed files (read lengths of ~23 bases) were joined.
miR quantify was run on these files, using the reference - miRbase v.22.1 and the preference - Danio rerio.
Normalization was executed using TMM (trimmed mean of M values). Annotation was carried out using Go Mapping RNAcentral v10.
Supplementary files format and content: excel file with Max Group Mean, Log2 Fold change, Fold change, p Value, FDR pvalue, Bonferroni for each miR in each model.
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| Submission date |
Jul 06, 2022 |
| Last update date |
Jul 19, 2023 |
| Contact name |
Ari Meerson |
| E-mail(s) |
arim@migal.org.il
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| Phone |
972-4-6955022
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| Organization name |
MIGALGalilee Research Institute
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| Street address |
2 Tarshish St.
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| City |
Kiryat Shmona |
| ZIP/Postal code |
11016 |
| Country |
Israel |
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| Platform ID |
GPL18413 |
| Series (2) |
| GSE207549 |
Transcriptome profiles of zebrafish larvae from a caffeine-induced anxiety model and a high fat-diet induced obesity model [miRNA-Seq] |
| GSE207550 |
Transcriptome profiles of zebrafish larvae from a caffeine-induced anxiety model and a high fat-diet induced obesity model |
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| Relations |
| BioSample |
SAMN29531892 |
| SRA |
SRX16037356 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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