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| Status |
Public on Dec 19, 2023 |
| Title |
Sp8 |
| Sample type |
SRA |
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| Source name |
Ventral part of telenchephalon, hypothalamus and pituitary
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| Organism |
Oryzias latipes |
| Characteristics |
tissue: Ventral part of telenchephalon, hypothalamus and pituitary
treatment: Spring equinox 14:00
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| Treatment protocol |
Samples were collected every 4 h for a 24-h period at the spring equinox, summer solstice, autumn equinox, and winter solstice.
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| Growth protocol |
Medaka were kept under outdoor natural conditions in the National Institute for Basic Biology, Okazaki, Japan (35.0°N, 137.2°E)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of brain (ventral part of telenchephalon, hypothalamus and pituitary) were isolated with elimination of DNA contamination using DNase.
mRNA was first purified from the total RNA using poly-T oligo-attached magnetic beads and then fragmented, after which cDNA synthesis was performed. Then the synthesized cDNA was used for the preparation of PE100 strand specific sequencing libraries.
Strand-specific RNA-seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| Data processing |
Clean reads were mapped on the Oryzias latipes reference assembly using bowtie2 (version 2.2.5)
The fragments per kilobase of exon per million fragments mapped (FPKM) was calculated using RSEM (version 1.2.12).
Assembly: Oryzias latipes reference assembly
Supplementary files format and content: Excel file include FPKM for each sample.
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| Submission date |
Jun 07, 2023 |
| Last update date |
Dec 19, 2023 |
| Contact name |
Takashi Yoshimura |
| E-mail(s) |
takashiy@agr.nagoya-u.ac.jp
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| Organization name |
Nagoya University
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| Street address |
Furo-cho, Chikusa-ku
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| City |
Nagoya |
| ZIP/Postal code |
4648601 |
| Country |
Japan |
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| Platform ID |
GPL33470 |
| Series (1) |
| GSE234400 |
Genome-wide transcriptome analysis of the brain (ventral part of telenchephalon, hypothalamus and pituitary) of medaka (Oryzias latipes) at the spring equinox, summer solstice, autumn equinox, and winter solstice [24h RNA-seq] |
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| Relations |
| BioSample |
SAMN35668108 |
| SRA |
SRX20635499 |
| 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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