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| Status |
Public on Oct 13, 2024 |
| Title |
liver, group, male, 7 wph, biol rep 4 |
| Sample type |
SRA |
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| Source name |
liver of group-housed males at 7 wph
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| Organism |
Nothobranchius furzeri |
| Characteristics |
tissue: liver of group-housed males at 7 wph
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with TRIzol reagent (Thermo Fisher Scientific), and subjected to DNase treatment with a TURBO DNA-free kit　(Invitrogen #AM1907) according to the manufacturer’s instructions.
For whole juvenile fish and livers, the libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490), NEBNext Ultra II Directional RNA Library Prep Kit (E7760), NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) (E6440). For ovaries and testes, the libraries were prepared using TruSeq stranded mRNA Library (Illumina, CA, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The quality check of raw sequencing data was performed using FastQC v0.11.8.
The raw data were processed using Trim-galore v0.6.4.
The processed reads were mapped to N. furzeri reference genome Nfu_20140520 using HISAT2 2.1.0.
The mapped reads were counted using featurecounts v.1.5.3.
Assembly: Nfu_20140520
Supplementary files format and content: tab-delimited text file including raw counts for each Sample
Supplementary files format and content: tab-delimited text file including TPM values for each Sample
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| Submission date |
Oct 16, 2023 |
| Last update date |
Oct 13, 2024 |
| Contact name |
Chika Takahashi |
| E-mail(s) |
[email protected]
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| Organization name |
RIKEN
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| Street address |
2-2-3 Minatojima-minamimachi,Chuo-ku
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| City |
Kobe |
| ZIP/Postal code |
650-0047 |
| Country |
Japan |
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| Platform ID |
GPL32658 |
| Series (2) |
| GSE245481 |
Effect of housing condition (group- or single-housing) on gene expression in African turquoise killifish II. |
| GSE245483 |
Effect of housing condition (group- or single-housing) on gene expression in African turquoise killifish |
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| Relations |
| BioSample |
SAMN37847228 |
| SRA |
SRX22104077 |
| 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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