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| Status |
Public on May 03, 2024 |
| Title |
Pool_ko, biological rep2 |
| Sample type |
SRA |
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| Source name |
Stage 40 Oryzias latipes (Medaka)
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| Organism |
Oryzias latipes |
| Characteristics |
Stage: Stage 40
gender: not determined
genotype/variation: KO for SEDL
tissue: embryo
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| Treatment protocol |
No treatment was performed
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| Growth protocol |
The Cab-strain of medaka fish (Oryzias latipes) was maintained as described in Avellino et al., 2013. Embryos were staged according to the method proposed by Iwamatsu (Iwamatsu, 2004). All studies on fish were conducted in strict accordance with the institutional guidelines for animal research and approved by the Italian Ministry of Health; Department of Public Health, Animal Health, Nutrition and Food Safety in accordance to the law on animal experimentation (D.Lgs. 26/2014). Furthermore, all animal treatments were reviewed and approved in advance by the Ethics Committee at the TIGEM Institute, (Pozzuoli (NA), Italy).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).
Total RNA (500 ng) from each sample was prepared using TruSeq RNA sample prep reagents (Illumina, San Diego, CA, USA) according to manufacturer's instructions
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
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| Description |
S3586
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| Data processing |
Sequence reads were trimmed using bbduk software(https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/usage-guide/) (bbmap suite 37.31) to remove adapter sequences, poly-A tails and low-quality end bases (regions with average quality below 6) and then aligned on mm10 reference sequence using STAR
Genome_build: oryLat2
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample
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| Submission date |
Oct 28, 2021 |
| Last update date |
May 06, 2024 |
| Contact name |
Rossella De Cegli |
| E-mail(s) |
[email protected]
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| Phone |
08119230692
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| Organization name |
Tigem
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| Street address |
Via Campi Flegrei 34
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| City |
Pozzuoli |
| ZIP/Postal code |
80078 |
| Country |
Italy |
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| Platform ID |
GPL21753 |
| Series (1) |
| GSE186769 |
Transcriptome profile of Stage 40 Oryzias latipes (Medaka) embryos II |
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| Relations |
| BioSample |
SAMN22657100 |
| SRA |
SRX12813803 |
| 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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