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| Status |
Public on Jan 01, 2023 |
| Title |
H1504-149-200C-mRNA |
| Sample type |
SRA |
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| Source name |
whole embryo
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| Organism |
Salvelinus alpinus |
| Characteristics |
cross type: SBxSB
family: H1504
individual: C
developmental timepoint: 200
sequencing batch: 3
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| Growth protocol |
embryos were reared in a common hatching tray
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the samples and enriched for small RNAs using the mirVana kit (Ambion).
The samples were divided into 3 batches, each containing 3 embryos per family, to produce the sequencing libraries.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-T7 |
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| Description |
RNA-seq data
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| Data processing |
reads quality assesment with FASTQC
adapter sequence removal with Cutadapt (only for miRNA files)
miRNA: transcripts quantification with MiRDeep2
miRNA: pre-processing and genome mapping with the MiRDeep2 Mapping module
miRNA: read couting with miRDeep2 Quantifier module, using the MiRBase reference database for all species
miRNA: removed sequences exhibiting at least 95% similarity across species using Cd-hit
mRNA: reads alignment with STAR, options --outSAMstrandField intronMotif --twopassMode Basic
mRNA: read counts with FeatureCounts, gene level
Genome_build: ASM291031v2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Jan 17, 2022 |
| Last update date |
Jan 01, 2023 |
| Contact name |
Quentin Horta-Lacueva |
| E-mail(s) |
qjb1@hi.is
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| Organization name |
University of Iceland
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| Street address |
Sturlugötu 7
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| City |
Reykjavík |
| ZIP/Postal code |
102 |
| Country |
Iceland |
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| Platform ID |
GPL31234 |
| Series (1) |
| GSE193797 |
Dominance in gene expression variability during ontogeny reveals the importance of canalization in adaptive divergence and speciation. |
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| Relations |
| BioSample |
SAMN25043985 |
| SRA |
SRX13813467 |
| 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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