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Recommendation on RNA-seq data for wild (untreated) Zebrafish developmental stages needed?

Hello Everyone. I am looking for recommendations on were I can download good RNA-seq data for the developmental stages of the model organism, Danio rerio. I know this is available but my searches havent been able to yield what I am looking for. NCBI has a tone of sra for zebrafish but atleast all that I saw are samples that have been treated with some chemical or a portion of a particular tissue. I also need seq data for the whole adult male and female. I will appreciate your suggestions and recommendations. Thanks

rna-seq sequencing danio rerio zebrafish mapping
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written by jaqx008 jaqx008

Search NCBI SRA, have patience and sift through hits looking for what you want.

You can try a different approach: search pubmed for RNAseq zebrafish developmantal stages or transcriptome zebrafish developmantal stages or some other variation, find the papers best matching what you want and see if they contain accession numbers for the sequencing data.

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written by h.mon h.mon

2 answers

https://elifesciences.org/articles/30860 should help. Sample names and their accessions are listed in supplementary file 1 (https://elifesciences.org/articles/30860/figures#supp1) and you'll want the samples with "RNASeq" in the last column, not "DETCT". https://www.ebi.ac.uk/gxa/experiments/E-ERAD-475/ is another way of getting at the data and there are also tracks in Ensembl.

I think our lab did do some RNA-seq on a whole adult male and female, but it was ages ago and probably doesn't count as good anymore. It's also in Ensembl and I assume the accessions are in https://genome.cshlp.org/content/22/10/2067.full but I'm not 100% sure.

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written by iansealy • iansealy

I came across this before but wasnt able to figure out what was what. Thanks for pointing out that the names are in the supplementary material1. Thanks

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written by jaqx008 jaqx008

One question though, Why does each library seem to have multiple small fastq files while I was downloading from ENA?

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written by jaqx008 jaqx008

Please could you delete this post, as it is not an answer and it is repeated above?

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written by h.mon h.mon

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